*>>>>>> Combined CHARMM All-Hydrogen Topology File for <<<<<<<<<
*>>>>>>>>> CHARMM22 Proteins and CHARMM27 Lipids <<<<<<<<<<
*>>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<
*from
*>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
*>>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
*>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
*>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu  <<<<<<<<<
*and
*  \\\\\\\ CHARMM27 All-Hydrogen Lipid Topology File ///////
*  \\\\\\\\\\\\\\\\\\ Developmental /////////////////////////
*              Alexander D. MacKerell Jr.
*                     August 1999
* All comments to ADM jr.  email: alex,mmiris.ab.umd.edu
*              telephone: 410-706-7442
*
27  1

!
! references
!
!PROTEINS
!
!MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.;
!Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.;
!Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos,
!C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III,
!W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.;
!Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M.  All-atom
!empirical potential for molecular modeling and dynamics Studies of
!proteins.  Journal of Physical Chemistry B, 1998, 102, 3586-3616.
!
!PHOSPHOTYROSINE
!
!Feng, M.-H., Philippopoulos, M., MacKerell, Jr., A.D. and Lim, C.
!Structural Characterization of the Phosphotyrosine Binding Region of a
!High-Affinity aSH2 Domain-Phosphopeptide Complex by Molecular Dynamics
!Simulation and Chemical Shift Calculations. Journal of the American
!Chemical Society, 1996, 118: 11265-11277.
!
!IONS (see lipid and nucleic acid topology and parameter files for
!additional ions
!
!ZINC
!
!Roland H. Stote and Martin Karplus, Zinc Binding in Proteins and
!Solution: A Simple but Accurate Nonbonded Representation, PROTEINS:
!Structure, Function, and Genetics 23:12-31 (1995)
!
!references
!
!LIPIDS
!
!Feller, S. and MacKerell, Jr., A.D. manuscript in preparation
!
!and
!
!Schlenkrich, M., Brickmann, J., MacKerell, Jr., A.D., and Karplus, M.
!Empirical Potential Energy Function for Phospholipids: Criteria for
!Parameter Optimization and Applications, in "Biological Membranes: A
!Molecular Perspective from Computation and Experiment," K.M. Merz and
!B. Roux, Eds. Birkhauser, Boston, 1996, pp 31-81.
!
!new ALKANES
!
!Yin, D. and MacKerell, Jr. A.D. Combined Ab initio/Empirical Approach
!for the Optimization of Lennard-Jones Parameters. Journal of
!Computational Chemistry, 1998, 19: 334-338.
!
!ALKENES
!
!Feller, S.E., Yin, D., Pastor, R.W., and MacKerell, Jr., A.D.,
!Molecular Dynamics Simulation of Unsaturated Lipids at Low Hydration:
!Parameterization and Comparison with Diffraction Studies.  Biophysical
!Journal, 73:2269-2279, 1997.
!
!new PHOSPHATE
!
!MacKerell, Jr., A.D. Influence of Water and Sodium on the Energetics
!of Dimethylphosphate and its Implications For DNA Structure, Journal
!de Chimie Physique, 1997, 94: 1436-1447.
!
!IONS
!
!all ions from Roux and coworkers
!
!Sodium
!
!Beglov, D. and Roux, B., Finite Representation of an Infinite
!Bulk System: Solvent Boundary Potential for Computer Simulations,
!Journal of Chemical Physics, 1994, 100: 9050-9063
! 

!NUCLEIC ACIDS
!
!Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for
!Nucleic Acids: 2) Parameter Optimization Based on Small Molecule and
!Condensed Phase Macromolecular Target Data.  Journal of Computational
!Chemistry, 2000, 21:86-104.
!
!and
!
!MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for
!Nucleic Acids: 2) Application to Molecular Dynamics Simulations of DNA
!and RNA in Solution. Journal of Computational
!Chemistry, 2000, 21:105-120.
!
!NAD(P)+, NAD(P)H and PPI
!
!Pavelites, J.J., Bash, P.A., Gao, J. and MacKerell, Jr., A.D. A
!Molecular Mechanics Force Field for NAD+, NADH, and the Pyrophosphate
!Groups of Nucleotides, Journal of Computational Chemistry, 1997, 18:
!221-239.
!



MASS     1 H      1.00800 H ! polar H
MASS     2 HC     1.00800 H ! N-ter H
MASS     3 HA     1.00800 H ! nonpolar H
MASS     4 HT     1.00800 H ! TIPS3P WATER HYDROGEN
MASS     5 HP     1.00800 H ! aromatic H
MASS     6 HB     1.00800 H ! backbone H
MASS     7 HR1    1.00800 H ! his he1, (+) his HG,HD2
MASS     8 HR2    1.00800 H ! (+) his HE1
MASS     9 HR3    1.00800 H ! neutral his HG, HD2
MASS    10 HS     1.00800 H ! thiol hydrogen
MASS    11 HE1    1.00800 H ! for alkene; RHC=CR
MASS    12 HE2    1.00800 H ! for alkene; H2C=CR
MASS    20 C     12.01100 C ! carbonyl C, peptide backbone
MASS    21 CA    12.01100 C ! aromatic C
MASS    22 CT1   12.01100 C ! aliphatic sp3 C for CH
MASS    23 CT2   12.01100 C ! aliphatic sp3 C for CH2
MASS    24 CT3   12.01100 C ! aliphatic sp3 C for CH3
MASS    25 CPH1  12.01100 C ! his CG and CD2 carbons
MASS    26 CPH2  12.01100 C ! his CE1 carbon
MASS    27 CPT   12.01100 C ! trp C between rings
MASS    28 CY    12.01100 C ! TRP C in pyrrole ring
MASS    29 CP1   12.01100 C ! tetrahedral C (proline CA)
MASS    30 CP2   12.01100 C ! tetrahedral C (proline CB/CG)
MASS    31 CP3   12.01100 C ! tetrahedral C (proline CD)
MASS    32 CC    12.01100 C ! carbonyl C, asn,asp,gln,glu,cter,ct2
MASS    33 CD    12.01100 C ! carbonyl C, pres aspp,glup,ct1
MASS    34 CPA   12.01100 C ! heme alpha-C
MASS    35 CPB   12.01100 C ! heme beta-C
MASS    36 CPM   12.01100 C ! heme meso-C
MASS    37 CM    12.01100 C ! heme CO carbon
MASS    38 CS    12.01100 C ! thiolate carbon
MASS    39 CE1   12.01100 C ! for alkene; RHC=CR
MASS    40 CE2   12.01100 C ! for alkene; H2C=CR
MASS    50 N     14.00700 N ! proline N
MASS    51 NR1   14.00700 N ! neutral his protonated ring nitrogen
MASS    52 NR2   14.00700 N ! neutral his unprotonated ring nitrogen
MASS    53 NR3   14.00700 N ! charged his ring nitrogen
MASS    54 NH1   14.00700 N ! peptide nitrogen
MASS    55 NH2   14.00700 N ! amide nitrogen
MASS    56 NH3   14.00700 N ! ammonium nitrogen
MASS    57 NC2   14.00700 N ! guanidinium nitroogen
MASS    58 NY    14.00700 N ! TRP N in pyrrole ring
MASS    59 NP    14.00700 N ! Proline ring NH2+ (N-terminal)
MASS    60 NPH   14.00700 N ! heme pyrrole N
MASS    70 O     15.99900 O ! carbonyl oxygen
MASS    71 OB    15.99900 O ! carbonyl oxygen in acetic acid
MASS    72 OC    15.99900 O ! carboxylate oxygen
MASS    73 OH1   15.99900 O ! hydroxyl oxygen
MASS    74 OS    15.99940 O ! ester oxygen
MASS    75 OT    15.99940 O ! TIPS3P WATER OXYGEN
MASS    76 OM    15.99900 O ! heme CO/O2 oxygen
MASS    81 S     32.06000 S ! sulphur
MASS    82 SM    32.06000 S ! sulfur C-S-S-C type
MASS    83 SS    32.06000 S ! thiolate sulfur
MASS    85 HE     4.00260 HE ! helium
MASS    86 NE    20.17970 NE ! neon
MASS    90 CAL   40.08000 CA ! calcium 2+
MASS    91 ZN    65.37000 ZN ! zinc (II) cation
MASS    92 FE    55.84700 Fe ! heme iron 56
MASS    99 DUM    0.00000 H ! dummy atom
!lipids section
MASS 101    HL    1.008000 H ! polar H (equivalent to protein H)
MASS 102    HCL   1.008000 H ! charged H for PE (equivalent to protein HC)
!MASS 3    HT    1.008000 H ! TIPS3P WATER HYDROGEN
MASS 104    HOL   1.008000 H ! Nucleic acid phosphate hydroxyl proton
MASS 105    HAL1  1.008000 H ! alphatic proton
MASS 106    HAL2  1.008000 H ! alphatic proton
MASS 107    HAL3  1.008000 H ! alphatic proton
MASS 108    HEL1  1.008000 H ! for alkene; RHC=CR
MASS 109    HEL2  1.008000 H ! for alkene; H2C=CR
MASS 120   CL   12.011000 C ! carbonyl C (acetic acid/methyl acetate)
MASS 121   CTL1 12.011000 C ! sp3 carbon with 1 H  (-CH1-)
MASS 122   CTL2 12.011000 C ! carbon of methylene group (-CH2-)
MASS 123   CTL3 12.011000 C ! carbon of methyl group (-CH3)
MASS 124   CTL5 12.011000 C ! carbon of methyl group (-CH3) for tetramethylammonium
MASS 125   CEL1 12.011000 C ! for alkene; RHC=CR
MASS 126   CEL2 12.011000 C ! for alkene; H2C=CR
MASS 140   NTL  14.007000 N ! ammonium nitrogen
MASS 141   NH3L 14.007000 N ! nitrogen phosphatidylethanolamine
MASS 160   OBL  15.999400 O ! acetic acid carboxyl oxygen (e. to protein OB)
MASS 161   OCL  15.999400 O ! acetate oxygen
!MASS 162   OT   15.999400 O ! TIPS3P WATER OXYGEN
MASS 163   OSL  15.999400 O ! Nucleic acid phosphate ester oxygen
MASS 164   O2L  15.999400 O ! Nucleic acid =O in phosphate or sulfate
MASS 165   OHL  15.999400 O ! Nucleic acid phosphate hydroxyl oxygen
MASS 180   PL   30.974000 P ! phosphorus
MASS 185   SL   32.060000 S ! Sulfate sulfur
MASS 190   CLA  35.450000 CL ! CHLORIDE Anion
MASS 191   SOD  22.989770 NA ! Sodium Ion
MASS 192   MG   24.305000 MG ! Magnesium Ion
MASS 193   POT  39.102000 K ! Potassium Ion
!MASS 199   DUM   0.000000 H ! dummy atom
!nucleic acid section
MASS 202    HN1   1.008000 H ! Nucleic acid amine proton
MASS 203    HN2   1.008000 H ! Nucleic acid ring nitrogen proton
MASS 204    HN3   1.008000 H ! Nucleic acid aromatic carbon proton
MASS 205    HN3B  1.008000 H ! NAD+ aromatic hydrogen
MASS 206    HN3C  1.008000 H ! Standard aromatic hydrogen (as in benzene)
MASS 207    HNP   1.008000 H ! pure aromatic H
MASS 208    HN4   1.008000 H ! Nucleic acid phosphate hydroxyl proton
MASS 209    HN5   1.008000 H ! Nucleic acid ribose hydroxyl proton
MASS 210   HN6   1.008000 H ! Nucleic acid ribose aliphatic proton
MASS 211   HN7   1.008000 H ! Nucleic acid proton (equivalent to protein HA)
MASS 212   HN8   1.008000 H ! Bound to CN8 in nucleic acids/model compounds
MASS 213   HN9   1.008000 H ! Bound to CN9 in nucleic acids/model compounds
MASS 214   HNE1  1.008000 H ! for alkene; RHC=CR (modified thy patch Sasha)
MASS 215   HNE2  1.008000 H ! for alkene; H2C=CR (modified thy patch Sasha)
MASS 220   CN1  12.011000 C ! Nucleic acid carbonyl carbon
MASS 221   CN1A 12.011000 C ! NAD+/NADH amide carbonyl carbon
MASS 222   CN1T 12.011000 C ! Nucleic acid carbonyl carbon (T/U C2)
MASS 223   CN2  12.011000 C ! Nucleic acid aromatic carbon to amide
MASS 224   CN3  12.011000 C ! Nucleic acid aromatic carbon 
MASS 225   CN3A 12.011000 C ! NAD+ aromatic carbon
MASS 226   CN3B 12.011000 C ! NAD+ aromatic carbon
MASS 227   CN3C 12.011000 C ! NADH aromatic carbon
MASS 228   CN3D 12.011000 C ! Nucleic acid aromatic carbon for 5MC
MASS 229   CN3T 12.011000 C ! Nucleic acid aromatic carbon, Thy C5
MASS 230   CN4  12.011000 C ! Nucleic acid purine C8 and ADE C2  
MASS 231   CN5  12.011000 C ! Nucleic acid purine C4 and C5
MASS 232   CN5G 12.011000 C ! Nucleic acid guanine C5
MASS 233   CN7  12.011000 C ! Nucleic acid carbon (equivalent to protein CT1)
MASS 234   CN7B 12.011000 C ! Nucleic acid aliphatic carbon for C1'
MASS 235   CN7C 12.011000 C ! C2' in arabinose 
MASS 236   CN7D 12.011000 C ! C2' in nucleic acids fluorine derivatives 
MASS 237   CN8  12.011000 C ! Nucleic acid carbon (equivalent to protein CT2)
MASS 238   CN8B 12.011000 C ! Nucleic acid carbon (equivalent to protein CT2)
MASS 239   CN9  12.011000 C ! Nucleic acid carbon (equivalent to protein CT3)
MASS 240   CNE1 12.011000 C ! for alkene; RHC=CR (modified thy patch Sasha)
MASS 241   CNE2 12.011000 C ! for alkene; H2C=CR (modified thy patch Sasha)
MASS 242   CNA  12.011000 C ! pure aromatic carbon
MASS 243   CNA2 12.011000 C ! pure aromatic carbon bound to F
MASS 250   NN1  14.007000 N ! Nucleic acid amide nitrogen
MASS 251   NN1C 14.007000 N ! Nucleic acid imino nitrogen (cyt taut Sasha)
MASS 252   NN2  14.007000 N ! Nucleic acid protonated ring nitrogen
MASS 253   NN2B 14.007000 N ! From NN2, for N9 in GUA different from ADE
MASS 254   NN2C 14.007000 N ! Nucleic acid protonated ring nitrogen (cyt taut Sasha)
MASS 255   NN2U 14.007000 N ! Nucleic acid protonated ring nitrogen, ura N3
MASS 256   NN2G 14.007000 N ! Nucleic acid protonated ring nitrogen, gua N1
MASS 257   NN3  14.007000 N ! Nucleic acid unprotonated ring nitrogen 
MASS 258   NN3A 14.007000 N ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3
MASS 259   NN3I 14.007000 N ! Nucleic acid unprotonated ring nitrogen, inosine N3
MASS 260   NN3G 14.007000 N ! Nucleic acid unprotonated ring nitrogen, gua N3
MASS 261   NN4  14.007000 N ! Nucleic acid purine N7
MASS 262   NN5  14.007000 N ! Nucleic acid sp2 amine nitrogen
MASS 263   NN6  14.007000 N ! Nucleic acid sp3 amine nitrogen (equiv to protein nh3)
!MASS 70   OT   15.999400 O ! TIPS3P WATER OXYGEN
MASS 271   ON1  15.999400 O ! Nucleic acid carbonyl oxygen
MASS 272   ON1C 15.999400 O ! Nucleic acid carbonyl oxygen, cyt O2
MASS 273   ON2  15.999400 O ! Nucleic acid phosphate ester oxygen
MASS 274   ON3  15.999400 O ! Nucleic acid =O in phosphate 
MASS 275   ON4  15.999400 O ! Nucleic acid phosphate hydroxyl oxygen
MASS 276   ON5  15.999400 O ! Nucleic acid ribose hydroxyl oxygen
MASS 277   ON6  15.999400 O ! Nucleic acid deoxyribose ring oxygen
MASS 278   ON6B 15.999400 O ! Nucleic acid ribose ring oxygen
MASS 279   ON2b 15.999400 O ! Nucleic acid phosphate ester oxygen (pres tp1/tp2)
MASS 280   FN1  18.998400 F ! Fluorine for sugar derivatives (NF) 
MASS 281   FNA  18.998400 F ! Aromatic fluorine
MASS 282   P    30.974000 P ! phosphorus
MASS 283   P2   30.974000 P ! pyrophosphate phosphorus
MASS 293   CES 132.900000 CS ! Cesium Ion

MASS 294   N_1  15.015000 N ! assuming N -> 14.00700 + 1.008 * 1 (Hs)
MASS 295   C_2  13.019000 C ! assuming C -> 12.01100 + 1.008 * 1 (Hs)
MASS 296   C_3  12.011000 C ! assuming C -> 12.01100 + 1.008 * 0 (Hs)
MASS 297   O_4  15.999000 O ! assuming O -> 15.99900 + 1.008 * 0 (Hs)
MASS 298   C_5  14.027000 C ! assuming C -> 12.01100 + 1.008 * 2 (Hs)
MASS 300   C_6  12.011000 C ! assuming C -> 12.01100 + 1.008 * 0 (Hs)
MASS 301   N_7  15.015000 N ! assuming N -> 14.00700 + 1.008 * 1 (Hs)
MASS 302   C_8  13.019000 C ! assuming C -> 12.01100 + 1.008 * 1 (Hs)
MASS 303   C_9  13.019000 C ! assuming C -> 12.01100 + 1.008 * 1 (Hs)
MASS 304   N_10 15.015000 N ! assuming N -> 14.00700 + 1.008 * 1 (Hs)
MASS 305   O_11 15.999000 O ! assuming O -> 15.99900 + 1.008 * 0 (Hs)

!MASS 99   DUM   0.001    H ! dummy atom
!MASS 102  CPH1 12.011000 C ! For imidazole model compound (NF)
!MASS 103  CPH2 12.011000 C ! For imidazole model compound (NF)
!MASS 104  HR3   1.008000 H ! For imidazole model compound (NF) 
!MASS 105  HR1   1.008000 H ! For imidazole model compound (NF) 
!MASS 106  NR1  14.007000 H ! For nitrogen in imidazol (NF)
!MASS 107  NR2  14.007000 H ! For nitrogen in imidazol (NF)


DECL -CA  
DECL -C  
DECL -O  
DECL +N  
DECL +HN  
DECL +CA  
DEFA FIRS NTER LAST CTER   
AUTO ANGLES DIHE   

!--------------------test for resi HIS-----------------------------
RESI HIS
 GROUP
 ATOM  N     N_1     0.00  ! Nr of Hs =  1
 ATOM  CA    C_2     0.00  ! Nr of Hs =  1
 ATOM  C     C_3     0.00  ! Nr of Hs =  0
 ATOM  O     O_4     0.00  ! Nr of Hs =  0
 ATOM  CB    C_5     0.00  ! Nr of Hs =  2
 ATOM  CG    C_6     0.00  ! Nr of Hs =  0
 ATOM  ND1   N_7     0.00  ! Nr of Hs =  1
 ATOM  CD2   C_8     0.00  ! Nr of Hs =  1
 ATOM  CE1   C_9     0.00  ! Nr of Hs =  1
 ATOM  NE2   N_10    0.00  ! Nr of Hs =  1
 ATOM  OXT   O_11    0.00  ! Nr of Hs =  0

 BOND  N    CA       CA   C        CA   CB       C    O
 BOND  C    OXT      CB   CG       CG   ND1     CG   CD2
 BOND  ND1  CE1      CD2  NE2      CE1  NE2

! DIHE  N    CA   CB   CG  ! flexible DIHE ???   -66.29
! DIHE  CA   CB   CG   ND1 ! flexible DIHE ???    69.41
  DIHE  CB   CG   ND1  CE1 ! flat ? (180 degrees = trans)   183.93
  DIHE  CD2  CG   ND1  CE1 ! flat ? (0 degrees = cis)     0.43
  DIHE  CB   CG   CD2  NE2 ! flat ? (180 degrees = trans)   175.62
  DIHE  ND1  CG   CD2  NE2 ! flat ? (0 degrees = cis)    -0.47
  DIHE  CG   ND1  CE1  NE2 ! flat ? (0 degrees = cis)    -0.21
  DIHE  CG   CD2  NE2  CE1 ! flat ? (0 degrees = cis)     0.36
  DIHE  ND1  CE1  NE2  CD2 ! flat ? (0 degrees = cis)    -0.09

 IMPR  CA   N    C    CB  ! chirality or flatness IMPR    33.91
 IMPR  C    CA   O    OXT ! chirality or flatness IMPR    -0.80
 IMPR  CG   CB   ND1  CD2 ! chirality or flatness IMPR     2.28


! DONOr H?1  N
 ACCEPTOR  O    C
! DONOr H?1  ND1
! DONOr H?1  NE2
 ACCEPTOR  OXT  C

!-------------------------------------------------------------------------------


RESI ALA          0.00
GROUP   
ATOM N    NH1    -0.47  !     |
ATOM HN   H       0.31  !  HN-N
ATOM CA   CT1     0.07  !     |     HB1
ATOM HA   HB      0.09  !     |    /
GROUP                   !  HA-CA--CB-HB2
ATOM CB   CT3    -0.27  !     |    \
ATOM HB1  HA      0.09  !     |     HB3
ATOM HB2  HA      0.09  !   O=C
ATOM HB3  HA      0.09  !     |
GROUP                   !
ATOM C    C       0.51
ATOM O    O      -0.51
BOND CB CA  N  HN  N  CA  
BOND C  CA  C  +N  CA HA  CB HB1  CB HB2  CB HB3 
DOUBLE O  C 
IMPR N -C CA HN  C CA +N O   
CMAP -C  N  CA  C   N  CA  C  +N
DONOR HN N   
ACCEPTOR O C   
IC -C   CA   *N   HN    1.3551 126.4900  180.0000 115.4200  0.9996
IC -C   N    CA   C     1.3551 126.4900  180.0000 114.4400  1.5390
IC N    CA   C    +N    1.4592 114.4400  180.0000 116.8400  1.3558
IC +N   CA   *C   O     1.3558 116.8400  180.0000 122.5200  1.2297
IC CA   C    +N   +CA   1.5390 116.8400  180.0000 126.7700  1.4613
IC N    C    *CA  CB    1.4592 114.4400  123.2300 111.0900  1.5461
IC N    C    *CA  HA    1.4592 114.4400 -120.4500 106.3900  1.0840
IC C    CA   CB   HB1   1.5390 111.0900  177.2500 109.6000  1.1109
IC HB1  CA   *CB  HB2   1.1109 109.6000  119.1300 111.0500  1.1119
IC HB1  CA   *CB  HB3   1.1109 109.6000 -119.5800 111.6100  1.1114

RESI ARG          1.00
GROUP   
ATOM N    NH1    -0.47  !     |                      HH11
ATOM HN   H       0.31  !  HN-N                       |
ATOM CA   CT1     0.07  !     |   HB1 HG1 HD1 HE     NH1-HH12
ATOM HA   HB      0.09  !     |   |   |   |   |    //(+)  
GROUP                   !  HA-CA--CB--CG--CD--NE--CZ
ATOM CB   CT2    -0.18  !     |   |   |   |         \
ATOM HB1  HA      0.09  !     |   HB2 HG2 HD2        NH2-HH22
ATOM HB2  HA      0.09  !   O=C                       |
GROUP                   !     |                      HH21
ATOM CG   CT2    -0.18
ATOM HG1  HA      0.09
ATOM HG2  HA      0.09
GROUP   
ATOM CD   CT2     0.20
ATOM HD1  HA      0.09
ATOM HD2  HA      0.09
ATOM NE   NC2    -0.70
ATOM HE   HC      0.44
ATOM CZ   C       0.64
ATOM NH1  NC2    -0.80
ATOM HH11 HC      0.46
ATOM HH12 HC      0.46
ATOM NH2  NC2    -0.80
ATOM HH21 HC      0.46
ATOM HH22 HC      0.46
GROUP   
ATOM C    C       0.51
ATOM O    O      -0.51
BOND CB  CA  CG  CB  CD CG  NE CD  CZ NE   
BOND NH2 CZ  N  HN  N  CA   
BOND C   CA  C  +N  CA HA  CB HB1   
BOND CB  HB2 CG  HG1 CG HG2 CD HD1 CD HD2   
BOND NE  HE  NH1 HH11  NH1 HH12  NH2 HH21  NH2 HH22 
DOUBLE O  C    CZ  NH1  
IMPR N  -C  CA  HN   C CA +N O   
CMAP -C  N  CA  C   N  CA  C  +N
IMPR CZ NH1 NH2 NE
DONOR HN N   
DONOR HE NE   
DONOR HH11 NH1   
DONOR HH12 NH1   
DONOR HH21 NH2   
DONOR HH22 NH2   
ACCEPTOR O C   
IC -C   CA   *N   HN    1.3496 122.4500  180.0000 116.6700  0.9973
IC -C   N    CA   C     1.3496 122.4500  180.0000 109.8600  1.5227
IC N    CA   C    +N    1.4544 109.8600  180.0000 117.1200  1.3511
IC +N   CA   *C   O     1.3511 117.1200  180.0000 121.4000  1.2271
IC CA   C    +N   +CA   1.5227 117.1200  180.0000 124.6700  1.4565
IC N    C    *CA  CB    1.4544 109.8600  123.6400 112.2600  1.5552
IC N    C    *CA  HA    1.4544 109.8600 -117.9300 106.6100  1.0836
IC N    CA   CB   CG    1.4544 110.7000  180.0000 115.9500  1.5475
IC CG   CA   *CB  HB1   1.5475 115.9500  120.0500 106.4000  1.1163
IC CG   CA   *CB  HB2   1.5475 115.9500 -125.8100 109.5500  1.1124
IC CA   CB   CG   CD    1.5552 115.9500  180.0000 114.0100  1.5384
IC CD   CB   *CG  HG1   1.5384 114.0100  125.2000 108.5500  1.1121
IC CD   CB   *CG  HG2   1.5384 114.0100 -120.3000 108.9600  1.1143
IC CB   CG   CD   NE    1.5475 114.0100  180.0000 107.0900  1.5034
IC NE   CG   *CD  HD1   1.5034 107.0900  120.6900 109.4100  1.1143
IC NE   CG   *CD  HD2   1.5034 107.0900 -119.0400 111.5200  1.1150
IC CG   CD   NE   CZ    1.5384 107.0900  180.0000 123.0500  1.3401
IC CZ   CD   *NE  HE    1.3401 123.0500  180.0000 113.1400  1.0065
IC CD   NE   CZ   NH1   1.5034 123.0500  180.0000 118.0600  1.3311
IC NE   CZ   NH1  HH11  1.3401 118.0600 -178.2800 120.6100  0.9903
IC HH11 CZ   *NH1 HH12  0.9903 120.6100  171.1900 116.2900  1.0023
IC NH1  NE   *CZ  NH2   1.3311 118.0600  178.6400 122.1400  1.3292
IC NE   CZ   NH2  HH21  1.3401 122.1400 -174.1400 119.9100  0.9899
IC HH21 CZ   *NH2 HH22  0.9899 119.9100  166.1600 116.8800  0.9914 

RESI ASN          0.00
GROUP   
ATOM N    NH1    -0.47  !     |       
ATOM HN   H       0.31  !  HN-N       
ATOM CA   CT1     0.07  !     |   HB1 OD1    HD21 (cis to OD1)
ATOM HA   HB      0.09  !     |   |   ||    /
GROUP                   !  HA-CA--CB--CG--ND2
ATOM CB   CT2    -0.18  !     |   |         \
ATOM HB1  HA      0.09  !     |   HB2        HD22 (trans to OD1)
ATOM HB2  HA      0.09  !   O=C           
GROUP                   !     |           
ATOM CG   CC      0.55
ATOM OD1  O      -0.55
GROUP   
ATOM ND2  NH2    -0.62
ATOM HD21 H       0.32
ATOM HD22 H       0.30
GROUP   
ATOM C    C       0.51
ATOM O    O      -0.51
BOND CB CA  CG CB   ND2 CG   
BOND N  HN  N  CA   C   CA    C +N   
BOND CA HA  CB HB1  CB  HB2  ND2 HD21  ND2 HD22 
DOUBLE C  O   CG  OD1  
IMPR N   -C  CA   HN    C   CA +N   O   
IMPR CG  ND2 CB   OD1   CG  CB ND2  OD1   
IMPR ND2 CG  HD21 HD22  ND2 CG HD22 HD21   
CMAP -C  N  CA  C   N  CA  C  +N
DONOR HN N   
DONOR HD21 ND2   
DONOR HD22 ND2   
ACCEPTOR OD1 CG   
ACCEPTOR O C   
IC -C   CA   *N   HN    1.3480 124.0500  180.0000 114.4900  0.9992
IC -C   N    CA   C     1.3480 124.0500  180.0000 105.2300  1.5245
IC N    CA   C    +N    1.4510 105.2300  180.0000 117.3800  1.3467
IC +N   CA   *C   O     1.3467 117.3800  180.0000 120.3200  1.2282
IC CA   C    +N   +CA   1.5245 117.3800  180.0000 124.8800  1.4528
IC N    C    *CA  CB    1.4510 105.2300  121.1800 113.0400  1.5627
IC N    C    *CA  HA    1.4510 105.2300 -115.5200 107.6300  1.0848
IC N    CA   CB   CG    1.4510 110.9100  180.0000 114.3000  1.5319
IC CG   CA   *CB  HB1   1.5319 114.3000  119.1700 107.8200  1.1120
IC CG   CA   *CB  HB2   1.5319 114.3000 -123.7400 110.3400  1.1091
IC CA   CB   CG   OD1   1.5627 114.3000  180.0000 122.5600  1.2323
IC OD1  CB   *CG  ND2   1.2323 122.5600 -179.1900 116.1500  1.3521
IC CB   CG   ND2  HD21  1.5319 116.1500 -179.2600 117.3500  0.9963
IC HD21 CG   *ND2 HD22  0.9963 117.3500  178.0200 120.0500  0.9951

RESI ASP         -1.00
GROUP   
ATOM N    NH1    -0.47  !     |       
ATOM HN   H       0.31  !  HN-N       
ATOM CA   CT1     0.07  !     |   HB1   OD1
ATOM HA   HB      0.09  !     |   |    //
GROUP                   !  HA-CA--CB--CG
ATOM CB   CT2    -0.28  !     |   |    \
ATOM HB1  HA      0.09  !     |   HB2   OD2(-)
ATOM HB2  HA      0.09  !   O=C           
ATOM CG   CC      0.62  !     |           
ATOM OD1  OC     -0.76
ATOM OD2  OC     -0.76
GROUP   
ATOM C    C       0.51
ATOM O    O      -0.51
BOND CB CA  CG CB  OD2 CG   
BOND N  HN  N  CA   C   CA  C +N   
BOND CA HA  CB HB1  CB HB2   
DOUBLE  O   C   CG  OD1
IMPR N   -C CA  HN  C CA +N O   
!IMPR OD1 CB OD2 CG
IMPR CG  CB OD2 OD1
CMAP -C  N  CA  C   N  CA  C  +N
DONOR HN N   
ACCEPTOR OD1 CG   
ACCEPTOR OD2 CG   
ACCEPTOR O C   
IC -C   CA   *N   HN    1.3465 125.3100  180.0000 112.9400  0.9966
IC -C   N    CA   C     1.3465 125.3100  180.0000 105.6300  1.5315
IC N    CA   C    +N    1.4490 105.6300  180.0000 117.0600  1.3478
IC +N   CA   *C   O     1.3478 117.0600  180.0000 120.7100  1.2330
IC CA   C    +N   +CA   1.5315 117.0600  180.0000 125.3900  1.4484
IC N    C    *CA  CB    1.4490 105.6300  122.3300 114.1000  1.5619
IC N    C    *CA  HA    1.4490 105.6300 -116.4000 106.7700  1.0841
IC N    CA   CB   CG    1.4490 111.1000  180.0000 112.6000  1.5218
IC CG   CA   *CB  HB1   1.5218 112.6000  119.2200 109.2300  1.1086
IC CG   CA   *CB  HB2   1.5218 112.6000 -121.6100 110.6400  1.1080
IC CA   CB   CG   OD1   1.5619 112.6000  180.0000 117.9900  1.2565
IC OD1  CB   *CG  OD2   1.2565 117.9900 -170.2300 117.7000  1.2541

RESI CYS          0.00
GROUP   
ATOM N    NH1    -0.47  !     |       
ATOM HN   H       0.31  !  HN-N       
ATOM CA   CT1     0.07  !     |   HB1
ATOM HA   HB      0.09  !     |   |  
GROUP                   !  HA-CA--CB--SG
ATOM CB   CT2    -0.11  !     |   |     \
ATOM HB1  HA      0.09  !     |   HB2    HG1
ATOM HB2  HA      0.09  !   O=C           
ATOM SG   S      -0.23  !     |           
ATOM HG1  HS      0.16
GROUP   
ATOM C    C       0.51
ATOM O    O      -0.51
BOND CB CA   SG CB   N HN  N  CA   
BOND C  CA   C +N  CA HA  CB HB1   
BOND CB HB2  SG HG1
DOUBLE O  C   
IMPR N -C CA HN  C CA +N O   
CMAP -C  N  CA  C   N  CA  C  +N
DONOR HN N   
DONOR HG1 SG   
ACCEPTOR O C   
IC -C   CA   *N   HN    1.3479 123.9300  180.0000 114.7700  0.9982
IC -C   N    CA   C     1.3479 123.9300  180.0000 105.8900  1.5202
IC N    CA   C    +N    1.4533 105.8900  180.0000 118.3000  1.3498
IC +N   CA   *C   O     1.3498 118.3000  180.0000 120.5900  1.2306
IC CA   C    +N   +CA   1.5202 118.3000  180.0000 124.5000  1.4548
IC N    C    *CA  CB    1.4533 105.8900  121.7900 111.9800  1.5584
IC N    C    *CA  HA    1.4533 105.8900 -116.3400 107.7100  1.0837
IC N    CA   CB   SG    1.4533 111.5600  180.0000 113.8700  1.8359
IC SG   CA   *CB  HB1   1.8359 113.8700  119.9100 107.2400  1.1134
IC SG   CA   *CB  HB2   1.8359 113.8700 -125.3200 109.8200  1.1124
IC CA   CB   SG   HG1   1.5584 113.8700  176.9600  97.1500  1.3341

RESI GLN          0.00
GROUP   
ATOM N    NH1    -0.47  !     |          
ATOM HN   H       0.31  !  HN-N          
ATOM CA   CT1     0.07  !     |   HB1 HG1 OE1   HE21 (cis to OE1)
ATOM HA   HB      0.09  !     |   |   |   ||    /
GROUP                   !  HA-CA--CB--CG--CD--NE2
ATOM CB   CT2    -0.18  !     |   |   |         \
ATOM HB1  HA      0.09  !     |   HB2 HG2       HE22 (trans to OE1)
ATOM HB2  HA      0.09  !   O=C          
GROUP                   !     |          
ATOM CG   CT2    -0.18
ATOM HG1  HA      0.09
ATOM HG2  HA      0.09
GROUP   
ATOM CD   CC      0.55
ATOM OE1  O      -0.55
GROUP   
ATOM NE2  NH2    -0.62
ATOM HE21 H       0.32
ATOM HE22 H       0.30
GROUP   
ATOM C    C       0.51
ATOM O    O      -0.51
BOND CB CA  CG  CB   CD  CG   NE2 CD   
BOND N  HN  N   CA   C   CA   
BOND C  +N  CA  HA   CB  HB1  CB  HB2  CG HG1   
BOND CG HG2 NE2 HE21 NE2 HE22   
DOUBLE O  C    CD  OE1  
IMPR N   -C  CA   HN    C   CA +N   O   
IMPR CD  NE2 CG   OE1   CD  CG NE2  OE1   
IMPR NE2 CD  HE21 HE22  NE2 CD HE22 HE21   
CMAP -C  N  CA  C   N  CA  C  +N
DONOR HN N   
DONOR HE21 NE2   
DONOR HE22 NE2   
ACCEPTOR OE1 CD   
ACCEPTOR O C   
IC -C   CA   *N   HN    1.3477 123.9300  180.0000 114.4500  0.9984
IC -C   N    CA   C     1.3477 123.9300  180.0000 106.5700  1.5180
IC N    CA   C    +N    1.4506 106.5700  180.0000 117.7200  1.3463
IC +N   CA   *C   O     1.3463 117.7200  180.0000 120.5900  1.2291
IC CA   C    +N   +CA   1.5180 117.7200  180.0000 124.3500  1.4461
IC N    C    *CA  CB    1.4506 106.5700  121.9100 111.6800  1.5538
IC N    C    *CA  HA    1.4506 106.5700 -116.8200 107.5300  1.0832
IC N    CA   CB   CG    1.4506 111.4400  180.0000 115.5200  1.5534
IC CG   CA   *CB  HB1   1.5534 115.5200  120.9300 106.8000  1.1147
IC CG   CA   *CB  HB2   1.5534 115.5200 -124.5800 109.3400  1.1140
IC CA   CB   CG   CD    1.5538 115.5200  180.0000 112.5000  1.5320
IC CD   CB   *CG  HG1   1.5320 112.5000  118.6900 110.4100  1.1112
IC CD   CB   *CG  HG2   1.5320 112.5000 -121.9100 110.7400  1.1094
IC CB   CG   CD   OE1   1.5534 112.5000  180.0000 121.5200  1.2294
IC OE1  CG   *CD  NE2   1.2294 121.5200  179.5700 116.8400  1.3530
IC CG   CD   NE2  HE21  1.5320 116.8400 -179.7200 116.8600  0.9959
IC HE21 CD   *NE2 HE22  0.9959 116.8600 -178.9100 119.8300  0.9943

RESI GLU         -1.00
GROUP   
ATOM N    NH1    -0.47  !     |          
ATOM HN   H       0.31  !  HN-N          
ATOM CA   CT1     0.07  !     |   HB1 HG1   OE1
ATOM HA   HB      0.09  !     |   |   |    //
GROUP                   !  HA-CA--CB--CG--CD
ATOM CB   CT2    -0.18  !     |   |   |    \
ATOM HB1  HA      0.09  !     |   HB2 HG2   OE2(-)
ATOM HB2  HA      0.09  !   O=C          
GROUP                   !     |          
ATOM CG   CT2    -0.28
ATOM HG1  HA      0.09
ATOM HG2  HA      0.09
ATOM CD   CC      0.62
ATOM OE1  OC     -0.76
ATOM OE2  OC     -0.76
GROUP   
ATOM C    C       0.51
ATOM O    O      -0.51
BOND CB CA  CG CB  CD CG  OE2 CD   
BOND N  HN  N  CA C   CA   
BOND C  +N  CA HA  CB HB1 CB  HB2 CG  HG1   
BOND CG HG2  
DOUBLE O  C   CD  OE1 
IMPR N   -C CA  HN  C CA +N O   
IMPR CD CG OE2 OE1
CMAP -C  N  CA  C   N  CA  C  +N
DONOR HN N   
ACCEPTOR OE1 CD   
ACCEPTOR OE2 CD   
ACCEPTOR O C   
IC -C   CA   *N   HN    1.3471 124.4500  180.0000 113.9900  0.9961
IC -C   N    CA   C     1.3471 124.4500  180.0000 107.2700  1.5216
IC N    CA   C    +N    1.4512 107.2700  180.0000 117.2500  1.3501
IC +N   CA   *C   O     1.3501 117.2500  180.0000 121.0700  1.2306
IC CA   C    +N   +CA   1.5216 117.2500  180.0000 124.3000  1.4530
IC N    C    *CA  CB    1.4512 107.2700  121.9000 111.7100  1.5516
IC N    C    *CA  HA    1.4512 107.2700 -118.0600 107.2600  1.0828
IC N    CA   CB   CG    1.4512 111.0400  180.0000 115.6900  1.5557
IC CG   CA   *CB  HB1   1.5557 115.6900  121.2200 108.1600  1.1145
IC CG   CA   *CB  HB2   1.5557 115.6900 -123.6500 109.8100  1.1131
IC CA   CB   CG   CD    1.5516 115.6900  180.0000 115.7300  1.5307
IC CD   CB   *CG  HG1   1.5307 115.7300  117.3800 109.5000  1.1053
IC CD   CB   *CG  HG2   1.5307 115.7300 -121.9600 111.0000  1.1081
IC CB   CG   CD   OE1   1.5557 115.7300  180.0000 114.9900  1.2590
IC OE1  CG   *CD  OE2   1.2590 114.9900 -179.1000 120.0800  1.2532

RESI GLY          0.00
GROUP   
ATOM N    NH1    -0.47  !     |
ATOM HN   H       0.31  !     N-H
ATOM CA   CT2    -0.02  !     |  
ATOM HA1  HB      0.09  !     |  
ATOM HA2  HB      0.09  ! HA1-CA-HA2
GROUP                   !     |  
ATOM C    C       0.51  !     |  
ATOM O    O      -0.51  !     C=O
                        !     |
BOND N HN  N  CA  C CA   
BOND C +N  CA HA1 CA HA2  
DOUBLE O  C 
IMPR N -C  CA HN  C CA   +N O   
CMAP -C  N  CA  C   N  CA  C  +N
DONOR HN N   
ACCEPTOR O C   
IC -C   CA   *N   HN    1.3475 122.8200  180.0000 115.6200  0.9992
IC -C   N    CA   C     1.3475 122.8200  180.0000 108.9400  1.4971
IC N    CA   C    +N    1.4553 108.9400  180.0000 117.6000  1.3479
IC +N   CA   *C   O     1.3479 117.6000  180.0000 120.8500  1.2289
IC CA   C    +N   +CA   1.4971 117.6000  180.0000 124.0800  1.4560
IC N    C    *CA  HA1   1.4553 108.9400  117.8600 108.0300  1.0814
IC N    C    *CA  HA2   1.4553 108.9400 -118.1200 107.9500  1.0817
PATCHING FIRS GLYP   

RESI HSD          0.00  ! neutral HIS, proton on ND1
GROUP   
ATOM N    NH1    -0.47  !     |          HD1    HE1
ATOM HN   H       0.31  !  HN-N           |     /
ATOM CA   CT1     0.07  !     |   HB1    ND1--CE1
ATOM HA   HB      0.09  !     |   |     /      ||
GROUP                   !  HA-CA--CB--CG       ||
ATOM CB   CT2    -0.09  !     |   |     \\     ||
ATOM HB1  HA      0.09  !     |   HB2    CD2--NE2
ATOM HB2  HA      0.09  !   O=C           |
ATOM ND1  NR1    -0.36  !     |          HD2
ATOM HD1  H       0.32
ATOM CG   CPH1   -0.05
GROUP   
ATOM CE1  CPH2    0.25
ATOM HE1  HR1     0.13
ATOM NE2  NR2    -0.70
ATOM CD2  CPH1    0.22
ATOM HD2  HR3     0.10
GROUP   
ATOM C    C       0.51
ATOM O    O      -0.51
BOND CB  CA   CG  CB   ND1 CG   CE1 ND1   
BOND NE2 CD2  N   HN   N   CA   
BOND C   CA   C   +N   CA  HA   CB  HB1   
BOND CB  HB2  ND1 HD1  CD2 HD2  CE1 HE1  
DOUBLE O  C   CG  CD2   CE1  NE2 
IMPR ND1 CG CE1 HD1  CD2 CG  NE2 HD2  CE1 ND1 NE2 HE1   
IMPR ND1 CE1 CG HD1  CD2 NE2 CG  HD2  CE1 NE2 ND1 HE1   
IMPR N   -C  CA HN   C   CA  +N  O   
CMAP -C  N  CA  C   N  CA  C  +N
DONOR HN N   
DONOR HD1 ND1   
ACCEPTOR NE2   
ACCEPTOR O C   
IC -C   CA   *N   HN    1.3475 123.2700  180.0000 115.2100  0.9988
IC -C   N    CA   C     1.3475 123.2700  180.0000 107.7000  1.5166
IC N    CA   C    +N    1.4521 107.7000  180.0000 117.5700  1.3509
IC +N   CA   *C   O     1.3509 117.5700  180.0000 120.2400  1.2273
IC CA   C    +N   +CA   1.5166 117.5700  180.0000 123.7200  1.4545
IC N    C    *CA  CB    1.4521 107.7000  122.4600 109.9900  1.5519
IC N    C    *CA  HA    1.4521 107.7000 -117.4900 107.3700  1.0830
IC N    CA   CB   CG    1.4521 112.1200  180.0000 114.0500  1.5041
IC CG   CA   *CB  HB1   1.5041 114.0500  121.1700 109.0100  1.1118
IC CG   CA   *CB  HB2   1.5041 114.0500 -122.3600 109.5300  1.1121
IC CA   CB   CG   ND1   1.5519 114.0500   90.0000 124.1000  1.3783
IC ND1  CB   *CG  CD2   1.3783 124.1000 -171.2900 129.6000  1.3597
IC CB   CG   ND1  CE1   1.5041 124.1000 -173.2100 107.0300  1.3549
IC CB   CG   CD2  NE2   1.5041 129.6000  171.9900 110.0300  1.3817
IC NE2  ND1  *CE1 HE1   1.3166 111.6300 -179.6300 123.8900  1.0932
IC CE1  CG   *ND1 HD1   1.3549 107.0300 -174.6500 126.2600  1.0005
IC NE2  CG   *CD2 HD2   1.3817 110.0300 -177.8500 129.6300  1.0834

RESI IMD          0.00  ! neutral imidazole, from HSD, proton on ND1
GROUP   
ATOM HG   HR3     0.09
ATOM ND1  NR1    -0.36  !         HD1    HE1 
ATOM HD1  H       0.32  !          |     /   
ATOM CG   CPH1   -0.05  !         ND1--CE1   
GROUP   	        !        /      ||   
ATOM CE1  CPH2    0.25  !  HG--CG       ||   
ATOM HE1  HR1     0.13  !        \\     ||   
ATOM NE2  NR2    -0.70  !         CD2--NE2   
ATOM CD2  CPH1    0.22  !          |	    
ATOM HD2  HR3     0.10  !         HD2        
BOND CG  HG   ND1 CG   CE1 ND1   
BOND NE2 CD2  
BOND ND1 HD1  CD2 HD2  CE1 HE1  
DOUBLE CG  CD2   CE1  NE2 
IMPR ND1 CG CE1 HD1  CD2 CG  NE2 HD2  CE1 ND1 NE2 HE1   
IMPR ND1 CE1 CG HD1  CD2 NE2 CG  HD2  CE1 NE2 ND1 HE1   
DONOR HD1 ND1   
ACCEPTOR NE2   
PATCHING FIRS NONE LAST NONE   

RESI IME          0.00  ! neutral imidazole, from HSE, proton on NE2
GROUP                 
ATOM HG   HR3     0.10  !                HE1
ATOM ND1  NR2    -0.70  !            __  /  
ATOM CG   CPH1    0.22  !         ND1--CE1  
ATOM CE1  CPH2    0.25  !        /      |   
ATOM HE1  HR1     0.13  !  HG--CG       |   
GROUP		        !        \\     |   
ATOM NE2  NR1    -0.36  !         CD2--NE2  
ATOM HE2  H       0.32  !          |     \  
ATOM CD2  CPH1   -0.05  !         HD2    HE2
ATOM HD2  HR3     0.09
BOND CG  HG   ND1 CG     
BOND NE2 CD2
BOND NE2 CE1
BOND NE2 HE2  CD2 HD2  CE1 HE1 
DOUBLE   CD2 CG   CE1 ND1
IMPR NE2 CD2 CE1 HE2  CD2 CG  NE2 HD2  CE1 ND1 NE2 HE1   
IMPR NE2 CE1 CD2 HE2  CD2 NE2 CG  HD2  CE1 NE2 ND1 HE1   
DONOR HE2 NE2   
ACCEPTOR ND1   
PATCHING FIRS NONE LAST NONE   

RESI HSE          0.00  ! neutral His, proton on NE2
GROUP   
ATOM N    NH1    -0.47  !     |                 HE1
ATOM HN   H       0.31  !  HN-N             __  /
ATOM CA   CT1     0.07  !     |   HB1    ND1--CE1
ATOM HA   HB      0.09  !     |   |     /      |
GROUP                   !  HA-CA--CB--CG       |
ATOM CB   CT2    -0.08  !     |   |     \\     |
ATOM HB1  HA      0.09  !     |   HB2    CD2--NE2
ATOM HB2  HA      0.09  !   O=C           |     \
ATOM ND1  NR2    -0.70  !     |          HD2    HE2
ATOM CG   CPH1    0.22
ATOM CE1  CPH2    0.25
ATOM HE1  HR1     0.13
GROUP
ATOM NE2  NR1    -0.36
ATOM HE2  H       0.32
ATOM CD2  CPH1   -0.05
ATOM HD2  HR3     0.09
GROUP   
ATOM C    C       0.51
ATOM O    O      -0.51
BOND CB  CA   CG  CB   ND1 CG     
BOND NE2 CD2  N   HN   N   CA      
BOND C   CA   C   +N   NE2 CE1  CA  HA   CB HB1   
BOND CB  HB2  NE2 HE2  CD2 HD2  CE1 HE1 
DOUBLE   O   C   CD2 CG   CE1 ND1
IMPR NE2 CD2 CE1 HE2  CD2 CG  NE2 HD2  CE1 ND1 NE2 HE1   
IMPR NE2 CE1 CD2 HE2  CD2 NE2 CG  HD2  CE1 NE2 ND1 HE1   
IMPR N   -C  CA  HN   C   CA  +N  O   
CMAP -C  N  CA  C   N  CA  C  +N
DONOR HN N   
DONOR HE2 NE2   
ACCEPTOR ND1   
ACCEPTOR O C   
IC -C   CA   *N   HN    1.3472 124.1600  180.0000 114.3600  0.9991
IC -C   N    CA   C     1.3472 124.1600  180.0000 106.4300  1.5166
IC N    CA   C    +N    1.4532 106.4300  180.0000 116.9700  1.3446
IC +N   CA   *C   O     1.3446 116.9700  180.0000 120.6800  1.2290
IC CA   C    +N   +CA   1.5166 116.9700  180.0000 124.9500  1.4505
IC N    C    *CA  CB    1.4532 106.4300  123.5200 111.6700  1.5578
IC N    C    *CA  HA    1.4532 106.4300 -116.4900 107.0800  1.0833
IC N    CA   CB   CG    1.4532 112.8200  180.0000 116.9400  1.5109
IC CG   CA   *CB  HB1   1.5109 116.9400  119.8000 107.9100  1.1114
IC CG   CA   *CB  HB2   1.5109 116.9400 -124.0400 109.5000  1.1101
IC CA   CB   CG   ND1   1.5578 116.9400   90.0000 120.1700  1.3859
IC ND1  CB   *CG  CD2   1.3859 120.1700 -178.2600 129.7100  1.3596
IC CB   CG   ND1  CE1   1.5109 120.1700 -179.2000 105.2000  1.3170
IC CB   CG   CD2  NE2   1.5109 129.7100  178.6600 105.8000  1.3782
IC NE2  ND1  *CE1 HE1   1.3539 111.7600  179.6900 124.5800  1.0929
IC CE1  CD2  *NE2 HE2   1.3539 107.1500 -178.6900 125.8600  0.9996
IC NE2  CG   *CD2 HD2   1.3782 105.8000 -179.3500 129.8900  1.0809

RESI HSP          1.00  ! Protonated His
GROUP   
ATOM N    NH1    -0.47  !     |          HD1    HE1
ATOM HN   H       0.31  !  HN-N           |     /
ATOM CA   CT1     0.07  !     |   HB1    ND1--CE1
ATOM HA   HB      0.09  !     |   |     /      ||
GROUP                   !  HA-CA--CB--CG       ||
ATOM CB   CT2    -0.05  !     |   |     \\     ||
ATOM HB1  HA      0.09  !     |   HB2    CD2--NE2(+)
ATOM HB2  HA      0.09  !   O=C           |     \
ATOM CD2  CPH1    0.19  !     |          HD2    HE2
ATOM HD2  HR1     0.13
ATOM CG   CPH1    0.19
GROUP
ATOM NE2  NR3    -0.51
ATOM HE2  H       0.44
ATOM ND1  NR3    -0.51
ATOM HD1  H       0.44
ATOM CE1  CPH2    0.32
ATOM HE1  HR2     0.18
GROUP   
ATOM C    C       0.51
ATOM O    O      -0.51
BOND CB  CA   CG  CB   ND1 CG   CE1 ND1   
BOND NE2 CD2  N   HN   N   CA   
BOND C   CA   C   +N  CA  HA  CB HB1   
BOND CB  HB2  ND1 HD1  NE2 HE2  CD2 HD2 CE1 HE1
DOUBLE  O   C   CD2 CG     NE2 CE1
IMPR ND1 CG  CE1 HD1  ND1 CE1 CG  HD1
IMPR NE2 CD2 CE1 HE2  NE2 CE1 CD2 HE2   
IMPR N   -C  CA  HN   C   CA  +N  O   
DONOR HN N   
DONOR HD1 ND1   
DONOR HE2 NE2   
ACCEPTOR O C   
IC -C   CA   *N   HN    1.3489 123.9300  180.0000 118.8000  1.0041
IC -C   N    CA   C     1.3489 123.9300  180.0000 112.0300  1.5225
IC N    CA   C    +N    1.4548 112.0300  180.0000 116.4900  1.3464
IC +N   CA   *C   O     1.3464 116.4900  180.0000 121.2000  1.2284
IC CA   C    +N   +CA   1.5225 116.4900  180.0000 124.2400  1.4521
IC N    C    *CA  CB    1.4548 112.0300  125.1300 109.3800  1.5533
IC N    C    *CA  HA    1.4548 112.0300 -119.2000 106.7200  1.0832
IC N    CA   CB   CG    1.4548 112.2500  180.0000 114.1800  1.5168
IC CG   CA   *CB  HB1   1.5168 114.1800  122.5000 108.9900  1.1116
IC CG   CA   *CB  HB2   1.5168 114.1800 -121.5100 108.9700  1.1132
IC CA   CB   CG   ND1   1.5533 114.1800   90.0000 122.9400  1.3718
IC ND1  CB   *CG  CD2   1.3718 122.9400 -165.2600 128.9300  1.3549
IC CB   CG   ND1  CE1   1.5168 122.9400 -167.6200 108.9000  1.3262
IC CB   CG   CD2  NE2   1.5168 128.9300  167.1300 106.9300  1.3727
IC NE2  ND1  *CE1 HE1   1.3256 108.5000  178.3900 125.7600  1.0799
IC CE1  CD2  *NE2 HE2   1.3256 108.8200 -172.9400 125.5200  1.0020
IC CE1  CG   *ND1 HD1   1.3262 108.9000  171.4900 126.0900  1.0018
IC NE2  CG   *CD2 HD2   1.3727 106.9300 -174.4900 128.4100  1.0867

RESI ILE          0.00
GROUP   
ATOM N    NH1    -0.47  !     |    HG21 HG22
ATOM HN   H       0.31  !  HN-N      | / 
ATOM CA   CT1     0.07  !     |     CG2--HG23
ATOM HA   HB      0.09  !     |    /
GROUP                   !  HA-CA--CB-HB    HD1
ATOM CB   CT1    -0.09  !     |    \       /
ATOM HB   HA      0.09  !     |     CG1--CD--HD2
GROUP                   !   O=C    / \     \	 
ATOM CG2  CT3    -0.27  !     | HG11 HG12  HD3
ATOM HG21 HA      0.09
ATOM HG22 HA      0.09
ATOM HG23 HA      0.09
GROUP   
ATOM CG1  CT2    -0.18
ATOM HG11 HA      0.09
ATOM HG12 HA      0.09
GROUP   
ATOM CD   CT3    -0.27
ATOM HD1  HA      0.09
ATOM HD2  HA      0.09
ATOM HD3  HA      0.09
GROUP   
ATOM C    C       0.51
ATOM O    O      -0.51
BOND CB  CA   CG1 CB   CG2 CB   CD  CG1   
BOND N   HN   N   CA    C   CA   C   +N   
BOND CA  HA   CB  HB   CG1 HG11 CG1 HG12 CG2 HG21   
BOND CG2 HG22 CG2 HG23 CD  HD1  CD  HD2  CD  HD3 
DOUBLE  O   C
IMPR N -C CA HN  C CA +N O   
CMAP -C  N  CA  C   N  CA  C  +N
DONOR HN N   
ACCEPTOR O C   
IC -C   CA   *N   HN    1.3470 124.1600  180.0000 114.1900  0.9978
IC -C   N    CA   C     1.3470 124.1600  180.0000 106.3500  1.5190
IC N    CA   C    +N    1.4542 106.3500  180.0000 117.9700  1.3465
IC +N   CA   *C   O     1.3465 117.9700  180.0000 120.5900  1.2300
IC CA   C    +N   +CA   1.5190 117.9700  180.0000 124.2100  1.4467
IC N    C    *CA  CB    1.4542 106.3500  124.2200 112.9300  1.5681
IC N    C    *CA  HA    1.4542 106.3500 -115.6300 106.8100  1.0826
IC N    CA   CB   CG1   1.4542 112.7900  180.0000 113.6300  1.5498
IC CG1  CA   *CB  HB    1.5498 113.6300  114.5500 104.4800  1.1195
IC CG1  CA   *CB  CG2   1.5498 113.6300 -130.0400 113.9300  1.5452
IC CA   CB   CG2  HG21  1.5681 113.9300 -171.3000 110.6100  1.1100
IC HG21 CB   *CG2 HG22  1.1100 110.6100  119.3500 110.9000  1.1102
IC HG21 CB   *CG2 HG23  1.1100 110.6100 -120.0900 110.9700  1.1105
IC CA   CB   CG1  CD    1.5681 113.6300  180.0000 114.0900  1.5381
IC CD   CB   *CG1 HG11  1.5381 114.0900  122.3600 109.7800  1.1130
IC CD   CB   *CG1 HG12  1.5381 114.0900 -120.5900 108.8900  1.1141
IC CB   CG1  CD   HD1   1.5498 114.0900 -176.7800 110.3100  1.1115
IC HD1  CG1  *CD  HD2   1.1115 110.3100  119.7500 110.6500  1.1113
IC HD1  CG1  *CD  HD3   1.1115 110.3100 -119.7000 111.0200  1.1103

RESI LEU          0.00
GROUP   
ATOM N    NH1    -0.47  !     |        HD11 HD12
ATOM HN   H       0.31  !  HN-N          | /
ATOM CA   CT1     0.07  !     |   HB1   CD1--HD13
ATOM HA   HB      0.09  !     |   |    /
GROUP                   !  HA-CA--CB--CG-HG
ATOM CB   CT2    -0.18  !     |   |    \ 
ATOM HB1  HA      0.09  !     |   HB2   CD2--HD23
ATOM HB2  HA      0.09  !   O=C          | \
GROUP                   !     |        HD21 HD22
ATOM CG   CT1    -0.09
ATOM HG   HA      0.09
GROUP   
ATOM CD1  CT3    -0.27
ATOM HD11 HA      0.09
ATOM HD12 HA      0.09
ATOM HD13 HA      0.09
GROUP   
ATOM CD2  CT3    -0.27
ATOM HD21 HA      0.09
ATOM HD22 HA      0.09
ATOM HD23 HA      0.09
GROUP   
ATOM C    C       0.51
ATOM O    O      -0.51
BOND CB  CA   CG  CB   CD1 CG   CD2 CG   
BOND N   HN   N   CA    C   CA   C +N   
BOND CA  HA   CB  HB1  CB  HB2  CG  HG   CD1 HD11   
BOND CD1 HD12 CD1 HD13 CD2 HD21 CD2 HD22 CD2 HD23
DOUBLE   O   C
IMPR N -C CA HN  C CA +N O   
CMAP -C  N  CA  C   N  CA  C  +N
DONOR HN N   
ACCEPTOR O C   
IC -C   CA   *N   HN    1.3474 124.3100  180.0000 114.2600  0.9979
IC -C   N    CA   C     1.3474 124.3100  180.0000 106.0500  1.5184
IC N    CA   C    +N    1.4508 106.0500  180.0000 117.9300  1.3463
IC +N   CA   *C   O     1.3463 117.9300  180.0000 120.5600  1.2299
IC CA   C    +N   +CA   1.5184 117.9300  180.0000 124.2600  1.4467
IC N    C    *CA  CB    1.4508 106.0500  121.5200 112.1200  1.5543
IC N    C    *CA  HA    1.4508 106.0500 -116.5000 107.5700  1.0824
IC N    CA   CB   CG    1.4508 111.1900  180.0000 117.4600  1.5472
IC CG   CA   *CB  HB1   1.5472 117.4600  120.9800 107.1700  1.1145
IC CG   CA   *CB  HB2   1.5472 117.4600 -124.6700 108.9800  1.1126
IC CA   CB   CG   CD1   1.5543 117.4600  180.0000 110.4800  1.5361
IC CD1  CB   *CG  CD2   1.5361 110.4800  120.0000 112.5700  1.5360
IC CD1  CD2  *CG  HG    1.5361 110.2600  120.0000 108.0200  1.1168
IC CB   CG   CD1  HD11  1.5472 110.4800  177.3300 110.5400  1.1111
IC HD11 CG   *CD1 HD12  1.1111 110.5400  119.9600 110.6200  1.1112
IC HD11 CG   *CD1 HD13  1.1111 110.5400 -119.8500 110.6900  1.1108
IC CB   CG   CD2  HD21  1.5472 112.5700  178.9600 110.3200  1.1116
IC HD21 CG   *CD2 HD22  1.1116 110.3200  119.7100 111.6900  1.1086
IC HD21 CG   *CD2 HD23  1.1116 110.3200 -119.6100 110.4900  1.1115

RESI LYS          1.00
GROUP   
ATOM N    NH1    -0.47  !     |                   
ATOM HN   H       0.31  !  HN-N                   
ATOM CA   CT1     0.07  !     |   HB1 HG1 HD1 HE1    HZ1
ATOM HA   HB      0.09  !     |   |   |   |   |     /   
GROUP                   !  HA-CA--CB--CG--CD--CE--NZ--HZ2
ATOM CB   CT2    -0.18  !     |   |   |   |   |     \
ATOM HB1  HA      0.09  !     |   HB2 HG2 HD2 HE2    HZ3
ATOM HB2  HA      0.09  !   O=C                  
GROUP                   !     |                  
ATOM CG   CT2    -0.18
ATOM HG1  HA      0.09
ATOM HG2  HA      0.09
GROUP   
ATOM CD   CT2    -0.18
ATOM HD1  HA      0.09
ATOM HD2  HA      0.09
GROUP   
ATOM CE   CT2     0.21
ATOM HE1  HA      0.05
ATOM HE2  HA      0.05
ATOM NZ   NH3    -0.30
ATOM HZ1  HC      0.33
ATOM HZ2  HC      0.33
ATOM HZ3  HC      0.33
GROUP   
ATOM C    C       0.51
ATOM O    O      -0.51
BOND CB CA   CG CB   CD CG   CE CD   NZ CE   
BOND N  HN   N  CA    C  CA   
BOND C  +N   CA HA   CB HB1  CB HB2  CG HG1   
BOND CG HG2  CD HD1  CD HD2  CE HE1  CE HE2 
DOUBLE   O  C   
BOND NZ HZ1  NZ HZ2  NZ HZ3   
IMPR N -C CA HN  C CA +N O   
CMAP -C  N  CA  C   N  CA  C  +N
DONOR HN N   
DONOR HZ1 NZ   
DONOR HZ2 NZ   
DONOR HZ3 NZ   
ACCEPTOR O C   
IC -C   CA   *N   HN    1.3482 123.5700  180.0000 115.1100  0.9988
IC -C   N    CA   C     1.3482 123.5700  180.0000 107.2900  1.5187
IC N    CA   C    +N    1.4504 107.2900  180.0000 117.2700  1.3478
IC +N   CA   *C   O     1.3478 117.2700  180.0000 120.7900  1.2277
IC CA   C    +N   +CA   1.5187 117.2700  180.0000 124.9100  1.4487
IC N    C    *CA  CB    1.4504 107.2900  122.2300 111.3600  1.5568
IC N    C    *CA  HA    1.4504 107.2900 -116.8800 107.3600  1.0833
IC N    CA   CB   CG    1.4504 111.4700  180.0000 115.7600  1.5435
IC CG   CA   *CB  HB1   1.5435 115.7600  120.9000 107.1100  1.1146
IC CG   CA   *CB  HB2   1.5435 115.7600 -124.4800 108.9900  1.1131
IC CA   CB   CG   CD    1.5568 115.7600  180.0000 113.2800  1.5397
IC CD   CB   *CG  HG1   1.5397 113.2800  120.7400 109.1000  1.1138
IC CD   CB   *CG  HG2   1.5397 113.2800 -122.3400 108.9900  1.1143
IC CB   CG   CD   CE    1.5435 113.2800  180.0000 112.3300  1.5350
IC CE   CG   *CD  HD1   1.5350 112.3300  122.2500 108.4100  1.1141
IC CE   CG   *CD  HD2   1.5350 112.3300 -121.5900 108.1300  1.1146
IC CG   CD   CE   NZ    1.5397 112.3300  180.0000 110.4600  1.4604
IC NZ   CD   *CE  HE1   1.4604 110.4600  119.9100 110.5100  1.1128
IC NZ   CD   *CE  HE2   1.4604 110.4600 -120.0200 110.5700  1.1123
IC CD   CE   NZ   HZ1   1.5350 110.4600  179.9200 110.0200  1.0404
IC HZ1  CE   *NZ  HZ2   1.0404 110.0200  120.2700 109.5000  1.0402
IC HZ1  CE   *NZ  HZ3   1.0404 110.0200 -120.1300 109.4000  1.0401

RESI MET          0.00
GROUP   
ATOM N    NH1    -0.47  !     |                   
ATOM HN   H       0.31  !  HN-N                   
ATOM CA   CT1     0.07  !     |   HB1 HG1     HE1 
ATOM HA   HB      0.09  !     |   |   |       |   
GROUP                   !  HA-CA--CB--CG--SD--CE--HE3
ATOM CB   CT2    -0.18  !     |   |   |       |   
ATOM HB1  HA      0.09  !     |   HB2 HG2     HE2 
ATOM HB2  HA      0.09  !   O=C                  
GROUP                   !     |                  
ATOM CG   CT2    -0.14
ATOM HG1  HA      0.09
ATOM HG2  HA      0.09
ATOM SD   S      -0.09
ATOM CE   CT3    -0.22
ATOM HE1  HA      0.09
ATOM HE2  HA      0.09
ATOM HE3  HA      0.09
GROUP   
ATOM C    C       0.51
ATOM O    O      -0.51
BOND CB CA   CG CB   SD CG   CE SD   
BOND N  HN   N  CA    C  CA   C  +N   
BOND CA HA   CB HB1  CB HB2  CG HG1  CG HG2   
BOND CE HE1  CE HE2  CE HE3  
DOUBLE   O  C   
IMPR N -C CA HN  C CA +N O   
CMAP -C  N  CA  C   N  CA  C  +N
DONOR HN N   
ACCEPTOR O C   
IC -C   CA   *N   HN    1.3478 124.2100  180.0000 114.3900  0.9978
IC -C   N    CA   C     1.3478 124.2100  180.0000 106.3100  1.5195
IC N    CA   C    +N    1.4510 106.3100  180.0000 117.7400  1.3471
IC +N   CA   *C   O     1.3471 117.7400  180.0000 120.6400  1.2288
IC CA   C    +N   +CA   1.5195 117.7400  180.0000 124.5200  1.4471
IC N    C    *CA  CB    1.4510 106.3100  121.6200 111.8800  1.5546
IC N    C    *CA  HA    1.4510 106.3100 -116.9800 107.5700  1.0832
IC N    CA   CB   CG    1.4510 111.2500  180.0000 115.9200  1.5460
IC CG   CA   *CB  HB1   1.5460 115.9200  120.5600 106.9000  1.1153
IC CG   CA   *CB  HB2   1.5460 115.9200 -124.8000 109.3800  1.1129
IC CA   CB   CG   SD    1.5546 115.9200  180.0000 110.2800  1.8219
IC SD   CB   *CG  HG1   1.8219 110.2800  120.5000 110.3400  1.1106
IC SD   CB   *CG  HG2   1.8219 110.2800 -121.1600 109.6400  1.1119
IC CB   CG   SD   CE    1.5460 110.2800  180.0000  98.9400  1.8206
IC CG   SD   CE   HE1   1.8219  98.9400 -179.4200 110.9100  1.1111
IC HE1  SD   *CE  HE2   1.1111 110.9100  119.9500 111.0300  1.1115
IC HE1  SD   *CE  HE3   1.1111 110.9100 -119.9500 111.0900  1.1112

RESI PHE          0.00
GROUP   
ATOM N    NH1    -0.47  !     |        HD1  HE1    
ATOM HN   H       0.31  !  HN-N         |    |   
ATOM CA   CT1     0.07  !     |   HB1  CD1--CE1
ATOM HA   HB      0.09  !     |   |    //     \\
GROUP                   !  HA-CA--CB--CG      CZ--HZ
ATOM CB   CT2    -0.18  !     |   |    \  __  /
ATOM HB1  HA      0.09  !     |   HB2  CD2--CE2
ATOM HB2  HA      0.09  !   O=C         |    |  
GROUP                   !     |        HD2  HE2   
ATOM CG   CA      0.00
GROUP   
ATOM CD1  CA     -0.115
ATOM HD1  HP      0.115
GROUP   
ATOM CE1  CA     -0.115
ATOM HE1  HP      0.115
GROUP
ATOM CZ   CA     -0.115
ATOM HZ   HP      0.115
GROUP
ATOM CD2  CA     -0.115
ATOM HD2  HP      0.115
GROUP
ATOM CE2  CA     -0.115
ATOM HE2  HP      0.115
GROUP   
ATOM C    C       0.51
ATOM O    O      -0.51
BOND CB  CA   CG CB   CD2 CG   CE1 CD1   
BOND CZ  CE2  N   HN   
BOND N   CA    C   CA   C   +N   CA  HA   
BOND CB  HB1  CB HB2  CD1 HD1  CD2 HD2  CE1 HE1  
DOUBLE   O  C    CD1 CG  CZ CE1   CE2 CD2
BOND CE2 HE2  CZ HZ   
IMPR N -C CA HN  C CA +N O   
CMAP -C  N  CA  C   N  CA  C  +N
DONOR HN N   
ACCEPTOR O C   
IC -C   CA   *N   HN    1.3476 123.8900  180.0000 114.4700  0.9987
IC -C   N    CA   C     1.3476 123.8900  180.0000 106.3800  1.5229
IC N    CA   C    +N    1.4504 106.3800  180.0000 117.6500  1.3483
IC +N   CA   *C   O     1.3483 117.6500  180.0000 120.4900  1.2287
IC CA   C    +N   +CA   1.5229 117.6500  180.0000 124.1000  1.4523
IC N    C    *CA  CB    1.4504 106.3800  122.4900 112.4500  1.5594
IC N    C    *CA  HA    1.4504 106.3800 -115.6300 107.0500  1.0832
IC N    CA   CB   CG    1.4504 111.6300  180.0000 112.7600  1.5109
IC CG   CA   *CB  HB1   1.5109 112.7600  118.2700 109.1000  1.1119
IC CG   CA   *CB  HB2   1.5109 112.7600 -123.8300 111.1100  1.1113
IC CA   CB   CG   CD1   1.5594 112.7600   90.0000 120.3200  1.4059
IC CD1  CB   *CG  CD2   1.4059 120.3200 -177.9600 120.7600  1.4062
IC CB   CG   CD1  CE1   1.5109 120.3200 -177.3700 120.6300  1.4006
IC CE1  CG   *CD1 HD1   1.4006 120.6300  179.7000 119.6500  1.0814
IC CB   CG   CD2  CE2   1.5109 120.7600  177.2000 120.6200  1.4002
IC CE2  CG   *CD2 HD2   1.4002 120.6200 -178.6900 119.9900  1.0811
IC CG   CD1  CE1  CZ    1.4059 120.6300   -0.1200 119.9300  1.4004
IC CZ   CD1  *CE1 HE1   1.4004 119.9300 -179.6900 120.0100  1.0808
IC CZ   CD2  *CE2 HE2   1.4000 119.9600 -179.9300 119.8700  1.0811
IC CE1  CE2  *CZ  HZ    1.4004 119.9800  179.5100 119.9700  1.0807

RESI PRO          0.00
GROUP                   !       HD1 HD2
ATOM N    N      -0.29  !     |   \ /
ATOM CD   CP3     0.00  !     N---CD   HG1  ATOM CA   CP1     0.02
ATOM HD1  HA      0.09  !     |     \  /
ATOM HD2  HA      0.09  !     |      CG
ATOM CA   CP1     0.02  !     |     /  \
ATOM HA   HB      0.09  !  HA-CA--CB   HG2
GROUP                   !     |   / \
ATOM CB   CP2    -0.18  !     | HB1 HB2
ATOM HB1  HA      0.09  !   O=C
ATOM HB2  HA      0.09  !     |
GROUP
ATOM CG   CP2    -0.18
ATOM HG1  HA      0.09
ATOM HG2  HA      0.09
GROUP   
ATOM C    C       0.51
ATOM O    O      -0.51
BOND C  CA  C   +N   
BOND N  CA  CA  CB  CB  CG  CG  CD  N   CD   
BOND HA CA  HG1 CG  HG2 CG  HD1 CD  HD2 CD  HB1 CB  HB2 CB
DOUBLE   O  C       
IMPR N -C CA CD   
IMPR C CA +N O   
CMAP -C  N  CA  C   N  CA  C  +N
ACCEPTOR O C   
IC -C   CA   *N   CD    1.3366 122.9400  178.5100 112.7500  1.4624
IC -C   N    CA   C     1.3366 122.9400  -76.1200 110.8600  1.5399
IC N    CA   C    +N    1.4585 110.8600  180.0000 114.7500  1.3569
IC +N   CA   *C   O     1.3569 114.7500  177.1500 120.4600  1.2316
IC CA   C    +N   +CA   1.5399 116.1200  180.0000 124.8900  1.4517
IC N    C    *CA  CB    1.4585 110.8600  113.7400 111.7400  1.5399
IC N    C    *CA  HA    1.4585 110.8600 -122.4000 109.0900  1.0837
IC N    CA   CB   CG    1.4585 102.5600   31.6100 104.3900  1.5322
IC CA   CB   CG   CD    1.5399 104.3900  -34.5900 103.2100  1.5317
IC N    CA   CB   HB1   1.4585 102.5600  -84.9400 109.0200  1.1131
IC N    CA   CB   HB2   1.4585 102.5600  153.9300 112.7400  1.1088
IC CA   CB   CG   HG1   1.5399 104.3900 -156.7200 112.9500  1.1077
IC CA   CB   CG   HG2   1.5399 104.3900   81.2600 109.2200  1.1143
IC CB   CG   CD   HD1   1.5322 103.2100  -93.5500 110.0300  1.1137
IC CB   CG   CD   HD2   1.5322 103.2100  144.5200 110.0000  1.1144
PATCHING FIRS PROP   

RESI SER          0.00
GROUP   
ATOM N    NH1    -0.47  !     |       
ATOM HN   H       0.31  !  HN-N       
ATOM CA   CT1     0.07  !     |   HB1
ATOM HA   HB      0.09  !     |   |  
GROUP                   !  HA-CA--CB--OG
ATOM CB   CT2     0.05  !     |   |     \
ATOM HB1  HA      0.09  !     |   HB2    HG1
ATOM HB2  HA      0.09  !   O=C           
ATOM OG   OH1    -0.66  !     |           
ATOM HG1  H       0.43
GROUP   
ATOM C    C       0.51
ATOM O    O      -0.51
BOND CB CA   OG CB  N HN  N  CA   
BOND C  CA  C +N  CA HA  CB HB1   
BOND CB HB2  OG HG1  
DOUBLE   O  C      
IMPR N -C CA HN  C CA +N O   
CMAP -C  N  CA  C   N  CA  C  +N
DONOR HN N   
DONOR HG1 OG   
ACCEPTOR OG   
ACCEPTOR O C   
IC -C   CA   *N   HN    1.3474 124.3700  180.0000 114.1800  0.9999
IC -C   N    CA   C     1.3474 124.3700  180.0000 105.8100  1.5166
IC N    CA   C    +N    1.4579 105.8100  180.0000 117.7200  1.3448
IC +N   CA   *C   O     1.3448 117.7200  180.0000 120.2500  1.2290
IC CA   C    +N   +CA   1.5166 117.7200  180.0000 124.6300  1.4529
IC N    C    *CA  CB    1.4579 105.8100  124.7500 111.4000  1.5585
IC N    C    *CA  HA    1.4579 105.8100 -115.5600 107.3000  1.0821
IC N    CA   CB   OG    1.4579 114.2800  180.0000 112.4500  1.4341
IC OG   CA   *CB  HB1   1.4341 112.4500  119.3200 108.1000  1.1140
IC OG   CA   *CB  HB2   1.4341 112.4500 -123.8600 110.3800  1.1136
IC CA   CB   OG   HG1   1.5585 112.4500  165.9600 107.0800  0.9655

RESI THR          0.00
GROUP   
ATOM N    NH1    -0.47  !     |  
ATOM HN   H       0.31  !  HN-N  
ATOM CA   CT1     0.07  !     |     OG1--HG1
ATOM HA   HB      0.09  !     |    /
GROUP                   !  HA-CA--CB-HB  
ATOM CB   CT1     0.14  !     |    \     
ATOM HB   HA      0.09  !     |     CG2--HG21
ATOM OG1  OH1    -0.66  !   O=C    / \    
ATOM HG1  H       0.43  !     | HG21 HG22 
GROUP                 
ATOM CG2  CT3    -0.27
ATOM HG21 HA      0.09
ATOM HG22 HA      0.09
ATOM HG23 HA      0.09
GROUP   
ATOM C    C       0.51
ATOM O    O      -0.51
BOND CB CA  OG1 CB   CG2 CB    N   HN   
BOND N  CA    C   CA    C   +N    CA  HA   
BOND CB HB  OG1 HG1  CG2 HG21  CG2 HG22  CG2 HG23
DOUBLE  O   C    
IMPR N -C CA HN  C CA +N O   
CMAP -C  N  CA  C   N  CA  C  +N
DONOR HN N   
DONOR HG1 OG1   
ACCEPTOR OG1   
ACCEPTOR O C   
IC -C   CA   *N   HN    1.3471 124.1200  180.0000 114.2600  0.9995
IC -C   N    CA   C     1.3471 124.1200  180.0000 106.0900  1.5162
IC N    CA   C    +N    1.4607 106.0900  180.0000 117.6900  1.3449
IC +N   CA   *C   O     1.3449 117.6900  180.0000 120.3000  1.2294
IC CA   C    +N   +CA   1.5162 117.6900  180.0000 124.6600  1.4525
IC N    C    *CA  CB    1.4607 106.0900  126.4600 112.7400  1.5693
IC N    C    *CA  HA    1.4607 106.0900 -114.9200 106.5300  1.0817
IC N    CA   CB   OG1   1.4607 114.8100  180.0000 112.1600  1.4252
IC OG1  CA   *CB  HB    1.4252 112.1600  116.3900 106.1100  1.1174
IC OG1  CA   *CB  CG2   1.4252 112.1600 -124.1300 115.9100  1.5324
IC CA   CB   OG1  HG1   1.5693 112.1600 -179.2800 105.4500  0.9633
IC CA   CB   CG2  HG21  1.5693 115.9100 -173.6500 110.8500  1.1104
IC HG21 CB   *CG2 HG22  1.1104 110.8500  119.5100 110.4100  1.1109
IC HG21 CB   *CG2 HG23  1.1104 110.8500 -120.3900 111.1100  1.1113

RESI TRP          0.00
GROUP   
ATOM N    NH1    -0.47  !     |                  HE3
ATOM HN   H       0.31  !  HN-N                   |
ATOM CA   CT1     0.07  !     |   HB1            CE3
ATOM HA   HB      0.09  !     |   |             /  \\
GROUP                   !  HA-CA--CB---CG-----CD2   CZ3-HZ3
ATOM CB   CT2    -0.18  !     |   |    ||     ||     |
ATOM HB1  HA      0.09  !     |   HB2  CD1    CE2   CH2-HH2
ATOM HB2  HA      0.09  !   O=C       /   \   / \  //
GROUP                   !     |     HD1    NE1   CZ2
ATOM CG   CY     -0.03  !                   |     |
ATOM CD1  CA      0.035 !                  HE1   HZ2
ATOM HD1  HP      0.115
ATOM NE1  NY     -0.61
ATOM HE1  H       0.38
ATOM CE2  CPT     0.13
ATOM CD2  CPT    -0.02
GROUP
ATOM CE3  CA     -0.115
ATOM HE3  HP      0.115
GROUP
ATOM CZ3  CA     -0.115
ATOM HZ3  HP      0.115
GROUP
ATOM CZ2  CA     -0.115
ATOM HZ2  HP      0.115
GROUP
ATOM CH2  CA     -0.115
ATOM HH2  HP      0.115
GROUP   
ATOM C    C       0.51
ATOM O    O      -0.51
BOND CB  CA   CG  CB   CD2 CG   NE1 CD1   
BOND CZ2 CE2   
BOND N   HN   N   CA     C   CA   C   +N   
BOND CZ3 CH2  CD2 CE3  NE1 CE2  CA  HA   CB  HB1   
BOND CB  HB2  CD1 HD1  NE1 HE1  CE3 HE3  CZ2 HZ2   
BOND CZ3 HZ3  CH2 HH2
DOUBLE  O   C   CD1 CG   CE2 CD2  CZ3 CE3  CH2 CZ2     
IMPR N -C CA HN  C CA +N O   
CMAP -C  N  CA  C   N  CA  C  +N
DONOR HN N   
DONOR HE1 NE1   
ACCEPTOR O C   
IC -C   CA   *N   HN    1.3482 123.5100  180.0000 115.0200  0.9972
IC -C   N    CA   C     1.3482 123.5100  180.0000 107.6900  1.5202
IC N    CA   C    +N    1.4507 107.6900  180.0000 117.5700  1.3505
IC +N   CA   *C   O     1.3505 117.5700  180.0000 121.0800  1.2304
IC CA   C    +N   +CA   1.5202 117.5700  180.0000 124.8800  1.4526
IC N    C    *CA  CB    1.4507 107.6900  122.6800 111.2300  1.5560
IC N    C    *CA  HA    1.4507 107.6900 -117.0200 106.9200  1.0835
IC N    CA   CB   CG    1.4507 111.6800  180.0000 115.1400  1.5233
IC CG   CA   *CB  HB1   1.5233 115.1400  119.1700 107.8400  1.1127
IC CG   CA   *CB  HB2   1.5233 115.1400 -124.7300 109.8700  1.1118
IC CA   CB   CG   CD2   1.5560 115.1400   90.0000 123.9500  1.4407
IC CD2  CB   *CG  CD1   1.4407 123.9500 -172.8100 129.1800  1.3679
IC CD1  CG   CD2  CE2   1.3679 106.5700   -0.0800 106.6500  1.4126
IC CG   CD2  CE2  NE1   1.4407 106.6500    0.1400 107.8700  1.3746
IC CE2  CG   *CD2 CE3   1.4126 106.6500  179.2100 132.5400  1.4011
IC CE2  CD2  CE3  CZ3   1.4126 120.8000   -0.2000 118.1600  1.4017
IC CD2  CE3  CZ3  CH2   1.4011 118.1600    0.1000 120.9700  1.4019
IC CE3  CZ3  CH2  CZ2   1.4017 120.9700    0.0100 120.8700  1.4030
IC CZ3  CD2  *CE3 HE3   1.4017 118.1600 -179.6200 121.8400  1.0815
IC CH2  CE3  *CZ3 HZ3   1.4019 120.9700 -179.8200 119.4500  1.0811
IC CZ2  CZ3  *CH2 HH2   1.4030 120.8700 -179.9200 119.5700  1.0811
IC CE2  CH2  *CZ2 HZ2   1.3939 118.4200  179.8700 120.0800  1.0790
IC CD1  CE2  *NE1 HE1   1.3752 108.8100  177.7800 124.6800  0.9767
IC CG   NE1  *CD1 HD1   1.3679 110.1000  178.1000 125.4300  1.0820

RESI TYR          0.00
GROUP   
ATOM N    NH1    -0.47  !     |        HD1  HE1    
ATOM HN   H       0.31  !  HN-N         |    |   
ATOM CA   CT1     0.07  !     |   HB1  CD1--CE1
ATOM HA   HB      0.09  !     |   |   //      \\
GROUP                   !  HA-CA--CB--CG      CZ--OH
ATOM CB   CT2    -0.18  !     |   |    \  __  /     \
ATOM HB1  HA      0.09  !     |   HB2  CD2--CE2     HH
ATOM HB2  HA      0.09  !   O=C         |    |  
GROUP                   !     |        HD2  HE2   
ATOM CG   CA      0.00
GROUP   
ATOM CD1  CA     -0.115
ATOM HD1  HP      0.115
GROUP   
ATOM CE1  CA     -0.115
ATOM HE1  HP      0.115
GROUP
ATOM CZ   CA      0.11
ATOM OH   OH1    -0.54
ATOM HH   H       0.43
GROUP
ATOM CD2  CA     -0.115
ATOM HD2  HP      0.115
GROUP
ATOM CE2  CA     -0.115
ATOM HE2  HP      0.115
GROUP   
ATOM C    C       0.51
ATOM O    O      -0.51
BOND CB  CA   CG  CB   CD2 CG   CE1 CD1   
BOND CZ  CE2  OH  CZ   
BOND N   HN   N   CA    C   CA   C   +N   
BOND CA  HA   CB  HB1  CB  HB2  CD1 HD1  CD2 HD2   
BOND CE1 HE1  CE2 HE2  OH  HH
DOUBLE   O   C   CD1 CG  CE1  CZ  CE2 CD2      
IMPR N -C CA HN  C CA +N O   
CMAP -C  N  CA  C   N  CA  C  +N
DONOR HN N   
DONOR HH OH   
ACCEPTOR OH   
ACCEPTOR O C   
IC -C   CA   *N   HN    1.3476 123.8100  180.0000 114.5400  0.9986
IC -C   N    CA   C     1.3476 123.8100  180.0000 106.5200  1.5232
IC N    CA   C    +N    1.4501 106.5200  180.0000 117.3300  1.3484
IC +N   CA   *C   O     1.3484 117.3300  180.0000 120.6700  1.2287
IC CA   C    +N   +CA   1.5232 117.3300  180.0000 124.3100  1.4513
IC N    C    *CA  CB    1.4501 106.5200  122.2700 112.3400  1.5606
IC N    C    *CA  HA    1.4501 106.5200 -116.0400 107.1500  1.0833
IC N    CA   CB   CG    1.4501 111.4300  180.0000 112.9400  1.5113
IC CG   CA   *CB  HB1   1.5113 112.9400  118.8900 109.1200  1.1119
IC CG   CA   *CB  HB2   1.5113 112.9400 -123.3600 110.7000  1.1115
IC CA   CB   CG   CD1   1.5606 112.9400   90.0000 120.4900  1.4064
IC CD1  CB   *CG  CD2   1.4064 120.4900 -176.4600 120.4600  1.4068
IC CB   CG   CD1  CE1   1.5113 120.4900 -175.4900 120.4000  1.4026
IC CE1  CG   *CD1 HD1   1.4026 120.4000  178.9400 119.8000  1.0814
IC CB   CG   CD2  CE2   1.5113 120.4600  175.3200 120.5600  1.4022
IC CE2  CG   *CD2 HD2   1.4022 120.5600 -177.5700 119.9800  1.0813
IC CG   CD1  CE1  CZ    1.4064 120.4000   -0.1900 120.0900  1.3978
IC CZ   CD1  *CE1 HE1   1.3978 120.0900  179.6400 120.5800  1.0799
IC CZ   CD2  *CE2 HE2   1.3979 119.9200 -178.6900 119.7600  1.0798
IC CE1  CE2  *CZ  OH    1.3978 120.0500 -178.9800 120.2500  1.4063
IC CE1  CZ   OH   HH    1.3978 119.6800  175.4500 107.4700  0.9594

RESI VAL          0.00
GROUP   
ATOM N    NH1    -0.47  !     |    HG11 HG12
ATOM HN   H       0.31  !  HN-N      | / 
ATOM CA   CT1     0.07  !     |     CG1--HG13
ATOM HA   HB      0.09  !     |    /
GROUP                   !  HA-CA--CB-HB  
ATOM CB   CT1    -0.09  !     |    \     
ATOM HB   HA      0.09  !     |     CG2--HG21
GROUP                   !   O=C    / \   
ATOM CG1  CT3    -0.27  !     | HG21 HG22
ATOM HG11 HA      0.09
ATOM HG12 HA      0.09
ATOM HG13 HA      0.09
GROUP   
ATOM CG2  CT3    -0.27
ATOM HG21 HA      0.09
ATOM HG22 HA      0.09
ATOM HG23 HA      0.09
GROUP   
ATOM C    C       0.51
ATOM O    O      -0.51
BOND CB  CA    CG1 CB    CG2 CB    N   HN   
BOND N   CA     C   CA    C   +N    CA HA   
BOND CB  HB    CG1 HG11  CG1 HG12  CG1 HG13  CG2 HG21   
BOND CG2 HG22  CG2 HG23
DOUBLE    O   C   
IMPR N -C CA HN C CA +N O   
CMAP -C  N  CA  C   N  CA  C  +N
DONOR HN N   
ACCEPTOR O C   
IC -C   CA   *N   HN    1.3482 124.5700  180.0000 114.4100  0.9966
IC -C   N    CA   C     1.3482 124.5700  180.0000 105.5400  1.5180
IC N    CA   C    +N    1.4570 105.5400  180.0000 117.8300  1.3471
IC +N   CA   *C   O     1.3471 117.8300  180.0000 120.7000  1.2297
IC CA   C    +N   +CA   1.5180 117.8300  180.0000 124.0800  1.4471
IC N    C    *CA  CB    1.4570 105.5400  122.9500 111.2300  1.5660
IC N    C    *CA  HA    1.4570 105.5400 -117.2400 107.4600  1.0828
IC N    CA   CB   CG1   1.4570 113.0500  180.0000 113.9700  1.5441
IC CG1  CA   *CB  CG2   1.5441 113.9700  123.9900 112.1700  1.5414
IC CG1  CA   *CB  HB    1.5441 113.9700 -119.1700 107.5700  1.1178
IC CA   CB   CG1  HG11  1.5660 113.9700  177.8300 110.3000  1.1114
IC HG11 CB   *CG1 HG12  1.1114 110.3000  119.2500 111.6700  1.1097
IC HG11 CB   *CG1 HG13  1.1114 110.3000 -119.4900 110.7000  1.1110
IC CA   CB   CG2  HG21  1.5660 112.1700 -177.7800 110.7100  1.1108
IC HG21 CB   *CG2 HG22  1.1108 110.7100  120.0800 110.5600  1.1115
IC HG21 CB   *CG2 HG23  1.1108 110.7100 -119.5500 111.2300  1.1098

RESI ALAD        0.00 ! Alanine dipeptide, with CMAP term
GROUP
ATOM CL   CT3   -0.27
ATOM HL1  HA     0.09
ATOM HL2  HA     0.09
ATOM HL3  HA     0.09
GROUP
ATOM CLP  C      0.51
ATOM OL   O     -0.51
GROUP
ATOM NL   NH1   -0.47
ATOM HL   H      0.31
ATOM CA   CT1    0.07
ATOM HA   HB     0.09
GROUP
ATOM CB   CT3   -0.27  !     HL1     OL           OR           HR1
ATOM HB1  HA     0.09  !       \     ||   HL  HA  ||   HR      /
ATOM HB2  HA     0.09  !        \    ||   |   |   ||   |      /
ATOM HB3  HA     0.09  !   HL2---CL--CLP--NL--CA--CRP--NR---CR---HR2
GROUP                  !        /             |               \
ATOM CRP  C      0.51  !       /         HB1--CB--HB3          \
ATOM OR   O     -0.51  !     HL3              |                HR3
GROUP                  !                     HB2
ATOM NR   NH1   -0.47
ATOM HR   H      0.31
ATOM CR   CT3   -0.11
ATOM HR1  HA     0.09
ATOM HR2  HA     0.09
ATOM HR3  HA     0.09

BOND CL  CLP   CLP NL    NL  CA
BOND CA  CRP   CRP NR    NR  CR
DOUBLE  CLP OL    CRP OR
BOND NL  HL    NR  HR
BOND CA  HA    CA  CB
BOND CL  HL1   CL  HL2   CL  HL3
BOND CB  HB1   CB  HB2   CB  HB3
BOND CR  HR1   CR  HR2   CR  HR3
IMPR CLP CL NL OL    NL CLP CA HL
IMPR CRP CA NR OR    NR CRP CR HR

CMAP CLP NL CA CRP NL CA CRP NR

ic clp nl  ca  crp  0.0 0.0  180.0  0.0 0.0 ! Phi
ic ca  clp *nl hl   0.0 0.0  180.0  0.0 0.0
ic hl  nl  ca  crp  0.0 0.0    0.0  0.0 0.0
ic nl  ca  crp nr   0.0 0.0  180.0  0.0 0.0 ! Psi
ic ca  nr  *crp or  0.0 0.0  180.0  0.0 0.0
ic nl  ca  crp or   0.0 0.0    0.0  0.0 0.0
ic cl  clp nl  ca   0.0 0.0  180.0  0.0 0.0 ! Omega Left
ic nl  cl  *clp ol  0.0 0.0  180.0  0.0 0.0
ic ol  clp nl  ca   0.0 0.0    0.0  0.0 0.0
ic ca  crp nr  cr   0.0 0.0  180.0  0.0 0.0 ! Omega Right
ic crp cr  *nr hr   0.0 0.0  180.0  0.0 0.0
ic ca  crp nr  hr   0.0 0.0  180.0  0.0 0.0
ic nl  crp *ca ha   0.0 0.0  240.0  0.0 0.0
ic nl  crp *ca cb   0.0 0.0  120.0  0.0 0.0
ic hl1 cl  clp nl   0.0 0.0  180.0  0.0 0.0
ic hl2 cl  clp nl   0.0 0.0   60.0  0.0 0.0
ic hl3 cl  clp ol   0.0 0.0  120.0  0.0 0.0
ic ha  ca  cb  hb1  0.0 0.0  180.0  0.0 0.0
ic nl  ca  cb  hb2  0.0 0.0  180.0  0.0 0.0
ic crp ca  cb  hb3  0.0 0.0  180.0  0.0 0.0
ic crp nr  cr  hr1  0.0 0.0  180.0  0.0 0.0
ic crp nr  cr  hr2  0.0 0.0   60.0  0.0 0.0
ic hr  nr  cr  hr3  0.0 0.0  120.0  0.0 0.0
ic ca  clp *nl hl   0.0 0.0  180.0  0.0 0.0
ic ca  nr  *crp or  0.0 0.0  180.0  0.0 0.0
ic hb1 hb2 *cb hb3  0.0 0.0  120.0  0.0 0.0
ic hl1 hl2 *cl hl3  0.0 0.0  240.0  0.0 0.0
ic hr1 hr2 *cr hr3  0.0 0.0  240.0  0.0 0.0
ic ha  ca  nl  hl   0.0 0.0  240.0  0.0 0.0
patch first none last none


RESI TIP3         0.000 ! tip3p water model, generate using noangle nodihedral
GROUP   
ATOM OH2  OT     -0.834
ATOM H1   HT      0.417
ATOM H2   HT      0.417
!BOND OH2 H1 OH2 H2 H1 H2    ! the last bond is needed for shake
BOND OH2 H1 OH2 H2 
ANGLE H1 OH2 H2             ! required
ACCEPTOR OH2   
PATCHING FIRS NONE LAST NONE 

RESI TP3M         0.000 ! "mmff" water model, as an analog of tip3p
GROUP   
ATOM OH2  OT     -0.834  ! these charges are replaced by the mmff setup   
ATOM H1   HT      0.417  ! these charges are replaced by the mmff setup
ATOM H2   HT      0.417  ! these charges are replaced by the mmff setup
BOND OH2 H1 OH2 H2          ! omits the H1-H2 bond, which is needed for shake with tip3p
ANGLE H1 OH2 H2             ! required
ACCEPTOR OH2   
PATCHING FIRS NONE LAST NONE     

RESI ZN2          2.00 ! Zinc ion
GROUP   
ATOM ZN   ZN      2.00
PATCHING FIRST NONE LAST NONE   

RESI HEME        -2.00 ! 6-liganded planar heme
GROUP   
ATOM FE   FE      0.24 !       O2A   O1A             O2D  O1D
ATOM NA   NPH    -0.18 !         \\ //                 \\ //
ATOM NB   NPH    -0.18 !          CGA                   CGD
ATOM NC   NPH    -0.18 !           |                     |
ATOM ND   NPH    -0.18 !    HBA1--CBA--HBA2  HA   HBD1--CBD--HBD2
ATOM C1A  CPA     0.12 !           |          |          |
ATOM C2A  CPB    -0.06 !    HAA1--CAA-HAA2  _CHA_ HAD1--CAD--HAD2
ATOM C3A  CPB    -0.06 !           |       /     \       |
ATOM C4A  CPA     0.12 !          C2A---C1A       C4D---C3D
ATOM C1B  CPA     0.12 !           |     |         |     |
ATOM C2B  CPB    -0.06 !HMA1\      |     |         |     |      /HMD1
ATOM C3B  CPB    -0.06 !HMA2-CMA--C3A    NA       ND    C2D--CMD-HMD2
ATOM C4B  CPA     0.12 !HMA3/       \   / \       / \   /       \HMD3
ATOM C1C  CPA     0.12 !             C4A   \     /   C1D
ATOM C2C  CPB    -0.06 !            /       \   /       \
ATOM C3C  CPB    -0.06 !      HB--CHB        FE         CHD--HD
ATOM C4C  CPA     0.12 !            \       /   \       /
ATOM C1D  CPA     0.12 !             C1B   /     \   C4C        HAC
ATOM C2D  CPB    -0.06 !HMB1\       /   \ /       \ /   \       /
ATOM C3D  CPB    -0.06 !HMB2-CMB--C2B    NB       NC    C3C--CAC
ATOM C4D  CPA     0.12 !HMB3/      |     |         |     |     \\  /HBC1
GROUP                  !           |     |         |     |      CBC
ATOM CHA  CPM    -0.10 !          C3B---C4B       C1C---C2C        \HBC2
ATOM HA   HA      0.10 !           |       \_CHC_/       |
GROUP                  !          CAB         |         CMC--HMC3
ATOM CHB  CPM    -0.10 !         //  \        HC       /  | 
ATOM HB   HA      0.10 !        CBB  HAB           HMC1  HMC2
GROUP                  !       /   \
ATOM CHC  CPM    -0.10 !    HBB1  HBB2
ATOM HC   HA      0.10 !
GROUP   
ATOM CHD  CPM    -0.10
ATOM HD   HA      0.10
GROUP   
ATOM CMA  CT3    -0.27
ATOM HMA1 HA      0.09
ATOM HMA2 HA      0.09
ATOM HMA3 HA      0.09
GROUP   
ATOM CAA  CT2    -0.18
ATOM HAA1 HA      0.09
ATOM HAA2 HA      0.09
GROUP   
ATOM CBA  CT2    -0.28
ATOM HBA1 HA      0.09
ATOM HBA2 HA      0.09
ATOM CGA  CC      0.62
ATOM O1A  OC     -0.76
ATOM O2A  OC     -0.76
GROUP   
ATOM CMB  CT3    -0.27
ATOM HMB1 HA      0.09
ATOM HMB2 HA      0.09
ATOM HMB3 HA      0.09
GROUP   
ATOM CAB  C      -0.20
ATOM HAB  HA      0.20
GROUP   
ATOM CBB  C      -0.20
ATOM HBB1 HA      0.10
ATOM HBB2 HA      0.10
GROUP   
ATOM CMC  CT3    -0.27
ATOM HMC1 HA      0.09
ATOM HMC2 HA      0.09
ATOM HMC3 HA      0.09
GROUP   
ATOM CAC  C      -0.20
ATOM HAC  HA      0.20
GROUP   
ATOM CBC  C      -0.20
ATOM HBC1 HA      0.10
ATOM HBC2 HA      0.10
GROUP   
ATOM CMD  CT3    -0.27
ATOM HMD1 HA      0.09
ATOM HMD2 HA      0.09
ATOM HMD3 HA      0.09
GROUP   
ATOM CAD  CT2    -0.18
ATOM HAD1 HA      0.09
ATOM HAD2 HA      0.09
GROUP   
ATOM CBD  CT2    -0.28
ATOM HBD1 HA      0.09
ATOM HBD2 HA      0.09
ATOM CGD  CC      0.62
ATOM O1D  OC     -0.76
ATOM O2D  OC     -0.76
BOND FE  NA    FE  NB    FE  NC    FE  ND    NA  C1A   
BOND C1A C2A   C2A C3A   C3A C4A   NA  C4A   C2A CAA   
BOND CAA CBA   CBA CGA   CGA O1A   CGA O2A   C3A CMA   
BOND CHB C4A   CHB C1B   NB  C1B   C1B C2B   C2B C3B   
BOND C3B C4B   NB  C4B   C2B CMB   C3B CAB   CAB CBB   
BOND CHC C4B   CHC C1C   NC  C1C   C1C C2C   C2C C3C   
BOND C3C C4C   NC  C4C   C2C CMC   C3C CAC   CAC CBC   
BOND CHD C4C   CHD C1D   ND  C1D   C1D C2D   C2D C3D   
BOND C3D C4D   ND  C4D   C2D CMD   C3D CAD   CAD CBD   
BOND CBD CGD   CGD O1D   CGD O2D   CHA C4D   CHA C1A   
BOND CHA HA    CHB HB    CHC HC    CHD HD   
BOND CAA HAA1  CAA HAA2  CBA HBA1  CBA HBA2   
BOND CMA HMA1  CMA HMA2  CMA HMA3   
BOND CMB HMB1  CMB HMB2  CMB HMB3   
BOND CAB HAB   CBB HBB1  CBB HBB2   
BOND CMC HMC1  CMC HMC2  CMC HMC3   
BOND CAC HAC   CBC HBC1  CBC HBC2   
BOND CMD HMD1  CMD HMD2  CMD HMD3   
BOND CAD HAD1  CAD HAD2  CBD HBD1  CBD HBD2   
IMPR C2A C1A C3A CAA  C3A C2A C4A CMA  C2B C1B C3B CMB   
IMPR C3B C2B C4B CAB  C2C C1C C3C CMC  C3C C2C C4C CAC   
IMPR C2D C1D C3D CMD  C3D C2D C4D CAD  
IMPR CGA CBA O2A O1A  CGD CBD O2D O1D
IMPR C4A NA C1A C2A  C1A NA C4A C3A   
IMPR C4B NB C1B C2B  C1B NB C4B C3B   
IMPR C4C NC C1C C2C  C1C NC C4C C3C   
IMPR C4D ND C1D C2D  C1D ND C4D C3D   
IMPR NA C1A C2A C3A  NA C4A C3A C2A   
IMPR NB C1B C2B C3B  NB C4B C3B C2B   
IMPR NC C1C C2C C3C  NC C4C C3C C2C   
IMPR ND C1D C2D C3D  ND C4D C3D C2D   
IMPR NA C1A CHA C4D  NA C4A CHB C1B   
IMPR NB C1B CHB C4A  NB C4B CHC C1C   
IMPR NC C1C CHC C4B  NC C4C CHD C1D   
IMPR ND C1D CHD C4C  ND C4D CHA C1A   
IMPR CHA C1A C4D HA   
IMPR CHB C1B C4A HB   
IMPR CHC C1C C4B HC   
IMPR CHD C1D C4C HD   
IMPR C1A C2A CHA NA  C4A C3A CHB NA   
IMPR C1B C2B CHB NB  C4B C3B CHC NB   
IMPR C1C C2C CHC NC  C4C C3C CHD NC   
IMPR C1D C2D CHD ND  C4D C3D CHA ND   
IMPR NA C1A C4A FE   
IMPR NB C1B C4B FE   
IMPR NC C1C C4C FE   
IMPR ND C1D C4D FE   
IMPR CAB CBB C3B HAB  HAB CAB CBB HBB2  CAB CBB HBB2 HBB1   
IMPR CAC CBC C3C HAC  HAC CAC CBC HBC2  CAC CBC HBC2 HBC1   
ACCEPTOR NA   
ACCEPTOR O1A    ! CGA
ACCEPTOR O2A    ! CGA
ACCEPTOR NB   
ACCEPTOR NC   
ACCEPTOR ND   
ACCEPTOR O1D    ! CGD
ACCEPTOR O2D    ! CGD
IC FE   NA   C4A  C3A   0.0000  0.0000  180.0000  0.0000  0.0000
IC C3A  C4A  NA   C1A   0.0000  0.0000    0.0000  0.0000  0.0000
IC FE   NA   C1A  C2A   0.0000  0.0000  180.0000  0.0000  0.0000
IC C4A  NA   FE   NB    0.0000  0.0000    0.0000  0.0000  0.0000
IC NA   FE   NB   C1B   0.0000  0.0000    0.0000  0.0000  0.0000
IC FE   NB   C1B  C2B   0.0000  0.0000  180.0000  0.0000  0.0000
IC C2B  C1B  NB   C4B   0.0000  0.0000    0.0000  0.0000  0.0000
IC FE   NB   C4B  C3B   0.0000  0.0000  180.0000  0.0000  0.0000
IC C4B  NB   FE   NC    0.0000  0.0000    0.0000  0.0000  0.0000
IC NB   FE   NC   C1C   0.0000  0.0000    0.0000  0.0000  0.0000
IC FE   NC   C1C  C2C   0.0000  0.0000  180.0000  0.0000  0.0000
IC C2C  C1C  NC   C4C   0.0000  0.0000    0.0000  0.0000  0.0000
IC FE   NC   C4C  C3C   0.0000  0.0000  180.0000  0.0000  0.0000
IC C4C  NC   FE   ND    0.0000  0.0000    0.0000  0.0000  0.0000
IC NC   FE   ND   C1D   0.0000  0.0000    0.0000  0.0000  0.0000
IC FE   ND   C1D  C2D   0.0000  0.0000  180.0000  0.0000  0.0000
IC C2D  C1D  ND   C4D   0.0000  0.0000    0.0000  0.0000  0.0000
IC FE   ND   C4D  C3D   0.0000  0.0000  180.0000  0.0000  0.0000
IC C4A  NA   FE   CHB   0.0000  0.0000    0.0000  0.0000  0.0000
IC NA   FE   CHB  HB    0.0000  0.0000    0.0000  0.0000  0.0000
IC C4B  NB   FE   CHC   0.0000  0.0000    0.0000  0.0000  0.0000
IC NB   FE   CHC  HC    0.0000  0.0000    0.0000  0.0000  0.0000
IC C4C  NC   FE   CHD   0.0000  0.0000    0.0000  0.0000  0.0000
IC NC   FE   CHD  HD    0.0000  0.0000    0.0000  0.0000  0.0000
IC C4D  ND   FE   CHA   0.0000  0.0000    0.0000  0.0000  0.0000
IC ND   FE   CHA  HA    0.0000  0.0000    0.0000  0.0000  0.0000
IC C3B  C1B  *C2B CMB   0.0000  0.0000  180.0000  0.0000  0.0000
IC C4B  C2B  *C3B CAB   0.0000  0.0000  180.0000  0.0000  0.0000
IC C2B  C3B  CAB  CBB   0.0000  0.0000  -45.0000  0.0000  0.0000 ! PREVENTS VINYL COLLISION
IC CHC  C1C  C2C  CMC   0.0000  0.0000    0.0000  0.0000  0.0000
IC C4C  C2C  *C3C CAC   0.0000  0.0000  180.0000  0.0000  0.0000
IC C2C  C3C  CAC  CBC   0.0000  0.0000  -45.0000  0.0000  0.0000 ! PREVENTS VINYL COLLISION
IC C4D  C2D  *C3D CAD   0.0000  0.0000  180.0000  0.0000  0.0000
IC C3D  C1D  *C2D CMD   0.0000  0.0000  180.0000  0.0000  0.0000
IC C2D  C3D  CAD  CBD   0.0000  0.0000 -120.0000  0.0000  0.0000
IC C3D  CAD  CBD  CGD   0.0000  0.0000  180.0000  0.0000  0.0000
IC CAD  CBD  CGD  O1D   0.0000  0.0000    0.0000  0.0000  0.0000
IC CAD  CBD  CGD  O2D   0.0000  0.0000  180.0000  0.0000  0.0000
IC C4A  C2A  *C3A CMA   0.0000  0.0000  180.0000  0.0000  0.0000
IC C3A  C1A  *C2A CAA   0.0000  0.0000  180.0000  0.0000  0.0000
IC C1A  C2A  CAA  CBA   0.0000  0.0000  120.0000  0.0000  0.0000
IC C2A  CAA  CBA  CGA   0.0000  0.0000  180.0000  0.0000  0.0000
IC CAA  CBA  CGA  O1A   0.0000  0.0000    0.0000  0.0000  0.0000
IC CAA  CBA  CGA  O2A   0.0000  0.0000  180.0000  0.0000  0.0000
IC C3C  C1C  *C2C CMC   0.0000  0.0000  180.0000  0.0000  0.0000
IC CBA  O1A  *CGA O2A   0.0000  0.0000  180.0000  0.0000  0.0000
IC CBD  O1D  *CGD O2D   0.0000  0.0000  180.0000  0.0000  0.0000
PATCHING FIRS NONE LAST NONE   

PRES NTER         1.00 ! standard N-terminus
GROUP                  ! use in generate statement
ATOM N    NH3    -0.30 !
ATOM HT1  HC      0.33 !         HT1	
ATOM HT2  HC      0.33 !     (+)/
ATOM HT3  HC      0.33 ! --CA--N--HT2
ATOM CA   CT1     0.21 !   |    \
ATOM HA   HB      0.10 !   HA    HT3
DELETE ATOM HN   
BOND HT1 N HT2 N HT3 N   
DONOR HT1 N   
DONOR HT2 N   
DONOR HT3 N   
IC HT1  N    CA   C     0.0000  0.0000  180.0000  0.0000  0.0000
IC HT2  CA   *N   HT1   0.0000  0.0000  120.0000  0.0000  0.0000
IC HT3  CA   *N   HT2   0.0000  0.0000  120.0000  0.0000  0.0000

PRES GLYP         1.00 ! Glycine N-terminus
GROUP                  ! use in generate statement
ATOM N    NH3    -0.30 !
ATOM HT1  HC      0.33 !   HA1   HT1
ATOM HT2  HC      0.33 !   | (+)/
ATOM HT3  HC      0.33 ! --CA--N--HT2
ATOM CA   CT2     0.13 !   |    \
ATOM HA1  HB      0.09 !   HA2   HT3
ATOM HA2  HB      0.09 !
DELETE ATOM HN   
BOND HT1 N HT2 N HT3 N   
DONOR HT1 N   
DONOR HT2 N   
DONOR HT3 N   
IC HT1  N    CA   C     0.0000  0.0000  180.0000  0.0000  0.0000
IC HT2  CA   *N   HT1   0.0000  0.0000  120.0000  0.0000  0.0000
IC HT3  CA   *N   HT2   0.0000  0.0000  120.0000  0.0000  0.0000

PRES PROP         1.00 ! Proline N-Terminal
GROUP                  ! use in generate statement
ATOM N    NP     -0.07 !   HA
ATOM HN1  HC      0.24 !   |
ATOM HN2  HC      0.24 !  -CA   HN1
ATOM CD   CP3     0.16 !  /  \ /
ATOM HD1  HA      0.09 !       N(+)
ATOM HD2  HA      0.09 !      / \
ATOM CA   CP1     0.16 !  -CD    HN2
ATOM HA   HB      0.09 !   | \
BOND HN1 N HN2 N       !  HD1 HD2
DONOR HN1 N   
DONOR HN2 N   
IC HN1  CA   *N   CD    0.0000  0.0000  120.0000  0.0000  0.0000
IC HN2  CA   *N   HN1   0.0000  0.0000  120.0000  0.0000  0.0000

PRES ACE          0.00 ! acetylated N-terminus (to create dipeptide)
GROUP                  ! use in generate statement
ATOM CAY  CT3    -0.27 !
ATOM HY1  HA      0.09 ! HY1 HY2 HY3
ATOM HY2  HA      0.09 !    \ | /
ATOM HY3  HA      0.09 !     CAY
GROUP                  !      |
ATOM CY   C       0.51 !      CY=OY
ATOM OY   O      -0.51 !      |
                       !
BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3
DOUBLE OY CY
IMPR CY CAY N OY
IMPR N CY CA HN
CMAP CY  N  CA  C   N  CA  C  NT
ACCEPTOR OY CY
IC CY   N    CA   C     0.0000  0.0000  -60.0000  0.0000  0.0000
IC CY   CA   *N   HN    0.0000  0.0000  180.0000  0.0000  0.0000
IC CAY  CY   N    CA    0.0000  0.0000  180.0000  0.0000  0.0000
IC N    CAY  *CY  OY    0.0000  0.0000  180.0000  0.0000  0.0000
IC OY   CY   CAY  HY1   0.0000  0.0000  180.0000  0.0000  0.0000
IC OY   CY   CAY  HY2   0.0000  0.0000   60.0000  0.0000  0.0000
IC OY   CY   CAY  HY3   0.0000  0.0000  -60.0000  0.0000  0.0000

PRES ACP          0.00 ! acetylated N-terminus (for proline dipeptide)
GROUP                  ! use in generate statement
ATOM CAY  CT3    -0.27 !
ATOM HY1  HA      0.09 ! HY1 HY2 HY3
ATOM HY2  HA      0.09 !    \ | /
ATOM HY3  HA      0.09 !     CAY
GROUP                  !      |
ATOM CY   C       0.51 !      CY=OY
ATOM OY   O      -0.51 !      |
                       !
BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3
DOUBLE OY CY
IMPR CY CAY N OY
IMPR N CY CA CD
CMAP CY  N  CA  C   N  CA  C  NT
ACCEPTOR OY CY
IC CY   N    CA   C     0.0000  0.0000  -60.0000  0.0000  0.0000
IC CY   CA   *N   CD    0.0000  0.0000  180.0000  0.0000  0.0000
IC CAY  CY   N    CA    0.0000  0.0000  180.0000  0.0000  0.0000
IC N    CAY  *CY  OY    0.0000  0.0000  180.0000  0.0000  0.0000
IC OY   CY   CAY  HY1   0.0000  0.0000  180.0000  0.0000  0.0000
IC OY   CY   CAY  HY2   0.0000  0.0000   60.0000  0.0000  0.0000
IC OY   CY   CAY  HY3   0.0000  0.0000  -60.0000  0.0000  0.0000

PRES CTER        -1.00 ! standard C-terminus
GROUP                  ! use in generate statement
ATOM C    CC      0.34 !   OT2(-)
ATOM OT1  OC     -0.67 !  /
ATOM OT2  OC     -0.67 ! -C
DELETE ATOM O          !  \\
BOND C OT2             !   OT1
DOUBLE  C OT1
IMPR C CA OT2 OT1
ACCEPTOR OT1 C   
ACCEPTOR OT2 C   
IC N    CA   C    OT2   0.0000  0.0000  180.0000  0.0000  0.0000
IC OT2  CA   *C   OT1   0.0000  0.0000  180.0000  0.0000  0.0000

PRES CT1          0.00 ! methylated C-terminus from methyl acetate
GROUP                  ! use in generate statement
ATOM N    NH1    -0.47 !
ATOM HN   H       0.31 !          OT1
ATOM CA   CT1     0.17 !     |   //
ATOM HA   HB      0.09 ! -N--CA--C       HT1
ATOM C    CD      0.63 !  |  |    \      /
ATOM OT1  OB     -0.52 ! HN  HA    OT2--CT--HT2
ATOM OT2  OS     -0.34 !                 \
ATOM CT   CT3    -0.14 !                 HT3
ATOM HT1  HA      0.09 !
ATOM HT2  HA      0.09 !
ATOM HT3  HA      0.09 !
DELETE ATOM O   
BOND  C  OT2  OT2 CT   
BOND CT HT1  CT HT2  CT  HT3
DOUBLE C  OT1    
IMPR C CA OT2 OT1
ACCEPTOR OT1 C   
ACCEPTOR OT2 C   
IC N    CA   C    OT2   0.0000  0.0000  180.0000  0.0000  0.0000
IC OT2  CA   *C   OT1   0.0000  0.0000  180.0000  0.0000  0.0000
IC CA   C    OT2  CT    0.0000  0.0000  180.0000  0.0000  0.0000
IC C    OT2  CT   HT1   0.0000  0.0000    0.0000  0.0000  0.0000
IC C    OT2  CT   HT2   0.0000  0.0000  120.0000  0.0000  0.0000
IC C    OT2  CT   HT3   0.0000  0.0000  240.0000  0.0000  0.0000

PRES CT2          0.00 ! amidated C-terminus
GROUP                  ! use in generate statement
ATOM C    CC      0.55 !        
ATOM O    O      -0.55 !     |
GROUP                  !   O=C
ATOM NT   NH2    -0.62 !     |
ATOM HT1  H       0.32 !     NT
ATOM HT2  H       0.30 !    / \
BOND C NT              !  HT1 HT2 (HT1 is cis to O)
BOND NT HT1 NT HT2     !
IMPR C NT CA O C CA NT O   
IMPR NT C HT1 HT2 NT C HT2 HT1   
DONOR HT1 NT   
DONOR HT2 NT   
IC N    CA   C    O     0.0000  0.0000  180.0000  0.0000  0.0000
IC NT   CA   *C   O     0.0000  0.0000  180.0000  0.0000  0.0000
IC CA   C    NT   HT1   0.0000  0.0000  180.0000  0.0000  0.0000
IC HT1  C    *NT  HT2   0.0000  0.0000  180.0000  0.0000  0.0000

PRES CT3          0.00 ! N-Methylamide C-terminus
GROUP                  ! use in generate statement
ATOM C    C       0.51 !
ATOM O    O      -0.51 !      |
GROUP                  !      C=O
ATOM NT   NH1    -0.47 !      | 
ATOM HNT  H       0.31 !      NT-HNT
ATOM CAT  CT3    -0.11 !      |
ATOM HT1  HA      0.09 ! HT1-CAT-HT3
ATOM HT2  HA      0.09 !      | 
ATOM HT3  HA      0.09 !     HT2
                       !
BOND C NT  NT HNT  NT CAT  CAT HT1  CAT HT2  CAT HT3   
IMPR NT C CAT HNT C CA NT O   
CMAP -C  N  CA  C   N  CA  C  NT
DONOR HNT NT   
IC N    CA   C    O     0.0000  0.0000  180.0000  0.0000  0.0000
IC NT   CA   *C   O     0.0000  0.0000  180.0000  0.0000  0.0000
IC C    CAT  *NT  HNT   0.0000  0.0000  180.0000  0.0000  0.0000
IC CA   C    NT   CAT   0.0000  0.0000  180.0000  0.0000  0.0000
IC C    NT   CAT  HT1   0.0000  0.0000   60.0000  0.0000  0.0000
IC C    NT   CAT  HT2   0.0000  0.0000  180.0000  0.0000  0.0000
IC C    NT   CAT  HT3   0.0000  0.0000  -60.0000  0.0000  0.0000

PRES ASPP         0.00 ! patch for protonated aspartic acid, proton on od2
GROUP                  ! via acetic acid, use in a patch statement
ATOM CB   CT2    -0.21 !
ATOM HB1  HA      0.09 ! HB1    OD1
ATOM HB2  HA      0.09 !  |    //
ATOM CG   CD      0.75 ! -CB--CG
ATOM OD1  OB     -0.55 !  |     \
ATOM OD2  OH1    -0.61 ! HB2     OD2-HD2
ATOM HD2  H       0.44 !
BOND OD2 HD2   
ANGLE HD2 OD2 CG   
DIHE HD2 OD2 CG OD1  HD2 OD2 CG CB   
DONOR HD2 OD2   
IC HD2  OD2  CG   OD1   0.0000  0.0000  0.0000  0.0000  0.0000

PRES GLUP         0.00 ! patch for protonated glutamic acid, proton on oe2
GROUP                  ! via acetic acid, use in a patch statement
ATOM CG   CT2    -0.21 !
ATOM HG1  HA      0.09 ! HG1    OE1
ATOM HG2  HA      0.09 !  |    //
ATOM CD   CD      0.75 ! -CG--CD
ATOM OE1  OB     -0.55 !  |     \
ATOM OE2  OH1    -0.61 ! HG2     OE2-HE2
ATOM HE2  H       0.44 !
BOND OE2 HE2   
ANGLE HE2 OE2 CD   
DIHE HE2 OE2 CD OE1  HE2 OE2 CD CG   
DONOR HE2 OE2   
IC HE2  OE2  CD   OE1   0.0000  0.0000  0.0000  0.0000  0.0000

PRES LINK         0.00 ! linkage for IMAGES or for joining segments
                       ! 1 refers to previous (N terminal)
                       ! 2 refers to next (C terminal)
                       ! use in a patch statement
BOND 1C 2N   
ANGLE 1C 2N 2CA  1CA 1C 2N   
ANGLE 1O 1C 2N   1C  2N 2HN   
DIHE 1C  2N  2CA 2C   1C  2N  2CA 2HA  1C  2N  2CA 2CB   
DIHE 1HA 1CA 1C  2N   1N  1CA 1C  2N   1CB 1CA 1C  2N   
DIHE 1CA 1C  2N  2HN  1CA 1C  2N  2CA   
DIHE 1O  1C  2N  2HN  1O  1C  2N  2CA   
IMPR 2N 1C 2CA 2HN  1C 1CA 2N 1O   
IC 1N   1CA  1C   2N    0.0000  0.0000  180.0000  0.0000  0.0000
IC 2N   1CA  *1C  1O    0.0000  0.0000  180.0000  0.0000  0.0000
IC 1CA  1C   2N   2CA   0.0000  0.0000  180.0000  0.0000  0.0000
IC 1C   2N   2CA  2C    0.0000  0.0000  180.0000  0.0000  0.0000
IC 1C   2CA  *2N  2HN   0.0000  0.0000  180.0000  0.0000  0.0000

PRES CYSD        -1.0 ! patch for deprotonated CYS
GROUP                 ! The charges are invented!!!
ATOM CB  CT2    -0.39 !
ATOM SG  SM     -0.79 !           2SG--2CB--
DELETE ATOM HG1

PRES DISU        -0.36 ! patch for disulfides. Patch must be 1-CYS and 2-CYS.
GROUP                  ! use in a patch statement
ATOM 1CB  CT2    -0.10 !
ATOM 1SG  SM     -0.08 !           2SG--2CB--
GROUP                  !          /
ATOM 2SG  SM     -0.08 ! -1CB--1SG
ATOM 2CB  CT2    -0.10 !
DELETE ATOM 1HG1   
DELETE ATOM 2HG1   
BOND 1SG 2SG   
ANGLE 1CB 1SG 2SG 1SG 2SG 2CB   
DIHE 1HB1 1CB 1SG 2SG 1HB2 1CB 1SG 2SG   
DIHE 2HB1 2CB 2SG 1SG 2HB2 2CB 2SG 1SG   
DIHE 1CA 1CB 1SG 2SG 1SG 2SG 2CB 2CA   
DIHE 1CB 1SG 2SG 2CB   
!DIHE 1CB 1SG 2SG 2CB   
IC 1CA  1CB  1SG  2SG   0.0000  0.0000  180.0000  0.0000  0.0000
IC 1CB  1SG  2SG  2CB   0.0000  0.0000   90.0000  0.0000  0.0000
IC 1SG  2SG  2CB  2CA   0.0000  0.0000  180.0000  0.0000  0.0000

PRES HS2          0.00 ! Patch for neutral His, move proton from ND1 to NE2
GROUP                  ! use in a patch statement
ATOM CE1  CPH2    0.25 !                 HE1
ATOM HE1  HR1     0.13 !                 /
ATOM ND1  NR2    -0.70 !   HB1    ND1--CE1
ATOM CG   CPH1    0.22 !   |     /      |
ATOM CB   CT2    -0.08 !  -CB--CG       |
ATOM HB1  HA      0.09 !   |     \      |
ATOM HB2  HA      0.09 !   HB2    CD2--NE2
GROUP                  !           |     \
ATOM NE2  NR1    -0.36 !          HD2    HE2
ATOM HE2  H       0.32
ATOM CD2  CPH1   -0.05
ATOM HD2  HR3     0.09
DELETE ATOM HD1   
DELETE ACCE NE2   
BOND NE2 HE2   
ANGLE CD2 NE2 HE2  CE1 NE2 HE2   
DIHE HE2 NE2 CE1 HE1  HE2 NE2 CE1 ND1  HE2 NE2 CD2 HD2   
DIHE HE2 NE2 CD2 CG   
IMPR NE2 CD2 CE1 HE2  NE2 CE1 CD2 HE2   
DONOR HE2 NE2   
ACCEPTOR ND1   
IC CE1  CD2  *NE2 HE2   0.0000  0.0000  180.0000  0.0000  0.0000

RESI O2           0.00 ! O2 ligand for heme
GROUP                
ATOM O1   OM      0.021
ATOM O2   OM     -0.021
BOND O1 O2   
PATCHING FIRS NONE LAST NONE   

RESI CO           0.00 ! CO ligand for heme
GROUP   
ATOM C    CM      0.021
ATOM O    OM     -0.021
TRIPLE C O   
PATCHING FIRS NONE LAST NONE   

PRES FHEM         0.00 ! FIX UP THE HEME BY DELETING UNWANTED AUTOGENERATED ANGLES
                       ! unliganded heme patch
DELETE ANGLE 1NA 1FE 1NC  1NB 1FE 1ND   

PRES PHEM         0.00 ! Patch for HEME to His link.
                       ! Patch residues must be 1-HIS, and 2-HEME.
DELETE ANGLE 2NA 2FE 2NC  2NB 2FE 2ND 
BOND 1NE2 2FE   
ANGLE 1CD2 1NE2 2FE  1CE1 1NE2 2FE  1NE2 2FE 2NA  1NE2 2FE 2NB   
ANGLE 1NE2 2FE  2NC  1NE2 2FE  2ND   
IC 1CD2 1NE2 2FE  2NA   0.0000  0.0000    0.0000  0.0000  0.0000
IC 1CD2 1NE2 2FE  2NB   0.0000  0.0000    0.0000  0.0000  0.0000
IC 1CD2 1NE2 2FE  2NB   0.0000  0.0000    0.0000  0.0000  0.0000
IC 1CD2 1NE2 2FE  2NB   0.0000  0.0000    0.0000  0.0000  0.0000
IC 1CE1 1NE2 2FE  2NA   0.0000  0.0000    0.0000  0.0000  0.0000

PRES PLO2         0.00 ! Patch residue for Heme ligand.  Residues must be
                       ! 1-O2 , 2-HEME , and 3-HIS
                       ! O1 of the oxygen is bonded to the iron.
BOND 1O1 2FE        
ANGLE 1O2 1O1 2FE  1O1 2FE 2NA  1O1 2FE 2NB 
ANGLE 1O1 2FE 2NC  1O1 2FE 2ND   
DIHE 1O2 1O1 2FE 2NA   
IC 1O2  1O1  2FE  2NA   0.0000  0.0000    0.0000  0.0000  0.0000
IC 1O2  1O1  2FE  3NE2  0.0000  0.0000    0.0000  0.0000  0.0000

PRES PLIG         0.00 ! Patch residue for Heme ligand. Residues must be,
                       ! 1-CO , 2-HEME , and 3-HIS
BOND 1C 2FE          
ANGLE 1C 2FE 3NE2    
ANGLE 1O 1C  2FE  1C 2FE 2NA  1C 2FE 2NB   
ANGLE 1C 2FE 2NC  1C 2FE 2ND   
IC 1O   1C   2FE  2NA   0.0000  0.0000    0.0000  0.0000  0.0000
IC 1O   1C   2FE  3NE2  0.0000  0.0000    0.0000  0.0000  0.0000

! patches for cyclic peptides
PRES LIG1     0.00000 ! linkage for cyclic peptide
                !       1 refers to the C terminus which is a glycine
                !       2 refers to the N terminus 
                !       use in a patch statement, perform initial
                !       generation using first NONE last NONE
BOND 1C 2N
ANGLE 1C 2N 2CA 1CA 1C 2N
ANGLE 1O 1C 2N 1C 2N 2HN
DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA 1C 2N 2CA 2CB
DIHE 1HA1 1CA 1C 2N 1N 1CA 1C 2N 1HA2 1CA 1C 2N
DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA
DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA
DIHE 1CA 1C 2N 2CA
IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O
IC 1N   1CA  1C   2N    0.0000  0.0000 180.0000  0.0000  0.0000
IC 2N   1CA  *1C  1O    0.0000  0.0000 180.0000  0.0000  0.0000
IC 1CA  1C   2N   2CA   0.0000  0.0000 180.0000  0.0000  0.0000
IC 1C   2N   2CA  2C    0.0000  0.0000 180.0000  0.0000  0.0000
IC 1C   2CA  *2N  2HN   0.0000  0.0000 180.0000  0.0000  0.0000

PRES LIG2     0.00000 ! linkage for cyclic peptide
                !       1 refers to the C terminus
                !       2 refers to the N terminus which is a glycine
                !       use in a patch statement, perform initial
                !       generation using first NONE last NONE
BOND 1C 2N
ANGLE 1C 2N 2CA 1CA 1C 2N
ANGLE 1O 1C 2N 1C 2N 2HN
DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA1 1C 2N 2CA 2HA2
DIHE 1HA 1CA 1C 2N 1N 1CA 1C 2N 1CB 1CA 1C 2N
DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA
DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA
DIHE 1CA 1C 2N 2CA
IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O
IC 1N   1CA  1C   2N    0.0000  0.0000 180.0000  0.0000  0.0000
IC 2N   1CA  *1C  1O    0.0000  0.0000 180.0000  0.0000  0.0000
IC 1CA  1C   2N   2CA   0.0000  0.0000 180.0000  0.0000  0.0000
IC 1C   2N   2CA  2C    0.0000  0.0000 180.0000  0.0000  0.0000
IC 1C   2CA  *2N  2HN   0.0000  0.0000 180.0000  0.0000  0.0000

PRES LIG3     0.00000 ! linkage for cyclic peptide
                !       1 refers to the C terminus which is a glycine
                !       2 refers to the N terminus which is a glycine
                !       use in a patch statement, perform initial
                !       generation using first NONE last NONE
BOND 1C 2N
ANGLE 1C 2N 2CA 1CA 1C 2N
ANGLE 1O 1C 2N 1C 2N 2HN
DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA1 1C 2N 2CA 2HA2
DIHE 1HA1 1CA 1C 2N 1N 1CA 1C 2N 1HA2 1CA 1C 2N
DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA
DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA
DIHE 1CA 1C 2N 2CA
IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O
IC 1N   1CA  1C   2N    0.0000  0.0000 180.0000  0.0000  0.0000
IC 2N   1CA  *1C  1O    0.0000  0.0000 180.0000  0.0000  0.0000
IC 1CA  1C   2N   2CA   0.0000  0.0000 180.0000  0.0000  0.0000
IC 1C   2N   2CA  2C    0.0000  0.0000 180.0000  0.0000  0.0000
IC 1C   2CA  *2N  2HN   0.0000  0.0000 180.0000  0.0000  0.0000

RESI DUM       0.00 ! DUMMY ATOM
GROUP
ATOM DUM DUM   0.00
PATCHING FIRST NONE LAST NONE

!END
!phosphotyrosine information deleted
!

!lipids section
RESI MAS          0.00 ! methylacetate
GROUP                  !
ATOM C1   CTL3   -0.17 !           H22
ATOM C    CL      0.63 !           |
ATOM OM   OSL    -0.34 !       H21-C2-H23
ATOM C2   CTL3   -0.14 !             \
ATOM O    OBL    -0.52 !             OM
ATOM H11  HAL3    0.09 !            /
ATOM H12  HAL3    0.09 !         O=C
ATOM H13  HAL3    0.09 !           |
ATOM H21  HAL3    0.09 !       H11-C1-H13
ATOM H22  HAL3    0.09 !           |
ATOM H23  HAL3    0.09 !           H12
 
BOND C1   C       C    OM      OM    C2
DOUBLE C    O
BOND C1   H11     C1   H12     C1   H13
BOND C2   H21     C2   H22     C2   H23
IMPR C OM C1 O
! internal coordinates from experiment for heavy atoms
IC C1   C    OM   C2   1.520     109.0     180.0     114.8     1.437
IC O    C    OM   C2   1.200     125.9       0.0     114.8     1.437
IC H11  C1   C    OM   1.1       108.9     180.0     109.0     1.334
IC H12  C1   C    OM   1.1       109.75     60.4     109.0     1.334
IC H13  C1   C    OM   1.1       109.75    -60.4     109.0     1.334
IC H21  C2   OM   C    1.0788    109.94    180.0     114.8     1.334
IC H22  C2   OM   C    1.0802    110.50     60.5     114.8     1.334
IC H23  C2   OM   C    1.0802    110.50    -60.5     114.8     1.334

RESI ETAC         0.00 ! Ethylacetate
                       !            H213
GROUP                  !             |
ATOM C1   CTL3   -0.17 !        H211-C21-H212
ATOM C    CL      0.63 !             /
ATOM OM   OSL    -0.34 !        H22-C2-H23
ATOM C2   CTL2   -0.05 !             \
ATOM O    OBL    -0.52 !             OM
ATOM H11  HAL3    0.09 !            /
ATOM H12  HAL3    0.09 !         O=C
ATOM H13  HAL3    0.09 !            \
ATOM H22  HAL2    0.09 !         H11-C1-H13
ATOM H23  HAL2    0.09 !             |
GROUP                  !             H12
ATOM C21  CTL3   -0.27 
ATOM H211 HAL3    0.09
ATOM H212 HAL3    0.09
ATOM H213 HAL3    0.09
BOND C1   C       C    OM      OM    C2
DOUBLE C    O
BOND C1   H11     C1   H12     C1   H13
BOND C2   C21     C2   H22     C2   H23
BOND C21  H211    C21  H212    C21  H213
IMPR C OM C1 O 
! internal coordinates from experiment for heavy atoms
IC C1   C    OM   C2   1.520     109.0     180.0     114.8     1.437
IC O    C    OM   C2   1.200     125.9       0.0     114.8     1.437
IC H11  C1   C    OM   1.1       108.9     180.0     109.0     1.334
IC H12  C1   C    OM   1.1       109.75     60.4     109.0     1.334
IC H13  C1   C    OM   1.1       109.75    -60.4     109.0     1.334
IC C21  C2   OM   C    1.520     109.94    180.0     114.8     1.334
IC H22  C2   OM   C    1.0802    110.50     60.5     114.8     1.334
IC H23  C2   OM   C    1.0802    110.50    -60.5     114.8     1.334
IC H211 C21  C2   OM   1.1       108.90    180.0     116.7     1.437
IC H212 C21  C2   OM   1.1       108.90     60.0     116.7     1.437
IC H213 C21  C2   OM   1.1       108.90    -60.0     116.7     1.437

RESI MPRO         0.00 ! Methylpropionate
GROUP                  !
ATOM C1   CTL2   -0.08 !           H22
ATOM C    CL      0.63 !           |
ATOM OM   OSL    -0.34 !       H21-C2-H23
ATOM C2   CTL3   -0.14 !             \
ATOM O    OBL    -0.52 !             OM
ATOM H12  HAL2    0.09 !            /
ATOM H13  HAL2    0.09 !         O=C
ATOM H21  HAL3    0.09 !            \
ATOM H22  HAL3    0.09 !         H12-C1-H13
ATOM H23  HAL3    0.09 !            /
GROUP                  !     H112-C11-H111
ATOM C11  CTL3   -0.27 !           |
ATOM H111 HAL3    0.09 !          H113
ATOM H112 HAL3    0.09 !
ATOM H113 HAL3    0.09 ! 
BOND C1   C       C    OM      C    O      OM    C2
BOND C1   C11     C1   H12     C1   H13
BOND C11  H111    C11  H112    C11  H113
BOND C2   H21     C2   H22     C2   H23
IMPR C OM C1 O
! internal coordinates from experiment for heavy atoms
IC C1   C    OM   C2   1.520     109.0     180.0     114.8     1.437
IC O    C    OM   C2   1.200     125.9       0.0     114.8     1.437
IC C11  C1   C    OM   1.520     108.9     180.0     109.0     1.334
IC H12  C1   C    OM   1.1       109.75     60.4     109.0     1.334
IC H13  C1   C    OM   1.1       109.75    -60.4     109.0     1.334
IC H21  C2   OM   C    1.0788    109.94    180.0     114.8     1.334
IC H22  C2   OM   C    1.0802    110.50     60.5     114.8     1.334
IC H23  C2   OM   C    1.0802    110.50    -60.5     114.8     1.334
IC H111 C11  C1   C    1.1       109.75    180.0     109.0     1.520
IC H112 C11  C1   C    1.1       109.75     60.4     109.0     1.520
IC H113 C11  C1   C    1.1       109.75    -60.4     109.0     1.520
 
RESI ACEH         0.00 ! acetic acid
                       ! atoms in proper order for molvib input
GROUP                  !
ATOM C2   CT3    -0.30 !
ATOM C1   CD      0.75 !   H21      O2
ATOM H21  HA      0.09 !      \    //
ATOM H22  HA      0.09 !  H22-C2--C1
ATOM H23  HA      0.09 !      /     \
ATOM O2   OB     -0.55 !   H23       O1-HO1
ATOM O1   OH1    -0.61 !
ATOM HO1  H       0.44 !
BOND C1 O1  O1 HO1  C1 C2  C2 H21  C2 H22  C2 H23
DOUBLE C1 O2
IMPR C1 O1 C2 O2
IC O2   C1   C2   H21   0.0000  0.0000   0.0000  0.0000  0.0000
IC HO1  O1   C1   O2    0.0000  0.0000   0.0000  0.0000  0.0000
IC HO1  O1   C1   C2    0.0000  0.0000 180.0000  0.0000  0.0000
IC O1   C1   C2   H21   0.0000  0.0000 180.0000  0.0000  0.0000
IC O1   C1   C2   H22   0.0000  0.0000  60.0000  0.0000  0.0000
IC O1   C1   C2   H23   0.0000  0.0000 -60.0000  0.0000  0.0000

RESI ACT         -1.00  ! acetate, from CTER
GROUP                 
ATOM C2   CT3    -0.27  !       H21   O1   
ATOM H21  HA      0.09  !       |    //	    
ATOM H22  HA      0.09  !  H22--C2--C1	      
ATOM H23  HA      0.09  !       |    \	      
ATOM C1   CC      0.34  !       H23   O2(-)            
ATOM O1   OC     -0.67
ATOM O2   OC     -0.67
BOND C1 C2  O2  C1
BOND C2 H21 C2 H22  C2 H23 
DOUBLE  C1  O1
IMPR C1  C2  O2  O1
ACCEPTOR O1 C1   
ACCEPTOR O2 C1   
PATCHING FIRS NONE LAST NONE   

RESI DMPA        -1.00 ! Dimethylphosphate
GROUP                  !
ATOM P1   PL      1.50 !
ATOM O3   O2L    -0.78 !
ATOM O4   O2L    -0.78 !           H11
ATOM O1   OSL    -0.57 !            |
ATOM O2   OSL    -0.57 !       H13- C1-H12
                       !             \
ATOM C1   CTL3   -0.17 !     (-) O3   O1
ATOM H11  HAL3    0.09 !          \ /
ATOM H12  HAL3    0.09 !           P1 (+)
ATOM H13  HAL3    0.09 !          /  \
                       !     (-) O4   O2
ATOM C2   CTL3   -0.17 !             /
ATOM H21  HAL3    0.09 !        H23-C2-H22
ATOM H22  HAL3    0.09 !            |
ATOM H23  HAL3    0.09 !           H21
                       !
BOND P1   O1     P1   O2    P1   O3    P1   O4    O1   C1    O2   C2
BOND C1   H11    C1   H12   C1   H13   C2   H21   C2   H22   C2   H23

! IC FOR THE g,g conformation (3-21G* opt. structure)
IC O3   P1   O1   C1   1.4723    107.31    000.0     117.79    1.4356
IC O4   P1   O2   C2   1.4722    000.0     000.0     117.79    1.4357
IC O1   P1   O2   C2   1.6343    000.0      73.8     117.79    1.4357
IC O2   P1   O1   C1   1.6344    000.0      73.7     117.79    1.4356
IC H11  C1   O1   P1   1.0827    107.8     174.8     117.79    1.6343
IC H12  C1   O1   P1   1.0800    110.4      54.1     117.79    1.6343
IC H13  C1   O1   P1   1.0848    110.7     294.3     117.79    1.6343
IC H21  C2   O2   P1   1.0827    107.9     174.7     117.79    1.6344
IC H22  C2   O2   P1   1.0800    110.4      54.1     117.79    1.6344
IC H23  C2   O2   P1   1.0848    110.7     294.2     117.79    1.6344
 
RESI MP_1        -1.00 ! Methylphosphate, anionic
GROUP                  !
! atom order for molvib
ATOM C1   CTL3   -0.17  !
ATOM O1   OSL    -0.62  !                 H11
ATOM P1   PL      1.50  !                  |
ATOM O2   OHL    -0.68  !            H13--C1--H12
ATOM O3   O2L    -0.82  !                  |
ATOM O4   O2L    -0.82  !                 O1
ATOM H11  HAL3    0.09  !                  |
ATOM H12  HAL3    0.09  !             O4==P1==O3 (-)
ATOM H13  HAL3    0.09  !                  |
ATOM H2   HOL     0.34  !                 O2
                        !                   \
                        !                    H2

BOND P1   O1     P1   O2    P1   O3    P1   O4    O1   C1
BOND C1   H11    C1   H12   C1   H13   O2   H2

IC O3   P1   O1   C1   0.0000    000.00    000.0     000.00    0.0000
IC O4   P1   O1   C1   0.0000    000.00    000.0     000.00    0.0000
IC O2   P1   O1   C1   0.0000    000.00    000.0     000.00    0.0000
IC H11  C1   O1   P1   0.0000    000.00    000.0     000.00    0.0000
IC H12  C1   O1   P1   0.0000    000.00    000.0     000.00    0.0000
IC H13  C1   O1   P1   0.0000    000.00    000.0     000.00    0.0000
IC H2   O2   P1   O1   0.0000    000.00    000.0     000.00    0.0000
 
RESI MP_2        -2.00 ! Methylphosphate, dianionic
GROUP                  !
ATOM P1   PL      1.10 !
ATOM O1   OSL    -0.40 !                 H11
ATOM O2   O2L    -0.90 !                  |
ATOM O3   O2L    -0.90 !            H13--C1--H12
ATOM O4   O2L    -0.90 !                  |
GROUP                  !                  O1
ATOM C1   CTL3   -0.27 !                  |
ATOM H11  HAL3    0.09 !          (-) O4--P1(+)--O3 (-)
ATOM H12  HAL3    0.09 !                  |
ATOM H13  HAL3    0.09 !                  O2 (-)
                       !
BOND P1   O1     P1   O2    P1   O3    P1   O4    O1   C1
BOND C1   H11    C1   H12   C1   H13

IC O3   P1   O1   C1   0.0000    000.00    000.0     000.00    0.0000
IC O4   P1   O1   C1   0.0000    000.00    000.0     000.00    0.0000
IC O2   P1   O1   C1   0.0000    000.00    000.0     000.00    0.0000
IC H11  C1   O1   P1   0.0000    000.00    000.0     000.00    0.0000
IC H12  C1   O1   P1   0.0000    000.00    000.0     000.00    0.0000
IC H13  C1   O1   P1   0.0000    000.00    000.0     000.00    0.0000
! dummy to analyze cetain angles
IC O3   P1   O4   O1   0.0         0.0       0.0       0.0     0.0
 
RESI  MSO4       -1.00 ! Methylsulfate
GROUP                  !
ATOM S    SL      1.33 !           OS2(-1)
ATOM OS1  OSL    -0.28 !            |
ATOM OS2  O2L    -0.65 ! (-1) OS2--S(+2)--OS4 (-1)
ATOM OS3  O2L    -0.65 !            |
ATOM OS4  O2L    -0.65 !           OS1
ATOM C1   CTL3   -0.37 !             \
ATOM H11  HAL3    0.09 !         H11-C1-H13
ATOM H12  HAL3    0.09 !              |
ATOM H13  HAL3    0.09 !             H12
                       !
BOND  S  OS1  S  OS2  S  OS3  S  OS4  OS1  C1
BOND  C1 H11  C1 H12  C1 H13
ACCE  OS1
ACCE  OS2
ACCE  OS3
ACCE  OS4

IC OS4  S    OS2  OS1   0.0000  0.0000   60.0000  0.0000  0.0000
IC OS2  S    OS2  OS3   0.0000  0.0000  -60.0000  0.0000  0.0000
IC OS3  S    OS1  OS4   0.0000  0.0000   60.0000  0.0000  0.0000
IC OS1  S   OS3   OS2   0.0000  0.0000   60.0000  0.0000  0.0000
IC C1   OS1   S   OS2   0.0000  0.0000   60.0000  0.0000  0.0000
IC S    OS1  C1   OS3   0.0000  0.0000   60.0000  0.0000  0.0000
IC OS1  S    OS4  OS2   0.0000  0.0000  180.0000  0.0000  0.0000
IC OS1  S    OS2  OS3   0.0000  0.0000  180.0000  0.0000  0.0000
IC OS1  S    OS3  OS2   0.0000  0.0000  180.0000  0.0000  0.0000
IC OS4  S    OS2  OS1   0.0000  0.0000   60.0000  0.0000  0.0000
IC OS4  S    OS3  OS1   0.0000  0.0000   60.0000  0.0000  0.0000
IC OS3  S    OS2  OS1   0.0000  0.0000   60.0000  0.0000  0.0000
IC OS4  S    OS1  C1    0.0000  0.0000   60.0000  0.0000  0.0000
IC OS2  S    OS1  C1    0.0000  0.0000   60.0000  0.0000  0.0000
IC OS3  S    OS1  C1    0.0000  0.0000   60.0000  0.0000  0.0000

Resi BUTA        0.00  ! BUTANE
Group
Atom  h11 HAL3    0.09 !    H2
Atom  h12 HAL3    0.09 !     |
Atom  h13 HAL3    0.09 ! H1-C1-H3
Atom  c1  CTL3   -0.27 !     |
Group                  !     |
Atom  h21 HAL2    0.09 ! H4-C2-H5
Atom  h22 HAL2    0.09 !     |
Atom  c2  CTL2   -0.18 !     |
Group                  !     |
Atom  h31 HAL2    0.09 ! H6-C3-H7
Atom  h32 HAL2    0.09 !     |
atom  c3  CTL2   -0.18 !     |
Group                  !     |
atom  h41 HAL3    0.09 ! H8-C4-H10
atom  h42 HAL3    0.09 !     |
atom  h43 HAL3    0.09 !    H9
atom  c4  CTL3   -0.27 !
Bond h11 c1  h12 c1  h13 c1  c1 c2
Bond h21 c2  h22 c2  c2  c3
Bond h31 c3  h32 c3  c3  c4
Bond h41 c4  h42 c4  h43 c4
ic  c1  c2  c3  c4  0.00  0.00  180.0  0.00 0.00
ic  c2  c3  c4  h41 0.00  0.00  180.0  0.00 0.00
ic  c3  h41 *c4 h42 0.00  0.00  120.0  0.00 0.00
ic  c3  h41 *c4 h43 0.00  0.00 -120.0  0.00 0.00
ic  c3  c2  c1  h11 0.00  0.00  180.0  0.00 0.00
ic  c2  h11 *c1 h12 0.00  0.00  120.0  0.00 0.00
ic  c2  h11 *c1 h13 0.00  0.00 -120.0  0.00 0.00
ic  c1  c3  *c2 h21 0.00  0.00  120.0  0.00 0.00
ic  c1  c3  *c2 h22 0.00  0.00 -120.0  0.00 0.00
ic  c2  c4  *c3 h31 0.00  0.00  120.0  0.00 0.00
ic  c2  c4  *c3 h32 0.00  0.00 -120.0  0.00 0.00

Resi HEXA         0.00 ! hexane
Group
Atom  h11 HAL3    0.09 !    H2
Atom  h12 HAL3    0.09 !     |
Atom  h13 HAL3    0.09 ! H1-C1-H3
Atom  c1  CTL3   -0.27 !     |
Group                  !     |
Atom  h21 HAL2    0.09 ! H4-C2-H5
Atom  h22 HAL2    0.09 !     |
Atom  c2  CTL2   -0.18 !     |
Group                  !     |
Atom  h31 HAL2    0.09 ! H6-C3-H7
Atom  h32 HAL2    0.09 !     |
atom  c3  CTL2   -0.18 !     |
Group                  !     |
atom  h41 HAL2    0.09 ! H8-C4-H10
atom  h42 HAL2    0.09 !     |
atom  c4  CTL2   -0.18 !     |
Group                  !     |
atom  h51 HAL2    0.09 ! H51-C5-H152
atom  h52 HAL2    0.09 !     |
atom  c5  CTL2   -0.18 !     |
Group                  !     |
atom  h61 HAL2    0.09 ! H61-C4-H62
atom  h62 HAL2    0.09 !     |
atom  h63 HAL2    0.09 !    H63
atom  c6  CTL2   -0.27 !
Bond h11 c1  h12 c1  h13 c1  c1 c2
Bond h21 c2  h22 c2  c2  c3
Bond h31 c3  h32 c3  c3  c4
Bond h41 c4  h42 c4  c4  c5
Bond h51 c5  h52 c5  c5  c6
Bond h61 c6  h62 c6  c6  h63
ic  c1  c2  c3  c4  0.00  0.00  180.0   0.00 0.00
ic  c2  c3  c4  c5  0.00  0.00  180.0   0.00 0.00
ic  c3  c4  c5  c6  0.00  0.00  180.0   0.00 0.00
ic  c3  c2  c1  h11 0.00  0.00  180.0   0.00 0.00
ic  h11 c2 *c1  h12 0.00  0.00  120.0   0.00 0.00
ic  h11 c2 *c1  h13 0.00  0.00  240.0   0.00 0.00
ic  c1  c3 *c2  h21 0.00  0.00  120.0   0.00 0.00
ic  c1  c3 *c2  h22 0.00  0.00  240.0   0.00 0.00
ic  c2  c4 *c3  h31 0.00  0.00  120.0   0.00 0.00
ic  c2  c4 *c3  h32 0.00  0.00  240.0   0.00 0.00
ic  c3  c5 *c4  h41 0.00  0.00  120.0   0.00 0.00
ic  c3  c5 *c4  h42 0.00  0.00  240.0   0.00 0.00
ic  c4  c6 *c5  h51 0.00  0.00  120.0   0.00 0.00
ic  c4  c6 *c5  h52 0.00  0.00  240.0   0.00 0.00
ic  c4  c5  c6  h61 0.00  0.00  180.0   0.00 0.00
ic  h61 c5 *c6  h62 0.00  0.00  120.0   0.00 0.00
ic  h61 c5 *c6  h63 0.00  0.00  240.0   0.00 0.00

Resi ETHE       0.00 ! ethylene, yin/adm jr.
Group 
 Atom c1  cel2 -0.42 !
 Atom h11 hel2  0.21 !  H11     H21
 Atom h12 hel2  0.21 !    \     /
Group                !     C1=C2
 Atom c2  cel2 -0.42 !    /     \
 Atom h21 hel2  0.21 !  H12     H22
 Atom h22 hel2  0.21 !
Bond c1 h11  c1 h12
Double c1 c2
Bond c2 h21  c2 h22
IMPR c1 c2 h12 h11
IMPR c1 c2 h11 h12
IMPR c2 c1 h22 h21
IMPR c2 c1 h21 h22
ic h11 c1 c2  h21  0.00 0.00  180.0 0.0  0.0
ic h12 c2 *c1 h11  0.00 0.00  180.0 0.0  0.0
ic h22 c1 *c2 h21  0.00 0.00  180.0 0.0  0.0
ic c1  c2 h21 h22  0.00 0.00  180.0 0.0  0.0
patc firs none last none

Resi PRPE       0.00 ! propene, yin/adm jr.
Group
 Atom c1  cel2 -0.42 !
 Atom h11 hel2  0.21 ! H11     H21
 Atom h12 hel2  0.21 !   \     /
Group                !    C1=C2   H31
 Atom c2  cel1 -0.15 !   /     \  /
 Atom h21 HEL1  0.15 ! H12      C3
Group                !         /  \
 Atom c3  ctl3 -0.27 !       H33  H32
 Atom h31 HAL3  0.09 !
 Atom h32 HAL3  0.09 !
 Atom h33 HAL3  0.09 !
Bond c1 h11  c1 h12
Double c1 c2
Bond c2 h21
Bond c2 c3
bond c3 h31  c3 h32  c3 h33
ic h11 c1 c2  h21  0.00 0.00  180.0 0.0  0.0
ic h12 c2 *c1 h11  0.00 0.00  180.0 0.0  0.0
ic c3  c1 *c2 h21  0.00 0.00  180.0 0.0  0.0
ic h31 c3 c2  c1   0.00 0.00    0.0 0.0  0.0
ic h32 c3 c2  c1   0.00 0.00  120.0 0.0  0.0
ic h33 c3 c2  c1   0.00 0.00 -120.0 0.0  0.0
patc firs none last none

Resi BTE1       0.00 ! 1-Butene, yin/adm jr.
Group        
 Atom c1  cel2 -0.42 !
 Atom h11 hel2  0.21 ! H11     H21 H41
 Atom h12 hel2  0.21 !   \     /    |
Group                !    C1=C2    C4-H42
 Atom c2  cel1 -0.15 !   /     \  /  \
 Atom h21 HEL1  0.15 ! H12      C3    H43
Group                !         /  \
 Atom c3  ctl2 -0.18 !       H31  H32
 Atom h31 HAL2  0.09 !
 Atom h32 HAL2  0.09 !
Group
 Atom c4  ctl3 -0.27
 Atom h41 HAL3  0.09
 Atom h42 HAL3  0.09
 Atom h43 HAL3  0.09
BOND c1 h11  c1 h12
Double c1 c2
BOND c2 h21
BOND c2 c3
BOND c3 h31  c3 h32
BOND c3 c4
BOND c4 h41  c4 h42  c4 h43
ic  c1   c2 c3  c4   0.00 0.00    0.0 0.00 0.00
ic  h11  c1 c2  c3   0.00 0.00  180.0 0.00 0.00
ic  h12  c1 c2  c3   0.00 0.00    0.0 0.00 0.00
ic  h21  c1 *c2 c3   0.00 0.00  180.0 0.00 0.00
ic  h31  c2 *c3 c4   0.00 0.00  120.0 0.00 0.00
ic  h32  c2 *c3 c4   0.00 0.00 -120.0 0.00 0.00
ic  h41  c4 c3  c2   0.00 0.00  180.0 0.00 0.00
ic  h42  c4 c3  c2   0.00 0.00   60.0 0.00 0.00
ic  h43  c4 c3  c2   0.00 0.00  -60.0 0.00 0.00
patc firs none last none


Resi BTE2       0.00 ! 2-Butene, yin/adm jr.
Group
 Atom c1  ctl3 -0.27 !  H12 H13
 Atom h11 HAL3  0.09 !    \ |
 Atom h12 HAL3  0.09 ! H13-C1      H31
 Atom h13 HAL3  0.09 !       \     /
Group                !        C2=C3
 Atom c2  cel1 -0.15 !       /     \
 Atom h21 HEL1  0.15 !     H21      C4-H41
Group                !              | \
 Atom c3  cel1 -0.15 !            H43 H42
 Atom h31 HEL1  0.15 !
Group
 Atom c4  ctl3 -0.27
 Atom h41 HAL3  0.09
 Atom h42 HAL3  0.09
 Atom h43 HAL3  0.09
BOND c1 h11  c1 h12  c1 h13
BOND c1 c2
BOND c2 h21
DOUBLE c2 c3
BOND c3 h31
BOND c3 c4
BOND c4 h41  c4 h42  c4 h43
ic  c1   c2 c3  c4   0.00 0.00  180.0 0.00 0.00
ic  h11  c1 c2  c3   0.00 0.00    0.0 0.00 0.00
ic  h12  c1 c2  c3   0.00 0.00  120.0 0.00 0.00
ic  h13  c1 c2  c3   0.00 0.00 -120.0 0.00 0.00
ic  h21  c1 *c2 c3   0.00 0.00  180.0 0.00 0.00
ic  h31  c4 *c3 c2   0.00 0.00  120.0 0.00 0.00
ic  h41  c4 c3  c2   0.00 0.00    0.0 0.00 0.00
ic  h42  c4 c3  c2   0.00 0.00  120.0 0.00 0.00
ic  h43  c4 c3  c2   0.00 0.00 -120.0 0.00 0.00
patc firs none last none

Resi HXE2       0.00 ! 2-hexene, yin/adm jr.
Group
 Atom c1  ctl3 -0.27 !  H12 H13
 Atom h11 HAL3  0.09 !    \ |
 Atom h12 HAL3  0.09 ! H13-C1    H31 H51 H52
 Atom h13 HAL3  0.09 !       \    /    \ /
Group                !        C2=C3    C5    H61
 Atom c2  cel1 -0.15 !       /     \  /  \  /
 Atom h21 HEL1  0.15 !     H21      C4    C6-H62
Group                !             / \      \
 Atom c3  cel1 -0.15 !           H41 H42     H63
 Atom h31 HEL1  0.15 !
Group
 Atom c4  ctl2 -0.18
 Atom h41 HAL2  0.09
 Atom h42 HAL2  0.09
Group
 Atom c5  ctl2 -0.18
 Atom h51 HAL2  0.09
 Atom h52 HAL2  0.09
Group
 Atom c6  ctl3 -0.27
 Atom h61 HAL3  0.09
 Atom h62 HAL3  0.09
 Atom h63 HAL3  0.09

BOND c1 h11  c1 h12  c1 h13
BOND c1 c2
BOND c2 h21
DOUBLE c2 c3
BOND c3 h31
BOND c3 c4
BOND c4 h41  c4 h42
BOND c4 c5   c5 h51  c5 h52
BOND c5 c6   c6 h61  c6 h62  c6 h63
! all trans
ic  c1   c2 c3  c4   0.00 0.00  180.0 0.00 0.00
ic  h11  c1 c2  c3   0.00 0.00    0.0 0.00 0.00
ic  h12  c1 c2  c3   0.00 0.00  120.0 0.00 0.00
ic  h13  c1 c2  c3   0.00 0.00 -120.0 0.00 0.00
ic  h21  c1 *c2 c3   0.00 0.00  180.0 0.00 0.00
ic  h31  c4 *c3 c2   0.00 0.00  120.0 0.00 0.00
ic  c2   c3 c4  c5   0.00 0.00  180.0 0.00 0.00
ic  c3   c5 *c4 h41  0.00 0.00  120.0 0.00 0.00
ic  c3   c5 *c4 h42  0.00 0.00 -120.0 0.00 0.00
ic  c3   c4 c5  c6   0.00 0.00  180.0 0.00 0.00
ic  c4   c6 *c5 h51  0.00 0.00  120.0 0.00 0.00
ic  c4   c6 *c5 h52  0.00 0.00 -120.0 0.00 0.00
ic  h61  c6 c5  c4   0.00 0.00  180.0 0.00 0.00
ic  h62  c6 c5  c4   0.00 0.00   60.0 0.00 0.00
ic  h63  c6 c5  c4   0.00 0.00  300.0 0.00 0.00
patc firs none last none

!RESI TIP3         0.00 ! TIPS3P WATER MODEL
!                       ! GENERATE USING NOANGLE NODIHEDRAL
!GROUP                  !
!ATOM OH2  OT     -0.834
!ATOM H1   HT      0.417
!ATOM H2   HT      0.417
!BOND OH2  H1     OH2  H2    H1   H2    ! THE LAST BOND IS NEEDED FOR SHAKE
!ANGLE H1 OH2 H2    ! REQUIRED
!ACCEPTOR OH2
!PATCHING FIRS NONE LAST NONE
 
!RESI TP3M         0.000 ! "mmff" water model, as an analog of tip3p
!GROUP   
!ATOM OH2  OT     -0.834  ! these charges are replaced by the mmff setup   
!ATOM H1   HT      0.417  ! these charges are replaced by the mmff setup
!ATOM H2   HT      0.417  ! these charges are replaced by the mmff setup
!BOND OH2 H1 OH2 H2          ! omits the H1-H2 bond, which is needed for shake with tip3p
!ANGLE H1 OH2 H2             ! required
!ACCEPTOR OH2   
!PATCHING FIRS NONE LAST NONE     


RESI NC4          1.00 ! tetramethylammonium
GROUP                  ! 
ATOM N    NTL    -0.60 !                H32
ATOM C1   CTL5   -0.35 !                 |
ATOM C2   CTL5   -0.35 !            H31-C3-H33
ATOM C3   CTL5   -0.35 !         H23     |      H41
ATOM C4   CTL5   -0.35 !         |       |      |
ATOM H11  HL      0.25 !     H22-C2------N------C4-H42    (+)
ATOM H12  HL      0.25 !         |       |      |
ATOM H13  HL      0.25 !         H21     |      H43
ATOM H21  HL      0.25 !            H11-C1-H13
ATOM H22  HL      0.25 !                 |
ATOM H23  HL      0.25 !                 H12
ATOM H31  HL      0.25
ATOM H32  HL      0.25
ATOM H33  HL      0.25
ATOM H41  HL      0.25
ATOM H42  HL      0.25
ATOM H43  HL      0.25
BOND N C1 N C2 N C3 N C4
BOND C1 H11 C1 H12 C1 H13
BOND C2 H21 C2 H22 C2 H23
BOND C3 H31 C3 H32 C3 H33
BOND C4 H41 C4 H42 C4 H43
! internal are wrong
IC C2   N    C1   H11   0.0000  0.0000  180.0000  0.0000  0.0000
IC C2   N    C1   H12   0.0000  0.0000  -60.0000  0.0000  0.0000
IC C2   N    C1   H13   0.0000  0.0000   60.0000  0.0000  0.0000
IC C2   C1   *N   C3    0.0000  0.0000  120.0000  0.0000  0.0000
IC C2   C1   *N   C4    0.0000  0.0000 -120.0000  0.0000  0.0000
IC C3   N    C2   H21   0.0000  0.0000    0.0000  0.0000  0.0000
IC C3   N    C2   H22   0.0000  0.0000 -120.0000  0.0000  0.0000
IC C3   N    C2   H23   0.0000  0.0000  120.0000  0.0000  0.0000
IC C4   N    C3   H31   0.0000  0.0000    0.0000  0.0000  0.0000
IC C4   N    C3   H32   0.0000  0.0000 -120.0000  0.0000  0.0000
IC C4   N    C3   H33   0.0000  0.0000  120.0000  0.0000  0.0000
IC C1   N    C4   H41   0.0000  0.0000    0.0000  0.0000  0.0000
IC C1   N    C4   H42   0.0000  0.0000 -120.0000  0.0000  0.0000
IC C1   N    C4   H43   0.0000  0.0000  120.0000  0.0000  0.0000
 
RESI NC5          1.00 ! tetramethylammonium ethyl analog 
GROUP
ATOM N    NTL    -0.60 !
ATOM C1   CTL2   -0.10 !                 |
ATOM C2   CTL5   -0.35 !               -C3-
ATOM C3   CTL5   -0.35 !                 |
ATOM C4   CTL5   -0.35 !            |    |   |
ATOM H11  HL      0.25 !           -C2---N---C4-     (+)
ATOM H12  HL      0.25 !            |    |   |
ATOM H21  HL      0.25 !                 |
ATOM H22  HL      0.25 !               -C1-
ATOM H23  HL      0.25 !                 |
ATOM H31  HL      0.25 !                 |
ATOM H32  HL      0.25 !               -C5-
ATOM H33  HL      0.25 !                 |
ATOM H41  HL      0.25
ATOM H42  HL      0.25
ATOM H43  HL      0.25
GROUP
ATOM C5   CTL3   -0.27
ATOM H51  HAL3    0.09
ATOM H52  HAL3    0.09
ATOM H53  HAL3    0.09
BOND N C1 N C2 N C3 N C4
BOND C1 H11 C1 H12 C1 C5
BOND C2 H21 C2 H22 C2 H23
BOND C3 H31 C3 H32 C3 H33
BOND C4 H41 C4 H42 C4 H43
BOND C5 H51 C5 H52 C5 H53
! ab-initio HF/6-31G* structure
IC C4    N     C1    C5     1.4967  107.80  180.00  115.98   1.5217
IC C5    C1    N     C2     1.5217  115.98  -61.05  111.12   1.4950
IC C5    C1    N     C3     1.5217  115.98   61.05  111.12   1.4950
IC C4    N     C1    H11    1.4967  107.80   57.27  105.76   1.0809
IC C4    N     C1    H12    1.4967  107.80  -57.27  105.76   1.0809
IC C1    N     C2    H21    1.5176  111.12 -174.50  108.75   1.0795
IC C1    N     C2    H22    1.5176  111.12   65.81  109.69   1.0773
IC C1    N     C2    H23    1.5176  111.12  -54.79  109.07   1.0797
IC C1    N     C3    H31    1.5176  111.12  174.50  108.75   1.0795
IC C1    N     C3    H32    1.5176  111.12  -65.81  109.69   1.0773
IC C1    N     C3    H33    1.5176  111.12   54.79  109.07   1.0797
IC C1    N     C4    H41    1.5176  107.80  180.00  109.11   1.0793
IC C1    N     C4    H42    1.5176  107.80   60.03  109.12   1.0793
IC C1    N     C4    H43    1.5176  107.80  -60.03  109.12   1.0793
IC N     C1    C5    H51    1.5176  115.98  180.00  107.05   1.0836
IC N     C1    C5    H52    1.5176  115.98   62.29  112.91   1.0820
IC N     C1    C5    H53    1.5176  115.98  -62.29  112.91   1.0820

RESI CHOL         1.00 ! choline
GROUP                  !
ATOM N    NTL    -0.60 !
ATOM C1   CTL2   -0.10 !                 |
ATOM C2   CTL5   -0.35 !               -C3-
ATOM C3   CTL5   -0.35 !                 |
ATOM C4   CTL5   -0.35 !            |    |   |
ATOM H11  HL      0.25 !           -C2---N---C4-     (+)
ATOM H12  HL      0.25 !            |    |   |
ATOM H21  HL      0.25 !                 |
ATOM H22  HL      0.25 !               -C1-
ATOM H23  HL      0.25 !                 |
ATOM H31  HL      0.25 !                 |
ATOM H32  HL      0.25 !                 |
ATOM H33  HL      0.25 !                 |
ATOM H41  HL      0.25 !                 |
ATOM H42  HL      0.25 !                 |
ATOM H43  HL      0.25 !                 |
GROUP                  !                 |
ATOM C5   CTL2    0.05 !                 |
ATOM H51  HAL2    0.09 !               -C5-
ATOM H52  HAL2    0.09 !                 |
ATOM OH1  OHL    -0.66 !                 OH1---HO1
ATOM HO1  HOL     0.43 !
BOND N C1 N C2 N C3 N C4
BOND C1 H11 C1 H12 C1 C5
BOND C2 H21 C2 H22 C2 H23
BOND C3 H31 C3 H32 C3 H33
BOND C4 H41 C4 H42 C4 H43
BOND C5 H51 C5 H52
BOND C5 OH1 OH1 HO1
! ab-initio HF/6-31G* geometry  of gauche conformer
IC C4    N     C1    C5     1.4964  107.76  161.60  116.58   1.5208
IC C5    C1    N     C2     1.5208  116.58  -80.13  111.04   1.5031
IC C5    C1    N     C3     1.5208  116.58   42.05  111.71   1.4945
IC N     C1    C5    OH1    1.5158  116.58   56.02  109.57   1.3947
IC C1    C5    OH1   HO1    1.5208  109.57  169.05  110.84   0.9491
IC C2    N     C1    H11    1.5031  111.04  158.76  106.72   1.0813
IC C3    N     C1    H12    1.4945  111.71  165.25  106.14   1.0802
IC C1    N     C2    H21    1.5158  111.04 -179.38  108.21   1.0796
IC C3    N     C2    H22    1.4945  109.20  -63.85  109.22   1.0746
IC C4    N     C2    H23    1.4964  108.15   57.69  108.56   1.0794
IC C1    N     C3    H31    1.5158  111.71  173.42  108.53   1.0794
IC C2    N     C3    H32    1.5031  109.20  177.22  109.23   1.0800
IC C4    N     C3    H33    1.4964  108.88  174.14  109.12   1.0773
IC C1    N     C4    H41    1.5158  107.76  175.04  109.01   1.0793
IC C2    N     C4    H42    1.5031  108.15  -64.86  109.05   1.0796
IC C3    N     C4    H43    1.4945  108.88   56.40  109.30   1.0794
IC N     C1    C5    H51    1.5158  116.58  176.61  105.66   1.0855
IC N     C1    C5    H52    1.5158  116.58  -67.32  110.89   1.0847
 
RESI ACHO         1.00 ! acetylcholine
GROUP                  !
ATOM N    NTL    -0.60 !
ATOM C1   CTL2   -0.10 !                 |
ATOM C2   CTL5   -0.35 !               -C3-
ATOM C3   CTL5   -0.35 !                 |
ATOM C4   CTL5   -0.35 !            |    |   |
ATOM H11  HL      0.25 !           -C2---N---C4-     (+)
ATOM H12  HL      0.25 !            |    |   |
ATOM H21  HL      0.25 !                 |
ATOM H22  HL      0.25 !               -C1-
ATOM H23  HL      0.25 !                 |
ATOM H31  HL      0.25 !                 |
ATOM H32  HL      0.25 !                 |
ATOM H33  HL      0.25 !                 |
ATOM H41  HL      0.25 !                 |
ATOM H42  HL      0.25 !                 |
ATOM H43  HL      0.25 !                 |
GROUP                  !                 |  
ATOM C5   CTL2   -0.05 !               -C5- 
ATOM OM   OSL    -0.34 !                 |  
ATOM C    CL      0.63 !                OM
ATOM C7   CTL3   -0.17 !                /
ATOM O    OBL    -0.52 !            O==C
ATOM H51  HAL2    0.09 !               |
ATOM H52  HAL2    0.09 !             --C7--
ATOM H71  HAL3    0.09 !               |
ATOM H72  HAL3    0.09 !
ATOM H73  HAL3    0.09 !
BOND N C1   N C2   N C3   N C4
BOND C1 H11 C1 H12 C1 C5
BOND C2 H21 C2 H22 C2 H23
BOND C3 H31 C3 H32 C3 H33
BOND C4 H41 C4 H42 C4 H43
BOND C5 H51 C5 H52
BOND C7   C       C    OM      OM    C5
DOUBLE C   O
BOND C7   H71     C7   H72     C7   H73
IMPR C OM C7 O
IC C4    N     C1    C5     0.0000  000.00  161.60  000.00   0.0000
IC C5    C1    N     C2     0.0000  000.00  -80.13  000.00   0.0000
IC C5    C1    N     C3     0.0000  000.00   42.05  000.00   0.0000
IC C2    N     C1    H11    0.0000  000.00  158.76  000.00   0.0000
IC C3    N     C1    H12    0.0000  000.00  165.25  000.00   0.0000
IC C1    N     C2    H21    0.0000  000.00 -179.38  000.00   0.0000
IC C3    N     C2    H22    0.0000  000.00  -63.85  000.00   0.0000
IC C4    N     C2    H23    0.0000  000.00   57.69  000.00   0.0000
IC C1    N     C3    H31    0.0000  000.00  173.42  000.00   0.0000
IC C2    N     C3    H32    0.0000  000.00  177.22  000.00   0.0000
IC C4    N     C3    H33    0.0000  000.00  174.14  000.00   0.0000
IC C1    N     C4    H41    0.0000  000.00  175.04  000.00   0.0000
IC C2    N     C4    H42    0.0000  000.00  -64.86  000.00   0.0000
IC C3    N     C4    H43    0.0000  000.00   56.40  000.00   0.0000
IC N     C1    C5    H51    0.0000  000.00  180.00  000.00   0.0000
IC N     C1    C5    H52    0.0000  000.00  -60.0   000.00   0.0000
IC N     C1    C5    OM     0.0000  000.00   72.0   000.00   0.0000
IC C1    C5    OM    C      0.0000  000.00  166.9   000.00   0.0000
IC C7    C     OM    C5     0.0000  000.00   20.0   000.00   0.0000
IC O     C     OM    C5     0.0000  000.00 -160.0   000.00   0.0000
IC H71   C7    C     OM     0.0000  000.00  180.0   000.00   0.0000
IC H72   C7    C     OM     0.0000  000.00   60.4   000.00   0.0000
IC H73   C7    C     OM     0.0000  000.00  -60.4   000.00   0.0000
 
RESI PC           0.00 ! phosphatidylcholine
GROUP                  !
ATOM N    NTL    -0.60 !
ATOM C1   CTL2   -0.10 !                 |
ATOM C2   CTL5   -0.35 !               -C3-
ATOM C3   CTL5   -0.35 !                 |
ATOM C4   CTL5   -0.35 !            |    |   |
ATOM H11  HL      0.25 !           -C2---N---C4-     (+)
ATOM H12  HL      0.25 !            |    |   |
ATOM H21  HL      0.25 !                 |
ATOM H22  HL      0.25 !               -C1-
ATOM H23  HL      0.25 !                 |
ATOM H31  HL      0.25 !                 |
ATOM H32  HL      0.25 !                 |
ATOM H33  HL      0.25 !                 |
ATOM H41  HL      0.25 !                 |
ATOM H42  HL      0.25 !                 |
ATOM H43  HL      0.25 !                 |
GROUP                  !                 |
ATOM C5   CTL2   -0.08 !                 |
ATOM H51  HAL2    0.09 !          H52---C5---H51
ATOM H52  HAL2    0.09 !                 |
GROUP                  !                 |
ATOM P1   PL      1.50 !       (-) O3   O1
ATOM O3   O2L    -0.78 !             \ /
ATOM O4   O2L    -0.78 !              P1 (+)
ATOM O1   OSL    -0.57 !             / \
ATOM O2   OSL    -0.57 !       (-) O4   O2
GROUP                  !                 |
ATOM C6   CTL3   -0.17 !                 |
ATOM H61  HAL3    0.09 !            H63-C6-H62
ATOM H62  HAL3    0.09 !                 |
ATOM H63  HAL3    0.09 !                H61
                       !
BOND N C1 N C2 N C3 N C4
BOND C1 H11 C1 H12 C1 C5
BOND C2 H21 C2 H22 C2 H23
BOND C3 H31 C3 H32 C3 H33
BOND C4 H41 C4 H42 C4 H43
BOND C5 H51 C5 H52
BOND P1   O1     P1   O2    P1   O3    P1   O4    O1   C5    O2   C6
BOND C6   H61    C6   H62   C6   H63

IC C4    N     C1    C5     0.0000  000.00  112.00  000.00   0.0000
IC C5    C1    N     C2     0.0000  000.00 -121.00  000.00   0.0000
IC C5    C1    N     C3     0.0000  000.00    0.00  000.00   0.0000
IC C2    N     C1    H11    0.0000  000.00  120.00  000.00   0.0000
IC C3    N     C1    H12    0.0000  000.00  120.00  000.00   0.0000
IC C1    N     C2    H21    0.0000  000.00  180.00  000.00   0.0000
IC C3    N     C2    H22    0.0000  000.00  -60.00  000.00   0.0000
IC C4    N     C2    H23    0.0000  000.00   60.00  000.00   0.0000
IC C1    N     C3    H31    0.0000  000.00  180.00  000.00   0.0000
IC C2    N     C3    H32    0.0000  000.00  180.00  000.00   0.0000
IC C4    N     C3    H33    0.0000  000.00  180.00  000.00   0.0000
IC C1    N     C4    H41    0.0000  000.00  180.00  000.00   0.0000
IC C2    N     C4    H42    0.0000  000.00  -60.00  000.00   0.0000
IC C3    N     C4    H43    0.0000  000.00   60.00  000.00   0.0000
IC N     C1    C5    H51    0.0000  000.00 -150.00  000.00   0.0000
IC N     C1    C5    H52    0.0000  000.00  100.00  000.00   0.0000
IC N     C1    C5    O1     0.0000  000.00  -30.00  000.00   0.0000
IC C1    C5    O1    P1     0.0000  000.00  130.00  000.00   0.0000
IC C5    O1    P1    O2     0.0000  000.00 -160.0   000.00   0.0000
IC O3    P1    O1    C5     0.0000  000.00   80.00  000.00   0.0000
IC O4    P1    O1    C5     0.0000  000.00  -60.00  000.00   0.0000
IC O1    P1    O2    C6     0.0000  000.00  180.00  000.00   0.0000
IC H61   C6    O2    P1     0.0000  000.00    0.00  000.00   0.0000
IC H62   C6    O2    P1     0.0000  000.00  120.00  000.00   0.0000
IC H63   C6    O2    P1     0.0000  000.00 -120.00  000.00   0.0000
  
RESI GPC          0.00 ! glycerolphosphorylcholine
GROUP                  !
ATOM N    NTL    -0.60 !
ATOM C1   CTL2   -0.10 !             |
ATOM C2   CTL5   -0.35 !           -C3-
ATOM C3   CTL5   -0.35 !             |
ATOM C4   CTL5   -0.35 !        |    |   |
ATOM H11  HL      0.25 !       -C2---N---C4-     (+)
ATOM H12  HL      0.25 !        |    |   |
ATOM H21  HL      0.25 !             |
ATOM H22  HL      0.25 !           -C1-
ATOM H23  HL      0.25 !             |
ATOM H31  HL      0.25 !             |
ATOM H32  HL      0.25 !             |
ATOM H33  HL      0.25 !             |
ATOM H41  HL      0.25 !             |
ATOM H42  HL      0.25 !             |
ATOM H43  HL      0.25 !             |
GROUP                  !             |
ATOM C5   CTL2   -0.08 !             |
ATOM H51  HAL2    0.09 !       H51---C5---H52
ATOM H52  HAL2    0.09 !             |
ATOM P    PL      1.50 !    (-) O3   O1
ATOM O3   O2L    -0.78 !          \ /
ATOM O4   O2L    -0.78 !           P (+)
ATOM O1   OSL    -0.57 !          / \
ATOM O2   OSL    -0.57 !    (-) O4   O2
ATOM CG1  CTL2   -0.08 !             |
ATOM HG11 HAL2    0.09 !        HG11-CG1-HG12
ATOM HG12 HAL2    0.09 !             |
GROUP                  !             | 
ATOM CG2  CTL1    0.14 !             |
ATOM HG21 HAL1    0.09 !        HG21-CG2-OG2-HO2
ATOM OG2  OHL    -0.66 !             |
ATOM HO2  HOL     0.43 !             |       
GROUP                  !             |  
ATOM CG3  CTL2    0.05 !             |
ATOM HG31 HAL2    0.09 !        HG31-CG3-OG3-HO3
ATOM HG32 HAL2    0.09 !             |
ATOM OG3  OHL    -0.66 !             HG32
ATOM HO3  HOL     0.43 !
BOND CG1 O2   CG1 HG11  CG1 HG12
BOND CG2 CG1  CG2 HG21  CG2 OG2   OG2 HO2
BOND CG3 CG2  CG3 HG31  CG3 HG32  CG3 OG3  OG3 HO3
BOND N   C1   N   C2    N   C3    N   C4
BOND C1 H11 C1 H12 C1 C5
BOND C2 H21 C2 H22 C2 H23
BOND C3 H31 C3 H32 C3 H33
BOND C4 H41 C4 H42 C4 H43
BOND C5 H51 C5 H52
BOND P   O1   P   O2    P   O3    P   O4    O1   C5

! internal coordinates for analysis
! see H.Hauser,I.Pascher,R.H.Pearson,S.Sundell, BBA 650, 21-51 (1981)
!  glycerol backbone
IC O2   CG1  CG2  CG3   0.      0.        0.      0.      0. !  t1
IC O2   CG1  CG2  OG2   0.      0.        0.      0.      0. !  t2
IC CG1  CG2  CG3  OG3   0.      0.        0.      0.      0. !  t3
IC OG2  CG2  CG3  OG3   0.      0.        0.      0.      0. !  t3
!
!  zwitterionic headgroup
IC P    O2   CG1  CG2   0.      0.        0.      0.      0. !  a1
IC O1   P    O2   CG1   0.      0.        0.      0.      0. !  a2
IC O2   P    O1   C5    0.      0.        0.      0.      0. !  a3
IC C1   C5   O1   P     0.      0.        0.      0.      0. !  a4
IC N    C1   C5   O1    0.      0.        0.      0.      0. !  a5
IC C2   N    C1   C5    0.      0.        0.      0.      0. !  a6
IC C3   N    C1   C5    0.      0.        0.      0.      0. !  a6
IC C4   N    C1   C5    0.      0.        0.      0.      0. !  a6
IC O1   O2   *P   O3    0.      0.      120.      0.      0. 
IC O1   O2   *P   O4    0.      0.     -120.      0.      0. 
  
RESI LPPC        0.00 ! deoxylysophosphatidylcholine 
! Polar Head and glycerol backbone
GROUP                 !          H15B
ATOM N    NTL   -0.60 !            |
ATOM C13  CTL5  -0.35 !      H15A-C15-H15C
ATOM H13A HL     0.25 !            | 
ATOM H13B HL     0.25 !    H13B    |    H14A
ATOM H13C HL     0.25 !      |     |     |
ATOM C14  CTL5  -0.35 !H13A-C13----N----C14-H14B     (+)
ATOM H14A HL     0.25 !      |     |     |
ATOM H14B HL     0.25 !    H13C    |    H14C
ATOM H14C HL     0.25 !            |
ATOM C15  CTL5  -0.35 !            |
ATOM H15A HL     0.25 !            |    alpha6
ATOM H15B HL     0.25 !            |  
ATOM H15C HL     0.25 !            |
ATOM C12  CTL2  -0.10 !     H12A--C12---H12B     
ATOM H12A HL     0.25 !            |
ATOM H12B HL     0.25 !            |    
GROUP                 !                  alpha5
ATOM C11  CTL2  -0.08 !            |
ATOM H11A HAL2   0.09 !     H11A--C11---H11B
ATOM H11B HAL2   0.09 !            |     alpha4
ATOM P    PL     1.50 !   (-) O13  O12
ATOM O13  O2L   -0.78 !         \ /      alpha3
ATOM O14  O2L   -0.78 !          P (+)
ATOM O11  OSL   -0.57 !         / \      alpha2
ATOM O12  OSL   -0.57 !   (-) O14  O11
ATOM C1   CTL2  -0.08 !            |     alpha1
ATOM HA   HAL2   0.09 !       HA---C1---HB
ATOM HB   HAL2   0.09 !            |     theta1
GROUP                 !            |
ATOM C2   CTL2  -0.18 !       HR---C2----HS
ATOM HS   HAL2   0.09 !            | 
ATOM HR   HAL2   0.09 !            | 
GROUP                 !            |
ATOM C3   CTL2  -0.05 !       HX---C3---HY 
ATOM HX   HAL2   0.09 !            |
ATOM HY   HAL2   0.09 !            |   gamma1
ATOM O31  OSL   -0.34 !      O32  O31
ATOM C31  CL     0.63 !       \\ /    gamma2
ATOM O32  OBL   -0.52 !        C31
ATOM C32  CTL2  -0.08 !         |     gamma3
ATOM H2X  HAL2   0.09 !  H2X---C32---H2Y
ATOM H2Y  HAL2   0.09 !         |
GROUP                 !
ATOM C33  CTL2  -0.18 !         |
ATOM H3X  HAL2   0.09 !  H3X---C33---H3Y 
ATOM H3Y  HAL2   0.09 !         |
GROUP                 !
ATOM C34  CTL2  -0.18 !         |
ATOM H4X  HAL2   0.09 !  H4X---C34---H4Y
ATOM H4Y  HAL2   0.09 !         |
GROUP                 !
ATOM C35  CTL2  -0.18 !         |
ATOM H5X  HAL2   0.09 !  H5X---C35---H5Y
ATOM H5Y  HAL2   0.09 !         |
GROUP                 !
ATOM C36  CTL2  -0.18 !         |
ATOM H6X  HAL2   0.09 !  H6X---C36---H6Y
ATOM H6Y  HAL2   0.09 !         |
GROUP                 !
ATOM C37  CTL2  -0.18 !         |
ATOM H7X  HAL2   0.09 !  H7X---C37---H7Y
ATOM H7Y  HAL2   0.09 !         |
GROUP                 !
ATOM C38  CTL2  -0.18 !         |
ATOM H8X  HAL2   0.09 !  H8X---C38---H8Y
ATOM H8Y  HAL2   0.09 !         |
GROUP                 !
ATOM C39  CTL2  -0.18 !         |
ATOM H9X  HAL2   0.09 !  H9X---C39---H9Y 
ATOM H9Y  HAL2   0.09 !         |
GROUP                 !
ATOM C310 CTL2  -0.18 !         |
ATOM H10X HAL2   0.09 ! H10X---C310--H10Y
ATOM H10Y HAL2   0.09 !         |
GROUP                 !
ATOM C311 CTL2  -0.18 !         |
ATOM H11X HAL2   0.09 ! H11X---C311--H11Y
ATOM H11Y HAL2   0.09 !         |
GROUP                 !
ATOM C312 CTL3  -0.27 !         |
ATOM H12X HAL3   0.09 ! H12X---C312--H12Y
ATOM H12Y HAL3   0.09 !         |
ATOM H12Z HAL3   0.09 !        H12Z
                      !
! Polar Head
BOND  N    C13       N    C14       N    C15       
BOND  C13  H13A      C13  H13B      C13  H13C 
BOND  C14  H14A      C14  H14B      C14  H14C 
BOND  C15  H15A      C15  H15B      C15  H15C 
BOND  N    C12
BOND  C12  H12A      C12  H12B      C12  C11
BOND  C11  H11A      C11  H11B      C11  O12   
BOND  O12  P         P    O11       P    O13       P    O14 
! Glycerol Backbone
BOND  C1   HA        C1    HB       C1   C2        C1   O11       
BOND  C2   HS        C2    HR       C2   C3
BOND  C3   HX        C3    HY       C3   O31

! Chain #3
BOND  O31  C31
BOND  C31  C32
DOUBLE  C31  O32
BOND  C32  H2X       C32  H2Y       C32  C33 
BOND  C33  H3X       C33  H3Y       C33  C34 
BOND  C34  H4X       C34  H4Y       C34  C35 
BOND  C35  H5X       C35  H5Y       C35  C36 
BOND  C36  H6X       C36  H6Y       C36  C37 
BOND  C37  H7X       C37  H7Y       C37  C38 
BOND  C38  H8X       C38  H8Y       C38  C39 
BOND  C39  H9X       C39  H9Y       C39  C310
BOND  C310 H10X      C310 H10Y      C310 C311
BOND  C311 H11X      C311 H11Y      C311 C312
BOND  C312 H12X      C312 H12Y      C312 H12Z

IMPR C31 O31 C32 O32 

! Polar head (angle names from Sundaralingam)
IC       C2    C1    O11   P      0.0  0.0  180.0  0.0  0.0 !alpha1
IC       C1    O11   P     O12    0.0  0.0  180.0  0.0  0.0 !alpha2
IC       O11   O12  *P     O13    0.0  0.0  120.0  0.0  0.0
IC       O11   O12  *P     O14    0.0  0.0  240.0  0.0  0.0
IC       O11   P     O12   C11    0.0  0.0  180.0  0.0  0.0 !alpha3
IC       O12   C12  *C11   H11A   0.0  0.0  120.0  0.0  0.0
IC       O12   C12  *C11   H11B   0.0  0.0  240.0  0.0  0.0
IC       P     O12   C11   C12    0.0  0.0  180.0  0.0  0.0 !alpha4
IC       N     C11  *C12   H12A   0.0  0.0  120.0  0.0  0.0
IC       N     C11  *C12   H12B   0.0  0.0  240.0  0.0  0.0
IC       O12   C11   C12   N      0.0  0.0  180.0  0.0  0.0 !alpha5
IC       C11   C12   N     C13    0.0  0.0  180.0  0.0  0.0 !alpha6
IC       C12   C13  *N     C14    0.0  0.0  120.0  0.0  0.0
IC       C12   C13  *N     C15    0.0  0.0  240.0  0.0  0.0

! Glycerol
IC       O11   C1    C2    C3     0.0  0.0  120.0  0.0  0.0 !theta1
IC       C1    C2    C3    O31    0.0  0.0  180.0  0.0  0.0 !theta3

! Chain 3
IC       C2    C3    O31   C31    0.0  0.0 -120.0  0.0  0.0 !gamma1
IC       C3    O31   C31   C32    0.0  0.0  180.0  0.0  0.0 !gamma2
IC       O31   C31   C32   C33    0.0  0.0  180.0  0.0  0.0 !gamma3
IC       C32   O31  *C31   O32    0.0  0.0  180.0  0.0  0.0
IC       C31   C32   C33   C34    0.0  0.0  180.0  0.0  0.0 !gamma4
IC       C32   C33   C34   C35    0.0  0.0  180.0  0.0  0.0 !gamma5
IC       C33   C34   C35   C36    0.0  0.0  180.0  0.0  0.0 !gamma6
IC       C34   C35   C36   C37    0.0  0.0  180.0  0.0  0.0 !gamma7
IC       C35   C36   C37   C38    0.0  0.0  180.0  0.0  0.0 !gamma8
IC       C36   C37   C38   C39    0.0  0.0  180.0  0.0  0.0 !gamma9
IC       C37   C38   C39   C310   0.0  0.0  180.0  0.0  0.0 !gamma10
IC       C38   C39   C310  C311   0.0  0.0  180.0  0.0  0.0 !gamma11
IC       C39   C310  C311  C312   0.0  0.0  180.0  0.0  0.0 !gamma12

RESI ETAM       1.00 ! ethanolamine
GROUP                !
ATOM N    NH3L -0.30 !           HN2
ATOM HN1  HCL   0.33 !            |
ATOM HN2  HCL   0.33 !  (+) HN1---N---HN3
ATOM HN3  HCL   0.33 !            |
ATOM C1   CTL2  0.13 !            |
ATOM H11  HAL2  0.09 !     H12---C1---H11
ATOM H12  HAL2  0.09 !            |
GROUP                !            |
ATOM C5   CTL2  0.05 !            |
ATOM H51  HAL2  0.09 !      H52---C5---H51
ATOM H52  HAL2  0.09 !            |
ATOM OH1  OHL  -0.66 !            OH1---HO1
ATOM HO1  HOL   0.43 !
BOND N HN1 N HN2 N HN3 N C1
BOND C1 H11 C1 H12 C1 C5
BOND C5 H51 C5 H52
BOND C5 OH1 OH1 HO1
! HF/6-31G* OPTIMIZED STRUCTURE:
IC N    C1    C5    OH1    1.5084  107.86   48.44  104.92   1.3987
IC C1   C5    OH1   HO1    1.5191  104.92  173.19  111.99   0.9495
IC HN1  N     C1    C5     1.0145  108.35  -49.03  107.86   1.5191
IC HN2  N     C1    C5     1.0107  112.05   69.23  107.86   1.5191
IC HN3  N     C1    C5     1.0102  112.39 -169.37  107.86   1.5191
IC N    C5    *C1   H11    0.0000  000.00  120.00  000.00   0.0000
IC N    C5    *C1   H12    0.0000  000.00 -120.00  000.00   0.0000
IC OH1  C1    *C5   H51    0.0000  000.00  120.00  000.00   0.0000
IC OH1  C1    *C5   H52    0.0000  000.00 -120.00  000.00   0.0000

RESI GPE          0.00 ! L-alpha-glycerylphosphorylethanolamine
!
GROUP                  !
ATOM N     NH3L  -0.30 !           HN2
ATOM HN1   HCL    0.33 !            |
ATOM HN2   HCL    0.33 !  (+) HN1---N---HN3
ATOM HN3   HCL    0.33 !            |
ATOM C12   CTL2   0.13 !            |
ATOM H12A  HAL2   0.09 !     H12A--C12---H12B
ATOM H12B  HAL2   0.09 !            |
GROUP                  !            |     alpha5
ATOM C11  CTL2   -0.08 !            |
ATOM H11A HAL2    0.09 !     H11A--C11---H11B
ATOM H11B HAL2    0.09 !            |     alpha4
ATOM P    PL      1.50 !   (-) O13  O12
ATOM O13  O2L    -0.78 !         \ /      alpha3
ATOM O14  O2L    -0.78 !          P (+)
ATOM O11  OSL    -0.57 !         / \      alpha2
ATOM O12  OSL    -0.57 !   (-) O14  O11
ATOM C1   CTL2   -0.08 !            |     alpha1
ATOM HA   HAL2    0.09 !       HA---C1---HB
ATOM HB   HAL2    0.09 !            |     theta1
GROUP                  !            | 
ATOM C2  CTL1     0.14 !            |
ATOM HS  HAL1     0.09 !         HS-C2-OH2-HO2
ATOM OH2  OHL    -0.66 !            |
ATOM HO2  HOL     0.43 !            |       
GROUP                  !            |  
ATOM C3  CTL2     0.05 !            |
ATOM HX  HAL2     0.09 !         HX-C3-OH3-HO3
ATOM HY  HAL2     0.09 !            |
ATOM OH3  OHL    -0.66 !            HY
ATOM HO3  HOL     0.43 !
! Polar Head
BOND  N    HN1       N    HN2       N    HN3       N    C12
BOND  C12  H12A      C12  H12B      C12  C11
BOND  C11  H11A      C11  H11B      C11  O12
BOND  O12  P         P    O11       P    O13       P    O14
! Glycerol Backbone
BOND  C1   HA        C1    HB       C1   C2        C1   O11
BOND  C2   HS        C2    C3       C2   OH2
BOND  C3   HX        C3    HY       C3   OH3
BOND  OH2  HO2
BOND  OH3  HO3
!
! Polar head (angle names from Sundaralingam)
IC       C2    C1    O11   P      0.0  0.0  180.0  0.0  0.0 !alpha1
IC       C1    O11   P     O12    0.0  0.0  180.0  0.0  0.0 !alpha2
IC       O11   O12  *P     O13    0.0  0.0  120.0  0.0  0.0
IC       O11   O12  *P     O14    0.0  0.0  240.0  0.0  0.0
IC       O11   P     O12   C11    0.0  0.0  180.0  0.0  0.0 !alpha3
IC       O12   C12  *C11   H11A   0.0  0.0  120.0  0.0  0.0
IC       O12   C12  *C11   H11B   0.0  0.0  240.0  0.0  0.0
IC       P     O12   C11   C12    0.0  0.0  180.0  0.0  0.0 !alpha4
IC       N     C11  *C12   H12A   0.0  0.0  120.0  0.0  0.0
IC       N     C11  *C12   H12B   0.0  0.0  240.0  0.0  0.0
IC       O12   C11   C12   N      0.0  0.0  180.0  0.0  0.0 !alpha5
IC       C11   C12   N     HN1    0.0  0.0  180.0  0.0  0.0 !alpha6
IC       C12   HN1  *N     HN2    0.0  0.0  120.0  0.0  0.0
IC       C12   HN1  *N     HN3    0.0  0.0  240.0  0.0  0.0
! Glycerol
IC       O11   C1    C2    C3     0.0  0.0  120.0  0.0  0.0 !theta1
IC       C1    C2    C3    OH3    0.0  0.0  180.0  0.0  0.0 !theta3
IC       C1    C3   *C2    OH2    0.0  0.0 -120.0  0.0  0.0
! for stereo-specific phopholipid at carbon C2 (labeled hydrogen S)
IC       O11   C2   *C1    HA     0.0  0.0 +120.0  0.0  0.0
IC       O11   C2   *C1    HB     0.0  0.0 -120.0  0.0  0.0
IC       OH2   C1   *C2    HS     0.0  0.0 +120.0  0.0  0.0
IC       OH3   C2   *C3    HX     0.0  0.0 +120.0  0.0  0.0
IC       OH3   C2   *C3    HY     0.0  0.0 -120.0  0.0  0.0
IC       C1    C2    OH2   HO2    0.0  0.0  180.0  0.0  0.0 !beta1
IC       C2    C3    OH3   HO3    0.0  0.0 -120.0  0.0  0.0 !gamma1

RESI DLPE         0.00 ! 1,2 dilauroyl-DL-Phosphatidylethanolamine
!
!  R1 - CH2        
!       |          (angles and atom names from Sundaralingam)
!  R2 - CH
!       |
!       CH2 - PO4 - CH2 - CH2 - NH3
!
! Polar Head and glycerol backbone
GROUP                  !
ATOM N     NH3L  -0.30 !           HN2
ATOM HN1   HCL    0.33 !            |
ATOM HN2   HCL    0.33 !  (+) HN1---N---HN3
ATOM HN3   HCL    0.33 !            |
ATOM C12   CTL2   0.13 !            |
ATOM H12A  HAL2   0.09 !     H12A--C12---H12B
ATOM H12B  HAL2   0.09 !            |
GROUP                  !            |     alpha5
ATOM C11  CTL2   -0.08 !            |
ATOM H11A HAL2    0.09 !     H11A--C11---H11B
ATOM H11B HAL2    0.09 !            |     alpha4
ATOM P    PL      1.50 !   (-) O13  O12
ATOM O13  O2L    -0.78 !         \ /      alpha3
ATOM O14  O2L    -0.78 !          P (+)
ATOM O11  OSL    -0.57 !         / \      alpha2
ATOM O12  OSL    -0.57 !   (-) O14  O11
ATOM C1   CTL2   -0.08 !            |     alpha1
ATOM HA   HAL2    0.09 !      H1A---C1---H1B
ATOM HB   HAL2    0.09 !            |     theta1
GROUP                  !            |
ATOM C2   CTL1    0.04 !       HS---C2- - - - - - -
ATOM HS   HAL1    0.09 !            | beta1        |
ATOM O21  OSL    -0.34 !       O22  O21          theta3
ATOM C21  CL      0.63 !        \\ /  beta2        |
ATOM O22  OBL    -0.52 !          C21
ATOM C22  CTL2   -0.08 !          |   beta3        |
ATOM H2R  HAL2    0.09 !   H2R---C22---H2S
ATOM H2S  HAL2    0.09 !          |                |
GROUP                  !              beta4
ATOM C3   CTL2   -0.05 !          |                |
ATOM HX   HAL2    0.09 !                      HX---C3---HY
ATOM HY   HAL2    0.09 !          |                |   gamma1
ATOM O31  OSL    -0.34 !                      O32  O31
ATOM C31  CL      0.63 !          |            \\ /    gamma2
ATOM O32  OBL    -0.52 !                         C31
ATOM C32  CTL2   -0.08 !          |              |     gamma3
ATOM H2X  HAL2    0.09 !                  H2X---C32---H2Y
ATOM H2Y  HAL2    0.09 !          |              |
GROUP                  !                               gamma4
ATOM C23  CTL2   -0.18 !          |              |
ATOM H3R  HAL2    0.09 !   H3R ---C23---H3S
ATOM H3S  HAL2    0.09 !          |              |
GROUP                  !
ATOM C24  CTL2   -0.18 !          |
ATOM H4R  HAL2    0.09 !   H4R ---C24---H4S      |
ATOM H4S  HAL2    0.09 !          |
GROUP                  !
ATOM C25  CTL2   -0.18 !          |              |
ATOM H5R  HAL2    0.09 !   H5R ---C25---H5S
ATOM H5S  HAL2    0.09 !          |              |
GROUP                  !
ATOM C26  CTL2   -0.18 !          |
ATOM H6R  HAL2    0.09 !   H6R ---C26---H6S      |
ATOM H6S  HAL2    0.09 !          |
GROUP                  !
ATOM C27  CTL2   -0.18 !          |              |
ATOM H7R  HAL2    0.09 !   H7R ---C27---H7S
ATOM H7S  HAL2    0.09 !          |              |
GROUP                  !
ATOM C28  CTL2   -0.18 !          |
ATOM H8R  HAL2    0.09 !   H8R ---C28---H8S      |
ATOM H8S  HAL2    0.09 !          |
GROUP                  !
ATOM C29  CTL2   -0.18 !          |              |
ATOM H9R  HAL2    0.09 !   H9R ---C29---H9S
ATOM H9S  HAL2    0.09 !          |              |
GROUP                  !
ATOM C210 CTL2   -0.18 !          |
ATOM H10R HAL2    0.09 !   H10R---C210--H10S     |
ATOM H10S HAL2    0.09 !          |
GROUP                  !
ATOM C211 CTL2   -0.18 !          |              |
ATOM H11R HAL2    0.09 !   H11R---C211--H11S
ATOM H11S HAL2    0.09 !          |              |
GROUP                  !
ATOM C212 CTL3   -0.27 !          |
ATOM H12R HAL3    0.09 !   H12R---C212--H12S     |
ATOM H12S HAL3    0.09 !          |
ATOM H12T HAL3    0.09 !         H12T            |
GROUP                  !
ATOM C33  CTL2   -0.18 !                         |
ATOM H3X  HAL2    0.09 !                  H3X ---C33---H3Y
ATOM H3Y  HAL2    0.09 !                         |
GROUP                  !
ATOM C34  CTL2   -0.18 !                         |
ATOM H4X  HAL2    0.09 !                  H4X ---C34---H4Y
ATOM H4Y  HAL2    0.09 !                         |
GROUP                  !
ATOM C35  CTL2   -0.18 !                         |
ATOM H5X  HAL2    0.09 !                  H5X ---C35---H5Y
ATOM H5Y  HAL2    0.09 !                         |
GROUP                  !
ATOM C36  CTL2   -0.18 !                         |
ATOM H6X  HAL2    0.09 !                  H6X ---C36---H6Y
ATOM H6Y  HAL2    0.09 !                         |
GROUP                  !
ATOM C37  CTL2   -0.18 !                         |
ATOM H7X  HAL2    0.09 !                  H7X ---C37---H7Y
ATOM H7Y  HAL2    0.09 !                         |
GROUP                  !
ATOM C38  CTL2   -0.18 !                         |
ATOM H8X  HAL2    0.09 !                  H8X ---C38---H8Y
ATOM H8Y  HAL2    0.09 !                         |
GROUP                  !
ATOM C39  CTL2   -0.18 !                         |
ATOM H9X  HAL2    0.09 !                  H9X ---C39---H9Y
ATOM H9Y  HAL2    0.09 !                         |
GROUP                  !
ATOM C310 CTL2   -0.18 !                         |
ATOM H10X HAL2    0.09 !                  H10X---C310--H10Y
ATOM H10Y HAL2    0.09 !                         |
GROUP                  !
ATOM C311 CTL2   -0.18 !                         |
ATOM H11X HAL2    0.09 !                  H11X---C311--H11Y
ATOM H11Y HAL2    0.09 !                         |
GROUP                  !
ATOM C312 CTL3   -0.27 !                         |
ATOM H12X HAL3    0.09 !                  H12X---C312--H12Y
ATOM H12Y HAL3    0.09 !                         |
ATOM H12Z HAL3    0.09 !                         H12Z
 
! Polar Head
BOND  N    HN1       N    HN2       N    HN3       N    C12
BOND  C12  H12A      C12  H12B      C12  C11
BOND  C11  H11A      C11  H11B      C11  O12
BOND  O12  P         P    O11       P    O13       P    O14
! Glycerol Backbone
BOND  C1   HA        C1    HB       C1   C2        C1   O11
BOND  C2   HS        C2    C3       C2   O21
BOND  C3   HX        C3    HY       C3   O31
! Chain #2
BOND  O21  C21
BOND  C21  C22
DOUBLE  C21  O22
BOND  C22  H2R       C22  H2S       C22  C23
BOND  C23  H3R       C23  H3S       C23  C24
BOND  C24  H4R       C24  H4S       C24  C25
BOND  C25  H5R       C25  H5S       C25  C26
BOND  C26  H6R       C26  H6S       C26  C27
BOND  C27  H7R       C27  H7S       C27  C28
BOND  C28  H8R       C28  H8S       C28  C29
BOND  C29  H9R       C29  H9S       C29  C210
BOND  C210 H10R      C210 H10S      C210 C211
BOND  C211 H11R      C211 H11S      C211 C212
BOND  C212 H12R      C212 H12S      C212 H12T
! Chain #3
BOND  O31  C31
BOND  C31  C32
DOUBLE  C31  O32
BOND  C32  H2X       C32  H2Y       C32  C33
BOND  C33  H3X       C33  H3Y       C33  C34
BOND  C34  H4X       C34  H4Y       C34  C35
BOND  C35  H5X       C35  H5Y       C35  C36
BOND  C36  H6X       C36  H6Y       C36  C37
BOND  C37  H7X       C37  H7Y       C37  C38
BOND  C38  H8X       C38  H8Y       C38  C39
BOND  C39  H9X       C39  H9Y       C39  C310
BOND  C310 H10X      C310 H10Y      C310 C311
BOND  C311 H11X      C311 H11Y      C311 C312
BOND  C312 H12X      C312 H12Y      C312 H12Z

IMPR C21 O21 C22 O22    C31 O31 C32 O32 
! Polar head (angle names from Sundaralingam)
IC       C2    C1    O11   P      0.0  0.0  180.0  0.0  0.0 !alpha1
IC       C1    O11   P     O12    0.0  0.0  180.0  0.0  0.0 !alpha2
IC       O11   O12  *P     O13    0.0  0.0  120.0  0.0  0.0
IC       O11   O12  *P     O14    0.0  0.0  240.0  0.0  0.0
IC       O11   P     O12   C11    0.0  0.0  180.0  0.0  0.0 !alpha3
IC       O12   C12  *C11   H11A   0.0  0.0  120.0  0.0  0.0
IC       O12   C12  *C11   H11B   0.0  0.0  240.0  0.0  0.0
IC       P     O12   C11   C12    0.0  0.0  180.0  0.0  0.0 !alpha4
IC       N     C11  *C12   H12A   0.0  0.0  120.0  0.0  0.0
IC       N     C11  *C12   H12B   0.0  0.0  240.0  0.0  0.0
IC       O12   C11   C12   N      0.0  0.0  180.0  0.0  0.0 !alpha5
IC       C11   C12   N     HN1    0.0  0.0  180.0  0.0  0.0 !alpha6
IC       C12   HN1  *N     HN2    0.0  0.0  120.0  0.0  0.0
IC       C12   HN1  *N     HN3    0.0  0.0  240.0  0.0  0.0
! Glycerol
IC       O11   C1    C2    C3     0.0  0.0  120.0  0.0  0.0 !theta1
IC       C1    C2    C3    O31    0.0  0.0  180.0  0.0  0.0 !theta3
IC       C1    C3   *C2    O21    0.0  0.0 -120.0  0.0  0.0
! for stereo-specific phopholipid at carbon C2 (labeled hydrogen S)
IC       O11   C2   *C1    HA     0.0  0.0 +120.0  0.0  0.0
IC       O11   C2   *C1    HB     0.0  0.0 -120.0  0.0  0.0
IC       O21   C1   *C2    HS     0.0  0.0 +120.0  0.0  0.0
IC       O31   C2   *C3    HX     0.0  0.0 +120.0  0.0  0.0
IC       O31   C2   *C3    HY     0.0  0.0 -120.0  0.0  0.0
! Chain 1
IC       C1    C2    O21   C21    0.0  0.0  180.0  0.0  0.0 !beta1
IC       C2    O21   C21   C22    0.0  0.0  120.0  0.0  0.0 !beta2
IC       O21   C21   C22   C23    0.0  0.0  180.0  0.0  0.0 !beta3
IC       C22   O21  *C21   O22    0.0  0.0  180.0  0.0  0.0
IC       C21   C22   C23   C24    0.0  0.0  180.0  0.0  0.0 !beta4
IC       C22   C23   C24   C25    0.0  0.0  180.0  0.0  0.0 !beta5
IC       C23   C24   C25   C26    0.0  0.0  180.0  0.0  0.0 !beta6
IC       C24   C25   C26   C27    0.0  0.0  180.0  0.0  0.0 !beta7
IC       C25   C26   C27   C28    0.0  0.0  180.0  0.0  0.0 !beta8
IC       C26   C27   C28   C29    0.0  0.0  180.0  0.0  0.0 !beta9
IC       C27   C28   C29   C210   0.0  0.0  180.0  0.0  0.0 !beta10
IC       C28   C29   C210  C211   0.0  0.0  180.0  0.0  0.0 !beta11
IC       C29   C210  C211  C212   0.0  0.0  180.0  0.0  0.0 !beta12
! Chain 2
IC       C2    C3    O31   C31    0.0  0.0 -120.0  0.0  0.0 !gamma1
IC       C3    O31   C31   C32    0.0  0.0  180.0  0.0  0.0 !gamma2
IC       O31   C31   C32   C33    0.0  0.0  180.0  0.0  0.0 !gamma3
IC       C32   O31  *C31   O32    0.0  0.0  180.0  0.0  0.0
IC       C31   C32   C33   C34    0.0  0.0  180.0  0.0  0.0 !gamma4
IC       C32   C33   C34   C35    0.0  0.0  180.0  0.0  0.0 !gamma5
IC       C33   C34   C35   C36    0.0  0.0  180.0  0.0  0.0 !gamma6
IC       C34   C35   C36   C37    0.0  0.0  180.0  0.0  0.0 !gamma7
IC       C35   C36   C37   C38    0.0  0.0  180.0  0.0  0.0 !gamma8
IC       C36   C37   C38   C39    0.0  0.0  180.0  0.0  0.0 !gamma9
IC       C37   C38   C39   C310   0.0  0.0  180.0  0.0  0.0 !gamma10
IC       C38   C39   C310  C311   0.0  0.0  180.0  0.0  0.0 !gamma11
IC       C39   C310  C311  C312   0.0  0.0  180.0  0.0  0.0 !gamma12

RESI DMPC         0.00 ! 1,2 dimiristoyl-SN-glycero-3-Phosphorylcholine
!
!  R1 - CH2        
!       |          (angles and atom names from Sundaralingam)
!  R2 - CH
!       |
!       CH2 - PO4 - CH2 - CH2 - N(CH3)3
!
! Polar Head and glycerol backbone
GROUP                 !          H15B
ATOM N    NTL   -0.60 !            |
ATOM C13  CTL5  -0.35 !      H15A-C15-H15C
ATOM H13A HL     0.25 !            | 
ATOM H13B HL     0.25 !    H13B    |    H14A
ATOM H13C HL     0.25 !      |     |     |
ATOM C14  CTL5  -0.35 !H13A-C13----N----C14-H14B     (+)
ATOM H14A HL     0.25 !      |     |     |
ATOM H14B HL     0.25 !    H13C    |    H14C
ATOM H14C HL     0.25 !            |
ATOM C15  CTL5  -0.35 !            |
ATOM H15A HL     0.25 !            |    alpha6
ATOM H15B HL     0.25 !            |  
ATOM H15C HL     0.25 !            |
ATOM C12  CTL2  -0.10 !     H12A--C12---H12B     
ATOM H12A HL     0.25 !            |
ATOM H12B HL     0.25 !            |    
GROUP                 !                  alpha5
ATOM C11  CTL2  -0.08 !            |
ATOM H11A HAL2   0.09 !     H11A--C11---H11B
ATOM H11B HAL2   0.09 !            |     alpha4
ATOM P    PL     1.50 !   (-) O13  O12
ATOM O13  O2L   -0.78 !         \ /      alpha3
ATOM O14  O2L   -0.78 !          P (+)
ATOM O11  OSL   -0.57 !         / \      alpha2
ATOM O12  OSL   -0.57 !   (-) O14  O11
ATOM C1   CTL2  -0.08 !            |     alpha1
ATOM HA   HAL2   0.09 !       HA---C1---HB
ATOM HB   HAL2   0.09 !            |     theta1
GROUP                 !            |
ATOM C2   CTL1   0.04 !       HS---C2- - - - - - -
ATOM HS   HAL1   0.09 !            | beta1        |
ATOM O21  OSL   -0.34 !       O22  O21          theta3
ATOM C21  CL     0.63 !        \\ /  beta2        |
ATOM O22  OBL   -0.52 !          C21
ATOM C22  CTL2  -0.08 !          |   beta3        |
ATOM H2R  HAL2   0.09 !   H2R---C22---H2S
ATOM H2S  HAL2   0.09 !          |                |
GROUP                 !              beta4
ATOM C3   CTL2  -0.05 !          |                |
ATOM HX   HAL2   0.09 !                      HX---C3---HY
ATOM HY   HAL2   0.09 !          |                |   gamma1
ATOM O31  OSL   -0.34 !                      O32  O31
ATOM C31  CL     0.63 !          |            \\ /    gamma2
ATOM O32  OBL   -0.52 !                         C31
ATOM C32  CTL2  -0.08 !          |              |     gamma3
ATOM H2X  HAL2   0.09 !                  H2X---C32---H2Y
ATOM H2Y  HAL2   0.09 !          |              |
GROUP                 !                               gamma4
ATOM C23  CTL2  -0.18 !          |              |
ATOM H3R  HAL2   0.09 !   H3R ---C23---H3S
ATOM H3S  HAL2   0.09 !          |              |
GROUP                 !
ATOM C24  CTL2  -0.18 !          |
ATOM H4R  HAL2   0.09 !   H4R ---C24---H4S      |
ATOM H4S  HAL2   0.09 !          |
GROUP                 !
ATOM C25  CTL2  -0.18 !          |              |
ATOM H5R  HAL2   0.09 !   H5R ---C25---H5S
ATOM H5S  HAL2   0.09 !          |              |
GROUP                 !
ATOM C26  CTL2  -0.18 !          |
ATOM H6R  HAL2   0.09 !   H6R ---C26---H6S      |
ATOM H6S  HAL2   0.09 !          |
GROUP                 !
ATOM C27  CTL2  -0.18 !          |              |
ATOM H7R  HAL2   0.09 !   H7R ---C27---H7S
ATOM H7S  HAL2   0.09 !          |              |
GROUP                 !
ATOM C28  CTL2  -0.18 !          |
ATOM H8R  HAL2   0.09 !   H8R ---C28---H8S      |
ATOM H8S  HAL2   0.09 !          |
GROUP                 !
ATOM C29  CTL2  -0.18 !          |              |
ATOM H9R  HAL2   0.09 !   H9R ---C29---H9S
ATOM H9S  HAL2   0.09 !          |              |
GROUP                 !
ATOM C210 CTL2  -0.18 !          |
ATOM H10R HAL2   0.09 !   H10R---C210--H10S     |
ATOM H10S HAL2   0.09 !          |
GROUP                 !
ATOM C211 CTL2  -0.18 !          |              |
ATOM H11R HAL2   0.09 !   H11R---C211--H11S
ATOM H11S HAL2   0.09 !          |              |
GROUP                 !
ATOM C212 CTL2  -0.18 !          |
ATOM H12R HAL2   0.09 !   H12R---C212--H12S     |
ATOM H12S HAL2   0.09 !          |
GROUP                 !
ATOM C213 CTL2  -0.18 !          |              |
ATOM H13R HAL2   0.09 !   H13R---C213--H13S
ATOM H13S HAL2   0.09 !          |              |
GROUP                 !
ATOM C214 CTL3  -0.27 !          |
ATOM H14R HAL3   0.09 !   H14R---C214--H14S     |
ATOM H14S HAL3   0.09 !          |
ATOM H14T HAL3   0.09 !         H14T            |
GROUP                 !
ATOM C33  CTL2  -0.18 !                         |
ATOM H3X  HAL2   0.09 !                  H3X ---C33---H3Y
ATOM H3Y  HAL2   0.09 !                         |
GROUP                 !
ATOM C34  CTL2  -0.18 !                         |
ATOM H4X  HAL2   0.09 !                  H4X ---C34---H4Y
ATOM H4Y  HAL2   0.09 !                         |
GROUP                 !
ATOM C35  CTL2  -0.18 !                         |
ATOM H5X  HAL2   0.09 !                  H5X ---C35---H5Y
ATOM H5Y  HAL2   0.09 !                         |
GROUP                 !
ATOM C36  CTL2  -0.18 !                         |
ATOM H6X  HAL2   0.09 !                  H6X ---C36---H6Y
ATOM H6Y  HAL2   0.09 !                         |
GROUP                 !
ATOM C37  CTL2  -0.18 !                         |
ATOM H7X  HAL2   0.09 !                  H7X ---C37---H7Y
ATOM H7Y  HAL2   0.09 !                         |
GROUP                 !
ATOM C38  CTL2  -0.18 !                         |
ATOM H8X  HAL2   0.09 !                  H8X ---C38---H8Y
ATOM H8Y  HAL2   0.09 !                         |
GROUP                 !
ATOM C39  CTL2  -0.18 !                         |
ATOM H9X  HAL2   0.09 !                  H9X ---C39---H9Y
ATOM H9Y  HAL2   0.09 !                         |
GROUP                 !
ATOM C310 CTL2  -0.18 !                         |
ATOM H10X HAL2   0.09 !                  H10X---C310--H10Y
ATOM H10Y HAL2   0.09 !                         |
GROUP                 !
ATOM C311 CTL2  -0.18 !                         |
ATOM H11X HAL2   0.09 !                  H11X---C311--H11Y
ATOM H11Y HAL2   0.09 !                         |
GROUP                 !
ATOM C312 CTL2  -0.18 !                         |
ATOM H12X HAL2   0.09 !                  H12X---C312--H12Y
ATOM H12Y HAL2   0.09 !                         |
GROUP                 !
ATOM C313 CTL2  -0.18 !                         |
ATOM H13X HAL2   0.09 !                  H13X---C313--H13Y
ATOM H13Y HAL2   0.09 !                         |
GROUP                 !
ATOM C314 CTL3  -0.27 !                         |
ATOM H14X HAL3   0.09 !                  H14X---C314--H14Y
ATOM H14Y HAL3   0.09 !                         |
ATOM H14Z HAL3   0.09 !                         H14Z
 
! Polar Head
BOND  N    C13       N    C14       N    C15       
BOND  C13  H13A      C13  H13B      C13  H13C 
BOND  C14  H14A      C14  H14B      C14  H14C 
BOND  C15  H15A      C15  H15B      C15  H15C 
BOND  N    C12
BOND  C12  H12A      C12  H12B      C12  C11
BOND  C11  H11A      C11  H11B      C11  O12   
BOND  O12  P         P    O11       P    O13       P    O14 
! Glycerol Backbone
BOND  C1   HA        C1    HB       C1   C2        C1   O11
BOND  C2   HS        C2    C3       C2   O21
BOND  C3   HX        C3    HY       C3   O31
! Chain #2
BOND  O21  C21
BOND  C21  C22
DOUBLE C21  O22 
BOND  C22  H2R       C22  H2S       C22  C23
BOND  C23  H3R       C23  H3S       C23  C24
BOND  C24  H4R       C24  H4S       C24  C25
BOND  C25  H5R       C25  H5S       C25  C26
BOND  C26  H6R       C26  H6S       C26  C27
BOND  C27  H7R       C27  H7S       C27  C28
BOND  C28  H8R       C28  H8S       C28  C29
BOND  C29  H9R       C29  H9S       C29  C210
BOND  C210 H10R      C210 H10S      C210 C211
BOND  C211 H11R      C211 H11S      C211 C212
BOND  C212 H12R      C212 H12S      C212 C213
BOND  C213 H13R      C213 H13S      C213 C214
BOND  C214 H14R      C214 H14S      C214 H14T
! Chain #3
BOND  O31  C31
BOND  C31  C32
DOUBLE  C31  O32
BOND  C32  H2X       C32  H2Y       C32  C33
BOND  C33  H3X       C33  H3Y       C33  C34
BOND  C34  H4X       C34  H4Y       C34  C35
BOND  C35  H5X       C35  H5Y       C35  C36
BOND  C36  H6X       C36  H6Y       C36  C37
BOND  C37  H7X       C37  H7Y       C37  C38
BOND  C38  H8X       C38  H8Y       C38  C39
BOND  C39  H9X       C39  H9Y       C39  C310
BOND  C310 H10X      C310 H10Y      C310 C311
BOND  C311 H11X      C311 H11Y      C311 C312
BOND  C312 H12X      C312 H12Y      C312 C313
BOND  C313 H13X      C313 H13Y      C313 C314
BOND  C314 H14X      C314 H14Y      C314 H14Z

IMPR C21 O21 C22 O22   C31 O31 C32 O32

! Polar head (angle names from Sundaralingam)
IC       C2    C1    O11   P      0.0  0.0  180.0  0.0  0.0 !alpha1
IC       C1    O11   P     O12    0.0  0.0  180.0  0.0  0.0 !alpha2
IC       O11   O12  *P     O13    0.0  0.0  120.0  0.0  0.0
IC       O11   O12  *P     O14    0.0  0.0  240.0  0.0  0.0
IC       O11   P     O12   C11    0.0  0.0  180.0  0.0  0.0 !alpha3
IC       O12   C12  *C11   H11A   0.0  0.0  120.0  0.0  0.0
IC       O12   C12  *C11   H11B   0.0  0.0  240.0  0.0  0.0
IC       P     O12   C11   C12    0.0  0.0  180.0  0.0  0.0 !alpha4
IC       N     C11  *C12   H12A   0.0  0.0  120.0  0.0  0.0
IC       N     C11  *C12   H12B   0.0  0.0  240.0  0.0  0.0
IC       O12   C11   C12   N      0.0  0.0  180.0  0.0  0.0 !alpha5
IC       C11   C12   N     C13    0.0  0.0  180.0  0.0  0.0 !alpha6
IC       C12   C13  *N     C14    0.0  0.0  120.0  0.0  0.0
IC       C12   C13  *N     C15    0.0  0.0  240.0  0.0  0.0

! Glycerol
IC       O11   C1    C2    C3     0.0  0.0  120.0  0.0  0.0 !theta1
IC       C1    C2    C3    O31    0.0  0.0  180.0  0.0  0.0 !theta3
IC       C1    C3   *C2    O21    0.0  0.0 -120.0  0.0  0.0
! for stereo-specific phopholipid at carbon C2 (labeled hydrogen S)
IC       O11   C2   *C1    HA     0.0  0.0 +120.0  0.0  0.0
IC       O11   C2   *C1    HB     0.0  0.0 -120.0  0.0  0.0
IC       O21   C1   *C2    HS     0.0  0.0 +120.0  0.0  0.0
IC       O31   C2   *C3    HX     0.0  0.0 +120.0  0.0  0.0
IC       O31   C2   *C3    HY     0.0  0.0 -120.0  0.0  0.0
! Chain 1
IC       C1    C2    O21   C21    0.0  0.0  180.0  0.0  0.0 !beta1
IC       C2    O21   C21   C22    0.0  0.0  120.0  0.0  0.0 !beta2
IC       O21   C21   C22   C23    0.0  0.0  180.0  0.0  0.0 !beta3
IC       C22   O21  *C21   O22    0.0  0.0  180.0  0.0  0.0
IC       C21   C22   C23   C24    0.0  0.0  180.0  0.0  0.0 !beta4
IC       C22   C23   C24   C25    0.0  0.0  180.0  0.0  0.0 !beta5
IC       C23   C24   C25   C26    0.0  0.0  180.0  0.0  0.0 !beta6
IC       C24   C25   C26   C27    0.0  0.0  180.0  0.0  0.0 !beta7
IC       C25   C26   C27   C28    0.0  0.0  180.0  0.0  0.0 !beta8
IC       C26   C27   C28   C29    0.0  0.0  180.0  0.0  0.0 !beta9
IC       C27   C28   C29   C210   0.0  0.0  180.0  0.0  0.0 !beta10
IC       C28   C29   C210  C211   0.0  0.0  180.0  0.0  0.0 !beta11
IC       C29   C210  C211  C212   0.0  0.0  180.0  0.0  0.0 !beta12
IC       C210  C211  C212  C213   0.0  0.0  180.0  0.0  0.0 !beta13
IC       C211  C212  C213  C214   0.0  0.0  180.0  0.0  0.0 !beta14
! Chain 2
IC       C2    C3    O31   C31    0.0  0.0 -120.0  0.0  0.0 !gamma1
IC       C3    O31   C31   C32    0.0  0.0  180.0  0.0  0.0 !gamma2
IC       O31   C31   C32   C33    0.0  0.0  180.0  0.0  0.0 !gamma3
IC       C32   O31  *C31   O32    0.0  0.0  180.0  0.0  0.0
IC       C31   C32   C33   C34    0.0  0.0  180.0  0.0  0.0 !gamma4
IC       C32   C33   C34   C35    0.0  0.0  180.0  0.0  0.0 !gamma5
IC       C33   C34   C35   C36    0.0  0.0  180.0  0.0  0.0 !gamma6
IC       C34   C35   C36   C37    0.0  0.0  180.0  0.0  0.0 !gamma7
IC       C35   C36   C37   C38    0.0  0.0  180.0  0.0  0.0 !gamma8
IC       C36   C37   C38   C39    0.0  0.0  180.0  0.0  0.0 !gamma9
IC       C37   C38   C39   C310   0.0  0.0  180.0  0.0  0.0 !gamma10
IC       C38   C39   C310  C311   0.0  0.0  180.0  0.0  0.0 !gamma11
IC       C39   C310  C311  C312   0.0  0.0  180.0  0.0  0.0 !gamma12
IC       C310  C311  C312  C313   0.0  0.0  180.0  0.0  0.0 !gamma13
IC       C311  C312  C313  C314   0.0  0.0  180.0  0.0  0.0 !gamma14
 
RESI SDS         -1.00 ! Dodecylsulphate
                       ! based on methylsulfate
GROUP
ATOM S    SL      1.33 !           OS2(-1)
ATOM OS1  OSL    -0.28 !             |
ATOM OS2  O2L    -0.65 !   (-) OS2--S(+2)--OS4 (-)
ATOM OS3  O2L    -0.65 !             |
ATOM OS4  O2L    -0.65 !            OS1
ATOM C1   CTL2   -0.28 !              \
ATOM H11  HAL2    0.09 !          H11-C1-H12
ATOM H12  HAL2    0.09 !               |
GROUP                  !               |
ATOM C2   CTL2   -0.18 !          H21-C2-H22
ATOM H21  HAL2    0.09 !               |
ATOM H22  HAL2    0.09 !               |
GROUP                  !               |
ATOM C3   CTL2   -0.18 !          H31-C3-H32
ATOM H31  HAL2    0.09 !               |
ATOM H32  HAL2    0.09 !               |
GROUP                  !               |
ATOM C4   CTL2   -0.18 !          H41-C4-H42
ATOM H41  HAL2    0.09 !               |
ATOM H42  HAL2    0.09 !               |
GROUP                  !               |
ATOM C5   CTL2   -0.18 !          H51-C5-H52
ATOM H51  HAL2    0.09 !               |
ATOM H52  HAL2    0.09 !               |
GROUP                  !               |
ATOM C6   CTL2   -0.18 !          H61-C6-H62
ATOM H61  HAL2    0.09 !               |
ATOM H62  HAL2    0.09 !               |
GROUP                  !               |
ATOM C7   CTL2   -0.18 !          H71-C7-H72
ATOM H71  HAL2    0.09 !               |
ATOM H72  HAL2    0.09 !               |
GROUP                  !               |
ATOM C8   CTL2   -0.18 !          H81-C8-H82
ATOM H81  HAL2    0.09 !               |
ATOM H82  HAL2    0.09 !               |
GROUP                  !               |
ATOM C9   CTL2   -0.18 !          H91-C9-H92
ATOM H91  HAL2    0.09 !               |
ATOM H92  HAL2    0.09 !               |
GROUP                  !               |
ATOM C10  CTL2   -0.18 !         H101-C10-H102
ATOM H101 HAL2    0.09 !               |
ATOM H102 HAL2    0.09 !               |
GROUP                  !               |
ATOM C11  CTL2   -0.18 !         H111-C11-H112
ATOM H111 HAL2    0.09 !               |
ATOM H112 HAL2    0.09 !               |
GROUP                  !               |
ATOM C12  CTL3   -0.27 !         H121-C12-H123
ATOM H121 HAL3    0.09 !               |
ATOM H122 HAL3    0.09 !             H122
ATOM H123 HAL3    0.09 !

BOND  S   OS1 S   OS2  S   OS3  S  OS4 
BOND  OS1 C1  C1  H11  C1  H12  
BOND  C1  C2  C2  H21  C2  H22
BOND  C2  C3  C3  H31  C3  H32
BOND  C3  C4  C4  H41  C4  H42
BOND  C4  C5  C5  H51  C5  H52
BOND  C5  C6  C6  H61  C6  H62
BOND  C6  C7  C7  H71  C7  H72
BOND  C7  C8  C8  H81  C8  H82
BOND  C8  C9  C9  H91  C9  H92
BOND  C9  C10 C10 H101 C10 H102
BOND  C10 C11 C11 H111 C11 H112
BOND  C11 C12 C12 H121 C12 H122 C12 H123

ACCE  OS1
ACCE  OS2
ACCE  OS3
ACCE  OS4

IC C2   OS1  OS2  S    2.56     179.99      0.0      40.1      0.00
IC OS1  OS2  *S   OS3  2.37      40.1     120.0       0.00     0.00
IC OS1  OS2  *S   OS4  2.37      40.1    -120.0       0.00     0.00
IC OS2  S    OS1  C1   0.00       0.00    180.0       0.00     0.00
IC OS4  S    OS2  OS1  1.4530   113.50   -113.75     40.11     2.3733
IC OS2  S    OS2  OS3  1.4522     0.00      0.00     33.26     2.4296
IC OS3  S    OS1  OS4  1.4530   105.51    121.17     35.54     2.4088
IC OS1  S    OS3  OS2  1.5716   105.51    112.45     33.24     2.4296
IC C1   OS1  S    OS2  1.4263   114.59   -180.00    103.34     1.4522
IC S    OS1  C1   OS3  1.5716   114.59    -30.52     56.05     2.8947
IC OS1  S    OS4  OS2  1.5716   105.51   -112.45     33.24     2.4296
IC OS1  S    OS2  OS3  1.5716   103.34   -113.75     33.26     2.4296
IC OS1  S    OS3  OS2  1.5716   105.51    112.45     33.24     2.4296
IC OS4  S    OS2  OS1  1.4530   113.50   -113.75     40.11     2.3733
IC OS4  S    OS3  OS1  1.4530   114.15    115.37     38.95     2.4088
IC OS3  S    OS2  OS1  1.4530   113.50    113.75     40.11     2.3733
IC OS4  S    OS1  C1   1.4530   105.51    -60.58     114.59    1.4263
IC OS2  S    OS1  C1   1.4522   103.34   -180.00     114.59    1.4263
IC OS3  S    OS1  C1   1.4530   105.51     60.58     114.59    1.4263
! REMAINDER IS ALL TRANS
IC S    OS1  C1   C2   0.0        0.00    180.00       0.0     0.0
IC OS1  C1   C2   C3   0.0        0.00    180.00       0.0     0.0
IC C1   C2   C3   C4   0.0        0.00    180.00       0.0     0.0
IC C2   C3   C4   C5   0.0        0.00    180.00       0.0     0.0
IC C3   C4   C5   C6   0.0        0.00    180.00       0.0     0.0
IC C4   C5   C6   C7   0.0        0.00    180.00       0.0     0.0
IC C5   C6   C7   C8   0.0        0.00    180.00       0.0     0.0
IC C6   C7   C8   C9   0.0        0.00    180.00       0.0     0.0
IC C7   C8   C9   C10  0.0        0.00    180.00       0.0     0.0
IC C8   C9   C10  C11  0.0        0.00    180.00       0.0     0.0
IC C9   C10  C11  C12  0.0        0.00    180.00       0.0     0.0
IC OS1  C2   *C1  H11  0.0        0.00    120.00       0.0     0.0
IC OS1  C2   *C1  H12  0.0        0.00   -120.00       0.0     0.0
IC C1   C3   *C2  H21  0.0        0.00    120.00       0.0     0.0
IC C1   C3   *C2  H22  0.0        0.00   -120.00       0.0     0.0
IC C2   C4   *C3  H31  0.0        0.00    120.00       0.0     0.0
IC C2   C4   *C3  H32  0.0        0.00   -120.00       0.0     0.0
IC C3   C5   *C4  H41  0.0        0.00    120.00       0.0     0.0
IC C3   C5   *C4  H42  0.0        0.00   -120.00       0.0     0.0
IC C4   C6   *C5  H51  0.0        0.00    120.00       0.0     0.0
IC C4   C6   *C5  H52  0.0        0.00   -120.00       0.0     0.0
IC C5   C7   *C6  H61  0.0        0.00    120.00       0.0     0.0
IC C5   C7   *C6  H62  0.0        0.00   -120.00       0.0     0.0
IC C6   C8   *C7  H71  0.0        0.00    120.00       0.0     0.0
IC C6   C8   *C7  H72  0.0        0.00   -120.00       0.0     0.0
IC C7   C9   *C8  H81  0.0        0.00    120.00       0.0     0.0
IC C7   C9   *C8  H82  0.0        0.00   -120.00       0.0     0.0
IC C8   C10  *C9  H91  0.0        0.00    120.00       0.0     0.0
IC C8   C10  *C9  H92  0.0        0.00   -120.00       0.0     0.0
IC C9   C11  *C10 H101 0.0        0.00    120.00       0.0     0.0
IC C9   C11  *C10 H102 0.0        0.00   -120.00       0.0     0.0
IC C10  C12  *C11 H111 0.0        0.00    120.00       0.0     0.0
IC C10  C12  *C11 H112 0.0        0.00   -120.00       0.0     0.0
IC C10  C11  C12  H121 0.0        0.00    180.00       0.0     0.0
IC C11  H121 *C12 H122 0.0        0.00    120.00       0.0     0.0
IC C11  H121 *C12 H123 0.0        0.00   -120.00       0.0     0.0

RESI POPC         0.00 ! 1-palmytoil-2-oleoyl-sn-glycero-
!                        3-Phosphatidylcholine
!
! (May 14, 1999 Carlos F. Lopez)
! No IC's (read in coordinates from file)
!
!  Palmytoil - CH2        
!              |  
!      Oleyl - CH
!              |     (-)              (+)
!              CH2 - PO4 - CH2 - CH2 - N-(CH3)3
!
! Polar Head and glycerol backbone
GROUP                  !                 H31
ATOM N    NTL    -0.60 !                 |
ATOM C11  CTL2   -0.10 !             H33-C13-H32
ATOM C12  CTL5   -0.35 !                 |
ATOM C13  CTL5   -0.35 !           H21   |   H43
ATOM C14  CTL5   -0.35 !            |    |   |
ATOM H11  HL      0.25 !       H22-C12---N---C14-H42   (+)
ATOM H12  HL      0.25 !            |    |   |
ATOM H21  HL      0.25 !            H23  |   H41
ATOM H22  HL      0.25 !                 |
ATOM H23  HL      0.25 !                 |
ATOM H31  HL      0.25 !                 |
ATOM H32  HL      0.25 !             H11-C11-H12
ATOM H33  HL      0.25 !                 |
ATOM H41  HL      0.25 !                 |
ATOM H42  HL      0.25 !                 |
ATOM H43  HL      0.25 !                 |
GROUP                  !                 |
ATOM C15  CTL2   -0.08 !                 |
ATOM H51  HAL2    0.09 !           H51---C15---H52
ATOM H52  HAL2    0.09 !                 |
GROUP                  !                 |
ATOM P1   PL      1.50 !       (-) O3   O1
ATOM O3   O2L    -0.78 !             \ /
ATOM O4   O2L    -0.78 !              P1 (+)
ATOM O1   OSL    -0.57 !             / \
ATOM O2   OSL    -0.57 !       (-) O4   O2
GROUP                  !                 |
ATOM C1   CTL2   -0.08 !                 |     alpha1
ATOM HA   HAL2    0.09 !            HA---C1---HB
ATOM HB   HAL2    0.09 !                 |     theta1
GROUP                  !                 |
ATOM C2   CTL1    0.04 !            HS---C2--------------
ATOM HS   HAL1    0.09 !                 | beta1        |
ATOM O21  OSL    -0.34 !            O22  O21          theta3
ATOM C21  CL      0.63 !             \\ /  beta2        |
ATOM O22  OBL    -0.52 !               C21              |
ATOM C22  CTL2   -0.08 !               |   beta3        |
ATOM H2R  HAL2    0.09 !        H2R---C22---H2S         |
ATOM H2S  HAL2    0.09 !               |                |
GROUP                  !               |    beta4       |
ATOM C3   CTL2   -0.05 !               |                |
ATOM HX   HAL2    0.09 !               |           HX---C3---HY
ATOM HY   HAL2    0.09 !               |                |   gamma1
ATOM O31  OSL    -0.34 !               |           O32  O31
ATOM C31  CL      0.63 !               |            \\ /    gamma2
ATOM O32  OBL    -0.52 !               |              C31
ATOM C32  CTL2   -0.08 !               |              |     gamma3
ATOM H2X  HAL2    0.09 !               |        H2X---C32---H2Y
ATOM H2Y  HAL2    0.09 !               |              |
GROUP                  !               |              |      gamma4
ATOM C23  CTL2   -0.18 !               |              |
ATOM H3R  HAL2    0.09 !        H3R ---C23---H3S      |
ATOM H3S  HAL2    0.09 !               |              |
GROUP                  !               |              |
ATOM C24  CTL2   -0.18 !               |              |
ATOM H4R  HAL2    0.09 !        H4R ---C24---H4S      |
ATOM H4S  HAL2    0.09 !               |              |
GROUP                  !               |              |
ATOM C25  CTL2   -0.18 !               |              |
ATOM H5R  HAL2    0.09 !        H5R ---C25---H5S      |
ATOM H5S  HAL2    0.09 !               |              |
GROUP                  !               |              |
ATOM C26  CTL2   -0.18 !               |              |
ATOM H6R  HAL2    0.09 !        H6R ---C26---H6S      |
ATOM H6S  HAL2    0.09 !               |              |
GROUP                  !               |              |
ATOM C27  CTL2   -0.18 !               |              |
ATOM H7R  HAL2    0.09 !        H7R ---C27---H7S      |
ATOM H7S  HAL2    0.09 !               |              |
GROUP                  !               |              |
ATOM C28  CTL2   -0.18 !               |              |
ATOM H8R  HAL2    0.09 !        H8R ---C28---H8S      |
ATOM H8S  HAL2    0.09 !               |              |
GROUP                  !               |              |
ATOM C29  CEL1   -0.15 !               |              |
ATOM H91  HEL1    0.15 !        H91 ---C29            |
GROUP                  !               ||  (CIS)      |
ATOM C210 CEL1   -0.15 !               ||             |
ATOM H101 HEL1    0.15 !        H101---C210           |
GROUP                  !               |              |
ATOM C211 CTL2   -0.18 !               |              |
ATOM H11R HAL2    0.09 !        H11R---C211--H11S     |
ATOM H11S HAL2    0.09 !               |              |
GROUP                  !               |              |
ATOM C212 CTL2   -0.18 !               |              |
ATOM H12R HAL2    0.09 !        H12R---C212--H12S     |
ATOM H12S HAL2    0.09 !               |              |
GROUP                  !               |              |
ATOM C213 CTL2   -0.18 !               |              |
ATOM H13R HAL2    0.09 !        H13R---C213--H13S     |
ATOM H13S HAL2    0.09 !               |              |
GROUP                  !               |              |
ATOM C214 CTL2   -0.18 !               |              |
ATOM H14R HAL2    0.09 !        H14R---C214--H14S     |
ATOM H14S HAL2    0.09 !               |              |
GROUP                  !               |              |
ATOM C215 CTL2   -0.18 !               |              |
ATOM H15R HAL2    0.09 !        H15R---C215--H15S     |
ATOM H15S HAL2    0.09 !               |              |
GROUP                  !               |              |
ATOM C216 CTL2   -0.18 !               |              |
ATOM H16R HAL2    0.09 !        H16R---C216--H16S     |
ATOM H16S HAL2    0.09 !               |              |
GROUP                  !               |              |
ATOM C217 CTL2   -0.18 !               |              |
ATOM H17R HAL2    0.09 !        H17R---C217--H17S     |
ATOM H17S HAL2    0.09 !               |              |
GROUP                  !               |              |
ATOM C218 CTL3   -0.27 !               |              |
ATOM H18R HAL3    0.09 !        H18R---C218--H18S     |
ATOM H18S HAL3    0.09 !               |              |
ATOM H18T HAL3    0.09 !              H18T            |
GROUP                  !                              |
ATOM C33  CTL2   -0.18 !                              |
ATOM H3X  HAL2    0.09 !                       H3X ---C33---H3Y
ATOM H3Y  HAL2    0.09 !                              |
GROUP                  !                              |
ATOM C34  CTL2   -0.18 !                              |
ATOM H4X  HAL2    0.09 !                       H4X ---C34---H4Y
ATOM H4Y  HAL2    0.09 !                              |
GROUP                  !                              |
ATOM C35  CTL2   -0.18 !                              |
ATOM H5X  HAL2    0.09 !                       H5X ---C35---H5Y
ATOM H5Y  HAL2    0.09 !                              |
GROUP                  !                              |
ATOM C36  CTL2   -0.18 !                              |
ATOM H6X  HAL2    0.09 !                       H6X ---C36---H6Y
ATOM H6Y  HAL2    0.09 !                              |
GROUP                  !                              |
ATOM C37  CTL2   -0.18 !                              |
ATOM H7X  HAL2    0.09 !                       H7X ---C37---H7Y
ATOM H7Y  HAL2    0.09 !                              |
GROUP                  !                              |
ATOM C38  CTL2   -0.18 !                              |
ATOM H8X  HAL2    0.09 !                       H8X ---C38---H8Y
ATOM H8Y  HAL2    0.09 !                              |
GROUP                  !                              |
ATOM C39  CTL2   -0.18 !                              |
ATOM H9X  HAL2    0.09 !                       H9X ---C39---H9Y
ATOM H9Y  HAL2    0.09 !                              |
GROUP                  !                              |
ATOM C310 CTL2   -0.18 !                              |
ATOM H10X HAL2    0.09 !                       H10X---C310--H10Y
ATOM H10Y HAL2    0.09 !                              |
GROUP                  !                              |
ATOM C311 CTL2   -0.18 !                              |
ATOM H11X HAL2    0.09 !                       H11X---C311--H11Y
ATOM H11Y HAL2    0.09 !                              |
GROUP                  !                              |
ATOM C312 CTL2   -0.18 !                              |
ATOM H12X HAL2    0.09 !                       H12X---C312--H12Y
ATOM H12Y HAL2    0.09 !                              |
GROUP                  !                              |
ATOM C313 CTL2   -0.18 !                              |
ATOM H13X HAL2    0.09 !                       H13X---C313--H13Y
ATOM H13Y HAL2    0.09 !                              |
GROUP                  !                              |
ATOM C314 CTL2   -0.18 !                              |
ATOM H14X HAL2    0.09 !                       H14X---C314--H14Y
ATOM H14Y HAL2    0.09 !                              |
GROUP                  !                              |
ATOM C315 CTL2   -0.18 !                              |
ATOM H15X HAL2    0.09 !                       H15X---C315--H15Y
ATOM H15Y HAL2    0.09 !                              |
GROUP                  !                              |
ATOM C316 CTL3   -0.27 !                              |
ATOM H16X HAL3    0.09 !                       H16X---C316--H16Y
ATOM H16Y HAL3    0.09 !                              |
ATOM H16Z HAL3    0.09 !                              H16Z
 
!BONDING FROM PC
BOND N     C11       N     C12      N     C13     N     C14
BOND C11   H11       C11   H12      C11   C15
BOND C12   H21       C12   H22      C12   H23
BOND C13   H31       C13   H32      C13   H33
BOND C14   H41       C14   H42      C14   H43
BOND C15   H51       C15   H52
BOND P1    O1        P1    O2       P1    O3      P1    O4    
BOND O1    C15       O2    C1

! Glycerol Backbone
BOND  C1   HA        C1    HB       C1   C2        
BOND  C2   HS        C2    C3       C2   O21
BOND  C3   HX        C3    HY       C3   O31
! Chain from C2
BOND  O21  C21
BOND  C21  C22
DOUBLE  C21  O22
BOND  C22  H2R       C22  H2S       C22  C23
BOND  C23  H3R       C23  H3S       C23  C24
BOND  C24  H4R       C24  H4S       C24  C25
BOND  C25  H5R       C25  H5S       C25  C26
BOND  C26  H6R       C26  H6S       C26  C27
BOND  C27  H7R       C27  H7S       C27  C28
BOND  C28  H8R       C28  H8S       C28  C29
BOND  C29  H91       
DOUBLE  C29 C210
BOND  C210 H101      C210 C211
BOND  C211 H11R      C211 H11S      C211 C212
BOND  C212 H12R      C212 H12S      C212 C213
BOND  C213 H13R      C213 H13S      C213 C214
BOND  C214 H14R      C214 H14S      C214 C215
BOND  C215 H15R      C215 H15S      C215 C216
BOND  C216 H16R      C216 H16S      C216 C217
BOND  C217 H17R      C217 H17S      C217 C218
BOND  C218 H18R      C218 H18S      C218 H18T
! Chain From C3
BOND  O31  C31
BOND  C31  C32
DOUBLE  C31  O32
BOND  C32  H2X       C32  H2Y       C32  C33
BOND  C33  H3X       C33  H3Y       C33  C34
BOND  C34  H4X       C34  H4Y       C34  C35
BOND  C35  H5X       C35  H5Y       C35  C36
BOND  C36  H6X       C36  H6Y       C36  C37
BOND  C37  H7X       C37  H7Y       C37  C38
BOND  C38  H8X       C38  H8Y       C38  C39
BOND  C39  H9X       C39  H9Y       C39  C310
BOND  C310 H10X      C310 H10Y      C310 C311
BOND  C311 H11X      C311 H11Y      C311 C312
BOND  C312 H12X      C312 H12Y      C312 C313
BOND  C313 H13X      C313 H13Y      C313 C314
BOND  C314 H14X      C314 H14Y      C314 C315
BOND  C315 H15X      C315 H15Y      C315 C316
BOND  C316 H16X      C316 H16Y      C316 H16Z

IMPR C21 O21 C22 O22    C31 O31 C32 O32

!IC table from IC generate, geometry is guessed
IC C12  C11  *N   C13  1.4999  109.15  122.15  111.71   1.4949
IC C12  C11  *N   C14  1.4999  109.15 -116.51  109.19   1.5011
IC C12  N    C11  C15  1.4999  109.15   43.57  118.04   1.5524
IC C15  N    *C11 H11  1.5524  118.04 -121.93  109.13   1.0811
IC H11  N    *C11 H12  1.0811  109.13 -117.56  108.83   1.0835
IC C11  N    C12  H21  1.5284  109.15  -59.57  108.41   1.0953
IC H21  N    *C12 H22  1.0953  108.41 -116.60  113.14   1.0854
IC H21  N    *C12 H23  1.0953  108.41  118.64  112.84   1.0777
IC C11  N    C13  H31  1.5284  111.71  -61.34  110.98   1.0826
IC H31  N    *C13 H32  1.0826  110.98  121.24  110.98   1.0826
IC H31  N    *C13 H33  1.0826  110.98 -119.19  110.09   1.0845
IC C11  N    C14  H41  1.5284  109.19  173.62  112.23   1.0785
IC H41  N    *C14 H42  1.0785  112.23  125.69  112.79   1.0778
IC H41  N    *C14 H43  1.0785  112.23 -117.12  108.08   1.0983
IC N    C11  C15  O1   1.5284  118.04   63.61  111.07   1.4249
IC O1   C11  *C15 H51  1.4249  111.07 -126.47  109.40   1.1165
IC H51  C11  *C15 H52  1.1165  109.40 -115.09  108.53   1.1137
IC C11  C15  O1   P1   1.5524  111.07 -132.50  121.66   1.5873
IC C15  O1   P1   O2   1.4249  121.66   95.32   99.37   1.5870
IC O2   O1   *P1  O3   1.5870   99.37 -113.40  108.96   1.4773
IC O2   O1   *P1  O4   1.5870   99.37  114.27  109.52   1.4735
IC O1   P1   O2   C1   1.5873   99.37 -136.11  119.34   1.4276
IC P1   O2   C1   C2   1.5870  119.34 -174.88  109.28   1.5468
IC C2   O2   *C1  HA   1.5468  109.28  119.70  111.34   1.1169
IC HA   O2   *C1  HB   1.1169  111.34  119.72  110.33   1.1141
IC O2   C1   C2   O21  1.4276  109.28 -167.70  109.50   1.4378
IC O21  C1   *C2  C3   1.4378  109.50 -121.42  111.45   1.5543
IC C3   C1   *C2  HS   1.5543  111.45 -117.17  108.32   1.1156
IC C1   C2   O21  C21  1.5468  109.50   90.28  116.64   1.3217
IC C2   O21  C21  C22  1.4378  116.64  174.47  109.18   1.5303
IC C22  O21  *C21 O22  1.5303  109.18 -178.13  126.27   1.2213
IC O21  C21  C22  C23  1.3217  109.18  -78.33  110.83   1.5447
IC C23  C21  *C22 H2R  1.5447  110.83  121.63  109.32   1.1103
IC H2R  C21  *C22 H2S  1.1103  109.32  117.81  107.94   1.1092
IC C1   C2   C3   O31  1.5468  111.45 -172.66  111.94   1.4454
IC O31  C2   *C3  HX   1.4454  111.94 -126.15  109.39   1.1150
IC HX   C2   *C3  HY   1.1150  109.39 -114.93  107.39   1.1133
IC C2   C3   O31  C31  1.5543  111.94  -96.66  116.55   1.3325
IC C3   O31  C31  C32  1.4454  116.55  177.97  109.29   1.5306
IC C32  O31  *C31 O32  1.5306  109.29 -179.43  126.40   1.2162
IC O31  C31  C32  C33  1.3325  109.29 -177.61  111.07   1.5445
IC C33  C31  *C32 H2X  1.5445  111.07  120.97  108.77   1.1094
IC H2X  C31  *C32 H2Y  1.1094  108.77  118.39  108.38   1.1099
IC C21  C22  C23  C24  1.5303  110.83  177.84  113.15   1.5345
IC C24  C22  *C23 H3R  1.5345  113.15 -120.52  109.51   1.1149
IC H3R  C22  *C23 H3S  1.1149  109.51 -117.98  109.32   1.1137
IC C22  C23  C24  C25  1.5447  113.15  174.44  112.06   1.5345
IC C25  C23  *C24 H4R  1.5345  112.06  121.05  109.09   1.1140
IC H4R  C23  *C24 H4S  1.1140  109.09  117.86  109.72   1.1131
IC C23  C24  C25  C26  1.5345  112.06  175.38  112.95   1.5340
IC C26  C24  *C25 H5R  1.5340  112.95 -121.08  109.34   1.1131
IC H5R  C24  *C25 H5S  1.1131  109.34 -117.43  108.99   1.1132
IC C24  C25  C26  C27  1.5345  112.95  174.94  112.21   1.5351
IC C27  C25  *C26 H6R  1.5351  112.21  121.27  109.00   1.1134
IC H6R  C25  *C26 H6S  1.1134  109.00  117.60  109.50   1.1130
IC C25  C26  C27  C28  1.5340  112.21  175.67  112.60   1.5394
IC C28  C26  *C27 H7R  1.5394  112.60 -121.40  108.58   1.1142
IC H7R  C26  *C27 H7S  1.1142  108.58 -116.93  108.44   1.1140
IC C26  C27  C28  C29  1.5351  112.60  178.25  111.01   1.5083
IC C29  C27  *C28 H8R  1.5083  111.01  119.62  107.18   1.1139
IC H8R  C27  *C28 H8S  1.1139  107.18  115.86  109.35   1.1118
IC C27  C28  C29  C210 1.5391  111.34 -141.40  127.31   1.3462
IC C210 C28  *C29 H91  1.3462  127.31 -176.71  114.35   1.1001
IC C28  C29  C210 C211 1.5073  127.31    1.24  127.43   1.5089
IC C211 C29  *C21 H101 1.5089  127.43  179.21  118.33   1.1011
IC C29  C210 C211 C212 1.3462  127.43 -120.91  110.88   1.5393
IC C212 C210 *C21 H11R 1.5393  110.88  121.06  112.51   1.1124
IC H11R C210 *C21 H11S 1.1124  112.51  119.00  109.81   1.1127
IC C210 C211 C212 C213 1.5089  110.88 -176.36  112.76   1.5347
IC C213 C211 *C21 H12R 1.5347  112.76 -120.93  109.33   1.1142
IC H12R C211 *C21 H12S 1.1142  109.33 -118.17  109.94   1.1138
IC C211 C212 C213 C214 1.5393  112.76 -179.47  112.21   1.5338
IC C214 C212 *C21 H13R 1.5338  112.21  121.29  109.31   1.1130
IC H13R C212 *C21 H13S 1.1130  109.31  117.74  109.05   1.1131
IC C212 C213 C214 C215 1.5347  112.21 -178.99  112.92   1.5339
IC C215 C213 *C21 H14R 1.5339  112.92 -121.37  109.00   1.1134
IC H14R C213 *C21 H14S 1.1134  109.00 -117.34  109.08   1.1132
IC C213 C214 C215 C216 1.5338  112.92  179.95  112.20   1.5339
IC C216 C214 *C21 H15R 1.5339  112.20  121.17  109.14   1.1131
IC H15R C214 *C21 H15S 1.1131  109.14  117.63  109.22   1.1132
IC C214 C215 C216 C217 1.5339  112.20  179.53  112.96   1.5328
IC C217 C215 *C21 H16R 1.5328  112.96 -121.41  109.07   1.1135
IC H16R C215 *C21 H16S 1.1135  109.07 -117.43  109.05   1.1130
IC C215 C216 C217 C218 1.5339  112.96 -179.21  113.03   1.5305
IC C218 C216 *C21 H17R 1.5305  113.03  121.55  108.80   1.1140
IC H17R C216 *C21 H17S 1.1140  108.80  116.88  108.83   1.1142
IC C216 C217 C218 H18R 1.5328  113.03   60.41  110.37   1.1113
IC H18R C217 *C21 H18S 1.1113  110.37 -119.78  110.49   1.1115
IC H18R C217 *C21 H18T 1.1113  110.37  120.07  110.59   1.1111
IC C31  C32  C33  C34  1.5333  111.40  179.66  112.54   1.5345
IC C34  C32  *C33 H3X  1.5345  112.54 -121.73  109.66   1.1133
IC H3X  C32  *C33 H3Y  1.1133  109.66 -117.45  109.37   1.1151
IC C32  C33  C34  C35  1.5440  112.54  178.40  112.54   1.5346
IC C35  C33  *C34 H4X  1.5346  112.54  121.75  110.03   1.1131
IC H4X  C33  *C34 H4Y  1.1131  110.03  117.75  108.84   1.1139
IC C33  C34  C35  C36  1.5345  112.54 -175.14  112.09   1.5349
IC C36  C34  *C35 H5X  1.5349  112.09 -122.26  109.27   1.1127
IC H5X  C34  *C35 H5Y  1.1127  109.27 -117.42  109.08   1.1138
IC C34  C35  C36  C37  1.5346  112.09  174.19  113.84   1.5368
IC C37  C35  *C36 H6X  1.5368  113.84  122.38  109.13   1.1124
IC H6X  C35  *C36 H6Y  1.1124  109.13  117.02  108.50   1.1143
IC C35  C36  C37  C38  1.5349  113.84   65.26  113.87   1.5343
IC C38  C36  *C37 H7X  1.5343  113.87  120.83  108.55   1.1137
IC H7X  C36  *C37 H7Y  1.1137  108.55  116.91  109.10   1.1132
IC C36  C37  C38  C39  1.5368  113.87  178.14  112.45   1.5354
IC C39  C37  *C38 H8X  1.5354  112.45  121.43  109.97   1.1123
IC H8X  C37  *C38 H8Y  1.1123  109.97  117.71  108.91   1.1127
IC C37  C38  C39  C310 1.5343  112.45 -176.66  111.96   1.5320
IC C310 C38  *C39 H9X  1.5320  111.96  120.68  109.20   1.1133
IC H9X  C38  *C39 H9Y  1.1133  109.20  117.81  109.34   1.1127
IC C38  C39  C310 C311 1.5354  111.96  178.35  113.81   1.5336
IC C311 C39  *C31 H10X 1.5336  113.81 -120.14  108.22   1.1126
IC H10X C39  *C31 H10Y 1.1126  108.22 -117.07  109.45   1.1132
IC C39  C310 C311 C312 1.5320  113.81 -175.46  111.16   1.5334
IC C312 C310 *C31 H11X 1.5334  111.16  120.27  109.12   1.1138
IC H11X C310 *C31 H11Y 1.1138  109.12  118.20  110.02   1.1119
IC C310 C311 C312 C313 1.5336  111.16  173.60  113.47   1.5330
IC C313 C311 *C31 H12X 1.5330  113.47 -120.74  108.01   1.1140
IC H12X C311 *C31 H12Y 1.1140  108.01 -116.85  109.45   1.1130
IC C311 C312 C313 C314 1.5334  113.47 -174.75  111.86   1.5335
IC C314 C312 *C31 H13X 1.5335  111.86  120.28  108.66   1.1135
IC H13X C312 *C31 H13Y 1.1135  108.66  118.03  110.08   1.1125
IC C312 C313 C314 C315 1.5330  111.86  175.21  113.05   1.5325
IC C315 C313 *C31 H14X 1.5325  113.05 -120.81  108.37   1.1133
IC H14X C313 *C31 H14Y 1.1133  108.37 -117.18  109.40   1.1131
IC C313 C314 C315 C316 1.5335  113.05 -177.76  112.89   1.5300
IC C316 C314 *C31 H15X 1.5300  112.89  121.41  108.55   1.1149
IC H15X C314 *C31 H15Y 1.1149  108.55  117.05  109.21   1.1136
IC C314 C315 C316 H16X 1.5325  112.89   57.15  110.07   1.1113
IC H16X C315 *C31 H16Y 1.1113  110.07 -119.27  110.55   1.1106
IC H16X C315 *C31 H16Z 1.1113  110.07  120.81  110.70   1.1116

RESI POPE         0.00 ! 1-palmytoil-2-oleoyl-sn-glycero-
!                        3-Phosphatidylethanolamine
!
! (May 14, 1999 Carlos F. Lopez)
!
!  Palmytoil - CH2        
!              |  
!      Oleyl - CH
!              |
!              CH2 - PO4 - CH2 - CH2 - NH3
!
! Polar Head and glycerol backbone
GROUP                  !
ATOM N     NH3L  -0.30 !           HN2
ATOM HN1   HCL    0.33 !            |
ATOM HN2   HCL    0.33 !  (+) HN1---N---HN3
ATOM HN3   HCL    0.33 !            |
ATOM C12   CTL2   0.13 !            |
ATOM H12A  HAL2   0.09 !     H12A--C12---H12B
ATOM H12B  HAL2   0.09 !            |
GROUP                  !            |     alpha5
ATOM C11  CTL2   -0.08 !            |
ATOM H11A HAL2    0.09 !     H11A--C11---H11B
ATOM H11B HAL2    0.09 !            |     alpha4
ATOM P    PL      1.50 !   (-) O13  O12
ATOM O13  O2L    -0.78 !         \ /      alpha3
ATOM O14  O2L    -0.78 !          P (+)
ATOM O11  OSL    -0.57 !         / \      alpha2
ATOM O12  OSL    -0.57 !   (-) O14  O11
ATOM C1   CTL2   -0.08 !            |     alpha1
ATOM HA   HAL2    0.09 !       HA---C1---HB
ATOM HB   HAL2    0.09 !            |     theta1
GROUP                  !            |
ATOM C2   CTL1    0.04 !       HS---C2--------------
ATOM HS   HAL1    0.09 !            | beta1        |
ATOM O21  OSL    -0.34 !       O22  O21          theta3
ATOM C21  CL      0.63 !        \\ /  beta2        |
ATOM O22  OBL    -0.52 !          C21              |
ATOM C22  CTL2   -0.08 !          |   beta3        |
ATOM H2R  HAL2    0.09 !   H2R---C22---H2S         |
ATOM H2S  HAL2    0.09 !          |                |
GROUP                  !          |    beta4       |
ATOM C3   CTL2   -0.05 !          |                |
ATOM HX   HAL2    0.09 !          |           HX---C3---HY
ATOM HY   HAL2    0.09 !          |                |   gamma1
ATOM O31  OSL    -0.34 !          |           O32  O31
ATOM C31  CL      0.63 !          |            \\ /    gamma2
ATOM O32  OBL    -0.52 !          |              C31
ATOM C32  CTL2   -0.08 !          |              |     gamma3
ATOM H2X  HAL2    0.09 !          |        H2X---C32---H2Y
ATOM H2Y  HAL2    0.09 !          |              |
GROUP                  !          |              |      gamma4
ATOM C23  CTL2   -0.18 !          |              |
ATOM H3R  HAL2    0.09 !   H3R ---C23---H3S      |
ATOM H3S  HAL2    0.09 !          |              |
GROUP                  !          |              |
ATOM C24  CTL2   -0.18 !          |              |
ATOM H4R  HAL2    0.09 !   H4R ---C24---H4S      |
ATOM H4S  HAL2    0.09 !          |              |
GROUP                  !          |              |
ATOM C25  CTL2   -0.18 !          |              |
ATOM H5R  HAL2    0.09 !   H5R ---C25---H5S      |
ATOM H5S  HAL2    0.09 !          |              |
GROUP                  !          |              |
ATOM C26  CTL2   -0.18 !          |              |
ATOM H6R  HAL2    0.09 !   H6R ---C26---H6S      |
ATOM H6S  HAL2    0.09 !          |              |
GROUP                  !          |              |
ATOM C27  CTL2   -0.18 !          |              |
ATOM H7R  HAL2    0.09 !   H7R ---C27---H7S      |
ATOM H7S  HAL2    0.09 !          |              |
GROUP                  !          |              |
ATOM C28  CTL2   -0.18 !          |              |
ATOM H8R  HAL2    0.09 !   H8R ---C28---H8S      |
ATOM H8S  HAL2    0.09 !          |              |
GROUP                  !          |              |
ATOM C29  CEL1   -0.15 !          |              |
ATOM H91  HEL1    0.15 !   H91 ---C29            |
GROUP                  !          ||  (CIS)      |
ATOM C210 CEL1   -0.15 !          ||             |
ATOM H101 HEL1    0.15 !   H101---C210           |
GROUP                  !          |              |
ATOM C211 CTL2   -0.18 !          |              |
ATOM H11R HAL2    0.09 !   H11R---C211--H11S     |
ATOM H11S HAL2    0.09 !          |              |
GROUP                  !          |              |
ATOM C212 CTL2   -0.18 !          |              |
ATOM H12R HAL2    0.09 !   H12R---C212--H12S     |
ATOM H12S HAL2    0.09 !          |              |
GROUP                  !          |              |
ATOM C213 CTL2   -0.18 !          |              |
ATOM H13R HAL2    0.09 !   H13R---C213--H13S     |
ATOM H13S HAL2    0.09 !          |              |
GROUP                  !          |              |
ATOM C214 CTL2   -0.18 !          |              |
ATOM H14R HAL2    0.09 !   H14R---C214--H14S     |
ATOM H14S HAL2    0.09 !          |              |
GROUP                  !          |              |
ATOM C215 CTL2   -0.18 !          |              |
ATOM H15R HAL2    0.09 !   H15R---C215--H15S     |
ATOM H15S HAL2    0.09 !          |              |
GROUP                  !          |              |
ATOM C216 CTL2   -0.18 !          |              |
ATOM H16R HAL2    0.09 !   H16R---C216--H16S     |
ATOM H16S HAL2    0.09 !          |              |
GROUP                  !          |              |
ATOM C217 CTL2   -0.18 !          |              |
ATOM H17R HAL2    0.09 !   H17R---C217--H17S     |
ATOM H17S HAL2    0.09 !          |              |
GROUP                  !          |              |
ATOM C218 CTL3   -0.27 !          |              |
ATOM H18R HAL3    0.09 !   H18R---C218--H18S     |
ATOM H18S HAL3    0.09 !          |              |
ATOM H18T HAL3    0.09 !         H18T            |
GROUP                  !                         |
ATOM C33  CTL2   -0.18 !                         |
ATOM H3X  HAL2    0.09 !                  H3X ---C33---H3Y
ATOM H3Y  HAL2    0.09 !                         |
GROUP                  !                         |
ATOM C34  CTL2   -0.18 !                         |
ATOM H4X  HAL2    0.09 !                  H4X ---C34---H4Y
ATOM H4Y  HAL2    0.09 !                         |
GROUP                  !                         |
ATOM C35  CTL2   -0.18 !                         |
ATOM H5X  HAL2    0.09 !                  H5X ---C35---H5Y
ATOM H5Y  HAL2    0.09 !                         |
GROUP                  !                         |
ATOM C36  CTL2   -0.18 !                         |
ATOM H6X  HAL2    0.09 !                  H6X ---C36---H6Y
ATOM H6Y  HAL2    0.09 !                         |
GROUP                  !                         |
ATOM C37  CTL2   -0.18 !                         |
ATOM H7X  HAL2    0.09 !                  H7X ---C37---H7Y
ATOM H7Y  HAL2    0.09 !                         |
GROUP                  !                         |
ATOM C38  CTL2   -0.18 !                         |
ATOM H8X  HAL2    0.09 !                  H8X ---C38---H8Y
ATOM H8Y  HAL2    0.09 !                         |
GROUP                  !                         |
ATOM C39  CTL2   -0.18 !                         |
ATOM H9X  HAL2    0.09 !                  H9X ---C39---H9Y
ATOM H9Y  HAL2    0.09 !                         |
GROUP                  !                         |
ATOM C310 CTL2   -0.18 !                         |
ATOM H10X HAL2    0.09 !                  H10X---C310--H10Y
ATOM H10Y HAL2    0.09 !                         |
GROUP                  !                         |
ATOM C311 CTL2   -0.18 !                         |
ATOM H11X HAL2    0.09 !                  H11X---C311--H11Y
ATOM H11Y HAL2    0.09 !                         |
GROUP                  !                         |
ATOM C312 CTL2   -0.18 !                         |
ATOM H12X HAL2    0.09 !                  H12X---C312--H12Y
ATOM H12Y HAL2    0.09 !                         |
GROUP                  !                         |
ATOM C313 CTL2   -0.18 !                         |
ATOM H13X HAL2    0.09 !                  H13X---C313--H13Y
ATOM H13Y HAL2    0.09 !                         |
GROUP                  !                         |
ATOM C314 CTL2   -0.18 !                         |
ATOM H14X HAL2    0.09 !                  H14X---C314--H14Y
ATOM H14Y HAL2    0.09 !                         |
GROUP                  !                         |
ATOM C315 CTL2   -0.18 !                         |
ATOM H15X HAL2    0.09 !                  H15X---C315--H15Y
ATOM H15Y HAL2    0.09 !                         |
GROUP                  !                         |
ATOM C316 CTL3   -0.27 !                         |
ATOM H16X HAL3    0.09 !                  H16X---C316--H16Y
ATOM H16Y HAL3    0.09 !                         |
ATOM H16Z HAL3    0.09 !                         H16Z
 
! Polar Head
BOND  N    HN1       N    HN2       N    HN3       N    C12
BOND  C12  H12A      C12  H12B      C12  C11
BOND  C11  H11A      C11  H11B      C11  O12
BOND  O12  P         P    O11       P    O13       P    O14
! Glycerol Backbone
BOND  C1   HA        C1    HB       C1   C2        C1   O11
BOND  C2   HS        C2    C3       C2   O21
BOND  C3   HX        C3    HY       C3   O31
! Chain from C2
BOND  O21  C21
BOND  C21  C22
DOUBLE  C21  O22
BOND  C22  H2R       C22  H2S       C22  C23
BOND  C23  H3R       C23  H3S       C23  C24
BOND  C24  H4R       C24  H4S       C24  C25
BOND  C25  H5R       C25  H5S       C25  C26
BOND  C26  H6R       C26  H6S       C26  C27
BOND  C27  H7R       C27  H7S       C27  C28
BOND  C28  H8R       C28  H8S       C28  C29
BOND  C29  H91       
DOUBLE  C29 C210
BOND  C210 H101      C210 C211
BOND  C211 H11R      C211 H11S      C211 C212
BOND  C212 H12R      C212 H12S      C212 C213
BOND  C213 H13R      C213 H13S      C213 C214
BOND  C214 H14R      C214 H14S      C214 C215
BOND  C215 H15R      C215 H15S      C215 C216
BOND  C216 H16R      C216 H16S      C216 C217
BOND  C217 H17R      C217 H17S      C217 C218
BOND  C218 H18R      C218 H18S      C218 H18T
! Chain From C3
BOND  O31  C31
BOND  C31  C32
DOUBLE  C31  O32
BOND  C32  H2X       C32  H2Y       C32  C33
BOND  C33  H3X       C33  H3Y       C33  C34
BOND  C34  H4X       C34  H4Y       C34  C35
BOND  C35  H5X       C35  H5Y       C35  C36
BOND  C36  H6X       C36  H6Y       C36  C37
BOND  C37  H7X       C37  H7Y       C37  C38
BOND  C38  H8X       C38  H8Y       C38  C39
BOND  C39  H9X       C39  H9Y       C39  C310
BOND  C310 H10X      C310 H10Y      C310 C311
BOND  C311 H11X      C311 H11Y      C311 C312
BOND  C312 H12X      C312 H12Y      C312 C313
BOND  C313 H13X      C313 H13Y      C313 C314
BOND  C314 H14X      C314 H14Y      C314 C315
BOND  C315 H15X      C315 H15Y      C315 C316
BOND  C316 H16X      C316 H16Y      C316 H16Z

IMPR C21 O21 C22 O22    C31 O31 C32 O32

!IC table from IC generate, geometry is guessed
IC HN1  C12  *N   HN2  1.0524  110.54  127.93  115.12   1.0338
IC HN1  C12  *N   HN3  1.0524  110.54 -112.33  100.76   1.0488
IC HN1  N    C12  C11  1.0524  110.54   70.07  107.99   1.5341
IC C11  N    *C12 H12A 1.5341  107.99 -122.80  109.40   1.1069
IC H12A N    *C12 H12B 1.1069  109.40 -119.69  107.75   1.1114
IC N    C12  C11  O12  1.5038  107.99   46.85  109.27   1.4315
IC O12  C12  *C11 H11A 1.4315  109.27 -121.18  109.30   1.1164
IC H11A C12  *C11 H11B 1.1164  109.30 -117.51  109.07   1.1179
IC C12  C11  O12  P    1.5341  109.27  178.59  119.49   1.5904
IC C11  O12  P    O11  1.4315  119.49  104.93  100.57   1.5835
IC O11  O12  *P   O13  1.5835  100.57 -114.66  107.37   1.4782
IC O11  O12  *P   O14  1.5835  100.57  115.52  107.48   1.4694
IC O12  P    O11  C1   1.5904  100.57  -68.41  122.45   1.4279
IC P    O11  C1   C2   1.5835  122.45  113.33  109.83   1.5458
IC C2   O11  *C1  HA   1.5458  109.83  118.28  108.95   1.1134
IC HA   O11  *C1  HB   1.1134  108.95  118.31  112.84   1.1153
IC O11  C1   C2   O21  1.4279  109.83 -169.38  109.43   1.4399
IC O21  C1   *C2  C3   1.4399  109.43 -120.76  111.51   1.5508
IC C3   C1   *C2  HS   1.5508  111.51 -116.85  107.06   1.1136
IC C1   C2   O21  C21  1.5458  109.43  123.06  117.42   1.3213
IC C2   O21  C21  C22  1.4399  117.42  163.64  109.74   1.5303
IC C22  O21  *C21 O22  1.5303  109.74 -176.86  126.01   1.2239
IC O21  C21  C22  C23  1.3213  109.74 -113.72  109.53   1.5428
IC C23  C21  *C22 H2R  1.5428  109.53  120.69  110.65   1.1107
IC H2R  C21  *C22 H2S  1.1107  110.65  118.78  108.83   1.1092
IC C1   C2   C3   O31  1.5458  111.51 -171.21  111.32   1.4465
IC O31  C2   *C3  HX   1.4465  111.32 -126.25  108.41   1.1159
IC HX   C2   *C3  HY   1.1159  108.41 -114.81  107.61   1.1132
IC C2   C3   O31  C31  1.5508  111.32 -117.52  117.59   1.3317
IC C3   O31  C31  C32  1.4465  117.59 -177.93  109.00   1.5333
IC C32  O31  *C31 O32  1.5333  109.00 -179.19  126.42   1.2107
IC O31  C31  C32  C33  1.3317  109.00 -176.00  111.40   1.5440
IC C33  C31  *C32 H2X  1.5440  111.40  120.79  108.80   1.1093
IC H2X  C31  *C32 H2Y  1.1093  108.80  118.57  108.70   1.1101
IC C21  C22  C23  C24  1.5303  109.53  168.08  112.83   1.5322
IC C24  C22  *C23 H3R  1.5322  112.83 -119.08  109.34   1.1146
IC H3R  C22  *C23 H3S  1.1146  109.34 -118.17  109.92   1.1133
IC C22  C23  C24  C25  1.5428  112.83  179.85  112.06   1.5333
IC C25  C23  *C24 H4R  1.5333  112.06  120.31  108.77   1.1150
IC H4R  C23  *C24 H4S  1.1150  108.77  117.76  110.16   1.1129
IC C23  C24  C25  C26  1.5322  112.06  172.89  112.33   1.5326
IC C26  C24  *C25 H5R  1.5326  112.33 -120.75  109.47   1.1135
IC H5R  C24  *C25 H5S  1.1135  109.47 -117.79  109.27   1.1131
IC C24  C25  C26  C27  1.5333  112.33  175.30  112.46   1.5342
IC C27  C25  *C26 H6R  1.5342  112.46  121.40  108.94   1.1138
IC H6R  C25  *C26 H6S  1.1138  108.94  117.47  109.32   1.1131
IC C25  C26  C27  C28  1.5326  112.46  176.92  112.22   1.5391
IC C28  C26  *C27 H7R  1.5391  112.22 -121.53  108.81   1.1141
IC H7R  C26  *C27 H7S  1.1141  108.81 -117.10  108.50   1.1141
IC C26  C27  C28  C29  1.5342  112.22  177.27  111.34   1.5073
IC C29  C27  *C28 H8R  1.5073  111.34  119.85  107.24   1.1140
IC H8R  C27  *C28 H8S  1.1140  107.24  115.81  109.06   1.1117
IC C27  C28  C29  C210 1.5391  111.34 -141.40  127.31   1.3462
IC C210 C28  *C29 H91  1.3462  127.31 -176.71  114.35   1.1001
IC C28  C29  C210 C211 1.5073  127.31    1.24  127.43   1.5089
IC C211 C29  *C21 H101 1.5089  127.43  179.21  118.33   1.1011
IC C29  C210 C211 C212 1.3462  127.43 -120.91  110.88   1.5393
IC C212 C210 *C21 H11R 1.5393  110.88  121.06  112.51   1.1124
IC H11R C210 *C21 H11S 1.1124  112.51  119.00  109.81   1.1127
IC C210 C211 C212 C213 1.5089  110.88 -176.36  112.76   1.5347
IC C213 C211 *C21 H12R 1.5347  112.76 -120.93  109.33   1.1142
IC H12R C211 *C21 H12S 1.1142  109.33 -118.17  109.94   1.1138
IC C211 C212 C213 C214 1.5393  112.76 -179.47  112.21   1.5338
IC C214 C212 *C21 H13R 1.5338  112.21  121.29  109.31   1.1130
IC H13R C212 *C21 H13S 1.1130  109.31  117.74  109.05   1.1131
IC C212 C213 C214 C215 1.5347  112.21 -178.99  112.92   1.5339
IC C215 C213 *C21 H14R 1.5339  112.92 -121.37  109.00   1.1134
IC H14R C213 *C21 H14S 1.1134  109.00 -117.34  109.08   1.1132
IC C213 C214 C215 C216 1.5338  112.92  179.95  112.20   1.5339
IC C216 C214 *C21 H15R 1.5339  112.20  121.17  109.14   1.1131
IC H15R C214 *C21 H15S 1.1131  109.14  117.63  109.22   1.1132
IC C214 C215 C216 C217 1.5339  112.20  179.53  112.96   1.5328
IC C217 C215 *C21 H16R 1.5328  112.96 -121.41  109.07   1.1135
IC H16R C215 *C21 H16S 1.1135  109.07 -117.43  109.05   1.1130
IC C215 C216 C217 C218 1.5339  112.96 -179.21  113.03   1.5305
IC C218 C216 *C21 H17R 1.5305  113.03  121.55  108.80   1.1140
IC H17R C216 *C21 H17S 1.1140  108.80  116.88  108.83   1.1142
IC C216 C217 C218 H18R 1.5328  113.03   60.41  110.37   1.1113
IC H18R C217 *C21 H18S 1.1113  110.37 -119.78  110.49   1.1115
IC H18R C217 *C21 H18T 1.1113  110.37  120.07  110.59   1.1111
IC C31  C32  C33  C34  1.5333  111.40  179.66  112.54   1.5345
IC C34  C32  *C33 H3X  1.5345  112.54 -121.73  109.66   1.1133
IC H3X  C32  *C33 H3Y  1.1133  109.66 -117.45  109.37   1.1151
IC C32  C33  C34  C35  1.5440  112.54  178.40  112.54   1.5346
IC C35  C33  *C34 H4X  1.5346  112.54  121.75  110.03   1.1131
IC H4X  C33  *C34 H4Y  1.1131  110.03  117.75  108.84   1.1139
IC C33  C34  C35  C36  1.5345  112.54 -175.14  112.09   1.5349
IC C36  C34  *C35 H5X  1.5349  112.09 -122.26  109.27   1.1127
IC H5X  C34  *C35 H5Y  1.1127  109.27 -117.42  109.08   1.1138
IC C34  C35  C36  C37  1.5346  112.09  174.19  113.84   1.5368
IC C37  C35  *C36 H6X  1.5368  113.84  122.38  109.13   1.1124
IC H6X  C35  *C36 H6Y  1.1124  109.13  117.02  108.50   1.1143
IC C35  C36  C37  C38  1.5349  113.84   65.26  113.87   1.5343
IC C38  C36  *C37 H7X  1.5343  113.87  120.83  108.55   1.1137
IC H7X  C36  *C37 H7Y  1.1137  108.55  116.91  109.10   1.1132
IC C36  C37  C38  C39  1.5368  113.87  178.14  112.45   1.5354
IC C39  C37  *C38 H8X  1.5354  112.45  121.43  109.97   1.1123
IC H8X  C37  *C38 H8Y  1.1123  109.97  117.71  108.91   1.1127
IC C37  C38  C39  C310 1.5343  112.45 -176.66  111.96   1.5320
IC C310 C38  *C39 H9X  1.5320  111.96  120.68  109.20   1.1133
IC H9X  C38  *C39 H9Y  1.1133  109.20  117.81  109.34   1.1127
IC C38  C39  C310 C311 1.5354  111.96  178.35  113.81   1.5336
IC C311 C39  *C31 H10X 1.5336  113.81 -120.14  108.22   1.1126
IC H10X C39  *C31 H10Y 1.1126  108.22 -117.07  109.45   1.1132
IC C39  C310 C311 C312 1.5320  113.81 -175.46  111.16   1.5334
IC C312 C310 *C31 H11X 1.5334  111.16  120.27  109.12   1.1138
IC H11X C310 *C31 H11Y 1.1138  109.12  118.20  110.02   1.1119
IC C310 C311 C312 C313 1.5336  111.16  173.60  113.47   1.5330
IC C313 C311 *C31 H12X 1.5330  113.47 -120.74  108.01   1.1140
IC H12X C311 *C31 H12Y 1.1140  108.01 -116.85  109.45   1.1130
IC C311 C312 C313 C314 1.5334  113.47 -174.75  111.86   1.5335
IC C314 C312 *C31 H13X 1.5335  111.86  120.28  108.66   1.1135
IC H13X C312 *C31 H13Y 1.1135  108.66  118.03  110.08   1.1125
IC C312 C313 C314 C315 1.5330  111.86  175.21  113.05   1.5325
IC C315 C313 *C31 H14X 1.5325  113.05 -120.81  108.37   1.1133
IC H14X C313 *C31 H14Y 1.1133  108.37 -117.18  109.40   1.1131
IC C313 C314 C315 C316 1.5335  113.05 -177.76  112.89   1.5300
IC C316 C314 *C31 H15X 1.5300  112.89  121.41  108.55   1.1149
IC H15X C314 *C31 H15Y 1.1149  108.55  117.05  109.21   1.1136
IC C314 C315 C316 H16X 1.5325  112.89   57.15  110.07   1.1113
IC H16X C315 *C31 H16Y 1.1113  110.07 -119.27  110.55   1.1106
IC H16X C315 *C31 H16Z 1.1113  110.07  120.81  110.70   1.1116

!The following two residues (PALM and PCGL) and the two subsequent
!patches (EST1 and EST2) are a modular way to create DPPC.  
!See the comments with EST1 and EST2 for more details. adm jr., Jul 99

RESI PALM        -1.00 ! Palmitate
                       ! based on methylsulfate

GROUP                               O1  O2 (-) 
ATOM C1   CL      0.62 !             \\ /
ATOM O1   OCL    -0.76 !              C1
ATOM O2   OCL    -0.76 !               |
                       !               |
ATOM C2   CTL2   -0.28 !          H2A-C2-H2B
ATOM H2A  HAL2    0.09 !               |
ATOM H2B  HAL2    0.09 !               |
GROUP                  !               |
ATOM C3   CTL2   -0.18 !          H3A-C3-H3B
ATOM H3A  HAL2    0.09 !               |
ATOM H3B  HAL2    0.09 !               |
GROUP                  !               |
ATOM C4   CTL2   -0.18 !          H4A-C4-H4B
ATOM H4A  HAL2    0.09 !               |
ATOM H4B  HAL2    0.09 !               |
GROUP                  !               |
ATOM C5   CTL2   -0.18 !          H5A-C5-H5B
ATOM H5A  HAL2    0.09 !               |
ATOM H5B  HAL2    0.09 !               |
GROUP                  !               |
ATOM C6   CTL2   -0.18 !          H6A-C6-H6B
ATOM H6A  HAL2    0.09 !               |
ATOM H6B  HAL2    0.09 !               |
GROUP                  !               |
ATOM C7   CTL2   -0.18 !          H7A-C7-H7B
ATOM H7A  HAL2    0.09 !               |
ATOM H7B  HAL2    0.09 !               |
GROUP                  !               |
ATOM C8   CTL2   -0.18 !          H8A-C8-H8B
ATOM H8A  HAL2    0.09 !               |
ATOM H8B  HAL2    0.09 !               |
GROUP                  !               |
ATOM C9   CTL2   -0.18 !          H9A-C9-H9B
ATOM H9A  HAL2    0.09 !               |
ATOM H9B  HAL2    0.09 !               |
GROUP                  !               |
ATOM C10  CTL2   -0.18 !         H10A-C10-H10B
ATOM H10A HAL2    0.09 !               |
ATOM H10B HAL2    0.09 !               |
GROUP                  !               |
ATOM C11  CTL2   -0.18 !         H11A-C11-H11B
ATOM H11A HAL2    0.09 !               |
ATOM H11B HAL2    0.09 !               |
GROUP                  !               |
ATOM C12  CTL2   -0.18 !         H12A-C12-H12B
ATOM H12A HAL2    0.09 !               |
ATOM H12B HAL2    0.09 !               |
GROUP                  !               |
ATOM C13  CTL2   -0.18 !         H13A-C13-H13B
ATOM H13A HAL2    0.09 !               |
ATOM H13B HAL2    0.09 !               |
GROUP                  !               |
ATOM C14  CTL2   -0.18 !         H14A-C14-H14B
ATOM H14A HAL2    0.09 !               |
ATOM H14B HAL2    0.09 !               |
GROUP                  !               |
ATOM C15  CTL2   -0.18 !         H15A-C15-H15B
ATOM H15A HAL2    0.09 !               |
ATOM H15B HAL2    0.09 !               |
GROUP                  !               |
ATOM C16  CTL3   -0.27 !         H16A-C16-H16B
ATOM H16A HAL3    0.09 !               |
ATOM H16B HAL3    0.09 !             H16C
ATOM H16C HAL3    0.09 !

BOND  C1  O1  C1  O2
BOND  C1  C2  C2  H2A  C2  H2B
BOND  C2  C3  C3  H3A  C3  H3B
BOND  C3  C4  C4  H4A  C4  H4B
BOND  C4  C5  C5  H5A  C5  H5B
BOND  C5  C6  C6  H6A  C6  H6B
BOND  C6  C7  C7  H7A  C7  H7B
BOND  C7  C8  C8  H8A  C8  H8B
BOND  C8  C9  C9  H9A  C9  H9B
BOND  C9  C10 C10 H10A C10 H10B
BOND  C10 C11 C11 H11A C11 H11B
BOND  C11 C12 C12 H12A C12 H12B
BOND  C12 C13 C13 H13A C13 H13B
BOND  C13 C14 C14 H14A C14 H14B
BOND  C14 C15 C15 H15A C15 H15B
BOND  C15 C16 C16 H16A C16 H16B C16 H16C
IMPR C1 O1 C2 O2
ACCE  O1
ACCE  O2
!IC table insufficent to create cartesian coordinates
IC O1   C2   *C1  O2   0.0000    0.00  180.00    0.00   0.0000
IC O1   C1   C2   C3   0.0000    0.00  180.00    0.00   0.0000
IC C3   C1   *C2  H2A  0.0000    0.00  120.00    0.00   0.0000
IC H2A  C1   *C2  H2B  0.0000    0.00 -120.00    0.00   0.0000
IC C1   C2   C3   C4   0.0000    0.00  180.00    0.00   0.0000
IC C4   C2   *C3  H3A  0.0000    0.00  120.00    0.00   0.0000
IC H3A  C2   *C3  H3B  0.0000    0.00 -120.00    0.00   0.0000
IC C2   C3   C4   C5   0.0000    0.00  180.00    0.00   0.0000
IC C5   C3   *C4  H4A  0.0000    0.00  120.00    0.00   0.0000
IC H4A  C3   *C4  H4B  0.0000    0.00 -120.00    0.00   0.0000
IC C3   C4   C5   C6   0.0000    0.00  180.00    0.00   0.0000
IC C6   C4   *C5  H5A  0.0000    0.00  120.00    0.00   0.0000
IC H5A  C4   *C5  H5B  0.0000    0.00 -120.00    0.00   0.0000
IC C4   C5   C6   C7   0.0000    0.00  180.00    0.00   0.0000
IC C7   C5   *C6  H6A  0.0000    0.00  120.00    0.00   0.0000
IC H6A  C5   *C6  H6B  0.0000    0.00 -120.00    0.00   0.0000
IC C5   C6   C7   C8   0.0000    0.00  180.00    0.00   0.0000
IC C8   C6   *C7  H7A  0.0000    0.00  120.00    0.00   0.0000
IC H7A  C6   *C7  H7B  0.0000    0.00 -120.00    0.00   0.0000
IC C6   C7   C8   C9   0.0000    0.00  180.00    0.00   0.0000
IC C9   C7   *C8  H8A  0.0000    0.00  120.00    0.00   0.0000
IC H8A  C7   *C8  H8B  0.0000    0.00 -120.00    0.00   0.0000
IC C7   C8   C9   C10  0.0000    0.00  180.00    0.00   0.0000
IC C10  C8   *C9  H9A  0.0000    0.00  120.00    0.00   0.0000
IC H9A  C8   *C9  H9B  0.0000    0.00 -120.00    0.00   0.0000
IC C8   C9   C10  C11  0.0000    0.00  180.00    0.00   0.0000
IC C11  C9   *C10 H10A 0.0000    0.00  120.00    0.00   0.0000
IC H10A C9   *C10 H10B 0.0000    0.00 -120.00    0.00   0.0000
IC C9   C10  C11  C12  0.0000    0.00  180.00    0.00   0.0000
IC C12  C10  *C11 H11A 0.0000    0.00  120.00    0.00   0.0000
IC H11A C10  *C11 H11B 0.0000    0.00 -120.00    0.00   0.0000
IC C10  C11  C12  C13  0.0000    0.00  180.00    0.00   0.0000
IC C13  C11  *C12 H12A 0.0000    0.00  120.00    0.00   0.0000
IC H12A C11  *C12 H12B 0.0000    0.00 -120.00    0.00   0.0000
IC C11  C12  C13  C14  0.0000    0.00  180.00    0.00   0.0000
IC C14  C12  *C13 H13A 0.0000    0.00  120.00    0.00   0.0000
IC H13A C12  *C13 H13B 0.0000    0.00 -120.00    0.00   0.0000
IC C12  C13  C14  C15  0.0000    0.00  180.00    0.00   0.0000
IC C15  C13  *C14 H14A 0.0000    0.00  120.00    0.00   0.0000
IC H14A C13  *C14 H14B 0.0000    0.00 -120.00    0.00   0.0000
IC C13  C14  C15  C16  0.0000    0.00  180.00    0.00   0.0000
IC C16  C14  *C15 H15A 0.0000    0.00  120.00    0.00   0.0000
IC H15A C14  *C15 H15B 0.0000    0.00 -120.00    0.00   0.0000
IC C14  C15  C16  H16A 0.0000    0.00  180.00    0.00   0.0000
IC H16A C15  *C16 H16B 0.0000    0.00  120.00    0.00   0.0000
IC H16A C15  *C16 H16C 0.0000    0.00 -120.00    0.00   0.0000
  
RESI PCGL         0.00 ! glycerolphosphorylcholine
                       ! nomenclature for creation of DPPC
GROUP                  ! from PALM and PCGL via patches EST1 and EST2
ATOM N    NTL    -0.60 !
ATOM C5   CTL2   -0.10 !             |
ATOM C6   CTL5   -0.35 !           -C7-
ATOM C7   CTL5   -0.35 !             |
ATOM C8   CTL5   -0.35 !        |    |   |
ATOM H5A  HL      0.25 !       -C6---N---C8-     (+)
ATOM H5B  HL      0.25 !        |    |   |
ATOM H6A  HL      0.25 !             |
ATOM H6B  HL      0.25 !           -C5-
ATOM H6C  HL      0.25 !             |
ATOM H7A  HL      0.25 !             |
ATOM H7B  HL      0.25 !             |
ATOM H7C  HL      0.25 !             |
ATOM H8A  HL      0.25 !             |
ATOM H8B  HL      0.25 !             |
ATOM H8C  HL      0.25 !             |
GROUP                  !             |
ATOM C4   CTL2   -0.08 !             |
ATOM H4A  HAL2    0.09 !       H4A---C4---H4B
ATOM H4B  HAL2    0.09 !             |
ATOM P    PL      1.50 !    (-) OP3  OP2
ATOM OP3  O2L    -0.78 !          \ /
ATOM OP4  O2L    -0.78 !           P (+)
ATOM OP1  OSL    -0.57 !          / \
ATOM OP2  OSL    -0.57 !    (-) OP4  OP1
ATOM C3   CTL2   -0.08 !             |
ATOM H3A  HAL2    0.09 !        H3A-C3-H3B
ATOM H3B  HAL2    0.09 !             |
GROUP                  !             | 
ATOM C2   CTL1    0.14 !             |
ATOM H2A  HAL1    0.09 !        H2A-C2-O2-H2
ATOM O2   OHL    -0.66 !             |
ATOM H2   HOL     0.43 !             |       
GROUP                  !             |  
ATOM C1   CTL2    0.05 !             |
ATOM H1A  HAL2    0.09 !        H1A-C1-O1-H1
ATOM H1B  HAL2    0.09 !             |
ATOM O1   OHL    -0.66 !             H1B
ATOM H1   HOL     0.43 !
BOND N   C5   N   C6    N   C7    N   C8
BOND C5  C4   C4  OP2   OP2 P     P   OP1
BOND P   OP3  P   OP4
BOND OP1 C3   C3  C2    C2  C1
BOND C2  O2   C1  O1
BOND O1  H1   O2  H2
BOND C1  H1A  C1  H1B
BOND C2  H2A
BOND C3  H3A  C3  H3B
BOND C4  H4A  C4  H4B
BOND C5  H5A  C5  H5B
BOND C6  H6A  C6  H6B  C6  H6C
BOND C7  H7A  C7  H7B  C7  H7C
BOND C8  H8A  C8  H8B  C8  H8C
!IC table insufficent to create cartesian coordinates
IC C6   C5   *N   C7   0.0000    0.00  120.00    0.00   0.0000
IC C6   C5   *N   C8   0.0000    0.00 -120.00    0.00   0.0000
IC C6   N    C5   C4   0.0000    0.00  180.00    0.00   0.0000
IC C4   N    *C5  H5A  0.0000    0.00  120.00    0.00   0.0000
IC C4   N    *C5  H5B  0.0000    0.00 -120.00    0.00   0.0000
IC C5   N    C6   H6A  0.0000    0.00  180.00    0.00   0.0000
IC H6A  N    *C6  H6B  0.0000    0.00  120.00    0.00   0.0000
IC H6A  N    *C6  H6C  0.0000    0.00 -120.00    0.00   0.0000
IC C5   N    C7   H7A  0.0000    0.00  180.00    0.00   0.0000
IC H7A  N    *C7  H7B  0.0000    0.00  120.00    0.00   0.0000
IC H7A  N    *C7  H7C  0.0000    0.00 -120.00    0.00   0.0000
IC C5   N    C8   H8A  0.0000    0.00  180.00    0.00   0.0000
IC H8A  N    *C8  H8B  0.0000    0.00  120.00    0.00   0.0000
IC H8A  N    *C8  H8C  0.0000    0.00 -120.00    0.00   0.0000
IC N    C5   C4   OP2  0.0000    0.00  180.00    0.00   0.0000
IC OP2  C5   *C4  H4A  0.0000    0.00  120.00    0.00   0.0000
IC OP2  C5   *C4  H4B  0.0000    0.00 -120.00    0.00   0.0000
IC C5   C4   OP2  P    0.0000    0.00  180.00    0.00   0.0000
IC C4   OP2  P    OP1  0.0000    0.00  180.00    0.00   0.0000
IC OP1  OP2  *P   OP3  0.0000    0.00  120.00    0.00   0.0000
IC OP1  OP2  *P   OP4  0.0000    0.00 -120.00    0.00   0.0000
IC OP2  P    OP1  C3   0.0000    0.00  180.00    0.00   0.0000
IC P    OP1  C3   C2   0.0000    0.00  180.00    0.00   0.0000
IC C2   OP1  *C3  H3A  0.0000    0.00  120.00    0.00   0.0000
IC C2   OP1  *C3  H3B  0.0000    0.00 -120.00    0.00   0.0000
IC OP1  C3   C2   C1   0.0000    0.00  180.00    0.00   0.0000
IC C1   C3   *C2  O2   0.0000    0.00  120.00    0.00   0.0000
IC C1   C3   *C2  H2A  0.0000    0.00 -120.00    0.00   0.0000
IC C3   C2   O2   H2   0.0000    0.00  180.00    0.00   0.0000
IC C3   C2   C1   O1   0.0000    0.00  180.00    0.00   0.0000
IC O1   C2   *C1  H1A  0.0000    0.00  120.00    0.00   0.0000
IC O1   C2   *C1  H1B  0.0000    0.00 -120.00    0.00   0.0000
IC C2   C1   O1   H1   0.0000    0.00  180.00    0.00   0.0000

PRES EST1        0.00 !patch to link O1 of PCGL to C1 of PALM
! residue 1 is PCGL, residue 2 is PALM
DELETE ATOM 1H1
DELETE ATOM 2O2
ATOM 1C1  CTL2  -0.05 !     1H1A--1C1--1H1B
ATOM 1H1A HAL2   0.09 !            |
ATOM 1H1B HAL2   0.09 !            |   
ATOM 1O1  OSL   -0.34 !      2O1  1O1
ATOM 2C1  CL     0.63 !       \\ /    
ATOM 2O1  OBL   -0.52 !        2C1
ATOM 2C2  CTL2  -0.08 !         |     
ATOM 2H2A HAL2   0.09 !  2H2A--2C2--2H2B
ATOM 2H2B HAL2   0.09 !         |
BOND 1O1  2C1

PRES EST2        0.00 !patch to link O2 of PCGL to C1 of PALM
! residue 1 is PCGL, residue 2 is PALM
DELETE ATOM 1H2
DELETE ATOM 2O2
GROUP
ATOM 1C2  CTL1   0.04 !     1H2A--1C2--
ATOM 1H2A HAL1   0.09 !            |
ATOM 1O2  OSL   -0.34 !      2O1  1O2
ATOM 2C1  CL     0.63 !       \\ /
ATOM 2O1  OBL   -0.52 !        2C1
ATOM 2C2  CTL2  -0.08 !         |
ATOM 2H2A HAL2   0.09 !  2H2A--2C2--2H2B
ATOM 2H2B HAL2   0.09 !         |
BOND 1O2  2C1


! Nucleic acids section
! -----------------------


! The following patches for phosphotyrosine must be used with a 
! parameter file containing both the protein and nucleic acid parameters.
! In addition, the commented parameters listed below must be included
! in the combined parameter file
!
!
! patch to convert tyrosine to phenolphosphate
!PATCH TP1 TYR 1 SETUP WARN
!
! this patch requires that the use of the following
!
!1) protein topology file that contains mass list of atoms in both
!   the protein and nucleic acid topology files and
!
! add to the topology file
!MASS 179   ON2b 15.999400 ! Nucleic acid phosphate ester oxygen (pres tp1/tp2)
!
!2) parameter file that contains both the protein and nucleic acid 
!   parameters plus the parameters listed below
!
! parameters to be added to the protein/nucleic acid parameter file
!
!bonds
!CA   ON2b  340.0       1.38    !phenol phosphate, 6/94, adm jr.
!ON2b P     270.0       1.61    !phenol phosphate, 6/94, adm jr.
!angles
!CA   CA   ON2b  75.0     120.0  !phenol phosphate, 6/94, adm jr.
!CA   ON2b P     90.0     120.0  20.   2.30 !phenol phosphate, 6/94, adm jr.
!ON4  P    ON2b  48.1     108.0  !phenol phosphate, 6/94, adm jr.
!ON3  P    ON2b  98.9     103.0  !phenol phosphate, 6/94, adm jr.
!dihedrals
!CA   CA   CA   ON2b      3.10    2   180.0  !phenol phosphate, 6/94, adm jr.
!HP   CA   CA   ON2b      4.20    2   180.0  !phenol phosphate, 6/94, adm jr.
!CA   CA   ON2b P         1.40    2   180.0  !phenol phosphate, 6/94, adm jr.
!CA   CA   ON2b P         0.20    3   180.0  !phenol phosphate, 6/94, adm jr.
!CA   ON2b P    ON4       0.95    2     0.0  !phenol phosphate, 6/94, adm jr.
!CA   ON2b P    ON4       0.50    3     0.0  !phenol phosphate, 6/94, adm jr.
!CA   ON2b P    ON3       0.10    3     0.0  !phenol phosphate, 6/94, adm jr.
!nonbonded
!ON2b     0.0       -0.1521    1.77   
!
! end of parameters to be added

!nucleic acid section
RESI GUA         -1.00  !               O6
ATOM P    P       1.50  !               ||   
ATOM O1P  ON3    -0.78  !               C6    
ATOM O2P  ON3    -0.78  !              /  \  
ATOM O5'  ON2    -0.57  !          H1-N1   C5--N7\\
ATOM C5'  CN8B   -0.08  !             |    ||     C8-H8
ATOM H5'  HN8     0.09  !             C2   C4--N9/
ATOM H5'' HN8     0.09  !            / \\ /      \
GROUP                   !      H21-N2   N3        \
ATOM C4'  CN7     0.16  !          |               \
ATOM H4'  HN7     0.09  !         H22               \
ATOM O4'  ON6B   -0.50  !                            \
ATOM C1'  CN7B    0.16  !        O1P    H5' H4'  O4'  \
ATOM H1'  HN7     0.09  !         |      |    \ /   \  \
GROUP                   !        -P-O5'-C5'---C4'    C1'
ATOM N9   NN2B   -0.02  !         |      |     \     / \
ATOM C4   CN5     0.26  !        O2P    H5''   C3'--C2' H1'
ATOM N2   NN1    -0.68  !               / \   / \
ATOM H21  HN1     0.32  !             O3' H3' O2' H2'' 
ATOM H22  HN1     0.35  !              |       |
ATOM N3   NN3G   -0.74  !                      H2'
ATOM C2   CN2     0.75  
ATOM N1   NN2G   -0.34  
ATOM H1   HN2     0.26  
ATOM C6   CN1     0.54 
ATOM O6   ON1    -0.51
ATOM C5   CN5G    0.00
ATOM N7   NN4    -0.60
ATOM C8   CN4     0.25
ATOM H8   HN3     0.16
GROUP
ATOM C2'  CN7B    0.14
ATOM H2'' HN7     0.09
ATOM O2'  ON5    -0.66 
ATOM H2'  HN5     0.43 
GROUP
ATOM C3'  CN7     0.01
ATOM H3'  HN7     0.09
ATOM O3'  ON2    -0.57 
BOND P    O1P       P    O2P       P     O5'
BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
BOND C1'  N9        C1'  C2'       N9   C4        N9   C8        C4   N3
BOND C2   N2        C2   N1        N2   H21
BOND N2   H22       N1   H1        N1   C6        C6   C5
BOND C5   N7        C2'  C3'       C3'  O3'       O3'  +P
BOND C2'  O2'       O2'  H2'
BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
BOND C5'  H5''      C8   H8  
DOUBLE   C2  N3     C4   C5        N7   C8        C6   O6
IMPR C2   N3   N1   N2        C6   N1   C5   O6        N2   H21  C2   H22
DONO H21  N2            
DONO H22  N2   
DONO H1   N1   
DONO H2'  O2'
ACCE O6   C6         
ACCE N3    
ACCE N7    
ACCE O1P  P
ACCE O2P  P       
ACCE O2'  
ACCE O3'
ACCE O4'
ACCE O5'
! Chi and sugar-phosphate backbone in B-DNA like conformation
BILD -O3' P    O5'  C5'    1.6001  101.45  -46.90  119.00   1.4401 !alpha
BILD -O3' O5'  *P   O1P    1.6001  101.45 -115.82  109.74   1.4802
BILD -O3' O5'  *P   O2P    1.6001  101.45  115.90  109.80   1.4801
BILD  P   O5'  C5'  C4'    1.5996  119.00 -146.00  110.04   1.5160 !beta
BILD O5'  C5'  C4'  C3'    1.4401  108.83   60.00  116.10   1.5284 !gamma
BILD C5'  C4'  C3'  O3'    1.5160  116.10  140.00  115.12   1.4212 !delta
BILD C4'  C3'  O3'  +P     1.5284  111.92  155.00  119.05   1.6001 !epsilon
BILD C3'  O3'  +P   +O5'   1.4212  119.05  -95.20  101.45   1.5996 !zeta
BILD O4'  C3'  *C4' C5'    1.4572  104.06 -120.04  116.10   1.5160
BILD C2'  C4'  *C3' O3'    1.5284  100.16 -124.08  115.12   1.4212
BILD C4'  C3'  C2'  C1'    1.5284  100.16  -30.00  102.04   1.5251 !puck
BILD C3'  C2'  C1'  N9     1.5284  101.97  147.80  113.71   1.4896
BILD O4'  C1'  N9   C4     1.5251  113.71  -97.2   125.59   1.3783 !chi
BILD C1'  C4   *N9  C8     1.4896  125.59 -179.99  106.0    1.374    
BILD C4   N9   C8   N7     1.377   106.0     0.0   113.5    1.304    
BILD C8   N9   C4   C5     1.374   106.0     0.0   105.6    1.377    
BILD N9   C5   *C4  N3     1.377   105.6   180.0   128.4    1.355    
BILD C5   C4   N3   C2     1.377   128.4     0.0   111.8    1.327    
BILD C4   N3   C2   N1     1.355   111.8     0.0   124.0    1.375    
BILD N1   N3   *C2  N2     1.375   124.0   180.0   119.7    1.341    
BILD N3   C2   N2   H21    1.327   119.7   180.0   127.0    1.01     
BILD H21  C2   *N2  H22    1.01    127.0  -180.0   116.5    1.01     
BILD N3   C2   N1   C6     1.327   124.0     0.0   124.9    1.393    
BILD C6   C2   *N1  H1     1.393   124.9   180.0   117.4    1.03     
BILD C5   N1   *C6  O6     1.415   111.7   180.0   120.0    1.239    
BILD N9   N7   *C8  H8     0.0       0.0   180.0     0.0    0.0
BILD C1'  C3'  *C2' O2'    1.5284  102.04 -114.67  110.81   1.4212 
BILD H2'  O2'  C2'  C3'    0.9600  114.97  148.63  111.92   1.5284 
BILD O4'  C2'  *C1' H1'    0.0       0.0  -115.0     0.0    0.0
BILD C1'  C3'  *C2' H2''   0.0       0.0   115.0     0.0    0.0
BILD C2'  C4'  *C3' H3'    0.0       0.0   115.0     0.0    0.0
BILD C3'  O4'  *C4' H4'    0.0       0.0  -115.0     0.0    0.0
BILD C4'  O5'  *C5' H5'    0.0       0.0  -115.0     0.0    0.0
BILD C4'  O5'  *C5' H5''   0.0       0.0   115.0     0.0    0.0

 
RESI ADE         -1.00  !             H61  H62!
ATOM P    P       1.50  !               \  /
ATOM O1P  ON3    -0.78  !                N6
ATOM O2P  ON3    -0.78  !                |
ATOM O5'  ON2    -0.57  !                C6
ATOM C5'  CN8B   -0.08  !              //  \
ATOM H5'  HN8     0.09  !              N1   C5--N7\\
ATOM H5'' HN8     0.09  !              |    ||     C8-H8
GROUP                   !              C2   C4--N9/
ATOM C4'  CN7     0.16  !             / \\ /     \
ATOM H4'  HN7     0.09  !           H2   N3       \
ATOM O4'  ON6B   -0.50  !                          \
ATOM C1'  CN7B    0.16  !                           \
ATOM H1'  HN7     0.09  !                            \
GROUP                   !        O1P    H5' H4'  O4'  \
ATOM N9   NN2    -0.05  !         |      |    \ /   \  \
ATOM C5   CN5     0.28  !        -P-O5'-C5'---C4'    C1'
ATOM N7   NN4    -0.71  !         |      |     \     / \
ATOM C8   CN4     0.34  !        O2P    H5''   C3'--C2' H1'
ATOM H8   HN3     0.12  !                     / \   / \
ATOM N1   NN3A   -0.74  !                  O3' H3' O2' H2''
ATOM C2   CN4     0.50  !                   |       |
ATOM H2   HN3     0.13  !                          H2'
ATOM N3   NN3A   -0.75  
ATOM C4   CN5     0.43  
ATOM C6   CN2     0.46  
ATOM N6   NN1    -0.77  
ATOM H61  HN1     0.38  
ATOM H62  HN1     0.38  
GROUP
ATOM C2'  CN7B    0.14
ATOM H2'' HN7     0.09
ATOM O2'  ON5    -0.66 
ATOM H2'  HN5     0.43 
GROUP
ATOM C3'  CN7     0.01
ATOM H3'  HN7     0.09
ATOM O3'  ON2    -0.57 
BOND P    O1P       P    O2P       P     O5'
BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
BOND C1'  N9        C1'  C2'       N9   C4        N9   C8        C4   N3
BOND C2   N1        C6   N6
BOND N6   H61       N6   H62       C6   C5        C5   N7
BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'       O3'  +P
BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
BOND C5'  H5''      C8   H8        C2   H2
DOUBLE  N1  C6      C2   N3        C4   C5        N7   C8
IMPR N6   C6   H61  H62        C6   N1   C5   N6        
DONO H61  N6   
DONO H62  N6   
DONO H2'  O2'
ACCE N3
ACCE N7
ACCE N1            
ACCE O1P  P
ACCE O2P  P
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
BILD -O3' P    O5'  C5'    1.6001  101.45  -46.90  119.00   1.4401 !alpha
BILD -O3' O5'  *P   O1P    1.6001  101.45 -115.82  109.74   1.4802
BILD -O3' O5'  *P   O2P    1.6001  101.45  115.90  109.80   1.4801
BILD  P   O5'  C5'  C4'    1.5996  119.00 -146.00  110.04   1.5160 !beta
BILD O5'  C5'  C4'  C3'    1.4401  108.83   60.00  116.10   1.5284 !gamma
BILD C5'  C4'  C3'  O3'    1.5160  116.10  140.00  115.12   1.4212 !delta
BILD C4'  C3'  O3'  +P     1.5284  111.92  155.00  119.05   1.6001 !epsilon
BILD C3'  O3'  +P   +O5'   1.4212  119.05  -95.20  101.45   1.5996 !zeta
BILD O4'  C3'  *C4' C5'    1.4572  104.06 -120.04  116.10   1.5160
BILD C2'  C4'  *C3' O3'    1.5284  100.16 -124.08  115.12   1.4212
BILD C4'  C3'  C2'  C1'    1.5284  100.16  -30.00  102.04   1.5251 !puck
BILD C3'  C2'  C1'  N9     1.5284  101.97  147.80  113.71   1.4896
BILD O4'  C1'  N9   C4     1.5251  113.71  -97.2   125.59   1.3783 !chi
BILD C1'  C4   *N9  C8     1.4896  125.97 -179.94  106.0    1.367  
BILD C4   N9   C8   N7     1.376   106.0     0.0   113.6    1.312  
BILD C8   N9   C4   C5     1.367   106.0     0.0   105.6    1.382  
BILD C8   N7   C5   C6     0.0       0.0   180.0     0.0    0.0
BILD N7   C5   C6   N1     0.0       0.0   180.0     0.0    0.0
BILD C5   C6   N1   C2     0.0       0.0     0.0     0.0    0.0
BILD N9   C5   *C4  N3     1.376   105.6  -180.0   126.9    1.342  
BILD C5   N1   *C6  N6     1.409   117.6  -180.0   121.2    1.337  
BILD N1   C6   N6   H61    1.337   121.2     0.0   119.0    1.01   
BILD H61  C6   *N6  H62    1.01    119.0   180.0   119.00   1.01   
BILD C5   N1   *C6  N6     1.409   117.6  -180.0   119.0    1.337  
BILD N1   C6   N6   H61    1.337   119.0     0.0   119.0    1.01   
BILD H61  C6   *N6  H62    1.01    119.0   180.0   121.00   1.01   
BILD N9   N7   *C8   H8    0.0       0.0   180.0     0.0    0.0
BILD N1   N3   *C2   H2    0.0       0.0   180.0     0.0    0.0
BILD C1'  C3'  *C2' O2'    1.5284  102.04 -114.67  110.81   1.4212 
BILD H2'  O2'  C2'  C3'    0.9600  114.97  148.63  111.92   1.5284 
BILD O4'  C2'  *C1' H1'    0.0       0.0  -115.0     0.0    0.0
BILD C1'  C3'  *C2' H2''   0.0       0.0   115.0     0.0    0.0
BILD C2'  C4'  *C3' H3'    0.0       0.0   115.0     0.0    0.0
BILD C3'  O4'  *C4' H4'    0.0       0.0  -115.0     0.0    0.0
BILD C4'  O5'  *C5' H5'    0.0       0.0  -115.0     0.0    0.0
BILD C4'  O5'  *C5' H5''   0.0       0.0   115.0     0.0    0.0
 
RESI CYT         -1.00
ATOM P    P       1.50  !
ATOM O1P  ON3    -0.78  !                      H42  H41
ATOM O2P  ON3    -0.78  !                        \  /    
ATOM O5'  ON2    -0.57  !                         N4
ATOM C5'  CN8B   -0.08  !                         |
ATOM H5'  HN8     0.09  !                         C4
ATOM H5'' HN8     0.09  !                        /  \\
GROUP                   !                    H5-C5   N3
ATOM C4'  CN7     0.16  !                       ||   |
ATOM H4'  HN7     0.09  !                    H6-C6   C2
ATOM O4'  ON6B   -0.50  !                        \  / \\
ATOM C1'  CN7B    0.16  !                         N1   O2
ATOM H1'  HN7     0.09  !                          \
GROUP                   !                           \
ATOM N1   NN2    -0.13  !                            \ 
ATOM C6   CN3     0.05  !        O1P    H5' H4'  O4'  \
ATOM H6   HN3     0.17  !         |      |    \ /   \  \
ATOM C5   CN3    -0.13  !        -P-O5'-C5'---C4'    C1'
ATOM H5   HN3     0.07  !         |      |     \     / \
ATOM C2   CN1     0.52  !        O2P    H5''   C3'--C2' H1'
ATOM O2   ON1C   -0.49  !                     / \   / \ 
ATOM N3   NN3    -0.66  !                  O3' H3' O2' H2'' 
ATOM C4   CN2     0.65  !                   |       |
ATOM N4   NN1    -0.75  !                          H2'
ATOM H41  HN1     0.37  
ATOM H42  HN1     0.33  
GROUP
ATOM C2'  CN7B    0.14
ATOM H2'' HN7     0.09
ATOM O2'  ON5    -0.66
ATOM H2'  HN5     0.43 
GROUP
ATOM C3'  CN7     0.01
ATOM H3'  HN7     0.09
ATOM O3'  ON2    -0.57 
BOND P    O1P       P    O2P       P     O5'
BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
BOND C1'  N1        C1'  C2'       N1   C2        N1   C6
BOND C2   N3        C4   N4        N4   H41       N4   H42
BOND C4   C5        C2'  C3'       C3'  O3'       O3'  +P
BOND C2'  O2'       O2'  H2'
BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
BOND C5'  H5''      C5   H5        C6   H6
DOUBLE   C2   O2    C5   C6        N3   C4
IMPR C2   N1   N3   O2        C4   N3   C5   N4
IMPR N4   C4   H41  H42      
DONO H42  N4   
DONO H2'  O2'
DONO H41  N4   
ACCE O2   C2
ACCE N3     
ACCE O1P  P
ACCE O2P  P       
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'

BILD -O3' P    O5'  C5'    1.6001  101.45  -46.90  119.00   1.4401 !alpha
BILD -O3' O5'  *P   O1P    1.6001  101.45 -115.82  109.74   1.4802
BILD -O3' O5'  *P   O2P    1.6001  101.45  115.90  109.80   1.4801
BILD  P   O5'  C5'  C4'    1.5996  119.00 -146.00  110.04   1.5160 !beta
BILD O5'  C5'  C4'  C3'    1.4401  108.83   60.00  116.10   1.5284 !gamma
BILD C5'  C4'  C3'  O3'    1.5160  116.10  140.00  115.12   1.4212 !delta
BILD C4'  C3'  O3'  +P     1.5284  111.92  155.00  119.05   1.6001 !epsilon
BILD C3'  O3'  +P   +O5'   1.4212  119.05  -95.20  101.45   1.5996 !zeta
BILD O4'  C3'  *C4' C5'    1.4572  104.06 -120.04  116.10   1.5160

BILD C2'  C4'  *C3' O3'    1.5284  100.16 -124.08  115.12   1.4212
BILD C4'  C3'  C2'  C1'    1.5284  100.16  -30.00  102.04   1.5251
BILD C3'  C2'  C1'  N1     1.5284  101.97  147.89  113.71   1.4896
BILD O4'  C1'  N1   C2     1.5251  113.71  -97.2   125.59   1.3783 !chi
BILD C1'  C2   *N1  C6     1.4896  117.79 -180.00  120.6    1.364   
BILD C2   N1   C6   C5     1.399   120.6     0.0   121.0    1.337   
BILD C6   N1   C2   N3     1.364   120.6     0.0   118.9    1.356   
BILD N1   N3   *C2  O2     1.399   118.9   180.0   121.9    1.237   
BILD N1   C2   N3   C4     1.399   118.9     0.0   120.0    1.334   
BILD C5   N3   *C4  N4     1.426   121.8   180.00  118.9    1.337   
BILD N3   C4   N4   H41    1.337   117.9     0.00  118.9    1.01    
BILD H41  C4   *N4  H42    1.01    118.9   180.00  120.7    1.01    
BILD C6   C4   *C5  H5     0.0       0.0   180.0     0.0    0.0
BILD N1   C5   *C6  H6     0.0       0.0   180.0     0.0    0.0
BILD C1'  C3'  *C2' O2'    1.5284  102.04 -114.67  110.81   1.4212 
BILD H2'  O2'  C2'  C3'    0.9600  114.97  148.63  111.92   1.5284 
BILD O4'  C2'  *C1' H1'    0.0       0.0  -115.0     0.0    0.0
BILD C1'  C3'  *C2' H2''   0.0       0.0   115.0     0.0    0.0
BILD C2'  C4'  *C3' H3'    0.0       0.0   115.0     0.0    0.0
BILD C3'  O4'  *C4' H4'    0.0       0.0  -115.0     0.0    0.0
BILD C4'  O5'  *C5' H5'    0.0       0.0  -115.0     0.0    0.0
BILD C4'  O5'  *C5' H5''   0.0       0.0   115.0     0.0    0.0
 
RESI THY         -1.00  !                  H51    O4
ATOM P    P       1.50  !                   |     ||
ATOM O1P  ON3    -0.78  !               H52-C5M   C4    H3
ATOM O2P  ON3    -0.78  !                   |  \ /  \  /
ATOM O5'  ON2    -0.57  !                  H53  C5   N3
ATOM C5'  CN8B   -0.08  !                       ||   |
ATOM H5'  HN8     0.09  !                    H6-C6   C2
ATOM H5'' HN8     0.09  !                        \  / \\  
GROUP                   !                         N1   O2
ATOM C4'  CN7     0.16  !                          \
ATOM H4'  HN7     0.09  !                           \
ATOM O4'  ON6B   -0.50  !                            \ 
ATOM C1'  CN7B    0.16  !        O1P    H5' H4'  O4'  \
ATOM H1'  HN7     0.09  !         |      |    \ /   \  \
GROUP                   !        -P-O5'-C5'---C4'    C1'
ATOM N1   NN2B   -0.34  !         |      |     \     / \
ATOM C6   CN3     0.17  !        O2P    H5''   C3'--C2' H1'
ATOM H6   HN3     0.17  !                     / \   / \
ATOM C2   CN1T    0.51  !                   O3' H3' O2' H2''
ATOM O2   ON1    -0.41  !                    |       | 
ATOM N3   NN2U   -0.46  !                           H2'
ATOM H3   HN2     0.36  !
ATOM C4   CN1     0.50  !
ATOM O4   ON1    -0.45  !
ATOM C5   CN3T   -0.15
ATOM C5M  CN9    -0.11
ATOM H51  HN9     0.07
ATOM H52  HN9     0.07
ATOM H53  HN9     0.07
GROUP
ATOM C2'  CN7B    0.14
ATOM H2'' HN7     0.09
ATOM O2'  ON5    -0.66 
ATOM H2'  HN5     0.43 
GROUP
ATOM C3'  CN7     0.01
ATOM H3'  HN7     0.09
ATOM O3'  ON2    -0.57 
BOND P    O1P       P    O2P       P     O5'
BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
BOND C1'  N1        C1'  C2'       N1   C2        N1   C6
BOND C2   N3        N3   H3        N3   C4       C4   C5
BOND C5   C5M       C2'  C3'       C3'  O3'       O3'  +P
BOND C2'  O2'       O2'  H2'
BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
BOND C5'  H5''      C6   H6        C5M  H51       C5M  H52       C5M  H53
DOUBLE  C2   O2     C4   O4        C5   C6
IMPR C2   N1   N3   O2        C4   N3   C5   O4        C5   C4   C6   C5M
DONO H3   N3   
DONO H2'  O2'
ACCE O2   C2
ACCE O4   C4
ACCE O1P  P
ACCE O2P  P       
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'

BILD -O3' P    O5'  C5'    1.6001  101.45  -46.90  119.00   1.4401 !alpha
BILD -O3' O5'  *P   O1P    1.6001  101.45 -115.82  109.74   1.4802
BILD -O3' O5'  *P   O2P    1.6001  101.45  115.90  109.80   1.4801
BILD  P   O5'  C5'  C4'    1.5996  119.00 -146.00  110.04   1.5160 !beta
BILD O5'  C5'  C4'  C3'    1.4401  108.83   60.00  116.10   1.5284
BILD C5'  C4'  C3'  O3'    1.5160  116.10  140.00  115.12   1.4212
BILD C4'  C3'  O3'  +P     1.5284  111.92  155.00  119.05   1.6001
BILD C3'  O3'  +P   +O5'   1.4212  119.05  -95.20  101.45   1.5996
BILD O4'  C3'  *C4' C5'    1.4572  104.06 -120.04  116.10   1.5160
BILD C2'  C4'  *C3' O3'    1.5284  100.16 -124.08  115.12   1.4212
BILD C4'  C3'  C2'  C1'    1.5284  100.16  -30.00  102.04   1.5251
BILD C3'  C2'  C1'  N1     1.5284  101.97  147.89  113.71   1.4896
BILD O4'  C1'  N1   C2     1.5251  113.71  -97.2   125.59   1.3783 !chi
BILD C1'  C2   *N1  C6     1.4896  117.06 -179.96  122.08   1.3704
BILD C2   N1   C6   C5     1.3746  122.08   -0.02  121.23   1.3432
BILD C6   N1   C2   N3     1.3704  122.08    0.06  115.38   1.3813
BILD N1   N3   *C2  O2     1.3746  115.38 -179.95  121.70   1.2191
BILD N1   C2   N3   C4     1.3746  115.38   -0.07  126.46   1.3795
BILD C5   N3   *C4  O4     1.4439  114.07  179.98  120.59   1.2327
BILD C2   C4   *N3  H3     1.3813  126.46  180.00  116.77   1.0900
BILD C4   C6   *C5  C5M    1.4439  120.78 -179.94  121.63   1.5000
BILD N1   C5   *C6  H6     0.0       0.0   180.0     0.0    0.0
BILD C6   C5   C5M  H51    0.0       0.0     0.0     0.0    0.0
BILD C5   H51  *C5M H52    0.0       0.0   115.0     0.0    0.0
BILD H51  H52  *C5M H53    0.0       0.0  -115.0     0.0    0.0
BILD C1'  C3'  *C2' O2'    1.5284  102.04 -114.67  110.81   1.4212
BILD H2'  O2'  C2'  C3'    0.9600  114.97  148.63  111.92   1.5284
BILD O4'  C2'  *C1' H1'    0.0       0.0  -115.0     0.0    0.0
BILD C1'  C3'  *C2' H2''   0.0       0.0   115.0     0.0    0.0
BILD C2'  C4'  *C3' H3'    0.0       0.0   115.0     0.0    0.0
BILD C3'  O4'  *C4' H4'    0.0       0.0  -115.0     0.0    0.0
BILD C4'  O5'  *C5' H5'    0.0       0.0  -115.0     0.0    0.0
BILD C4'  O5'  *C5' H5''   0.0       0.    115.0     0.0    0.0
 
RESI URA         -1.00  !                         O4                               
ATOM P    P       1.50  !                         ||
ATOM O1P  ON3    -0.78  !                         C4    H3
ATOM O2P  ON3    -0.78  !                        /  \  /
ATOM O5'  ON2    -0.57  !                    H5-C5   N3
ATOM C5'  CN8B   -0.08  !                       ||   |
ATOM H5'  HN8     0.09  !                    H6-C6   C2
ATOM H5'' HN8     0.09  !                        \  / \\    
GROUP                   !                         N1   O2
ATOM C4'  CN7     0.16  !                          \
ATOM H4'  HN7     0.09  !                           \
ATOM O4'  ON6B   -0.50  !                            \ 
ATOM C1'  CN7B    0.16  !        O1P    H5' H4'  O4'  \
ATOM H1'  HN7     0.09  !         |      |    \ /   \  \
GROUP                   !        -P-O5'-C5'---C4'    C1'
ATOM N1   NN2B   -0.34  !         |      |     \     / \
ATOM C6   CN3     0.20  !        O2P    H5''   C3'--C2' H1'
ATOM H6   HN3     0.14  !                     / \   / \
ATOM C2   CN1T    0.55  !                   O3' H3' O2' H2''
ATOM O2   ON1    -0.45  !                    |       | 
ATOM N3   NN2U   -0.46  !                           H2' 
ATOM H3   HN2     0.36  !
ATOM C4   CN1     0.53  !
ATOM O4   ON1    -0.48  !
ATOM C5   CN3    -0.15  !
ATOM H5   HN3     0.10  !
GROUP
ATOM C2'  CN7B    0.14
ATOM H2'' HN7     0.09
ATOM O2'  ON5    -0.66 
ATOM H2'  HN5     0.43 
GROUP
ATOM C3'  CN7     0.01
ATOM H3'  HN7     0.09
ATOM O3'  ON2    -0.57 
BOND P    O1P       P    O2P       P     O5'
BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
BOND C1'  N1        C1'  C2'       N1   C2        N1   C6
BOND C2   N3        N3   H3        N3   C4        C4   C5
BOND C2'  C3'       C3'  O3'       O3'  +P
BOND C2'  O2'       O2'  H2'
BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
BOND C5'  H5''      C5   H5        C6   H6
DOUBLE  C2   O2     C4   O4        C5   C6
IMPR C2   N1   N3   O2        C4   N3   C5   O4
DONO H3   N3   
DONO H2'  O2'
ACCE O2   C2
ACCE O4   C4
ACCE O1P  P
ACCE O2P  P
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
BILD -O3' P    O5'  C5'    1.6001  101.45  -39.25  119.00   1.4401
BILD -O3' O5'  *P   O1P    1.6001  101.45 -115.82  109.74   1.4802
BILD -O3' O5'  *P   O2P    1.6001  101.45  115.90  109.80   1.4801
BILD  P   O5'  C5'  C4'    1.5996  119.00 -151.39  110.04   1.5160
BILD O5'  C5'  C4'  C3'    1.4401  108.83 -179.85  116.10   1.5284
BILD C5'  C4'  C3'  O3'    1.5160  116.10   76.70  115.12   1.4212
BILD C4'  C3'  O3'  +P     1.5284  111.92  159.13  119.05   1.6001
BILD C3'  O3'  +P   +O5'   1.4212  119.05  -98.86  101.45   1.5996
BILD O4'  C3'  *C4' C5'    1.4572  104.06 -120.04  116.10   1.5160
BILD C2'  C4'  *C3' O3'    1.5284  100.16 -124.08  115.12   1.4212
BILD C4'  C3'  C2'  C1'    1.5284  100.16   39.58  102.04   1.5251
BILD C3'  C2'  C1'  N1     1.5284  101.97  144.39  113.71   1.4896
BILD O4'  C1'  N1   C2     1.5251  113.71  -96.0   117.06   1.3746
BILD C1'  C2   *N1  C6     1.4896  117.06 -180.0   121.3    1.379    
BILD C2   N1   C6   C5     1.379   121.3     0.0   122.8    1.338    
BILD C6   N1   C2   N3     1.380   121.3     0.0   114.8    1.373    
BILD N1   N3   *C2  O2     1.379   114.8  -180.0   122.0    1.218    
BILD N1   C2   N3   C4     1.379   114.8     0.0   127.0    1.383    
BILD C5   N3   *C4  O4     1.440   114.7   180.0   119.8    1.227    
BILD C2   C4   *N3  H3     1.373   127.0   180.0   116.5    1.03      
BILD C6   C4   *C5  H5     0.0       0.0   180.0     0.0    0.0
BILD N1   C5   *C6  H6     0.0       0.0   180.0     0.0    0.0
BILD C1'  C3'  *C2' O2'    1.5284  102.04 -114.67  110.81   1.4212   
BILD H2'  O2'  C2'  C3'    0.9600  114.97  148.63  111.92   1.5284   
BILD O4'  C2'  *C1' H1'    0.0       0.0  -115.0     0.0    0.0
BILD C1'  C3'  *C2' H2''   0.0       0.0   115.0     0.0    0.0
BILD C2'  C4'  *C3' H3'    0.0       0.0   115.0     0.0    0.0
BILD C3'  O4'  *C4' H4'    0.0       0.0  -115.0     0.0    0.0
BILD C4'  O5'  *C5' H5'    0.0       0.0  -115.0     0.0    0.0
BILD C4'  O5'  *C5' H5''   0.0       0.0   115.0     0.0    0.0
 
RESI MP_0         0.00   ! Methylphosphate, neutral
GROUP                    !
! atom order for molvib
ATOM C1   CN9    -0.17   !
ATOM O1   ON2    -0.56   !                 H11
ATOM P1   P       1.50   !                  |
ATOM O2   ON4    -0.63   !            H13--C1--H12
ATOM O3   ON4    -0.63   !                  |
ATOM O4   ON3    -0.64   !                 O1
ATOM H11  HN9     0.09   !                  |
ATOM H12  HN9     0.09   !             O4==P1--O3
ATOM H13  HN9     0.09   !                  |    \
ATOM H2   HN4     0.43   !                 O2     H3
ATOM H3   HN4     0.43   !                   \
                         !                    H2
                         !
BOND P1   O1     P1   O2    P1   O3    P1   O4    O1   C1
BOND C1   H11    C1   H12   C1   H13   O2   H2    O3   H3
IC O3   P1   O1   C1   0.0000    000.00    000.0     000.00    0.0000
IC O4   P1   O1   C1   0.0000    000.00    000.0     000.00    0.0000
IC O2   P1   O1   C1   0.0000    000.00    000.0     000.00    0.0000
IC H11  C1   O1   P1   0.0000    000.00    000.0     000.00    0.0000
IC H12  C1   O1   P1   0.0000    000.00    000.0     000.00    0.0000
IC H13  C1   O1   P1   0.0000    000.00    000.0     000.00    0.0000
IC H2   O2   P1   O1   0.0000    000.00    180.0     000.00    0.0000
IC H3   O3   P1   O1   0.0000    000.00    180.0     000.00    0.0000
! dummies to analyze cetain angles
IC O3   P1   O4   O1   0.0         0.0       0.0       0.0     0.0


! Ion parameters from Benoit Roux and Coworkers
! As of 8/98 no NBFIX terms required
! 
RESI SOD       1.00 ! Sodium Ion
GROUP   
ATOM SOD  SOD  1.00
PATCHING FIRST NONE LAST NONE   

RESI MG        2.00 ! Magnesium Ion
GROUP   
ATOM MG   MG   2.00
PATCHING FIRST NONE LAST NONE   

RESI POT       1.00 ! Potassium Ion
GROUP
ATOM POT   POT 1.00
PATCHING FIRST NONE LAST NONE

RESI CES       1.00 ! Cesium Ion
GROUP
ATOM CES  CES  1.00
PATCHING FIRST NONE LAST NONE

RESI CAL       2.00 ! Calcium Ion
GROUP
ATOM CAL  CAL  2.00
PATCHING FIRST NONE LAST NONE

RESI CLA      -1.00 ! Chloride Ion
GROUP
ATOM CLA  CLA -1.00
PATCHING FIRST NONE LAST NONE

! NOTE the option to regenerate all angles and dihedrals allows
! the explicit inclusion of the THET and DIHE terms to be omitted
! even if the PRES is used in a PATCH statement.  It is important to
! inspect the patches prior to use to determine if they should be used
! in a GENErate or PATCh statement and/or if the AUTOgeneration of 
! angles and dihedrals is required.
! see AUTOgen ANGLes DIHEdrals in STRUCTURE section of the
! documentation

RESI NIC         1.00  ! oxidized nicotinamide, jjp1/adm jr.
                       ! checked for consistency with new NA params, adm jr., 9/98
                       ! note that differences with respect to published results exist
                       ! due to new NA params
                       !
                       !       H15
GROUP                  !         \
ATOM H1   HN2     0.45 !     H16-N14     H8
ATOM N2   NN2    -0.52 !           \     |
ATOM C3   CN3B    0.16 !            C12  C7
ATOM H4   HN3B    0.19 !           // \ /  \\
ATOM C5   CN3    -0.10 !         O13   C9   C5-H6
ATOM H6   HN3B    0.16 !               ||   |
ATOM C7   CN3A   -0.05 !           H11-C10  C3-H4
ATOM H8   HN3B    0.16 !                \+ //
ATOM C9   CN3     0.05 !                 N2
ATOM C10  CN3B    0.18 !                 |
ATOM H11  HN3B    0.16 !                 H1
ATOM C12  CN1A    0.68 !
ATOM O13  ON1    -0.40 !
ATOM N14  NN1    -0.82 !
ATOM H15  HN1     0.34 ! trans to O13
ATOM H16  HN1     0.36 ! cis to O13
BOND N2  H1   C3  H4   C3  C5   C5  H6
BOND C7 H8   C7  C9   N2  C10
BOND C10 H11  C9 C12  C12 N14  N14 H15  N14 H16
DOUBLE C12 O13  C9 C10  C5 C7  N2 C3
! amide impropers
IMPR C12 N14 C9 O13   C12 C9  N14 O13
IMPR N14 C12 H16 H15  N14 C12 H15 H16
! ring hydrogen impropers
IMPR N2   C10  C3   H1    C3   N2   C5   H4    C5   C3   C7   H6
IMPR C7   C5   C9   H8    C10  C9   N2   H11
! ic table for analysis
IC N2   C3   C5   C7    0.0000  000.00  000.00  000.00  0.000
IC C3   C5   C7   C9    0.0000  000.00  000.00  000.00  0.000
IC C5   C7   C9   C10   0.0000  000.00  000.00  000.00  0.000
IC C7   C9   C10  N2    0.0000  000.00  000.00  000.00  0.000
IC C9   C10  N2   C3    0.0000  000.00  000.00  000.00  0.000
IC C10  N2   C3   C5    0.0000  000.00  000.00  000.00  0.000
IC C9   C10  N2   H1    0.0000  000.00  000.00  000.00  0.000
IC C10  N2   C3   H4    0.0000  000.00  000.00  000.00  0.000
IC N2   C3   C5   H6    0.0000  000.00  000.00  000.00  0.000
IC C3   C5   C7   H8    0.0000  000.00  000.00  000.00  0.000
IC C5   C7   C9   C12   0.0000  000.00  000.00  000.00  0.000
IC N2   C10  C9   C12   0.0000  000.00  000.00  000.00  0.000
IC C7   C9   C12  O13   0.0000  000.00  000.00  000.00  0.000
IC C7   C9   C12  N14   0.0000  000.00  000.00  000.00  0.000
IC O13  C12  N14  H15   0.0000  000.00  000.00  000.00  0.000
IC O13  C12  N14  H16   0.0000  000.00  000.00  000.00  0.000
patch first none last none

RESI NICH         0.00 ! reduced nicotinamide, jjp1/adm jr.
                       ! checked for consistency with new NA params, adm jr., 9/98
                       ! note that differences with respect to published results exist
                       ! due to new NA params
                       ! HN3 to HN6 atom type switch to maintain proper vdw params, 9/98
                       !
                       !       H15
GROUP                  !         \
ATOM H1   HN2     0.42 !     H16-N14   H8  H17
ATOM N2   NN2    -0.69 !           \    \  /
ATOM C3   CN3C   -0.06 !            C12  C7
ATOM H4   HN6     0.17 !           /  \ /  \
ATOM C5   CN3    -0.18 !         O13   C9   C5-H6
ATOM H6   HN6     0.14 !               ||   ||
ATOM C7   CN8    -0.28 !           H11-C10  C3-H4
ATOM H8   HN8     0.09 !                \  /
ATOM H17  HN8     0.09 !                 N2
ATOM C10  CN3C   -0.10 !                 |
ATOM H11  HN6     0.14 !                 H1
ATOM C9   CN3     0.36 !
ATOM C12  CN1A    0.55 !
ATOM O13  ON1    -0.51 !
ATOM N14  NN1    -0.72 !
ATOM H15  HN1     0.26 ! trans to O13
ATOM H16  HN1     0.32 ! cis to O13

BOND N2  H1   N2 C3   C3  H4   C5  H6
BOND C5  C7   C7 H8   C7  H17  C7  C9   N2  C10
BOND C10 H11  C9 C12  C12 N14  N14 H15  N14 H16
DOUBLE C12 O13   C9 C10   C3  C5
! amide impropers
IMPR C12 N14 C9 O13   C12 C9  N14 O13
IMPR N14 C12 H16 H15  N14 C12 H15 H16
! ring hydrogen impropers
IMPR N2   C10  C3   H1    C3   N2   C5   H4    C5   C3   C7   H6
IMPR C10  C9   N2   H11
! ic table for analysis
IC N2   C3   C5   C7    0.0000  000.00  000.00  000.00  0.000
IC C3   C5   C7   C9    0.0000  000.00  000.00  000.00  0.000
IC C5   C7   C9   C10   0.0000  000.00  000.00  000.00  0.000
IC C7   C9   C10  N2    0.0000  000.00  000.00  000.00  0.000
IC C9   C10  N2   C3    0.0000  000.00  000.00  000.00  0.000
IC C10  N2   C3   C5    0.0000  000.00  000.00  000.00  0.000
IC C9   C10  N2   H1    0.0000  000.00  000.00  000.00  0.000
IC C10  N2   C3   H4    0.0000  000.00  000.00  000.00  0.000
IC N2   C3   C5   H6    0.0000  000.00  000.00  000.00  0.000
IC C3   C5   C7   H8    0.0000  000.00  000.00  000.00  0.000
IC C3   C5   C7   H17   0.0000  000.00  000.00  000.00  0.000
IC C5   C7   C9   C12   0.0000  000.00  000.00  000.00  0.000
IC N2   C10  C9   C12   0.0000  000.00  000.00  000.00  0.000
IC C7   C9   C12  O13   0.0000  000.00  000.00  000.00  0.000
IC C7   C9   C12  N14   0.0000  000.00  000.00  000.00  0.000
IC O13  C12  N14  H15   0.0000  000.00  000.00  000.00  0.000
IC O13  C12  N14  H16   0.0000  000.00  000.00  000.00  0.000
patch first none last none

RESI PPI1        -3.00   ! Inorganic phosphate, jjp1/adm jr.
GROUP                    !
ATOM C1   CN9    -0.17   !
ATOM O11  ON2    -0.62   !
ATOM P1   P       1.50   !                 H11
ATOM O12  ON2    -0.74   !                  |
ATOM O13  ON3    -0.82   !            H13--C1--H12
ATOM O14  ON3    -0.82   !                  |
                         !                 O11
ATOM P2   P2      1.10   !                  |
ATOM O22  ON3    -0.90   !            O14==P1==O13  (-)
ATOM O23  ON3    -0.90   !                 |
ATOM O24  ON3    -0.90   !                 O12
                         !                 |
ATOM H11  HN9     0.09   !        (-) O24==P2==O23  (-)
ATOM H12  HN9     0.09   !                 ||
ATOM H13  HN9     0.09   !                 O22

BOND P1  O11   P1  O12   P1  O13   P1  O14   O11  C1
BOND C1  H11   C1  H12   C1  H13
BOND O12 P2    P2  O22   P2  O23   P2  O24
! IC Table
IC C1   O11  P1   O12  0.0000    000.00    180.0     000.00    0.0000
IC O11  P1   O12  P2   0.0000    000.00    180.0     000.00    0.0000
IC P1   O12  P2   O22  0.0000    000.00    180.0     000.00    0.0000
IC C1   O11  P1   O13  0.0000    000.00     60.0     000.00    0.0000
IC C1   O11  P1   O14  0.0000    000.00    -60.0     000.00    0.0000
IC P1   O12  P2   O23  0.0000    000.00     60.0     000.00    0.0000
IC P1   O12  P2   O24  0.0000    000.00    -60.0     000.00    0.0000
IC P1   O11  C1   H11  0.0000    000.00    180.0     000.00    0.0000
IC P1   O11  C1   H12  0.0000    000.00     60.0     000.00    0.0000
IC P1   O11  C1   H13  0.0000    000.00    -60.0     000.00    0.0000
PATC  FIRS NONE LAST NONE

RESI ADP         -3.00  ! adenosine diphosphate, jjp1/adm jr.
                        ! atom names correspond to pdb nomenclature
GROUP
ATOM C4'  CN7     0.16  !                       H61  H62
ATOM H4'  HN7     0.09  !                         \  /
ATOM O4'  ON6B   -0.50  !                          N6
ATOM C1'  CN7B    0.16  !                          |
ATOM H1'  HN7     0.09  !                          C6
GROUP                   !                        //  \
ATOM C5   CN5     0.28  !                        N1   C5--N7\\
ATOM N7   NN4    -0.71  !                        |    ||     C8-H8
ATOM C8   CN4     0.34  !                        C2   C4--N9/
ATOM H8   HN3     0.12  !                       / \\ /     \
ATOM N9   NN2    -0.05  !                     H2   N3       \
                        !                                    \
ATOM N1   NN3A   -0.74  !                                     \
ATOM C2   CN4     0.50  !                                      \
ATOM H2   HN3     0.13  !           O3B    O1A    H5' H4'  O4'  \
ATOM N3   NN3A   -0.75  !           |       |      |    \ /   \  \
ATOM C4   CN5     0.43  !      O1B=PB-O3A--PA-O5'-C5'---C4'    C1'
ATOM C6   CN2     0.46  !           |       |      |     \     / \
                        !           O2B    O2A    H5''   C3'--C2' H1'
ATOM N6   NN1    -0.77  !                               / \   / \
ATOM H61  HN1     0.38  !                            O3' H3' O2' H2''
ATOM H62  HN1     0.38  !                             |       |
GROUP                   !                            H3T     H2'
ATOM C2'  CN7     0.14  !
ATOM H2'' HN7     0.09
ATOM O2'  ON5    -0.66
ATOM H2'  HN5     0.43
GROUP
ATOM C3'  CN7     0.14
ATOM H3'  HN7     0.09
ATOM O3'  ON5    -0.66
ATOM H3T  HN5     0.43
GROUP
ATOM C5'  CN8    -0.08
ATOM H5'  HN8     0.09
ATOM H5'' HN8     0.09
ATOM O5'  ON2    -0.62
ATOM PA   P       1.50
ATOM O1A  ON3    -0.82
ATOM O2A  ON3    -0.82
ATOM O3A  ON2    -0.74
ATOM PB   P2      1.10
ATOM O1B  ON3    -0.90
ATOM O2B  ON3    -0.90
ATOM O3B  ON3    -0.90

BOND PB   O3A       PB   O1B       PB    O2B      PB   O3B       O3A  PA
BOND PA   O1A       PA   O2A       PA    O5'      O3'  H3T
BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
BOND C1'  N9        C1'  C2'       N9   C4        N9   C8        C4   N3
BOND C2   N1        C6   N6
BOND N6   H61       N6   H62       C6   C5        C5   N7
BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'
BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
BOND C5'  H5''      C8   H8        C2   H2
DOUBLE N1   C6    N3   C2    C4   C5        N7   C8
IMPR N6   C6   H61  H62       C6   N1   C5   N6        
DONO H61  N6
DONO H62  N6
DONO H2'  O2'
ACCE N3
ACCE N7
ACCE N1
ACCE O1A  PA
ACCE O2A  PA
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
ACCE O3A
ACCE O3B
ACCE O2B
ACCE O1B
IC PA   O3A  PB   O1B    0.0000  000.00  180.0   000.00   0.0000
IC C5'  O5'  PA   O1A    0.0000  000.00   60.0   000.00   0.0000
IC C5'  O5'  PA   O2A    0.0000  000.00  -60.0   000.00   0.0000
IC PA   O3A  PB   O2B    0.0000  000.00   60.0   000.00   0.0000
IC PA   O3A  PB   O3B    0.0000  000.00  -60.0   000.00   0.0000
IC PA   O5'  C5'  C4'    1.5996  119.00 -151.39  110.04   1.5160
IC O5'  C5'  C4'  C3'    1.4401  108.83 -179.85  116.10   1.5284
IC C5'  C4'  C3'  O3'    1.5160  116.10   76.70  115.12   1.4212
IC H3T  O3'  C3'  C4'    0.9650  105.47   38.18  111.98   1.5386
IC O4'  C3'  *C4' C5'    1.4572  104.06 -120.04  116.10   1.5160
IC C2'  C4'  *C3' O3'    1.5284  100.16 -124.08  115.12   1.4212
IC C4'  C3'  C2'  C1'    1.5284  100.16   39.58  102.04   1.5251
IC C3'  C2'  C1'  N9     1.5284  101.97  144.39  113.71   1.4896
IC O4'  C1'  N9   C4     1.5251  113.71  -96.00  125.97   1.3703
IC C1'  C4   *N9  C8     1.4896  125.97 -179.94  106.0    1.367
IC C4   N9   C8   N7     1.376   106.0     0.0   113.6    1.312
IC C8   N9   C4   C5     1.367   106.0     0.0   105.6    1.382
IC C8   N7   C5   C6     0.0       0.0   180.0     0.0    0.0
IC N7   C5   C6   N1     0.0       0.0   180.0     0.0    0.0
IC C5   C6   N1   C2     0.0       0.0     0.0     0.0    0.0
IC N9   C5   *C4  N3     1.376   105.6  -180.0   126.9    1.342
IC C5   N1   *C6  N6     1.409   117.6  -180.0   121.2    1.337
IC N1   C6   N6   H61    1.337   121.2     0.0   119.0    1.01
IC H61  C6   *N6  H62    1.01    119.0   180.0   119.00   1.01
IC C5   N1   *C6  N6     1.409   117.6  -180.0   119.0    1.337
IC N1   C6   N6   H61    1.337   119.0     0.0   119.0    1.01
IC H61  C6   *N6  H62    1.01    119.0   180.0   121.00   1.01
IC N9   N7   *C8   H8    0.0       0.0   180.0     0.0    0.0
IC N1   N3   *C2   H2    0.0       0.0   180.0     0.0    0.0
IC C1'  C3'  *C2' O2'    1.5284  102.04 -114.67  110.81   1.4212
IC H2'  O2'  C2'  C3'    0.9600  114.97  148.63  111.92   1.5284
IC O4'  C2'  *C1' H1'    0.0       0.0  -115.0     0.0    0.0
IC C1'  C3'  *C2' H2''   0.0       0.0   115.0     0.0    0.0
IC C2'  C4'  *C3' H3'    0.0       0.0   115.0     0.0    0.0
IC C3'  O4'  *C4' H4'    0.0       0.0  -115.0     0.0    0.0
IC C4'  O5'  *C5' H5'    0.0       0.0  -115.0     0.0    0.0
IC C4'  O5'  *C5' H5''   0.0       0.0   115.0     0.0    0.0
PATC  FIRS NONE LAST NONE

RESI ATP         -4.00  !adenosine triphosphate , jjp1/adm jr.
                        !atom names correspond to pdb nomenclature
                        !
GROUP
ATOM C4'  CN7     0.16  !                       H61  H62
ATOM H4'  HN7     0.09  !                         \  /
ATOM O4'  ON6B   -0.50  !                          N6
ATOM C1'  CN7B    0.16  !                          |
ATOM H1'  HN7     0.09  !                          C6
GROUP                   !                        //  \
ATOM C5   CN5     0.28  !                        N1   C5--N7\\
ATOM N7   NN4    -0.71  !                        |    ||     C8-H8
ATOM C8   CN4     0.34  !                        C2   C4--N9/
ATOM H8   HN3     0.12  !                       / \\ /     \
ATOM N9   NN2    -0.05  !                     H2   N3       \
                        !                                    \
ATOM N1   NN3A   -0.74  !                                     \
ATOM C2   CN4     0.50  !                                      \
ATOM H2   HN3     0.13  ! (-)O3G   O2B     O1A    H5' H4'  O4'  \
ATOM N3   NN3A   -0.75  !    |      |       |      |    \ /   \  \
ATOM C4   CN5     0.43  !O1G=PG-O3B-PB-O3A-PA-O5'-C5'---C4'    C1'
ATOM C6   CN2     0.46  !    |      |       |      |     \     / \
                        ! (-)O2G (-)O1B (-)O2A    H5''   C3'--C2' H1'
ATOM N6   NN1    -0.77  !                               / \   / \
ATOM H61  HN1     0.38  !                            O3' H3' O2' H2''
ATOM H62  HN1     0.38  !                             |       |
GROUP                   !                            H3T     H2'
ATOM C2'  CN7     0.14  !
ATOM H2'' HN7     0.09
ATOM O2'  ON5    -0.66
ATOM H2'  HN5     0.43
GROUP
ATOM C3'  CN7     0.14
ATOM H3'  HN7     0.09
ATOM O3'  ON5    -0.66
ATOM H3T  HN5     0.43
GROUP
ATOM C5'  CN8    -0.08
ATOM H5'  HN8     0.09
ATOM H5'' HN8     0.09
ATOM O5'  ON2    -0.62
ATOM PA   P       1.50
ATOM O1A  ON3    -0.82
ATOM O2A  ON3    -0.82
ATOM O3A  ON2    -0.74
ATOM PB   P2      1.50
ATOM O1B  ON3    -0.82
ATOM O2B  ON3    -0.82
ATOM O3B  ON2    -0.86 ! charge adjusted to yield total triP of -4.0
ATOM PG   P2      1.10
ATOM O1G  ON3    -0.90
ATOM O2G  ON3    -0.90
ATOM O3G  ON3    -0.90

BOND O5'  C5'       O5'  PA        PA   O1A       PA   O2A       PA   O3A
BOND O3A  PB        PB   O1B       PB   O2B       PB   O3B       O3B  PG
BOND PG   O1G       PG   O2G       PG   O3G
BOND C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
BOND C1'  N9        C1'  C2'       N9   C4        N9   C8        C4   N3
BOND C2   N1        C6   N6
BOND N6   H61       N6   H62       C6   C5        C5   N7
BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'       O3'  H3T
BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
BOND C5'  H5''      C8   H8        C2   H2
DOUBLE N1   C6    N3   C2    C4   C5        N7   C8
IMPR N6   C6   H61  H62       C6   N1   C5   N6       
DONO H61  N6
DONO H62  N6
DONO H2'  O2'
ACCE N3
ACCE N7
ACCE N1
ACCE O1A  PA
ACCE O2A  PA
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
ACCE O3A
ACCE O2B
ACCE O1B
ACCE O3B
ACCE O3G
ACCE O2G
ACCE O2G
IC PA   O3A  PB   O3B    0.0000  000.00  180.0   000.00   0.0000
IC O3A  PB   O3B  PG     0.0000  000.00  180.0   000.00   0.0000
IC PB   O3B  PG   O1G    0.0000  000.00  180.0   000.00   0.0000
IC C5'  O5'  PA   O1A    0.0000  000.00   60.0   000.00   0.0000
IC C5'  O5'  PA   O2A    0.0000  000.00  -60.0   000.00   0.0000
IC PA   O3A  PB   O1B    0.0000  000.00   60.0   000.00   0.0000
IC PA   O3A  PB   O2B    0.0000  000.00  -60.0   000.00   0.0000
IC PB   O3B  PG   O2G    0.0000  000.00   60.0   000.00   0.0000
IC PB   O3B  PG   O3G    0.0000  000.00  -60.0   000.00   0.0000
IC PA   O5'  C5'  C4'    1.5996  119.00 -151.39  110.04   1.5160
IC O5'  C5'  C4'  C3'    1.4401  108.83 -179.85  116.10   1.5284
IC C5'  C4'  C3'  O3'    1.5160  116.10   76.70  115.12   1.4212
IC H3T  O3'  C3'  C4'    0.9650  105.47   38.18  111.98   1.5386
IC O4'  C3'  *C4' C5'    1.4572  104.06 -120.04  116.10   1.5160
IC C2'  C4'  *C3' O3'    1.5284  100.16 -124.08  115.12   1.4212
IC C4'  C3'  C2'  C1'    1.5284  100.16   39.58  102.04   1.5251
IC C3'  C2'  C1'  N9     1.5284  101.97  144.39  113.71   1.4896
IC O4'  C1'  N9   C4     1.5251  113.71  -96.00  125.97   1.3703
IC C1'  C4   *N9  C8     1.4896  125.97 -179.94  106.0    1.367
IC C4   N9   C8   N7     1.376   106.0     0.0   113.6    1.312
IC C8   N9   C4   C5     1.367   106.0     0.0   105.6    1.382
IC C8   N7   C5   C6     0.0       0.0   180.0     0.0    0.0
IC N7   C5   C6   N1     0.0       0.0   180.0     0.0    0.0
IC C5   C6   N1   C2     0.0       0.0     0.0     0.0    0.0
IC N9   C5   *C4  N3     1.376   105.6  -180.0   126.9    1.342
IC C5   N1   *C6  N6     1.409   117.6  -180.0   121.2    1.337
IC N1   C6   N6   H61    1.337   121.2     0.0   119.0    1.01
IC H61  C6   *N6  H62    1.01    119.0   180.0   119.00   1.01
IC C5   N1   *C6  N6     1.409   117.6  -180.0   119.0    1.337
IC N1   C6   N6   H61    1.337   119.0     0.0   119.0    1.01
IC H61  C6   *N6  H62    1.01    119.0   180.0   121.00   1.01
IC N9   N7   *C8   H8    0.0       0.0   180.0     0.0    0.0
IC N1   N3   *C2   H2    0.0       0.0   180.0     0.0    0.0
IC C1'  C3'  *C2' O2'    1.5284  102.04 -114.67  110.81   1.4212
IC H2'  O2'  C2'  C3'    0.9600  114.97  148.63  111.92   1.5284
IC O4'  C2'  *C1' H1'    0.0       0.0  -115.0     0.0    0.0
IC C1'  C3'  *C2' H2''   0.0       0.0   115.0     0.0    0.0
IC C2'  C4'  *C3' H3'    0.0       0.0   115.0     0.0    0.0
IC C3'  O4'  *C4' H4'    0.0       0.0  -115.0     0.0    0.0
IC C4'  O5'  *C5' H5'    0.0       0.0  -115.0     0.0    0.0
IC C4'  O5'  *C5' H5''   0.0       0.0   115.0     0.0    0.0
PATC  FIRS NONE LAST NONE

RESI NAD         -1.00  ! oxidized nicotinamide adenine dinucleotide, jjp1/adm jr.
                        ! atom names correspond to pdb nomenclature
                        ! checked for consistency with new NA params, adm jr., 9/98
                        ! note that differences with respect to published results exist
                        ! due to new NA params
GROUP                   !
ATOM AC4' CN7     0.16  !                AH61  AH62
ATOM AH4' HN7     0.09  !                   \  /
ATOM AO4' ON6B   -0.50  !                   AN6
ATOM AC1' CN7B    0.16  !                    |
ATOM AH1' HN7     0.09  !                   AC6
GROUP                   !                  //  \
ATOM AC5  CN5     0.28  !                 AN1  AC5--AN7\\
ATOM AN7  NN4    -0.71  !                  |    ||     AC8-AH8
ATOM AC8  CN4     0.34  !                 AC2  AC4--AN9/
ATOM AH8  HN3     0.12  !                 / \\ /     \
ATOM AN9  NN2    -0.05  !              AH2  AN3       \
                        !                              \
ATOM AN1  NN3A   -0.74  !                               \
ATOM AC2  CN4     0.50  !                                \
ATOM AH2  HN3     0.13  !    NO1     AO1    AH5sAH4' AO4' \
ATOM AN3  NN3A   -0.75  !     |       |      |    \ /   \  \
ATOM AC4  CN5     0.43  ! NO5'NP-O3--AP-AO5'-AC5'-AC4'   AC1'
ATOM AC6  CN2     0.46  ! \   |       |      |     \     / \
                        !  \ NO2     AO2    AH5' AC3'-AC2' AH1'
ATOM AN6  NN1    -0.77  !   \                     / \   / \
ATOM AH61 HN1     0.38  !    \                AO3' AH3'AO2'AH2'
ATOM AH62 HN1     0.38  !     \                 |       |
GROUP                   !      \              AH3T     AH2T
ATOM AC2' CN7B    0.14  !       \                        NH71
ATOM AH2' HN7     0.09  !        \                          \ 
ATOM AO2' ON5    -0.66  !         \                    NH72-NN7    NH4
ATOM AH2T HN5     0.43  !          \                          \     |
GROUP                   !           \                         NC7  NC4
ATOM AC3' CN7     0.14  !            \                        / \  /  \
ATOM AH3' HN7     0.09  !             \                    NO7  NC3  NC5-NH5
ATOM AO3' ON5    -0.66  !              \                          |    |
ATOM AH3T HN5     0.43  !               \ NH5s NH4'NO4'      NH2-NC2 NC6-NH6
GROUP                   !                \ |    \ /   \            \+ /   
ATOM AC5' CN8B   -0.08  !                 NC5'--NC4'   NC1'---------NN1
ATOM AH5' HN8     0.09  !                  |     \     / \
ATOM AH5s HN8     0.09  !                 NH5'   NC3'-NC2'NH1'
ATOM AP   P       1.50  !                       / \   / \
ATOM AO1  ON3    -0.82  !                   NO3' NH3'NO2'NH2'
ATOM AO2  ON3    -0.82  !                    |       |
ATOM AO5' ON2    -0.62  !                   NH3T    NH2T
ATOM O3   ON2    -0.68
ATOM NP   P       1.50
ATOM NO1  ON3    -0.82
ATOM NO2  ON3    -0.82
ATOM NO5' ON2    -0.62
ATOM NC5' CN8B   -0.08
ATOM NH5s HN8     0.09
ATOM NH5' HN8     0.09 
GROUP                  
ATOM NC2' CN7B    0.14 
ATOM NH2' HN7     0.09 
ATOM NO2' ON5    -0.66
ATOM NH2T HN5     0.43
GROUP
ATOM NC3' CN7     0.14
ATOM NH3' HN7     0.09
ATOM NO3' ON5    -0.66
ATOM NH3T HN5     0.43
GROUP
ATOM NC1' CN7B    0.16
ATOM NH1' HN7     0.09
ATOM NC4' CN7     0.16
ATOM NH4' HN7     0.09
ATOM NO4' ON6B   -0.50
GROUP                  
ATOM NN1  NN2    -0.07
ATOM NC6  CN3B    0.16
ATOM NH6  HN3B    0.19
ATOM NC5  CN3    -0.10
ATOM NH5  HN3B    0.16
ATOM NC4  CN3A   -0.05
ATOM NH4  HN3B    0.16
ATOM NC3  CN3     0.05 
ATOM NC2  CN3B    0.18
ATOM NH2  HN3B    0.16
ATOM NC7  CN1A    0.68 
ATOM NO7  ON1    -0.40 
ATOM NN7  NN1    -0.82
ATOM NH71 HN1     0.34  ! trans to amide O
ATOM NH72 HN1     0.36  ! cis to amide O

BOND AN1  AC2       AN3  AC4       AC5  AC6
BOND AC6  AN6       AC5  AN7       AC8  AN9
BOND AN9  AC4       AC2  AH2       AN6  AH61      AN6  AH62      AC8  AH8
DOUBLE AC6  AN1       AC2  AN3       AC4  AC5      AN7  AC8
BOND AN9  AC1'      AC1' AC2'      AC2' AC3'      AC3' AC4'      AC4' AO4'
BOND AO4' AC1'      AC1' AH1'      AC2' AO2'      AO2' AH2T      AC2' AH2'
BOND AC3' AH3'      AC3' AO3'      AO3' AH3T      AC4' AH4'      AC4' AC5'
BOND AC5' AH5s      AC5' AH5'      AC5' AO5'      AO5' AP        AP   AO1
BOND AP   AO2       AP   O3        O3   NP        NP   NO1       NP   NO2
BOND NP   NO5'      NO5' NC5'      NC5' NH5s      NC5' NH5'      NC5' NC4'
BOND NC4' NO4'      NO4' NC1'      NC1' NC2'      NC2' NC3'      NC3' NC4'
BOND NC1' NH1'      NC2' NH2'      NC2' NO2'      NO2' NH2T      NC3' NH3'
BOND NC3' NO3'      NO3' NH3T      NC4' NH4'      NC1' NN1       NN1  NC2
BOND NC3  NC4       NC5  NC6
BOND NC2  NH2       NC3  NC7       NC7  NO7       NC7  NN7       NN7  NH71
BOND NN7  NH72      NC4  NH4       NC5  NH5       NC6  NH6
DOUBLE NC2  NC3       NC4  NC5       NC6  NN1
! adenine impropers
IMPR AN6  AC6  AH61 AH62     AC6   AN1   AC5  AN6       
! amide impropers
IMPR NC7   NN7   NC3  NO7    NC7   NC3   NN7   NO7 
IMPR NN7   NC7   NH71 NH72   NN7   NC7   NH72  NH71
! ring hydrogen impropers
IMPR NC6   NN1   NC5  NH6    NC5   NC6   NC4   NH5
IMPR NC4   NC5   NC3  NH4    NC2   NC3   NN1   NH2
DONO AH61 AN6
DONO AH62 AN6
DONO AH2T AO2'
DONO AH3T AO3'
ACCE AN1
ACCE AN3
ACCE AN7
ACCE AO4'
ACCE AO2'
ACCE AO3'
ACCE AO5'
ACCE AO1  AP
ACCE AO2  AP
ACCE O3
ACCE NO1  NP
ACCE NO2  NP
ACCE NO5'
ACCE NO4'
ACCE NO3'
ACCE NO2'
ACCE NO7
DONO NH2T NO2'
DONO NH3T NO3'
DONO NH71 NN7
DONO NH72 NN7
IC AP     O3     NP     NO5'   1.4863   65.28 -169.00   98.59   1.5977
IC AC5'   AO5'   AP     O3     1.4232  127.31 -165.10  103.27   1.4863
IC AC5'   AO5'   AP     AO2    1.4232  127.31   73.33  111.48   1.4836
IC AH5S   AC5'   AC4'   AC3'   0.9935  120.00  -58.20  111.58   1.6942
IC AP     O3     NP     NO1    1.4863   65.28   78.51  108.97   1.4756
IC AP     O3     NP     NO2    1.4863   65.28  -54.29  112.88   1.4636
IC AP     AO5'   AC5'   AC4'   1.5901  127.31  121.29  111.63   1.5491
IC AO1    AP     AO5'   AC5'   1.5901  127.31  121.29  127.31   1.4232
IC AO5'   AC5'   AC4'   AC3'   1.4232  111.63  -58.20  111.58   1.6942
IC AC5'   AC4'   AC3'   AO3'   1.5491  111.58  128.42  114.19   1.4337
IC AH3T   AO3'   AC3'   AC4'   0.9671   98.77  147.40  114.19   1.6942
IC AO4'   AC3'   *AC4   AC5'   1.8868  112.95 -118.10  111.58   1.5491
IC AC2'   AC4'   *AC3'  AO3'   1.5097   93.22 -117.72  114.19   1.4337
IC AC4'   AC3'   AC2'   AC1'   1.6942   93.22  -12.93  117.82   1.5415
IC AC3'   AC2'   AC1'   AN9    1.5097  117.82  135.56  115.01   1.4847
IC AO4'   AC1'   AN9    AC4    1.3646   95.44  -90.72  125.96   1.4013
IC AC1'   AC4    *AN9   AC8    1.4847  125.96 -176.52  105.34   1.3777
IC AC4    AN9    AC8    AN7    1.4013  105.34   -0.07  114.01   1.3282
IC AC8    AN9    AC4    AC5    1.3777  105.34    0.11  105.06   1.3782
IC AC8    AN7    AC5    AC6    1.3282  103.21 -179.92  130.78   1.4146
IC AN7    AC5    AC6    AN1    1.3814  130.78 -179.94  117.85   1.3482
IC AC5    AC6    AN1    AC2    1.4146  117.85   -0.14  118.87   1.3300
IC AN9    AC5    *AC4   AN3    1.4013  105.06 -179.67  126.14   1.3648
IC AC5    AN1    *AC6   AN6    1.4146  117.85  179.89  119.69   1.3419
IC AN1    AC6    AN6    AH61   1.3482  119.69   -0.39  116.60   0.9912
IC AH61   AC6    *AN6   AH62   0.9912  116.60 -179.02  116.94   0.9978
IC AC5    AN1    *AC6   AN6    1.4146  117.85  179.89  119.69   1.3419
IC AN1    AC6    AN6    AH61   1.3482  119.69   -0.39  116.60   0.9912
IC AH61   AC6    *AN6   AH62   0.9912  116.60 -179.02  116.94   0.9978
IC AN9    AN7    *AC8   AH8    1.3777  114.01 -179.37  126.34   1.0962
IC AN1    AN3    *AC2   AH2    1.3300  129.42  179.97  114.82   1.0928
IC AC1'   AC3'   *AC2   AO2'   1.5415  117.82 -145.06  114.13   1.4294
IC AH2'   AO2'   AC2'   AC3'   2.0386   31.12  -93.63  114.13   1.5097
IC AH2T   AO2'   AC2'   AC3'   0.9953   99.36  -93.63  114.13   1.5097
IC AO4'   AC2'   *AC1'  AH1'   1.3646  120.77 -114.99  109.65   1.1105
IC AC1'   AC3'   *AC2   AH2'   1.5415  117.82  108.23   86.44   1.0999
IC AC2'   AC4'   *AC3'  AH3'   1.5097   93.22  117.28  111.94   1.1110
IC AC3'   AO4'   *AC4   AH4'   1.6942  112.95 -140.26   57.99   1.0000
IC AC4'   AO5'   *AC5   AH5'   1.5491  111.63 -123.75  111.23   1.1111
IC AC4'   AO5'   *AC5   AH5'   1.5491  111.63 -123.75  111.23   1.1111
IC NC5'   NO5'   NP     NO2    1.4451  128.40  -49.72  108.83   1.4636
IC NH5S   NC5'   NO5'   NP     1.1110  109.50  115.00  128.40   1.5977
IC NH5'   NC5'   NO5'   NP     1.1110  109.50 -115.00  128.40   1.5977
IC NP     NO5'   NC5'   NC4'   1.5977  128.40    0.00  110.10   1.5160
IC NO5'   NC5'   NC4'   NC3'   1.4451  110.10    0.00  108.50   1.5160
IC NC5'   NC4'   NC3'   NC2'   1.5160  108.50    0.00  111.00   1.5160
IC NC4'   NC3'   NC2'   NC1'   1.5160  111.00    0.00  105.50   1.5270
IC NC3'   NC2'   NC1'   NO4'   1.5160  105.50    0.00  105.00   1.4100
IC NC2'   NC1'   NO4'   NC4'   1.5270  105.00    0.00  117.86   1.4712
IC NO2'   NC2'   NC1'   NO4'   1.4200  110.10  180.00  105.00   1.4100
IC NH2T   NO2'   NC2'   NC1'   0.9600  106.00  180.00  110.10   1.5270
IC NO4'   NC2'   *NC1'  NH1'   1.4100  105.00 -115.00  110.10   1.1110
IC NC1'   NC3'   *NC2   NH2'   1.5270  105.50  115.00  110.10   1.1110
IC NC2'   NC4'   *NC3   NH3'   1.5160  111.00  115.00  110.10   1.1110
IC NC3'   NO4'   *NC4   NH4'   1.5160  100.64 -115.00  107.24   1.1110
IC NC4'   NO5'   *NC5   NH5'   1.5160  110.10 -115.00  109.50   1.1110
IC NC4'   NO5'   *NC5   NH5S   1.5160  110.10  115.00  109.50   1.1110
IC NC3'   NC2'   NC1'   NN1    1.5160  105.50    0.00  113.70   1.4800
IC NO3'   NC3'   NC2'   NC1'   1.4200  110.10  180.00  105.50   1.5270
IC NH3T   NO3'   NC3'   NC2'   0.9600  106.00  180.00  110.10   1.5160
IC NC2'   NC1'   NN1    NC2    1.5270  113.70    0.00  121.70   1.3150
IC NC1'   NN1    NC2    NC3    1.4800  121.70    0.00  122.00   1.3500
IC NN1    NC2    NC3    NC4    1.3150  122.00    0.00  118.00   1.3600
IC NC2    NC3    NC4    NC5    1.3500  118.00    0.00  118.00   1.3600
IC NC3    NC4    NC5    NC6    1.3600  118.00    0.00  118.00   1.3500
IC NC4    NC5    NC6    NN1    1.3600  118.00    0.00  124.51   1.2199
IC NC5    NC6    NN1    NC2    1.3500  124.51    0.00  119.49   1.3150
IC NN1    NC2    NC3    NC7    1.3150  122.00    0.00  131.80   1.4800
IC NC2    NC3    NC7    NO7    1.3500  131.80    0.00  118.50   1.2300
IC NC2    NC3    NC7    NN7    1.3500  131.80    0.00  113.00   1.3600
IC NO7    NC7    NN7    NH71   1.2300    0.00  180.00  120.00   1.0000
IC NO7    NC7    NN7    NH72   1.2300    0.00    0.00  120.00   1.0000
IC NC2    NC3    NC4    NH4    1.3500  118.00    0.00  121.00   1.0900
IC NC3    NC4    NC5    NH5    1.3600  118.00    0.00  119.00   1.0900
IC NC4    NC5    NC6    NH6    1.3600  118.00    0.00  120.50   1.0900
IC NC6    NN1    NC2    NH2    1.2199  119.49    0.00  117.50   1.0900
PATCH FIRST NONE LAST NONE   

RESI NADH        -2.00  ! reduced nicotinamide adenine dinucleotide, jjp1/adm jr.
                        ! atom names correspond to pdb nomenclature
                        ! checked for consistency with new NA params, adm jr., 9/98
                        ! note that differences with respect to published results exist
                        ! due to new NA params
                        !
GROUP                   !
ATOM AC4' CN7     0.16  !                AH61  AH62
ATOM AH4' HN7     0.09  !                   \  /
ATOM AO4' ON6B   -0.50  !                   AN6
ATOM AC1' CN7B    0.16  !                    |
ATOM AH1' HN7     0.09  !                   AC6
GROUP                   !                  //  \
ATOM AC5  CN5     0.28  !                 AN1  AC5--AN7\\
ATOM AN7  NN4    -0.71  !                  |    ||     AC8-AH8
ATOM AC8  CN4     0.34  !                 AC2  AC4--AN9/
ATOM AH8  HN3     0.12  !                 / \\ /     \
ATOM AN9  NN2    -0.05  !              AH2  AN3       \
                        !                              \
ATOM AN1  NN3A   -0.74  !                               \
ATOM AC2  CN4     0.50  !                                \
ATOM AH2  HN3     0.13  !    NO1     AO1    AH5sAH4' AO4' \
ATOM AN3  NN3A   -0.75  !     |       |      |    \ /   \  \
ATOM AC4  CN5     0.43  ! NO5'NP-O3--AP-AO5'-AC5'-AC4'   AC1'
ATOM AC6  CN2     0.46  ! \   |       |      |     \     / \
                        !  \ NO2     AO2    AH5' AC3'-AC2' AH1'
ATOM AN6  NN1    -0.77  !   \                     / \   / \
ATOM AH61 HN1     0.38  !    \                AO3' AH3'AO2'AH2'
ATOM AH62 HN1     0.38  !     \                 |       |
GROUP                   !      \              AH3T     AH2T
ATOM AC2' CN7B    0.14  !       \                        NH71
ATOM AH2' HN7     0.09  !        \                          \
ATOM AO2' ON5    -0.66  !         \                    NH72-NN7  NH4 NH42
ATOM AH2T HN5     0.43  !          \                          \    \ /
GROUP                   !           \                         NC7  NC4
ATOM AC3' CN7     0.14  !            \                        / \  /  \
ATOM AH3' HN7     0.09  !             \                    NO7  NC3  NC5-NH5
ATOM AO3' ON5    -0.66  !              \                          |    |
ATOM AH3T HN5     0.43  !               \ NH5s NH4'NO4'      NH2-NC2 NC6-NH6
GROUP                   !                \ |    \ /   \            \  /
ATOM AC5' CN8B   -0.08  !                 NC5'--NC4'   NC1'---------NN1
ATOM AH5' HN8     0.09  !                  |     \     / \
ATOM AH5s HN8     0.09  !                 NH5'   NC3'-NC2'NH1'
ATOM AP   P       1.50  !                       / \   / \
ATOM AO1  ON3    -0.82  !                   NO3' NH3'NO2'NH2'
ATOM AO2  ON3    -0.82  !                    |       |
ATOM AO5' ON2    -0.62  !                   NH3T    NH2T
ATOM O3   ON2    -0.68
ATOM NP   P       1.50
ATOM NO1  ON3    -0.82
ATOM NO2  ON3    -0.82
ATOM NO5' ON2    -0.62
ATOM NC5' CN8B   -0.08
ATOM NH5s HN8     0.09
ATOM NH5' HN8     0.09
GROUP
ATOM NC2' CN7B    0.14
ATOM NH2' HN7     0.09
ATOM NO2' ON5    -0.66
ATOM NH2T HN5     0.43
GROUP
ATOM NC3' CN7     0.14
ATOM NH3' HN7     0.09
ATOM NO3' ON5    -0.66
ATOM NH3T HN5     0.43
GROUP
ATOM NC1' CN7B    0.16
ATOM NH1' HN7     0.09
ATOM NC4' CN7     0.16
ATOM NH4' HN7     0.09
ATOM NO4' ON6B   -0.50
GROUP
ATOM NN1  NN2    -0.27 !N2
ATOM NC6  CN3C   -0.06 !C3
ATOM NH6  HN6     0.17 !H4
ATOM NC5  CN3    -0.18 !C5
ATOM NH5  HN6     0.14 !H6
ATOM NC4  CN8    -0.28 !C7
ATOM NH4  HN8     0.09 !H8
ATOM NH42 HN8     0.09 !H17
ATOM NC3  CN3     0.36 !C9
ATOM NC2  CN3C   -0.10 !C10
ATOM NH2  HN6     0.14 !H11
ATOM NC7  CN1A    0.55 !C12
ATOM NO7  ON1    -0.51 !O13
ATOM NN7  NN1    -0.72 !N14
ATOM NH71 HN1     0.26 !H15  ! trans to amide O
ATOM NH72 HN1     0.32 !H16  ! cis to amide O

BOND AN1  AC2       AN3  AC4       AC5  AC6
BOND AC6  AN6       AC5  AN7       AC8  AN9
BOND AN9  AC4       AC2  AH2       AN6  AH61      AN6  AH62      AC8  AH8
DOUBLE  AC6  AN1      AC2  AN3      AC4  AC5      AN7  AC8
BOND AN9  AC1'      AC1' AC2'      AC2' AC3'      AC3' AC4'      AC4' AO4'
BOND AO4' AC1'      AC1' AH1'      AC2' AO2'      AO2' AH2T      AC2' AH2'
BOND AC3' AH3'      AC3' AO3'      AO3' AH3T      AC4' AH4'      AC4' AC5'
BOND AC5' AH5s      AC5' AH5'      AC5' AO5'      AO5' AP        AP   AO1
BOND AP   AO2       AP   O3        O3   NP        NP   NO1       NP   NO2
BOND NP   NO5'      NO5' NC5'      NC5' NH5s      NC5' NH5'      NC5' NC4'
BOND NC4' NO4'      NO4' NC1'      NC1' NC2'      NC2' NC3'      NC3' NC4'
BOND NC1' NH1'      NC2' NH2'      NC2' NO2'      NO2' NH2T      NC3' NH3'
BOND NC3' NO3'      NO3' NH3T      NC4' NH4'      NC1' NN1       NN1  NC2
BOND NC3  NC4       NC4  NC5       NC6  NN1
BOND NC2  NH2       NC3  NC7       NC7  NO7       NC7  NN7       NN7  NH71
BOND NN7  NH72      NC4  NH4       NC4  NH42      NC5  NH5       NC6  NH6
DOUBLE  NC2  NC3      NC5  NC6
! adenine impropers
IMPR AN6  AC6  AH61 AH62     AC6  AN1  AC5  AN6       
! amide impropers
IMPR NC7   NN7   NC3  NO7    NC7   NC3   NN7   NO7
IMPR NN7   NC7   NH71 NH72   NN7   NC7   NH72  NH71
! ring hydrogen impropers
IMPR NC6   NN1   NC5  NH6    NC5   NC6   NC4   NH5
IMPR NC4   NC5   NC3  NH4    NC2   NC3   NN1   NH2
DONO AH61 AN6
DONO AH62 AN6
DONO AH2T AO2'
DONO AH3T AO3'
ACCE AN1
ACCE AN3
ACCE AN7
ACCE AO4'
ACCE AO2'
ACCE AO3'
ACCE AO5'
ACCE AO1  AP
ACCE AO2  AP
ACCE O3
ACCE NO1  NP
ACCE NO2  NP
ACCE NO5'
ACCE NO4'
ACCE NO3'
ACCE NO2'
ACCE NO7
DONO NH2T NO2'
DONO NH3T NO3'
DONO NH71 NN7
DONO NH72 NN7
IC AP     O3     NP     NO5'   1.5477  110.11  175.47   98.59   1.5945
IC AC5'   AO5'   AP     O3     1.4379  124.23 -120.69   96.29   1.5477
IC AC5'   AO5'   AP     AO2    1.4379  124.23   -4.20  104.25   1.4838
IC AH5S   AC5'   AC4'   AC3'   1.1127  107.45 -172.00  111.64   1.5309
IC AP     O3     NP     NO1    1.5477  110.11   63.14  114.14   1.4739
IC AP     O3     NP     NO2    1.5477  110.11  -73.96  111.08   1.4835
IC AP     AO5'   AC5'   AC4'   1.5968  124.23  104.17  111.45   1.5366
IC AO1    AP     AO5'   AC5'   1.4736  106.06  122.59  124.23   1.4379
IC AO5'   AC5'   AC4'   AC3'   1.4379  111.45  -54.02  111.64   1.5309
IC AC5'   AC4'   AC3'   AO3'   1.5366  111.64  117.91  108.23   1.4176
IC AH3T   AO3'   AC3'   AC4'   0.9780  101.86  -77.83  108.23   1.5309
IC AO4'   AC3'   *AC4   AC5'   3.7210   30.68   12.44   22.46   6.0953
IC AC2'   AC4'   *AC3'  AO3'   1.5171  107.22 -123.00  108.23   1.4176
IC AC4'   AC3'   AC2'   AC1'   1.5309  107.22  -27.93   98.01   1.5397
IC AC3'   AC2'   AC1'   AN9    1.5171   98.01  168.03  114.25   1.4756
IC AO4'   AC1'   AN9    AC4    1.4308  112.85 -160.05  123.87   1.3958
IC AC1'   AC4    *AN9   AC8    1.4756  123.87  160.62  105.30   1.3614
IC AC4    AN9    AC8    AN7    1.3958  105.30    2.73  114.72   1.3222
IC AC8    AN9    AC4    AC5    1.3614  105.30   -0.85  105.33   1.3777
IC AC8    AN7    AC5    AC6    1.3222  102.89 -175.73  131.43   1.4163
IC AN7    AC5    AC6    AN1    1.3877  131.43  177.76  117.35   1.3499
IC AC5    AC6    AN1    AC2    1.4163  117.35    0.19  119.36   1.3330
IC AN9    AC5    *AC4   AN3    1.3958  105.33 -177.76  126.56   1.3567
IC AC5    AN1    *AC6   AN6    1.4163  117.35  178.91  119.82   1.3439
IC AN1    AC6    AN6    AH61   1.3499  119.82   -2.82  115.89   0.9932
IC AH61   AC6    *AN6   AH62   0.9932  115.89 -173.48  118.52   0.9961
IC AC5    AN1    *AC6   AN6    1.4163  117.35  178.91  119.82   1.3439
IC AN1    AC6    AN6    AH61   1.3499  119.82   -2.82  115.89   0.9932
IC AH61   AC6    *AN6   AH62   0.9932  115.89 -173.48  118.52   0.9961
IC AN9    AN7    *AC8   AH8    1.3614  114.72  173.63  127.58   1.0942
IC AN1    AN3    *AC2   AH2    1.3330  128.86  179.26  114.95   1.0940
IC AC1'   AC3'   *AC2   AO2'   4.3577   16.73   79.16   23.49   5.5426
IC AH2'   AO2'   AC2'   AC3'   2.0992   29.77  125.89  110.79   1.5171
IC AH2T   AO2'   AC2'   AC3'   0.9759  105.90    7.59  110.79   1.5171
IC AO4'   AC2'   *AC1'  AH1'   1.4308  104.32 -114.05  107.95   1.1153
IC AC1'   AC3'   *AC2   AH2'   4.3577   16.73  138.52   14.56   4.3331
IC AC2'   AC4'   *AC3'  AH3'   1.5171  107.22  118.77  114.33   1.1023
IC AC3'   AO4'   *AC4   AH4'   4.6236   30.68   55.38   18.92   5.2267
IC AC4'   AO5'   *AC5   AH5'   5.8410    8.40  125.34   12.50   6.6777
IC AC4'   AO5'   *AC5   AH5'   5.8410    8.40  125.34   12.50   6.6777
IC NC5'   NO5'   NP     NO2    1.4351  125.31   34.31  105.69   1.4835
IC NH5S   NC5'   NO5'   NP     1.1087  111.20   -6.79  125.31   1.5945
IC NH5'   NC5'   NO5'   NP     1.1115  107.95  108.24  125.31   1.5945
IC NP     NO5'   NC5'   NC4'   1.5945  125.31 -133.06  113.61   1.5644
IC NO5'   NC5'   NC4'   NC3'   1.4351  113.61   37.01  114.92   1.5111
IC NC5'   NC4'   NC3'   NC2'   1.5644  114.92   71.49   99.06   1.5369
IC NC4'   NC3'   NC2'   NC1'   1.5111   99.06   54.76   97.08   1.5500
IC NC3'   NC2'   NC1'   NO4'   1.5369   97.08  -39.12  103.14   1.4628
IC NC2'   NC1'   NO4'   NC4'   1.5500  103.14    9.47  109.09   1.4960
IC NO2'   NC2'   NC1'   NO4'   1.4207  114.02 -166.39  103.14   1.4628
IC NH2T   NO2'   NC2'   NC1'   0.9638  100.52  -89.37  114.02   1.5500
IC NO4'   NC2'   *NC1'  NH1'   1.4628  103.14 -111.22  105.40   1.1096
IC NC1'   NC3'   *NC2   NH2'   2.4663   46.96  -41.97   34.01   3.9460
IC NC2'   NC4'   *NC3   NH3'   3.9136   23.54 -115.76   16.12   3.6674
IC NC3'   NO4'   *NC4   NH4'   5.4003   24.61  -39.21   14.97   6.7904
IC NC4'   NO5'   *NC5   NH5'   5.9665   13.65  -41.47   15.17   7.7670
IC NC4'   NO5'   *NC5   NH5S   5.9665   13.65  -87.41   13.92   6.7251
IC NC3'   NC2'   NC1'   NN1    1.5369   97.08   88.64  116.58   1.5502
IC NO3'   NC3'   NC2'   NC1'   1.4176  119.76 -172.52   97.08   1.5500
IC NH3T   NO3'   NC3'   NC2'   0.9717  103.61   17.81  119.76   1.5369
IC NC2'   NC1'   NN1    NC2    1.5500  116.58  -19.65  116.34   1.3499
IC NC1'   NN1    NC2    NC3    1.5502  116.34  134.66  130.57   1.3607
IC NN1    NC2    NC3    NC4    1.3499  130.57    5.82  111.74   1.5356
IC NC2    NC3    NC4    NC5    1.3607  111.74   -1.05  119.26   1.5319
IC NC3    NC4    NC5    NC6    1.5356  119.26   -1.26  113.69   1.3745
IC NC4    NC5    NC6    NN1    1.5319  113.69   -0.29  128.15   1.3388
IC NC5    NC6    NN1    NC2    1.3745  128.15    4.14  116.26   1.3499
IC NN1    NC2    NC3    NC7    1.3499  130.57 -147.46  122.72   1.5282
IC NC2    NC3    NC7    NO7    1.3607  122.72 -140.47  119.41   1.2169
IC NC2    NC3    NC7    NN7    1.3607  122.72   46.61  116.68   1.3621
IC NO7    NC7    NN7    NH71   1.2169  123.49 -177.07  120.21   1.0093
IC NO7    NC7    NN7    NH72   1.2169  123.49   -4.94  119.16   1.0014
IC NC2    NC3    NC4    NH4    1.3607  111.74 -135.39  112.16   1.1099
IC NC2    NC3    NC4    NH42   1.3607  111.74  114.48  103.52   1.1129
IC NC3    NC4    NC5    NH5    1.5356  119.26 -171.18  122.65   1.0912
IC NC4    NC5    NC6    NH6    1.5319  113.69  179.92  118.00   1.0878
IC NC6    NN1    NC2    NH2    1.3388  116.26  162.03  117.47   1.0731
PATCH FIRST NONE LAST NONE

RESI NADP        -2.00  ! oxidized nicotinamide adenine dinucleotide,
                        ! NADP+, adm jr.
                        ! atom names correspond to pdb nomenclature
                        ! checked for consistency with new NA params, adm jr., 9/98
                        ! note that differences with respect to published results exist
                        ! due to new NA params
                        !
GROUP                   !
ATOM AC4' CN7     0.16  !                AH61  AH62
ATOM AH4' HN7     0.09  !                   \  /
ATOM AO4' ON6B   -0.50  !                   AN6
ATOM AC1' CN7B    0.16  !                    |
ATOM AH1' HN7     0.09  !                   AC6
GROUP                   !                  //  \
ATOM AC5  CN5     0.28  !                 AN1  AC5--AN7\\
ATOM AN7  NN4    -0.71  !                  |    ||     AC8-AH8
ATOM AC8  CN4     0.34  !                 AC2  AC4--AN9/
ATOM AH8  HN3     0.12  !                 / \\ /     \
ATOM AN9  NN2    -0.05  !              AH2  AN3       \
                        !                              \
ATOM AN1  NN3A   -0.74  !                               \
ATOM AC2  CN4     0.50  !                                \
ATOM AH2  HN3     0.13  !    NO1     AO1    AH5sAH4' AO4' \
ATOM AN3  NN3A   -0.75  !     |       |      |    \ /   \  \
ATOM AC4  CN5     0.43  ! NO5'NP-O3--AP-AO5'-AC5'-AC4'   AC1'
ATOM AC6  CN2     0.46  ! \   |       |      |     \     / \
                        !  \ NO2     AO2    AH5' AC3'-AC2' AH1'
ATOM AN6  NN1    -0.77  !   \                     / \   / \
ATOM AH61 HN1     0.38  !    \                AO3' AH3'AO2'AH2'
ATOM AH62 HN1     0.38  !     \                |        |
GROUP                   !      \             AH3T AO1P=AP2==AO2P (-)
ATOM AC2' CN7B    0.01  !       \                       |    NH71
ATOM AH2' HN7     0.09  !        \                AH2T-AO2T   /
ATOM AO2' ON2    -0.62  !         \                    NH72-NN7  NH4 NH42
ATOM AP2  P       1.50  !          \                          \    \ /
ATOM AO1P ON3    -0.82  !           \                         NC7  NC4
ATOM AO2P ON3    -0.82  !            \                        / \  /  \
ATOM AO2T ON4    -0.68  !             \                    NO7  NC3  NC5-NH5
ATOM AH2T HN4     0.34  !              \                          |    |
GROUP                   !               \                         |    |
ATOM AC3' CN7     0.14  !                \ NH5s NH4'NO4'      NH2-NC2 NC6-NH6
ATOM AH3' HN7     0.09  !                 \ |    \ /   \           \   /
ATOM AO3' ON5    -0.66  !                  NC5'--NC4'   NC1'--------NN1
ATOM AH3T HN5     0.43  !                   |     \     / \
GROUP                   !                 NH5'   NC3'-NC2'NH1'
ATOM AC5' CN8B   -0.08  !                        / \   / \  
ATOM AH5' HN8     0.09  !                    NO3' NH3'NO2'NH2'  
ATOM AH5s HN8     0.09  !                     |       |
ATOM AP   P       1.50  !                    NH3T    NH2T   
ATOM AO1  ON3    -0.82  !
ATOM AO2  ON3    -0.82  !
ATOM AO5' ON2    -0.62  !
ATOM O3   ON2    -0.68
ATOM NP   P       1.50
ATOM NO1  ON3    -0.82
ATOM NO2  ON3    -0.82
ATOM NO5' ON2    -0.62
ATOM NC5' CN8B   -0.08
ATOM NH5s HN8     0.09
ATOM NH5' HN8     0.09 
GROUP                  
ATOM NC2' CN7B    0.14 
ATOM NH2' HN7     0.09 
ATOM NO2' ON5    -0.66
ATOM NH2T HN5     0.43
GROUP
ATOM NC3' CN7     0.14
ATOM NH3' HN7     0.09
ATOM NO3' ON5    -0.66
ATOM NH3T HN5     0.43
GROUP
ATOM NC1' CN7B    0.16
ATOM NH1' HN7     0.09
ATOM NC4' CN7     0.16
ATOM NH4' HN7     0.09
ATOM NO4' ON6B   -0.50
GROUP                  
ATOM NN1  NN2    -0.07
ATOM NC6  CN3B    0.16
ATOM NH6  HN3B    0.19
ATOM NC5  CN3    -0.10
ATOM NH5  HN3B    0.16
ATOM NC4  CN3A   -0.05
ATOM NH4  HN3B    0.16
ATOM NC3  CN3     0.05 
ATOM NC2  CN3B    0.18
ATOM NH2  HN3B    0.16
ATOM NC7  CN1A    0.68 
ATOM NO7  ON1    -0.40 
ATOM NN7  NN1    -0.82
ATOM NH71 HN1     0.34  ! trans to amide O
ATOM NH72 HN1     0.36  ! cis to amide O

BOND AN1  AC2       AN3  AC4       AC5  AC6
BOND AC6  AN6       AC5  AN7       AC8  AN9
BOND AN9  AC4       AC2  AH2       AN6  AH61      AN6  AH62      AC8  AH8
DOUBLE AC6  AN1       AC2  AN3       AC4  AC5      AN7  AC8
BOND AN9  AC1'      AC1' AC2'      AC2' AC3'      AC3' AC4'      AC4' AO4'
BOND AO4' AC1'      AC1' AH1'      AC2' AO2'      AO2' AP2      AC2' AH2'
BOND AC3' AH3'      AC3' AO3'      AO3' AH3T      AC4' AH4'      AC4' AC5'
BOND AC5' AH5s      AC5' AH5'      AC5' AO5'      AO5' AP        AP   AO1
BOND AP   AO2       AP   O3        O3   NP        NP   NO1       NP   NO2
BOND NP   NO5'      NO5' NC5'      NC5' NH5s      NC5' NH5'      NC5' NC4'
BOND NC4' NO4'      NO4' NC1'      NC1' NC2'      NC2' NC3'      NC3' NC4'
BOND NC1' NH1'      NC2' NH2'      NC2' NO2'      NO2' NH2T      NC3' NH3'
BOND NC3' NO3'      NO3' NH3T      NC4' NH4'      NC1' NN1       NN1  NC2
BOND NC3  NC4       NC5  NC6
BOND NC2  NH2       NC3  NC7       NC7  NO7       NC7  NN7       NN7  NH71
BOND NN7  NH72      NC4  NH4       NC5  NH5       NC6  NH6
BOND AP2  AO1P      AP2  AO2P      AP2  AO2T      AO2T AH2T
DOUBLE NC2  NC3       NC4  NC5       NC6  NN1
! adenine impropers
IMPR AN6  AC6  AH61 AH62     AC6  AN1  AC5  AN6
! amide impropers
IMPR NC7   NN7   NC3  NO7    NC7   NC3   NN7   NO7 
IMPR NN7   NC7   NH71 NH72   NN7   NC7   NH72  NH71
! ring hydrogen impropers
IMPR NC6   NN1   NC5  NH6    NC5   NC6   NC4   NH5
IMPR NC4   NC5   NC3  NH4    NC2   NC3   NN1   NH2
DONO AH61 AN6
DONO AH62 AN6
DONO AH2T AO2'
DONO AH3T AO3'
ACCE AN1
ACCE AN3
ACCE AN7
ACCE AO4'
ACCE AO2'
ACCE AO3'
ACCE AO5'
ACCE AO1  AP
ACCE AO2  AP
ACCE O3
ACCE NO1  NP
ACCE NO2  NP
ACCE NO5'
ACCE NO4'
ACCE NO3'
ACCE NO2'
ACCE NO7
DONO NH2T NO2'
DONO NH3T NO3'
DONO NH71 NN7
DONO NH72 NN7
DONO AH2T AO2T
ACCE AO2T
ACCE AO1P
ACCE AO2P
ACCE AO2'
IC AP     O3     NP     NO5'   1.4863   65.28 -169.00   98.59   1.5977
IC AC5'   AO5'   AP     O3     1.4232  127.31 -165.10  103.27   1.4863
IC AC5'   AO5'   AP     AO2    1.4232  127.31   73.33  111.48   1.4836
IC AH5S   AC5'   AC4'   AC3'   0.9935  120.00  -58.20  111.58   1.6942
IC AP     O3     NP     NO1    1.4863   65.28   78.51  108.97   1.4756
IC AP     O3     NP     NO2    1.4863   65.28  -54.29  112.88   1.4636
IC AP     AO5'   AC5'   AC4'   1.5901  127.31  121.29  111.63   1.5491
IC AO1    AP     AO5'   AC5'   1.5901  127.31  121.29  127.31   1.4232
IC AO5'   AC5'   AC4'   AC3'   1.4232  111.63  -58.20  111.58   1.6942
IC AC5'   AC4'   AC3'   AO3'   1.5491  111.58  128.42  114.19   1.4337
IC AH3T   AO3'   AC3'   AC4'   0.9671   98.77  147.40  114.19   1.6942
IC AO4'   AC3'   *AC4   AC5'   1.8868  112.95 -118.10  111.58   1.5491
IC AC2'   AC4'   *AC3'  AO3'   1.5097   93.22 -117.72  114.19   1.4337
IC AC4'   AC3'   AC2'   AC1'   1.6942   93.22  -12.93  117.82   1.5415
IC AC3'   AC2'   AC1'   AN9    1.5097  117.82  135.56  115.01   1.4847
IC AO4'   AC1'   AN9    AC4    1.3646   95.44  -90.72  125.96   1.4013
IC AC1'   AC4    *AN9   AC8    1.4847  125.96 -176.52  105.34   1.3777
IC AC4    AN9    AC8    AN7    1.4013  105.34   -0.07  114.01   1.3282
IC AC8    AN9    AC4    AC5    1.3777  105.34    0.11  105.06   1.3782
IC AC8    AN7    AC5    AC6    1.3282  103.21 -179.92  130.78   1.4146
IC AN7    AC5    AC6    AN1    1.3814  130.78 -179.94  117.85   1.3482
IC AC5    AC6    AN1    AC2    1.4146  117.85   -0.14  118.87   1.3300
IC AN9    AC5    *AC4   AN3    1.4013  105.06 -179.67  126.14   1.3648
IC AC5    AN1    *AC6   AN6    1.4146  117.85  179.89  119.69   1.3419
IC AN1    AC6    AN6    AH61   1.3482  119.69   -0.39  116.60   0.9912
IC AH61   AC6    *AN6   AH62   0.9912  116.60 -179.02  116.94   0.9978
IC AC5    AN1    *AC6   AN6    1.4146  117.85  179.89  119.69   1.3419
IC AN1    AC6    AN6    AH61   1.3482  119.69   -0.39  116.60   0.9912
IC AH61   AC6    *AN6   AH62   0.9912  116.60 -179.02  116.94   0.9978
IC AN9    AN7    *AC8   AH8    1.3777  114.01 -179.37  126.34   1.0962
IC AN1    AN3    *AC2   AH2    1.3300  129.42  179.97  114.82   1.0928
IC AC1'   AC3'   *AC2   AO2'   1.5415  117.82 -145.06  114.13   1.4294
IC AH2'   AO2'   AC2'   AC3'   2.0386   31.12  -93.63  114.13   1.5097
IC AH2T   AO2'   AC2'   AC3'   0.9953   99.36  -93.63  114.13   1.5097
IC AO4'   AC2'   *AC1'  AH1'   1.3646  120.77 -114.99  109.65   1.1105
IC AC1'   AC3'   *AC2   AH2'   1.5415  117.82  108.23   86.44   1.0999
IC AC2'   AC4'   *AC3'  AH3'   1.5097   93.22  117.28  111.94   1.1110
IC AC3'   AO4'   *AC4   AH4'   1.6942  112.95 -140.26   57.99   1.0000
IC AC4'   AO5'   *AC5   AH5'   1.5491  111.63 -123.75  111.23   1.1111
IC AC4'   AO5'   *AC5   AH5'   1.5491  111.63 -123.75  111.23   1.1111
IC NC5'   NO5'   NP     NO2    1.4451  128.40  -49.72  108.83   1.4636
IC NH5S   NC5'   NO5'   NP     1.1110  109.50  115.00  128.40   1.5977
IC NH5'   NC5'   NO5'   NP     1.1110  109.50 -115.00  128.40   1.5977
IC NP     NO5'   NC5'   NC4'   1.5977  128.40    0.00  110.10   1.5160
IC NO5'   NC5'   NC4'   NC3'   1.4451  110.10    0.00  108.50   1.5160
IC NC5'   NC4'   NC3'   NC2'   1.5160  108.50    0.00  111.00   1.5160
IC NC4'   NC3'   NC2'   NC1'   1.5160  111.00    0.00  105.50   1.5270
IC NC3'   NC2'   NC1'   NO4'   1.5160  105.50    0.00  105.00   1.4100
IC NC2'   NC1'   NO4'   NC4'   1.5270  105.00    0.00  117.86   1.4712
IC NO2'   NC2'   NC1'   NO4'   1.4200  110.10  180.00  105.00   1.4100
IC NH2T   NO2'   NC2'   NC1'   0.9600  106.00  180.00  110.10   1.5270
IC NO4'   NC2'   *NC1'  NH1'   1.4100  105.00 -115.00  110.10   1.1110
IC NC1'   NC3'   *NC2   NH2'   1.5270  105.50  115.00  110.10   1.1110
IC NC2'   NC4'   *NC3   NH3'   1.5160  111.00  115.00  110.10   1.1110
IC NC3'   NO4'   *NC4   NH4'   1.5160  100.64 -115.00  107.24   1.1110
IC NC4'   NO5'   *NC5   NH5'   1.5160  110.10 -115.00  109.50   1.1110
IC NC4'   NO5'   *NC5   NH5S   1.5160  110.10  115.00  109.50   1.1110
IC NC3'   NC2'   NC1'   NN1    1.5160  105.50    0.00  113.70   1.4800
IC NO3'   NC3'   NC2'   NC1'   1.4200  110.10  180.00  105.50   1.5270
IC NH3T   NO3'   NC3'   NC2'   0.9600  106.00  180.00  110.10   1.5160
IC NC2'   NC1'   NN1    NC2    1.5270  113.70    0.00  121.70   1.3150
IC NC1'   NN1    NC2    NC3    1.4800  121.70    0.00  122.00   1.3500
IC NN1    NC2    NC3    NC4    1.3150  122.00    0.00  118.00   1.3600
IC NC2    NC3    NC4    NC5    1.3500  118.00    0.00  118.00   1.3600
IC NC3    NC4    NC5    NC6    1.3600  118.00    0.00  118.00   1.3500
IC NC4    NC5    NC6    NN1    1.3600  118.00    0.00  124.51   1.2199
IC NC5    NC6    NN1    NC2    1.3500  124.51    0.00  119.49   1.3150
IC NN1    NC2    NC3    NC7    1.3150  122.00    0.00  131.80   1.4800
IC NC2    NC3    NC7    NO7    1.3500  131.80    0.00  118.50   1.2300
IC NC2    NC3    NC7    NN7    1.3500  131.80    0.00  113.00   1.3600
IC NO7    NC7    NN7    NH71   1.2300    0.00  180.00  120.00   1.0000
IC NO7    NC7    NN7    NH72   1.2300    0.00    0.00  120.00   1.0000
IC NC2    NC3    NC4    NH4    1.3500  118.00    0.00  121.00   1.0900
IC NC3    NC4    NC5    NH5    1.3600  118.00    0.00  119.00   1.0900
IC NC4    NC5    NC6    NH6    1.3600  118.00    0.00  120.50   1.0900
IC NC6    NN1    NC2    NH2    1.2199  119.49    0.00  117.50   1.0900
IC AC3'   AC2'   AO2'   AP2    0.0000  000.00  180.00  000.00   0.0000
IC AC2'   AO2'   AP2    AO2T   0.0000  000.00  -39.52  000.00   0.0000
IC AO2T   AO2'   *AP2   AO1P   0.0000  000.00 -115.82  000.00   0.0000
IC AO2T   AO2'   *AP2   AO2P   0.0000  000.00  115.90  000.00   0.0000
IC AH2T   AO2T   AP2    AO2'   0.0000  000.00  180.00  000.00   0.0000
PATCH FIRST NONE LAST NONE   

RESI NDPH        -3.00  ! reduced nicotinamide adenine dinucleotide
                        ! NADPH, VARNAI/adm jr.
                        ! from RESI NADH and 3PHO
                        ! checked for consistency with new NA params, adm jr., 9/98
                        ! note that differences with respect to published results exist
                        ! due to new NA params
                        !
GROUP                   !
ATOM AC4' CN7     0.16  !                AH61  AH62
ATOM AH4' HN7     0.09  !                   \  /
ATOM AO4' ON6B   -0.50  !                   AN6
ATOM AC1' CN7B    0.16  !                    |
ATOM AH1' HN7     0.09  !                   AC6
GROUP                   !                  //  \
ATOM AC5  CN5     0.28  !                 AN1  AC5--AN7\\
ATOM AN7  NN4    -0.71  !                  |    ||     AC8-AH8
ATOM AC8  CN4     0.34  !                 AC2  AC4--AN9/
ATOM AH8  HN3     0.12  !                 / \\ /     \
ATOM AN9  NN2    -0.05  !              AH2  AN3       \
                        !                              \
ATOM AN1  NN3A   -0.74  !                               \
ATOM AC2  CN4     0.50  !                                \
ATOM AH2  HN3     0.13  !    NO1     AO1    AH5sAH4' AO4' \
ATOM AN3  NN3A   -0.75  !     |       |      |    \ /   \  \
ATOM AC4  CN5     0.43  ! NO5'NP-O3--AP-AO5'-AC5'-AC4'   AC1'
ATOM AC6  CN2     0.46  ! \   |       |      |     \     / \
                        !  \ NO2     AO2    AH5' AC3'-AC2' AH1'
ATOM AN6  NN1    -0.77  !   \                     / \   / \
ATOM AH61 HN1     0.38  !    \                AO3' AH3'AO2'AH2'
ATOM AH62 HN1     0.38  !     \                |        |
GROUP                   !      \             AH3T AO1P=AP2==AO2P (-)
ATOM AC2' CN7B    0.01  !       \                       |    NH71
ATOM AH2' HN7     0.09  !        \                AH2T-AO2T   /
ATOM AO2' ON2    -0.62  !         \                    NH72-NN7  NH4 NH42
ATOM AP2  P       1.50  !          \                          \    \ /
ATOM AO1P ON3    -0.82  !           \                         NC7  NC4
ATOM AO2P ON3    -0.82  !            \                        / \  /  \
ATOM AO2T ON4    -0.68  !             \                    NO7  NC3  NC5-NH5
ATOM AH2T HN4     0.34  !              \                          |    |
GROUP                   !               \                         |    |
ATOM AC3' CN7     0.14  !                \ NH5s NH4'NO4'      NH2-NC2 NC6-NH6
ATOM AH3' HN7     0.09  !                 \ |    \ /   \           \   /
ATOM AO3' ON5    -0.66  !                  NC5'--NC4'   NC1'--------NN1
ATOM AH3T HN5     0.43  !                   |     \     / \
GROUP                   !                 NH5'   NC3'-NC2'NH1'
ATOM AC5' CN8B   -0.08  !                        / \   / \  
ATOM AH5' HN8     0.09  !                    NO3' NH3'NO2'NH2'  
ATOM AH5s HN8     0.09  !                     |       |
ATOM AP   P       1.50  !                    NH3T    NH2T   
ATOM AO1  ON3    -0.82  !                   
ATOM AO2  ON3    -0.82  !                    
ATOM AO5' ON2    -0.62  !                   
ATOM O3   ON2    -0.68
ATOM NP   P       1.50
ATOM NO1  ON3    -0.82
ATOM NO2  ON3    -0.82
ATOM NO5' ON2    -0.62
ATOM NC5' CN8B   -0.08
ATOM NH5s HN8     0.09
ATOM NH5' HN8     0.09
GROUP
ATOM NC2' CN7B    0.14
ATOM NH2' HN7     0.09
ATOM NO2' ON5    -0.66
ATOM NH2T HN5     0.43
GROUP
ATOM NC3' CN7     0.14
ATOM NH3' HN7     0.09
ATOM NO3' ON5    -0.66
ATOM NH3T HN5     0.43
GROUP
ATOM NC1' CN7B    0.16
ATOM NH1' HN7     0.09
ATOM NC4' CN7     0.16
ATOM NH4' HN7     0.09
ATOM NO4' ON6B   -0.50
GROUP
ATOM NN1  NN2    -0.27 !N2
ATOM NC6  CN3C   -0.06 !C3
ATOM NH6  HN6     0.17 !H4
ATOM NC5  CN3    -0.18 !C5
ATOM NH5  HN6     0.14 !H6
ATOM NC4  CN8    -0.28 !C7
ATOM NH4  HN8     0.09 !H8
ATOM NH42 HN8     0.09 !H17
ATOM NC3  CN3     0.36 !C9
ATOM NC2  CN3C   -0.10 !C10
ATOM NH2  HN6     0.14 !H11
ATOM NC7  CN1A    0.55 !C12
ATOM NO7  ON1    -0.51 !O13
ATOM NN7  NN1    -0.72 !N14
ATOM NH71 HN1     0.26 !H15  ! trans to amide O
ATOM NH72 HN1     0.32 !H16  ! cis to amide O
BOND AN1  AC2       AN3  AC4       AC5  AC6
BOND AC6  AN6       AC5  AN7       AC8  AN9
BOND AN9  AC4       AC2  AH2       AN6  AH61      AN6  AH62      AC8  AH8
DOUBLE AC6  AN1       AC2  AN3       AC4  AC5      AN7  AC8
BOND AN9  AC1'      AC1' AC2'      AC2' AC3'      AC3' AC4'      AC4' AO4'
BOND AO4' AC1'      AC1' AH1'      AC2' AO2'      AO2' AP2       AC2' AH2'
BOND AC3' AH3'      AC3' AO3'      AO3' AH3T      AC4' AH4'      AC4' AC5'
BOND AC5' AH5s      AC5' AH5'      AC5' AO5'      AO5' AP        AP   AO1
BOND AP   AO2       AP   O3        O3   NP        NP   NO1       NP   NO2
BOND NP   NO5'      NO5' NC5'      NC5' NH5s      NC5' NH5'      NC5' NC4'
BOND NC4' NO4'      NO4' NC1'      NC1' NC2'      NC2' NC3'      NC3' NC4'
BOND NC1' NH1'      NC2' NH2'      NC2' NO2'      NO2' NH2T      NC3' NH3'
BOND NC3' NO3'      NO3' NH3T      NC4' NH4'      NC1' NN1       NN1  NC2
BOND NC3  NC4       NC5  NC6       
BOND NC2  NH2       NC3  NC7       NC7  NO7       NC7  NN7       NN7  NH71
BOND NN7  NH72      NC4  NH4       NC4  NH42      NC5  NH5       NC6  NH6
BOND AP2  AO1P      AP2  AO2P      AP2  AO2T      AO2T AH2T
DOUBLE NC2  NC3       NC4  NC5       NC6  NN1
! adenine impropers
IMPR AN6  AC6    AH61 AH62   AC6   AN1   AC5   AN6
! amide impropers
IMPR NC7   NN7   NC3  NO7    NC7   NC3   NN7   NO7
IMPR NN7   NC7   NH71 NH72   NN7   NC7   NH72  NH71
! ring hydrogen impropers
IMPR NC6   NN1   NC5  NH6    NC5   NC6   NC4   NH5
IMPR NC4   NC5   NC3  NH4    NC2   NC3   NN1   NH2
DONO AH61 AN6
DONO AH62 AN6
DONO AH3T AO3'
ACCE AN1
ACCE AN3
ACCE AN7
ACCE AO4'
ACCE AO3'
ACCE AO5'
ACCE AO1  AP
ACCE AO2  AP
ACCE O3
ACCE NO1  NP
ACCE NO2  NP
ACCE NO5'
ACCE NO4'
ACCE NO3'
ACCE NO2'
ACCE NO7
DONO NH2T NO2'
DONO NH3T NO3'
DONO NH71 NN7
DONO NH72 NN7
DONO AH2T AO2T
ACCE AO2T
ACCE AO1P
ACCE AO2P
ACCE AO2' 
! the following ICs will not totally IC BUILD NADPH
IC AP     O3     NP     NO5'   1.5477  110.11  175.47   98.59   1.5945
IC AC5'   AO5'   AP     O3     1.4379  124.23 -120.69   96.29   1.5477
IC AC5'   AO5'   AP     AO2    1.4379  124.23   -4.20  104.25   1.4838
IC AH5S   AC5'   AC4'   AC3'   1.1127  107.45 -172.00  111.64   1.5309
IC AP     O3     NP     NO1    1.5477  110.11   63.14  114.14   1.4739
IC AP     O3     NP     NO2    1.5477  110.11  -73.96  111.08   1.4835
IC AP     AO5'   AC5'   AC4'   1.5968  124.23  104.17  111.45   1.5366
IC AO1    AP     AO5'   AC5'   1.4736  106.06  122.59  124.23   1.4379
IC AO5'   AC5'   AC4'   AC3'   1.4379  111.45  -54.02  111.64   1.5309
IC AC5'   AC4'   AC3'   AO3'   1.5366  111.64  117.91  108.23   1.4176
IC AH3T   AO3'   AC3'   AC4'   0.9780  101.86  -77.83  108.23   1.5309
IC AO4'   AC3'   *AC4   AC5'   3.7210   30.68   12.44   22.46   6.0953
IC AC2'   AC4'   *AC3'  AO3'   1.5171  107.22 -123.00  108.23   1.4176
IC AC4'   AC3'   AC2'   AC1'   1.5309  107.22  -27.93   98.01   1.5397
IC AC3'   AC2'   AC1'   AN9    1.5171   98.01  168.03  114.25   1.4756
IC AO4'   AC1'   AN9    AC4    1.4308  112.85 -160.05  123.87   1.3958
IC AC1'   AC4    *AN9   AC8    1.4756  123.87  160.62  105.30   1.3614
IC AC4    AN9    AC8    AN7    1.3958  105.30    2.73  114.72   1.3222
IC AC8    AN9    AC4    AC5    1.3614  105.30   -0.85  105.33   1.3777
IC AC8    AN7    AC5    AC6    1.3222  102.89 -175.73  131.43   1.4163
IC AN7    AC5    AC6    AN1    1.3877  131.43  177.76  117.35   1.3499
IC AC5    AC6    AN1    AC2    1.4163  117.35    0.19  119.36   1.3330
IC AN9    AC5    *AC4   AN3    1.3958  105.33 -177.76  126.56   1.3567
IC AC5    AN1    *AC6   AN6    1.4163  117.35  178.91  119.82   1.3439
IC AN1    AC6    AN6    AH61   1.3499  119.82   -2.82  115.89   0.9932
IC AH61   AC6    *AN6   AH62   0.9932  115.89 -173.48  118.52   0.9961
IC AC5    AN1    *AC6   AN6    1.4163  117.35  178.91  119.82   1.3439
IC AN1    AC6    AN6    AH61   1.3499  119.82   -2.82  115.89   0.9932
IC AH61   AC6    *AN6   AH62   0.9932  115.89 -173.48  118.52   0.9961
IC AN9    AN7    *AC8   AH8    1.3614  114.72  173.63  127.58   1.0942
IC AN1    AN3    *AC2   AH2    1.3330  128.86  179.26  114.95   1.0940
IC AO4'   AC2'   *AC1'  AH1'   1.4308  104.32 -114.05  107.95   1.1153
IC AC1'   AC3'   *AC2   AH2'   4.3577   16.73  138.52   14.56   4.3331
IC AC2'   AC4'   *AC3'  AH3'   1.5171  107.22  118.77  114.33   1.1023
IC AC3'   AO4'   *AC4   AH4'   4.6236   30.68   55.38   18.92   5.2267
IC AC4'   AO5'   *AC5   AH5'   5.8410    8.40  125.34   12.50   6.6777
IC AC4'   AO5'   *AC5   AH5'   5.8410    8.40  125.34   12.50   6.6777
IC NC5'   NO5'   NP     NO2    1.4351  125.31   34.31  105.69   1.4835
IC NH5S   NC5'   NO5'   NP     1.1087  111.20   -6.79  125.31   1.5945
IC NH5'   NC5'   NO5'   NP     1.1115  107.95  108.24  125.31   1.5945
IC NP     NO5'   NC5'   NC4'   1.5945  125.31 -133.06  113.61   1.5644
IC NO5'   NC5'   NC4'   NC3'   1.4351  113.61   37.01  114.92   1.5111
IC NC5'   NC4'   NC3'   NC2'   1.5644  114.92   71.49   99.06   1.5369
IC NC4'   NC3'   NC2'   NC1'   1.5111   99.06   54.76   97.08   1.5500
IC NC3'   NC2'   NC1'   NO4'   1.5369   97.08  -39.12  103.14   1.4628
IC NC2'   NC1'   NO4'   NC4'   1.5500  103.14    9.47  109.09   1.4960
IC NO2'   NC2'   NC1'   NO4'   1.4207  114.02 -166.39  103.14   1.4628
IC NH2T   NO2'   NC2'   NC1'   0.9638  100.52  -89.37  114.02   1.5500
IC NO4'   NC2'   *NC1'  NH1'   1.4628  103.14 -111.22  105.40   1.1096
IC NC1'   NC3'   *NC2   NH2'   2.4663   46.96  -41.97   34.01   3.9460
IC NC2'   NC4'   *NC3   NH3'   3.9136   23.54 -115.76   16.12   3.6674
IC NC3'   NO4'   *NC4   NH4'   5.4003   24.61  -39.21   14.97   6.7904
IC NC4'   NO5'   *NC5   NH5'   5.9665   13.65  -41.47   15.17   7.7670
IC NC4'   NO5'   *NC5   NH5S   5.9665   13.65  -87.41   13.92   6.7251
IC NC3'   NC2'   NC1'   NN1    1.5369   97.08   88.64  116.58   1.5502
IC NO3'   NC3'   NC2'   NC1'   1.4176  119.76 -172.52   97.08   1.5500
IC NH3T   NO3'   NC3'   NC2'   0.9717  103.61   17.81  119.76   1.5369
IC NC2'   NC1'   NN1    NC2    1.5500  116.58  -19.65  116.34   1.3499
IC NC1'   NN1    NC2    NC3    1.5502  116.34  134.66  130.57   1.3607
IC NN1    NC2    NC3    NC4    1.3499  130.57    5.82  111.74   1.5356
IC NC2    NC3    NC4    NC5    1.3607  111.74   -1.05  119.26   1.5319
IC NC3    NC4    NC5    NC6    1.5356  119.26   -1.26  113.69   1.3745
IC NC4    NC5    NC6    NN1    1.5319  113.69   -0.29  128.15   1.3388
IC NC5    NC6    NN1    NC2    1.3745  128.15    4.14  116.26   1.3499
IC NN1    NC2    NC3    NC7    1.3499  130.57 -147.46  122.72   1.5282
IC NC2    NC3    NC7    NO7    1.3607  122.72 -140.47  119.41   1.2169
IC NC2    NC3    NC7    NN7    1.3607  122.72   46.61  116.68   1.3621
IC NO7    NC7    NN7    NH71   1.2169  123.49 -177.07  120.21   1.0093
IC NO7    NC7    NN7    NH72   1.2169  123.49   -4.94  119.16   1.0014
IC NC2    NC3    NC4    NH4    1.3607  111.74 -135.39  112.16   1.1099
IC NC2    NC3    NC4    NH42   1.3607  111.74  114.48  103.52   1.1129
IC NC3    NC4    NC5    NH5    1.5356  119.26 -171.18  122.65   1.0912
IC NC4    NC5    NC6    NH6    1.5319  113.69  179.92  118.00   1.0878
IC NC6    NN1    NC2    NH2    1.3388  116.26  162.03  117.47   1.0731
IC AC3'   AC2'   AO2'   AP2    0.0000  000.00  180.00  000.00   0.0000
IC AC2'   AO2'   AP2    AO2T   0.0000  000.00  -39.52  000.00   0.0000
IC AO2T   AO2'   *AP2   AO1P   0.0000  000.00 -115.82  000.00   0.0000
IC AO2T   AO2'   *AP2   AO2P   0.0000  000.00  115.90  000.00   0.0000
IC AH2T   AO2T   AP2    AO2'   0.0000  000.00  180.00  000.00   0.0000
PATCH FIRST NONE LAST NONE

! below are residues and patches added for the 97/98 optimization
! and extension of the na all-atom parameters

RESI THF          0.00  ! tetrahydrofuran, for MOLVIB
!
GROUP
ATOM O4'  ON6    -0.50  !      H41'  O4'  H11'
ATOM C4'  CN8     0.07  !        \  /  \  /
ATOM C3'  CN8    -0.18  !   H42'--C4'  C1'--H12'
ATOM C2'  CN8    -0.18  !          |    |
ATOM C1'  CN8     0.07  !   H31'--C3'--C2'--H21'
ATOM H11' HN8     0.09  !        /       \
ATOM H12' HN8     0.09  !      H32'      H22'
ATOM H21' HN8     0.09  !
ATOM H22' HN8     0.09  !
ATOM H31' HN8     0.09  !
ATOM H32' HN8     0.09  !
ATOM H41' HN8     0.09  !
ATOM H42' HN8     0.09  !

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'
BOND C1'  H11' 	C1'  H12' C2' H21' C2'  H22' C3'  H31' C3'  H32'
BOND C4'  H41'  C4'  H42'
PATC  FIRS NONE LAST NONE

RESI THFM       0.00 ! Methyl-tetrahydrofuran
GROUP
ATOM O4'  ON6    -0.50  !    H52' H53'
ATOM C1'  CN8     0.07  !      \  /
ATOM C2'  CN8    -0.18  !  H51'-C5'  O4'  H11'
ATOM C3'  CN8    -0.18  !        \  /  \  /
ATOM C4'  CN8     0.16  !   H42'--C4'  C1'--H12'
ATOM H11' HN8     0.09  !          |    |
ATOM H12' HN8     0.09  !   H31'--C3'--C2'--H21'
ATOM H21' HN8     0.09  !        /       \
ATOM H22' HN8     0.09  !      H32'      H22'
ATOM H31' HN8     0.09  !
ATOM H32' HN8     0.09  !
ATOM H42' HN7     0.09  !
GROUP                   !
ATOM C5'  CN9    -0.27  !
ATOM H51' HN9     0.09  !
ATOM H52' HN9     0.09  !
ATOM H53' HN9     0.09  !

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C4'  C5'
BOND C1'  H11' C1'  H12' C2'  H21' C2'  H22' C3'  H31' C3'  H32'
BOND C4'  H42' C5'  H51' C5'  H52' C5'  H53'

! methyl- tetrahydrofuran guess conformation
! From Nicolas: the following guess conformation contains a
! mistake because it builds the H3' and H3'' atoms at the same point.
! So, I have commented out the following ic table
!IC   C4'  O4' C1'   C2'    1.4556  110.31  -14.32  105.78   1.5315
!IC   O4'  C1' C2'   C3'    1.4200  105.78   32.55  102.71   1.5248
!IC   C1'  C2' C3'   C4'    1.5315  102.71  -36.74  101.19   1.5432
!IC   C2'  C3' C4'   O4'    1.5248  101.19   29.12  105.88   1.4556
!IC   C3'  C4' O4'   C1'    1.5432  105.88   -9.56  110.31   1.4200
!IC   H1'  C1' C2'   C3'    1.1024  109.82  -83.66  102.71   1.5248
!IC   H1'' C1' C2'   C3'    1.1024  109.82  154.66  102.71   1.5248
!IC   H2'  C2' C3'   C4'    1.0992  111.36 -156.17  101.19   1.5432
!IC   H2'' C2' C3'   C4'    1.0994  109.88   81.56  101.19   1.5432
!IC   H3'  C3' C4'   O4'    1.1016  110.76  146.70  105.88   1.4556
!IC   H3'' C3' C4'   O4'    1.1016  110.76  146.70  105.88   1.4556
!IC   H4'' C4' O4'   C1'    1.1012  107.70 -126.13  110.31   1.4200
!IC   C5'  C4' O4'   C1'    1.4102  105.70  139.13  110.31   1.4200
!IC   H51  C5' C4'   O4'    1.0802  110.70  175.13  105.31   1.4556
!IC   H52  C5' C4'   O4'    1.0802  110.70  -63.99  105.31   1.4556
!IC   H53  C5' C4'   O4'    1.0802  110.70   55.99  105.31   1.4556
! From Nicolas: the following ic table builds thfch3 in its
! energy minimized conformation, with the above ic table ('guess
! conformation as starting structure)
!IC   C4'     O4'     C1'     C2'    1.4416  109.61    0.45  106.74   1.5328
!IC   O4'     C1'     C2'     C3'    1.4471  106.74  -21.92  103.38   1.5200
!IC   C1'     C2'     C3'     C4'    1.5328  103.38   33.49  102.18   1.5321
!IC   C2'     C3'     C4'     O4'    1.5200  102.18  -34.11  105.43   1.4416
!IC   C3'     C4'     O4'     C1'    1.5321  105.43   21.23  109.61   1.4471
!IC   H1'     C1'     C2'     C3'    1.1099  113.03 -141.96  103.38   1.5200
!IC   H1''    C1'     C2'     C3'    1.1111  111.16   93.50  103.38   1.5200
!IC   H2'     C2'     C3'     C4'    1.1135  109.13  -81.76  102.18   1.5321
!IC   H2''    C2'     C3'     C4'    1.1076  113.49  155.97  102.18   1.5321
!IC   H3'     C3'     C4'     O4'    1.1127  108.68   81.68  105.43   1.4416
!IC   H3''    C3'     C4'     O4'    1.1069  112.41 -156.66  105.43   1.4416
!IC   H4''    C4'     O4'     C1'    1.1127  106.71  -95.75  109.61   1.4471
!IC   C5'     C4'     O4'     C1'    1.5325  108.43  144.82  109.61   1.4471
!IC   H51     C5'     C4'     O4'    1.1092  110.48 -179.98  108.43   1.4416
!IC   H52     C5'     C4'     O4'    1.1104  110.01  -59.66  108.43   1.4416
!IC   H53     C5'     C4'     O4'    1.1106  109.99   59.68  108.43   1.4416


PATC  FIRS NONE LAST NONE

RESI THFO       0.00  ! 3'-hydroxyl-tetrahydrofuran
                      ! Atom types for aliphatic hydrogens based on nucleotide
GROUP
ATOM O4'  ON6    -0.50 !      H41'  O4'  H11'
ATOM C1'  CN7B    0.07 !        \  /  \  /
ATOM C2'  CN8    -0.18 !   H42'--C4'  C1'--H12'
ATOM C4'  CN7     0.07 !          |    |
ATOM H11' HN7     0.09 !   H31'--C3'--C2'--H21'
ATOM H12' HN7     0.09 !        /       \
ATOM H21' HN8     0.09 !      O3'       H22'
ATOM H22' HN8     0.09 !       |
ATOM H41' HN7     0.09 !      H32'
ATOM H42' HN7     0.09
GROUP
ATOM C3'  CN7     0.14
ATOM H31' HN7     0.09
ATOM O3'  ON5    -0.66 
ATOM H32' HN5     0.43

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C3'  O3'
BOND C1'  H11' C1'  H12' C2'  H21' C2'  H22' C3'  H31' C4'  H41'  
BOND C4'  H42' O3'  H32'
!Nicolas: the following IC are for thf-oh as optimized via ab initio calculations
IC   C4'     O4'     C1'     C2'    1.4055  108.09   23.45  106.18   1.5457
IC   O4'     C1'     C2'     C3'    1.4127  106.18    3.96  103.11   1.5346
IC   C1'     C2'     C3'     C4'    1.5457  103.11  -26.93  100.86   1.5211
IC   C2'     C3'     C4'     O4'    1.5346  100.86   41.73  103.15   1.4055
IC   C3'     C4'     O4'     C1'    1.5211  103.15  -41.62  108.09   1.4127
IC   H11'    C1'     C2'     C3'    1.0856  111.62  123.53  103.11   1.5346
IC   H12'    C1'     C2'     C3'    1.0818  113.32 -114.11  103.11   1.5346
IC   H21'    C2'     C3'     C4'    1.0846  110.65   91.68  100.86   1.5211
IC   H22'    C2'     C3'     C4'    1.0822  110.88 -148.45  100.86   1.5211
IC   H31'    C3'     C4'     O4'    1.0806  113.53  162.89  103.15   1.4055
IC   H41'    C4'     O4'     C1'    1.0891  110.89   77.76  108.09   1.4127
IC   H42'    C4'     O4'     C1'    1.0808  108.72 -162.12  108.09   1.4127
IC   O3'     C3'     C4'     O4'    1.4028  110.98  -77.39  103.15   1.4055
IC   H32'    O3'     C3'     C4'    0.9492  108.72   44.80  110.98   1.5211
PATC  FIRS NONE LAST NONE

RESI THFI       0.00   ! imidazole analog with THF ring
! Sugar: transferred from thf; used for optimization of chi, therefore
! the sugar carbon atom types are not rigorously correct
! Atom types for aliphatic hydrogens based on nucleotide

GROUP   
ATOM O4'  ON6    -0.50 !      H41'  O4'  Imidazole
ATOM C1'  CN7B    0.16 !        \  /  \  /
ATOM H12' HN7     0.09 !   H42'--C4'  C1'--H12'
ATOM C4'  CN7     0.07 !          |    |
ATOM H41' HN7     0.09 !   H31'--C3'--C2'--H21'
ATOM H42' HN7     0.09 !        /       \
GROUP                  !      H32'      H22'
ATOM C2'  CN8    -0.18 !
ATOM H21' HN8     0.09 !
ATOM H22' HN8     0.09 !
GROUP                  !
ATOM C3'  CN7    -0.18 !
ATOM H31' HN7     0.09 !
ATOM H32' HN7     0.09 !
GROUP	! Imidazole: transferred from isolated imidazole (IMIA)
ATOM CG   CPH1  -0.05 !     C1'       HE1
ATOM HG   HR3    0.09 !       \       /
ATOM CD2  CPH1   0.22 !       ND1---CE1
ATOM HD2  HR3    0.10 !      /       |
ATOM ND1  NR1   -0.04 ! HG-CG        |
ATOM CE1  CPH2   0.25 !      \       |
ATOM HE1  HR1    0.13 !      CD2---NE2
ATOM NE2  NR2   -0.70 !       |
                      !      HD2

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C1'  ND1
BOND C1'  H12' C2'  H21' C2'  H22' C3'  H31' C3'  H32'
BOND C4'  H41' C4'  H42'
BOND ND1  CE1  CE1  NE2  NE2  CD2  CD2  CG  CG  ND1
BOND CE1  HE1  CD2  HD2  CG  HG
! KEEPS HYDROGENS IN RING PLANE
IMPR ND1  CG   CE1  C1'       ND1  CE1  CG   C1'
IMPR CD2  CG   NE2  HD2       CD2  NE2  CG   HD2
IMPR CE1  ND1  NE2  HE1       CE1  NE2  ND1  HE1
IMPR CG   CD2  ND1  HG        CG   ND1  CD2  HG
! ic table for thfim, from Nicolas:
IC 	C1'	C2'	C3'	C4' 	0.0 0.0 324.92 0.0 0.0
IC	C2'	C3'	C4' 	O4' 	0.0 0.0 33.390 0.0 0.0
IC 	H12'	C1'	C2'	C3' 	0.0 0.0 268.35 0.0 0.0
IC 	H21'	C2'	C3'	C4' 	0.0 0.0 82.530 0.0 0.0
IC 	H22'	C2'	C3'	C4' 	0.0 0.0 204.06 0.0 0.0
IC 	H31'	C3'	C4'	O4' 	0.0 0.0 155.99 0.0 0.0
IC 	H32'	C3'	C4'	O4' 	0.0 0.0 276.70 0.0 0.0
IC	H41'	C4'	O4'	C1' 	0.0 0.0 132.30 0.0 0.0
IC 	H42'	C4'	O4'	C1' 	0.0 0.0 220.70 0.0 0.0
IC	C4'	O4'	C1'	ND1 	0.0 0.0 256.98 0.0 0.0
IC 	O4'	C1'	ND1	CE1 	0.0 0.0 180.00 0.0 0.0
IC	C1'	ND1	CE1     NE2 	0.0 0.0 181.56 0.0 0.0
IC	ND1	CE1	NE2	CD2 	0.0 0.0   0.34 0.0 0.0
IC 	CE1	NE2	CD2	CG 	0.0 0.0   0.00 0.0 0.0 
IC 	HE1	CE1	NE2	CD2 	0.0 0.0 180.40 0.0 0.0
IC	CE1	NE2	CD2	HD2 	0.0 0.0 179.83 0.0 0.0
IC 	NE2 	CD2	CG 	HG 	0.0 0.0 178.45 0.0 0.0
PATC  FIRS NONE LAST NONE

RESI THMI       0.00   ! thf-ch3-imidazole
! C5' has been declared as CN8, and C3' as CN7, for compatibility
! with DNA, but these carbons are rigorously CN9 and CN8 respectively

! Atom types for aliphatic hydrogens based on nucleotide

GROUP   ! Sugar: transferred from thf
ATOM O4'  ON6    -0.50 !    H52' H53'
ATOM C1'  CN7B    0.16 !      \  /
ATOM H12' HN7     0.09 !  H51'-C5'  O4'  Imidazole
ATOM C4'  CN7     0.16 !        \  /  \  /
ATOM H42' HN7     0.09 !   H42'--C4'  C1'--H12'
GROUP                  !          |    |
ATOM C2'  CN8    -0.18 !   H31'--C3'--C2'--H21'
ATOM H21' HN8     0.09 !        /       \
ATOM H22' HN8     0.09 !      H32'      H22'
GROUP
ATOM C3'  CN7    -0.18
ATOM H31' HN7     0.09
ATOM H32' HN7     0.09
GROUP
ATOM C5'  CN8B   -0.27
ATOM H51' HN8     0.09
ATOM H52' HN8     0.09
ATOM H53' HN8     0.09
GROUP	! Imidazole: transferred from isolated imidazole (IMIA)
ATOM CG   CPH1   -0.05 !     C1'       HE1
ATOM HG   HR3     0.09 !       \       /
ATOM CD2  CPH1    0.22 !       ND1---CE1
ATOM HD2  HR3     0.10 !      /       ||
ATOM ND1  NR1    -0.04 !  HG-CG       ||
ATOM CE1  CPH2    0.25 !      \\      ||
ATOM HE1  HR1     0.13 !       CD2---NE2
ATOM NE2  NR2    -0.70 !        |
                       !       HD2

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C1'  ND1
BOND C1'  H12' C2'  H21' C2'  H22' C3'  H31' C3'  H32'
BOND C4'  H42' C4'  C5'  C5'  H51' C5'  H52' C5'  H53'
BOND ND1  CE1  NE2  CD2  CG  ND1
BOND CE1  HE1  CD2  HD2  CG  HG
DOUBLE CG  CD2   CE1  NE2

! KEEPS HYDROGENS IN RING PLANE
IMPR ND1  CG  CE1  C1'       ND1  CE1  CG   C1'
IMPR CD2  CG  NE2  HD2       CD2  NE2  CG   HD2
IMPR CE1  ND1 NE2  HE1       CE1  NE2  ND1  HE1
IMPR CG  CD2  ND1  HG        CG   ND1  CD2  HG
! ic table for thfim, from Nicolas:
IC 	C1'	C2'	C3'	C4' 	0.0 0.0 324.92 0.0 0.0
IC	C2'	C3'	C4' 	O4' 	0.0 0.0 33.390 0.0 0.0
IC 	H12'	C1'	C2'	C3' 	0.0 0.0 268.35 0.0 0.0
IC 	H21'	C2'	C3'	C4' 	0.0 0.0 82.530 0.0 0.0
IC 	H22'	C2'	C3'	C4' 	0.0 0.0 204.06 0.0 0.0
IC 	H31'	C3'	C4'	O4' 	0.0 0.0 155.99 0.0 0.0
IC 	H32'	C3'	C4'	O4' 	0.0 0.0 276.70 0.0 0.0
IC	C5'	C4'	O4'	C1' 	0.0 0.0 132.30 0.0 0.0
IC      H51'    C5'     C4'     O4'     0.0 0.0 -179.98 0.0 0.0
IC      H52'    C5'     C4'     O4'     0.0 0.0  -59.66 0.0 0.0
IC      H53'    C5'     C4'     O4'     0.0 0.0   59.68 0.0 0.0
IC 	H42'	C4'	O4'	C1' 	0.0 0.0 220.70 0.0 0.0
IC	C4'	O4'	C1'	ND1 	0.0 0.0 256.98 0.0 0.0
IC 	O4'	C1'	ND1	CE1 	0.0 0.0 180.00 0.0 0.0
IC	C1'	ND1	CE1     NE2 	0.0 0.0 181.56 0.0 0.0
IC	ND1	CE1	NE2	CD2 	0.0 0.0   0.34 0.0 0.0
IC 	CE1	NE2	CD2	CG 	0.0 0.0   0.00 0.0 0.0 
IC 	HE1	CE1	NE2	CD2 	0.0 0.0 180.40 0.0 0.0
IC	CE1	NE2	CD2	HD2 	0.0 0.0 179.83 0.0 0.0
IC 	NE2 	CD2	CG 	HG 	0.0 0.0 178.45 0.0 0.0
PATC  FIRS NONE LAST NONE

RESI THFC        0.00  ! THF-3'-OH-4'-CH3  

! Atom types for aliphatic hydrogens based on nucleotide

GROUP
ATOM O4'  ON6    -0.50 !    H52' H53'
ATOM C1'  CN8     0.07 !      \  /
ATOM H11' HN8     0.09 !  H51'-C5'  O4'  H11'
ATOM H12' HN8     0.09 !        \  /  \  /
ATOM C4'  CN7     0.16 !   H42'--C4'  C1'--H12'
ATOM H42' HN7     0.09 !          |    |
GROUP                  !   H31'--C3'--C2'--H21'
ATOM C2'  CN8    -0.18 !        /       \
ATOM H21' HN8     0.09 !      O3'       H22'
ATOM H22' HN8     0.09 !       |
GROUP                  !      H32'
ATOM H31' HN7     0.09
ATOM C3'  CN7     0.14 
ATOM O3'  ON5    -0.66
ATOM H32' HN5     0.43 
GROUP 
ATOM C5'  CN9    -0.27
ATOM H51' HN9     0.09
ATOM H52' HN9     0.09
ATOM H53' HN9     0.09
BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C4'  C5'
BOND C3'  O3'
BOND C1'  H11'      C1'  H12'
BOND C2'  H21'      C2'  H22'
BOND C3'  H31'
BOND C4'  H42'
BOND C5'  H51'      C5'  H52'      C5'  H53'
BOND O3'  H32'
PATC  FIRS NONE LAST NONE

RESI TH5P      -2.00 ! 5'-phosphate-methyl-tetrahydrofuran (phosphate -2)

! Atom types for aliphatic hydrogens based on nucleotide

GROUP                  !      O1P  (-2)
ATOM O4'  ON6    -0.50 !       ||
ATOM C1'  CN7B    0.07 !  O2P==P==O2P
ATOM H1'  HN7     0.09 !       |
ATOM H1'' HN7     0.09 !  H5'' |
ATOM C4'  CN7     0.16 !     \ |
ATOM H4'' HN7     0.09 ! H5'--C5'   O4'  H1'
GROUP                  !        \  /  \  /
ATOM C2'  CN8    -0.18 !    H4'--C4'  C1'--H1''
ATOM H2'  HN8     0.09 !          |    |
ATOM H2'' HN8     0.09 !    H3'--C3'--C2'--H2'
GROUP                  !        /       \
ATOM C3'  CN7    -0.18 !      H3''      H2''
ATOM H3'  HN7     0.09 !
ATOM H3'' HN7     0.09
GROUP
ATOM C5'  CN8B   -0.18
ATOM H5'  HN8     0.09
ATOM H5'' HN8     0.09
GROUP
ATOM O5'  ON2    -0.40
ATOM P    P       1.10
ATOM O1P  ON3    -0.90
ATOM O2P  ON3    -0.90
ATOM O3P  ON3    -0.90

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C4'  C5'
BOND C1'  H1'  C1'  H1'' C2'  H2'  C2'  H2'' C3'  H3'  C3'  H3'' 
BOND C4'  H4'' C5'  H5'  C5'  H5'' C5'  O5'  O5'  P    P    O1P
BOND P    O2P  P    O3P
IC   C4'     O4'     C1'     C2'    1.4416  109.61    0.45  106.74   1.5328
IC   O4'     C1'     C2'     C3'    1.4471  106.74  -21.92  103.38   1.5200
IC   C1'     C2'     C3'     C4'    1.5328  103.38   33.49  102.18   1.5321
IC   C2'     C3'     C4'     O4'    1.5200  102.18  -34.11  105.43   1.4416
IC   C3'     C4'     O4'     C1'    1.5321  105.43   21.23  109.61   1.4471
IC   H1'     C1'     C2'     C3'    1.1099  113.03 -141.96  103.38   1.5200
IC   H1''    C1'     C2'     C3'    1.1111  111.16   93.50  103.38   1.5200
IC   H2'     C2'     C3'     C4'    1.1135  109.13  -81.76  102.18   1.5321
IC   H2''    C2'     C3'     C4'    1.1076  113.49  155.97  102.18   1.5321
IC   H3'     C3'     C4'     O4'    1.1127  108.68   81.68  105.43   1.4416
IC   H3''    C3'     C4'     O4'    1.1069  112.41 -156.66  105.43   1.4416
IC   H4''    C4'     O4'     C1'    1.1127  106.71  -95.75  109.61   1.4471
IC   C5'     C4'     O4'     C1'    1.5325  108.43  144.82  109.61   1.4471
IC   H51'    C5'     C4'     O4'    1.1092  110.48  180.00  108.43   1.4416
IC   H52'    C5'     C4'     O4'    1.1104  110.01  -60.00  108.43   1.4416
IC   O4'     C4'     C5'     O5'    0.0       0.0    60.00    0.0    0.0   
IC   C4'     C5'     O5'     P      0.0       0.0   180.0     0.0    0.0 	
IC   C5'     O5'     P       O1P    0.0       0.0   -60.0     0.0    0.0
IC   C5'     O5'     P       O2P    0.0       0.0   180.0     0.0    0.0
IC   C5'     O5'     P       O3P    0.0       0.0   60.0      0.0    0.0 
PATC  FIRS NONE LAST NONE

RESI TH5H         0.00 ! 5'-hydroxy-methyl-tetrahydrofuran (phosphate -2)

! Atom types for aliphatic hydrogens based on nucleotide

                       !          H5T
GROUP                  !         /
ATOM O4'  ON6    -0.50 !  H5'' O5'
ATOM C1'  CN7B    0.07 !     \ |
ATOM H1'  HN7     0.09 ! H5'--C5'   O4'  H1'
ATOM H1'' HN7     0.09 !        \  /  \  /
ATOM C4'  CN7     0.16 !    H4'--C4'  C1'--H1''
ATOM H4'' HN7     0.09 !          |    |
GROUP                  !    H3'--C3'--C2'--H2'
ATOM C2'  CN8    -0.18 !        /       \
ATOM H2'  HN8     0.09 !      H3''      H2''
ATOM H2'' HN8     0.09 
GROUP
ATOM C3'  CN7    -0.18
ATOM H3'  HN7     0.09
ATOM H3'' HN7     0.09
GROUP
ATOM C5'  CN8B    0.05
ATOM H5'  HN8     0.09
ATOM H5'' HN8     0.09
ATOM O5'  ON5    -0.66
ATOM H5T  HN5     0.43

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C4'  C5'
BOND C1'  H1'  C1'  H1'' C2'  H2'  C2'  H2'' C3'  H3'  C3'  H3'' 
BOND C4'  H4'' C5'  H5'  C5'  H5'' C5'  O5'  O5'  H5T  

IC   C4'     O4'     C1'     C2'    1.4416  109.61    0.45  106.74   1.5328
IC   O4'     C1'     C2'     C3'    1.4471  106.74  -21.92  103.38   1.5200
IC   C1'     C2'     C3'     C4'    1.5328  103.38   33.49  102.18   1.5321
IC   C2'     C3'     C4'     O4'    1.5200  102.18  -34.11  105.43   1.4416
IC   C3'     C4'     O4'     C1'    1.5321  105.43   21.23  109.61   1.4471
IC   H1'     C1'     C2'     C3'    1.1099  113.03 -141.96  103.38   1.5200
IC   H1''    C1'     C2'     C3'    1.1111  111.16   93.50  103.38   1.5200
IC   H2'     C2'     C3'     C4'    1.1135  109.13  -81.76  102.18   1.5321
IC   H2''    C2'     C3'     C4'    1.1076  113.49  155.97  102.18   1.5321
IC   H3'     C3'     C4'     O4'    1.1127  108.68   81.68  105.43   1.4416
IC   H3''    C3'     C4'     O4'    1.1069  112.41 -156.66  105.43   1.4416
IC   H4''    C4'     O4'     C1'    1.1127  106.71  -95.75  109.61   1.4471
IC   C5'     C4'     O4'     C1'    1.5325  108.43  144.82  109.61   1.4471
IC   H5'     C5'     C4'     O4'    1.1092  110.48  180.00  108.43   1.4416
IC   H5''    C5'     C4'     O4'    1.1104  110.01  -60.00  108.43   1.4416
IC   O4'     C4'     C5'     O5'    0.0       0.0    60.00    0.0    0.0   
IC   C4'     C5'     O5'     H5T    0.0       0.0   180.0     0.0    0.0 	
PATC  FIRS NONE LAST NONE

RESI T5PH        -1.00 ! 5'-phosphate-methyl-tetrahydrofuran (phosphate -1)

! Atom types for aliphatic hydrogens based on nucleotide

GROUP
ATOM C5'  CN8B   -0.08 !
ATOM H5'  HN8     0.09 !      O1P    H5T
ATOM H5'' HN8     0.09 !      ||     /
ATOM O5'  ON2    -0.62 !  O2P==P==O3P
ATOM P    P       1.50 !       |
ATOM O1P  ON3    -0.82 !      O5'
ATOM O2P  ON3    -0.82 !       |
ATOM O3P  ON4    -0.68 !  H5'' |
ATOM H5T  HN4     0.34 !     \ |
GROUP                  ! H5'--C5'   O4'  H1'
ATOM O4'  ON6    -0.50 !        \  /  \  /
ATOM C1'  CN7B    0.07 !    H4'--C4'  C1'--H1''
ATOM H1'  HN7     0.09 !          |    |
ATOM H1'' HN7     0.09 !    H3'--C3'--C2'--H2'
ATOM C4'  CN7     0.16 !        /       \
ATOM H4'' HN7     0.09 !      H3''      H2''
GROUP                  !
ATOM C2'  CN8    -0.18
ATOM H2'  HN8     0.09
ATOM H2'' HN8     0.09 
GROUP
ATOM C3'  CN7    -0.18
ATOM H3'  HN7     0.09
ATOM H3'' HN7     0.09

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C4'  C5'
BOND C1'  H1'  C1'  H1'' C2'  H2'  C2'  H2'' C3'  H3'  C3'  H3'' 
BOND C4'  H4'' C5'  H5'  C5'  H5'' C5'  O5'  O5'  P    P    O1P
BOND P    O2P  P    O3P  O3P  H5T
IC   C4'     O4'     C1'     C2'    1.4416  109.61    0.45  106.74   1.5328
IC   O4'     C1'     C2'     C3'    1.4471  106.74  -21.92  103.38   1.5200
IC   C1'     C2'     C3'     C4'    1.5328  103.38   33.49  102.18   1.5321
IC   C2'     C3'     C4'     O4'    1.5200  102.18  -34.11  105.43   1.4416
IC   C3'     C4'     O4'     C1'    1.5321  105.43   21.23  109.61   1.4471
IC   H1'     C1'     C2'     C3'    1.1099  113.03 -141.96  103.38   1.5200
IC   H1''    C1'     C2'     C3'    1.1111  111.16   93.50  103.38   1.5200
IC   H2'     C2'     C3'     C4'    1.1135  109.13  -81.76  102.18   1.5321
IC   H2''    C2'     C3'     C4'    1.1076  113.49  155.97  102.18   1.5321
IC   H3'     C3'     C4'     O4'    1.1127  108.68   81.68  105.43   1.4416
IC   H3''    C3'     C4'     O4'    1.1069  112.41 -156.66  105.43   1.4416
IC   H4''    C4'     O4'     C1'    1.1127  106.71  -95.75  109.61   1.4471
IC   C5'     C4'     O4'     C1'    1.5325  108.43  144.82  109.61   1.4471
IC   H51'    C5'     C4'     O4'    1.1092  110.48  180.00  108.43   1.4416
IC   H52'    C5'     C4'     O4'    1.1104  110.01  -60.00  108.43   1.4416
IC   O4'     C4'     C5'     O5'    0.0       0.0    60.0     0.0    0.0   
IC   O4'     C4'     C5'     H5'    0.0       0.0   180.0     0.0    0.0   
IC   O4'     C4'     C5'     H5''   0.0       0.0   -60.0     0.0    0.0   
IC   C4'     C5'     O5'     P      0.0       0.0   180.0     0.0    0.0 	
IC   C5'     O5'     P       O1P    0.0       0.0   -60.0     0.0    0.0
IC   C5'     O5'     P       O2P    0.0       0.0   180.0     0.0    0.0
IC   C5'     O5'     P       O3P    0.0       0.0    60.0     0.0    0.0 
IC   O5'     P       O3P     H5T    0.0       0.0   180.0     0.0    0.0 
PATC  FIRS NONE LAST NONE

RESI TH3P        -2.00  ! 3'phosphate-hydroxyl-tetrahydrofuran (phosphate -2)
                        ! used to fit epsilon

! Atom types for aliphatic hydrogens based on nucleotide

GROUP
ATOM O4'  ON6    -0.50 !    H52' H53'
ATOM C1'  CN7B    0.07 !      \  /
ATOM H11' HN7     0.09 !  H51'-C5'  O4'  H11'
ATOM H12' HN7     0.09 !        \  /  \  /
ATOM C4'  CN7     0.07 !   H42'--C4'  C1'--H12'
ATOM H41' HN7     0.09 !          |    |
ATOM H42' HN7     0.09 !   H31'--C3'--C2'--H21'
GROUP                  !        /       \
ATOM C2'  CN8    -0.18 !      O3'       H22'
ATOM H21' HN8     0.09 !       |
ATOM H22' HN8     0.09 !  O1P==P==O2P
GROUP                  !       ||
ATOM C3'  CN7    -0.09 !      O3P (-2)
ATOM H31' HN7     0.09 !
GROUP
ATOM O3'  ON2    -0.40
ATOM P    P       1.10
ATOM O1P  ON3    -0.90
ATOM O2P  ON3    -0.90
ATOM O3P  ON3    -0.90

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C3'  O3'
BOND C1'  H11' C1'  H12' C2'  H21' C2'  H22' C3'  H31' C4'  H41'
BOND C4'  H42' O3'  P    P    O1P  P    O2P  P    O3P
IC   C4'     O4'     C1'     C2'    1.4055  108.09   23.45  106.18   1.5457
IC   O4'     C1'     C2'     C3'    1.4127  106.18    3.96  103.11   1.5346
IC   C1'     C2'     C3'     C4'    1.5457  103.11  -26.93  100.86   1.5211
IC   C2'     C3'     C4'     O4'    1.5346  100.86   41.73  103.15   1.4055
IC   C3'     C4'     O4'     C1'    1.5211  103.15  -41.62  108.09   1.4127
IC   H11'    C1'     C2'     C3'    1.0856  111.62  123.53  103.11   1.5346
IC   H12'    C1'     C2'     C3'    1.0818  113.32 -114.11  103.11   1.5346
IC   H21'    C2'     C3'     C4'    1.0846  110.65   91.68  100.86   1.5211
IC   H22'    C2'     C3'     C4'    1.0822  110.88 -148.45  100.86   1.5211
IC   H31'    C3'     C4'     O4'    1.0806  113.53  162.89  103.15   1.4055
IC   H41'    C4'     O4'     C1'    1.0891  110.89   77.76  108.09   1.4127
IC   H42'    C4'     O4'     C1'    1.0808  108.72 -162.12  108.09   1.4127
IC   O3'     C3'     C4'     O4'    1.4028  110.98  -77.39  103.15   1.4055
IC   P       O3'     C3'     C4'    0.0       0.0   180.00    0.0    0.0 
IC   O1P     P       O3'     C3'    0.0       0.0   -60.0     0.0    0.0
IC   O2P     P       O3'     C3'    0.0       0.0   180.0     0.0    0.0
IC   O3P     P       O3'     C3'    0.0       0.0    60.0     0.0    0.0
PATC  FIRS NONE LAST NONE

RESI T3PH        -1.00 ! monoanionic 3'phosphate-tetrahydrofuran 
                       ! used to fit epsilon

! Atom types for aliphatic hydrogens based on nucleotide

GROUP
ATOM O4'  ON6    -0.50 !
ATOM C1'  CN7B    0.07 !
ATOM H11' HN7     0.09 !      H41'  O4'  H11'
ATOM H12' HN7     0.09 !        \  /  \  /
ATOM C4'  CN7     0.07 !   H42'--C4'  C1'--H12'
ATOM H41' HN7     0.09 !          |    |
ATOM H42' HN7     0.09 !   H31'--C3'--C2'--H21'
GROUP                  !        /       \
ATOM C2'  CN8    -0.18 !      O3'       H22'
ATOM H21' HN8     0.09 !       |
ATOM H22' HN8     0.09 !  O1P==P==O2P
GROUP                  !       |
ATOM C3'  CN7     0.01 !      O3T  (-1)
ATOM H31' HN7     0.09 !        \
ATOM O3'  ON2    -0.62 !        H3T
ATOM P    P       1.50 !
ATOM O1P  ON3    -0.82
ATOM O2P  ON3    -0.82
ATOM O3T  ON4    -0.68
ATOM H3T  HN4     0.34

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C3'  O3'
BOND C1'  H11' C1'  H12' C2'  H21' C2'  H22' C3'  H31' C4'  H41'
BOND C4'  H42' O3'  P    P    O1P  P    O2P  P    O3T  O3T  H3T
IC   C4'     O4'     C1'     C2'    1.4055  108.09   23.45  106.18   1.5457
IC   O4'     C1'     C2'     C3'    1.4127  106.18    3.96  103.11   1.5346
IC   C1'     C2'     C3'     C4'    1.5457  103.11  -26.93  100.86   1.5211
IC   C2'     C3'     C4'     O4'    1.5346  100.86   41.73  103.15   1.4055
IC   C3'     C4'     O4'     C1'    1.5211  103.15  -41.62  108.09   1.4127
IC   H11'    C1'     C2'     C3'    1.0856  111.62  123.53  103.11   1.5346
IC   H12'    C1'     C2'     C3'    1.0818  113.32 -114.11  103.11   1.5346
IC   H21'    C2'     C3'     C4'    1.0846  110.65   91.68  100.86   1.5211
IC   H22'    C2'     C3'     C4'    1.0822  110.88 -148.45  100.86   1.5211
IC   H31'    C3'     C4'     O4'    1.0806  113.53  162.89  103.15   1.4055
IC   H41'    C4'     O4'     C1'    1.0891  110.89   77.76  108.09   1.4127
IC   H42'    C4'     O4'     C1'    1.0808  108.72 -162.12  108.09   1.4127
IC   O3'     C3'     C4'     O4'    1.4028  110.98  -77.39  103.15   1.4055
IC   P       O3'     C3'     C4'    0.0       0.0   180.00    0.0    0.0 
IC   O1P     P       O3'     C3'    0.0       0.0   -60.0     0.0    0.0
IC   O2P     P       O3'     C3'    0.0       0.0    60.0     0.0    0.0
IC   O3T     P       O3'     C3'    0.0       0.0   180.0     0.0    0.0
IC   H3T     O3T     P       O3'    0.0       0.0   180.0     0.0    0.0

PATC  FIRS NONE LAST NONE

RESI R3PH        -1.00 ! monoanionic 3'phosphate-tetrahydrofuran
                       ! with O2' hydroxyl. Used to fit C2'-O2' torsion in RNA

! Atom types for aliphatic hydrogens based on RNA nucleotide

GROUP
ATOM O4'  ON6B   -0.50 !
ATOM C1'  CN7B    0.07 !
ATOM H11' HN7     0.09 !      H41'  O4'  H11'
ATOM H12' HN7     0.09 !        \  /  \  /
ATOM C4'  CN7     0.07 !   H42'--C4'  C1'--H12'
ATOM H41' HN7     0.09 !          |    |
ATOM H42' HN7     0.09 !   H31'--C3'--C2'--H21'
GROUP                  !        /       \
ATOM C2'  CN7B    0.14 !      O3'       O2'
ATOM H21' HN7     0.09 !       |         |
ATOM O2'  ON5    -0.66 !  O1P==P==O2P   H22'
ATOM H22' HN5     0.43 !       |
GROUP                  !      O3T  (-1)
ATOM C3'  CN7     0.01 !        \
ATOM H31' HN7     0.09 !        H3T
ATOM O3'  ON2    -0.62 !
ATOM P    P       1.50
ATOM O1P  ON3    -0.82
ATOM O2P  ON3    -0.82
ATOM O3T  ON4    -0.68
ATOM H3T  HN4     0.34

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C3'  O3'
BOND C1'  H11' C1'  H12' C2'  H21' C2'  O2'  O2'  H22' C3'  H31' C4'  H41'
BOND C4'  H42' O3'  P    P    O1P  P    O2P  P    O3T  O3T  H3T
IC   C4'     O4'     C1'     C2'    1.4055  108.09   23.45  106.18   1.5457
IC   O4'     C1'     C2'     C3'    1.4127  106.18    3.96  103.11   1.5346
IC   C1'     C2'     C3'     C4'    1.5457  103.11  -26.93  100.86   1.5211
IC   C2'     C3'     C4'     O4'    1.5346  100.86   41.73  103.15   1.4055
IC   C3'     C4'     O4'     C1'    1.5211  103.15  -41.62  108.09   1.4127
IC   H11'    C1'     C2'     C3'    1.0856  111.62  123.53  103.11   1.5346
IC   H12'    C1'     C2'     C3'    1.0818  113.32 -114.11  103.11   1.5346
IC   H21'    C2'     C3'     C4'    1.0846  110.65   91.68  100.86   1.5211
IC   O2'     C2'     C3'     C4'    1.0822  110.88  283.41  100.86   1.5211
IC   H22'    O2'     C2'     C3'    1.0822  110.88    0.00  100.86   1.5211
IC   H31'    C3'     C4'     O4'    1.0806  113.53  162.89  103.15   1.4055
IC   H41'    C4'     O4'     C1'    1.0891  110.89   77.76  108.09   1.4127
IC   H42'    C4'     O4'     C1'    1.0808  108.72 -162.12  108.09   1.4127
IC   O3'     C3'     C4'     O4'    1.4028  110.98  -77.39  103.15   1.4055
IC   P       O3'     C3'     C4'    0.0       0.0   180.00    0.0    0.0
IC   O1P     P       O3'     C3'    0.0       0.0   -60.0     0.0    0.0
IC   O2P     P       O3'     C3'    0.0       0.0    60.0     0.0    0.0
IC   O3T     P       O3'     C3'    0.0       0.0   180.0     0.0    0.0
IC   H3T     O3T     P       O3'    0.0       0.0   180.0     0.0    0.0

PATC  FIRS NONE LAST NONE

RESI A3PH        -1.00 ! monoanionic 3'phosphate-tetrahydrofuran
                       ! with O2' hydroxyl in an arabinose (beta) conformation. 

! The furanose ring contains atom type CN7C, specific of arabinose 

GROUP
ATOM O4'  ON6    -0.50 !
ATOM C1'  CN7B    0.07 !
ATOM H11' HN7     0.09 !      H41'  O4'  H11'
ATOM H12' HN7     0.09 !        \  /  \  /
ATOM C4'  CN7     0.07 !   H42'--C4'  C1'--H12'
ATOM H41' HN7     0.09 !          |    |
ATOM H42' HN7     0.09 !   H31'--C3'--C2'--H21'
GROUP                  !        /       \
ATOM C2'  CN7C    0.14 !      O3'       O2'  O2' is beta
ATOM H22' HN7     0.09 !       |         |
ATOM O2'  ON5    -0.66 !  O1P==P==O2P   H22'
ATOM H21' HN5     0.43 !       |
GROUP                  !      O3T  (-1)
ATOM C3'  CN7     0.01 !        \
ATOM H31' HN7     0.09 !        H3T
ATOM O3'  ON2    -0.62 !
ATOM P    P       1.50
ATOM O1P  ON3    -0.82
ATOM O2P  ON3    -0.82
ATOM O3T  ON4    -0.68
ATOM H3T  HN4     0.34

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C3'  O3'
BOND C1'  H11' C1'  H12' C2'  H22' C2'  O2'  O2'  H21' C3'  H31' C4'  H41'
BOND C4'  H42' O3'  P    P    O1P  P    O2P  P    O3T  O3T  H3T
IC   C4'     O4'     C1'     C2'    1.4055  108.09   23.45  106.18   1.5457
IC   O4'     C1'     C2'     C3'    1.4127  106.18    3.96  103.11   1.5346
IC   C1'     C2'     C3'     C4'    1.5457  103.11  -26.93  100.86   1.5211
IC   C2'     C3'     C4'     O4'    1.5346  100.86   41.73  103.15   1.4055
IC   C3'     C4'     O4'     C1'    1.5211  103.15  -41.62  108.09   1.4127
IC   H11'    C1'     C2'     C3'    1.0856  111.62  123.53  103.11   1.5346
IC   H12'    C1'     C2'     C3'    1.0818  113.32 -114.11  103.11   1.5346
IC   H22'    C2'     C3'     C4'    1.0822  110.88  283.41  100.86   1.5211
IC   O2'     C2'     C3'     C4'    1.0846  110.65  120.00  100.86   1.5211
IC   H21'    O2'     C2'     C3'    1.0822  110.88  120.00  100.86   1.5211
IC   H31'    C3'     C4'     O4'    1.0806  113.53  162.89  103.15   1.4055
IC   H41'    C4'     O4'     C1'    1.0891  110.89   77.76  108.09   1.4127
IC   H42'    C4'     O4'     C1'    1.0808  108.72 -162.12  108.09   1.4127
IC   O3'     C3'     C4'     O4'    1.4028  110.98  -77.39  103.15   1.4055
IC   P       O3'     C3'     C4'    0.0       0.0   180.00    0.0    0.0
IC   O1P     P       O3'     C3'    0.0       0.0   -60.0     0.0    0.0
IC   O2P     P       O3'     C3'    0.0       0.0    60.0     0.0    0.0
IC   O3T     P       O3'     C3'    0.0       0.0   180.0     0.0    0.0
IC   H3T     O3T     P       O3'    0.0       0.0   180.0     0.0    0.0
PATC  FIRS NONE LAST NONE

RESI T3PM        -1.00 ! 3'phosphate-hydroxyl-tetrahydrofuran (phosphate -1)
                       ! capped with a methyl group. This is to investigate the differences
                       ! between BI and BII forms of DNA
                       ! C3T is defined as CN8B to miminck DNA
GROUP
ATOM O4'  ON6    -0.50 !
ATOM C1'  CN7B    0.07 !     H41'   O4'  H11'
ATOM H11' HN7     0.09 !        \  /  \  /
ATOM H12' HN7     0.09 !   H42'--C4'  C1'--H12'
ATOM C4'  CN7     0.07 !          |    |
ATOM H41' HN7     0.09 !   H31'--C3'--C2'--H21'
ATOM H42' HN7     0.09 !        /       \
GROUP                  !      O3'       H22'
ATOM C2'  CN8    -0.18 !       |
ATOM H21' HN8     0.09 !  O1P==P==O2P
ATOM H22' HN8     0.09 !       |
GROUP                  !      O3T  (-1)
ATOM C3'  CN7     0.01 !        \
ATOM H31' HN7     0.09 !        C3T--H3T3
GROUP                  !       /  \
ATOM O3'  ON2    -0.57 !    H3T1 H3T2
ATOM P    P       1.50 !
ATOM O1P  ON3    -0.78
ATOM O2P  ON3    -0.78
ATOM O3T  ON2    -0.57
ATOM C3T  CN8B   -0.17
ATOM H3T1 HN8     0.09
ATOM H3T2 HN8     0.09
ATOM H3T3 HN8     0.09

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C3'  O3'
BOND C1'  H11' C1'  H12' C2'  H21' C2'  H22' C3'  H31' C4'  H41'
BOND C4'  H42' O3'  P    P    O1P  P    O2P  P    O3T  O3T  C3T
BOND C3T  H3T1   C3T  H3T2  C3T  H3T3
IC   C4'     O4'     C1'     C2'    1.4055  108.09   23.45  106.18   1.5457
IC   O4'     C1'     C2'     C3'    1.4127  106.18    3.96  103.11   1.5346
IC   C1'     C2'     C3'     C4'    1.5457  103.11  -26.93  100.86   1.5211
IC   C2'     C3'     C4'     O4'    1.5346  100.86   41.73  103.15   1.4055
IC   C3'     C4'     O4'     C1'    1.5211  103.15  -41.62  108.09   1.4127
IC   H11'    C1'     C2'     C3'    1.0856  111.62  123.53  103.11   1.5346
IC   H12'    C1'     C2'     C3'    1.0818  113.32 -114.11  103.11   1.5346
IC   H21'    C2'     C3'     C4'    1.0846  110.65   91.68  100.86   1.5211
IC   H22'    C2'     C3'     C4'    1.0822  110.88 -148.45  100.86   1.5211
IC   H31'    C3'     C4'     O4'    1.0806  113.53  162.89  103.15   1.4055
IC   H41'    C4'     O4'     C1'    1.0891  110.89   77.76  108.09   1.4127
IC   H42'    C4'     O4'     C1'    1.0808  108.72 -162.12  108.09   1.4127
IC   O3'     C3'     C4'     O4'    1.4028  110.98  -77.39  103.15   1.4055
IC   P       O3'     C3'     C4'    0.0000  000.00  180.00  000.00   0.0000
IC   C3'     O3'     P       O3T    0.0000  000.00  -95.22  000.00   0.0000
IC   O3T     O3'     *P      O1P    0.0000  000.00 -115.82  000.00   0.0000
IC   O3T     O3'     *P      O2P    0.0000  000.00  115.90  000.00   0.0000
IC   C3T     O3T     P       O3'    0.0000  000.00  -46.90  000.00   0.0000
IC   H3T1    C3T     O3T     P      0.0000  000.00  180.00  000.00   0.0000
IC   H3T2    C3T     O3T     P      0.0000  000.00   60.00  000.00   0.0000
IC   H3T3    C3T     O3T     P      0.0000  000.00  -60.00  000.00   0.0000
PATC  FIRS NONE LAST NONE

RESI TM3P        -2.00 ! 4'-methyl,3'-phosphate tetrahydrofuran (phosphate -2)

! This is the DNA version (the RNA version is RM3P, see below)

GROUP
ATOM O4'  ON6    -0.50 !    H52' H53'
ATOM C1'  CN7B    0.07 !      \  /
ATOM H11' HN7     0.09 !  H51'-C5'  O4'  H11'
ATOM H12' HN7     0.09 !        \  /  \  /
ATOM C4'  CN7     0.16 !   H42'--C4'  C1'--H12'
ATOM H42' HN7     0.09 !          |    |
GROUP                  !   H31'--C3'--C2'--H21'
ATOM C2'  CN8    -0.18 !        /       \
ATOM H21' HN8     0.09 !      O3'       H22'
ATOM H22' HN8     0.09 !       |
GROUP                  !  O1P==P==O2P
ATOM C3'  CN7    -0.09 !       ||
ATOM H31' HN7     0.09 !      O3P (-2)
GROUP                  !
ATOM O3'  ON2    -0.40
ATOM P    P       1.10
ATOM O1P  ON3    -0.90
ATOM O2P  ON3    -0.90
ATOM O3P  ON3    -0.90
GROUP                 
ATOM C5'  CN8B   -0.27
ATOM H51' HN8     0.09
ATOM H52' HN8     0.09
ATOM H53' HN8     0.09

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C3'  O3'
BOND C1'  H11' C1'  H12' C2'  H21' C2'  H22' C3'  H31' C4'  H42' 
BOND O3'  P    P    O1P  P    O2P  P    O3P
BOND C4'  C5'  C5'  H51' C5'  H52' C5'  H53'
IC   C4'     O4'     C1'     C2'    1.4055  108.09   23.45  106.18   1.5457
IC   O4'     C1'     C2'     C3'    1.4127  106.18    3.96  103.11   1.5346
IC   C1'     C2'     C3'     C4'    1.5457  103.11  -26.93  100.86   1.5211
IC   C2'     C3'     C4'     O4'    1.5346  100.86   41.73  103.15   1.4055
IC   C3'     C4'     O4'     C1'    1.5211  103.15  -41.62  108.09   1.4127
IC   H11'    C1'     C2'     C3'    1.0856  111.62  123.53  103.11   1.5346
IC   H12'    C1'     C2'     C3'    1.0818  113.32 -114.11  103.11   1.5346
IC   H21'    C2'     C3'     C4'    1.0846  110.65   91.68  100.86   1.5211
IC   H22'    C2'     C3'     C4'    1.0822  110.88 -148.45  100.86   1.5211
IC   H31'    C3'     C4'     O4'    1.0806  113.53  162.89  103.15   1.4055
IC   C5'     C4'     O4'     C1'    0.0000  000.00   77.76  108.09   1.4127
IC   H51'    C5'     C4'     O4'    0.0       0.0   180.0     0.0    0.0
IC   H52'    C5'     C4'     O4'    0.0       0.0   -60.0     0.0    0.0
IC   H53'    C5'     C4'     O4'    0.0       0.0    60.0     0.0    0.0
IC   H42'    C4'     O4'     C1'    1.0808  108.72 -162.12  108.09   1.4127
IC   O3'     C3'     C4'     O4'    1.4028  110.98  -77.39  103.15   1.4055
IC   P       O3'     C3'     C4'    0.0       0.0   180.00    0.0    0.0
IC   O1P     P       O3'     C3'    0.0       0.0   -60.0     0.0    0.0
IC   O2P     P       O3'     C3'    0.0       0.0   180.0     0.0    0.0
IC   O3P     P       O3'     C3'    0.0       0.0    60.0     0.0    0.0
PATC  FIRS NONE LAST NONE

RESI RM3P        -2.00 ! 4'-methyl,3'-phosphate tetrahydrofuran (phosphate -2)

! This is the RNA version of TM3P: NOTE that it does NOT have a 2'hydroxyl to
! allow for the determination of the influence of the ring dihedrals on the
! sugar puckering energetics in the absence of the 2' hydroxyl

GROUP
ATOM O4'  ON6B   -0.50
ATOM C1'  CN7B    0.07
ATOM H11' HN7     0.09
ATOM H12' HN7     0.09
ATOM C4'  CN7     0.16
ATOM H42' HN7     0.09
GROUP                 
ATOM C2'  CN7B   -0.18
ATOM H21' HN7     0.09
ATOM H22' HN7     0.09
GROUP                 
ATOM C3'  CN7    -0.09
ATOM H31' HN7     0.09
GROUP                 
ATOM O3'  ON2    -0.40
ATOM P    P       1.10
ATOM O1P  ON3    -0.90
ATOM O2P  ON3    -0.90
ATOM O3P  ON3    -0.90
GROUP                 
ATOM C5'  CN8B   -0.27
ATOM H51' HN8     0.09
ATOM H52' HN8     0.09
ATOM H53' HN8     0.09

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C3'  O3'
BOND C1'  H11' C1'  H12' C2'  H21' C2'  H22' C3'  H31' C4'  H42' 
BOND O3'  P    P    O1P  P    O2P  P    O3P
BOND C4'  C5'  C5'  H51' C5'  H52' C5'  H53'
IC   C4'     O4'     C1'     C2'    1.4055  108.09   23.45  106.18   1.5457
IC   O4'     C1'     C2'     C3'    1.4127  106.18    3.96  103.11   1.5346
IC   C1'     C2'     C3'     C4'    1.5457  103.11  -26.93  100.86   1.5211
IC   C2'     C3'     C4'     O4'    1.5346  100.86   41.73  103.15   1.4055
IC   C3'     C4'     O4'     C1'    1.5211  103.15  -41.62  108.09   1.4127
IC   H11'    C1'     C2'     C3'    1.0856  111.62  123.53  103.11   1.5346
IC   H12'    C1'     C2'     C3'    1.0818  113.32 -114.11  103.11   1.5346
IC   H21'    C2'     C3'     C4'    1.0846  110.65   91.68  100.86   1.5211
IC   H22'    C2'     C3'     C4'    1.0822  110.88 -148.45  100.86   1.5211
IC   H31'    C3'     C4'     O4'    1.0806  113.53  162.89  103.15   1.4055
IC   C5'     C4'     O4'     C1'    0.0000  000.00   77.76  108.09   1.4127
IC   H51'    C5'     C4'     O4'    0.0     0.0     180.0     0.0    0.0
IC   H52'    C5'     C4'     O4'    0.0     0.0      -60.0    0.0    0.0
IC   H53'    C5'     C4'     O4'    0.0     0.0       60.0    0.0    0.0
IC   H42'    C4'     O4'     C1'    1.0808  108.72 -162.12  108.09   1.4127
IC   O3'     C3'     C4'     O4'    1.4028  110.98  -77.39  103.15   1.4055
IC   P       O3'     C3'     C4'    0.0       0.0   180.00    0.0    0.0
IC   O1P     P       O3'     C3'    0.0       0.0   -60.0     0.0    0.0
IC   O2P     P       O3'     C3'    0.0       0.0   180.0     0.0    0.0
IC   O3P     P       O3'     C3'    0.0       0.0    60.0     0.0    0.0
PATC  FIRS NONE LAST NONE

RESI T35P        -4.00 ! 5'-phosphate-3'-phosphate-
                       ! methyl-tetrahydrofuran (phosphate -2)
GROUP                 
ATOM O4'  ON6    -0.50 !
ATOM C1'  CN7B    0.07 !      O1P (-2)
ATOM H1'  HN7     0.09 !      ||
ATOM H1'' HN7     0.09 !  O2P==P==O2P
ATOM C4'  CN7     0.16 !       |
ATOM H4'' HN7     0.09 ! H5'' O5'
GROUP                  !     \ |
ATOM C2'  CN8    -0.18 ! H5'--C5'   O4'  H1'
ATOM H2'  HN8     0.09 !        \  /  \  /
ATOM H2'' HN8     0.09 !    H4'--C4'  C1'--H1''
GROUP                  !          |    |
ATOM C3'  CN7    -0.09 !    H3'--C3'--C2'--H2'
ATOM H3'  HN7     0.09 !        /       \
GROUP                  !      O3'       H22'
ATOM O3'  ON2    -0.40 !       |
ATOM P3   P       1.10 ! O31P==P==O32P
ATOM O31P ON3    -0.90 !       ||
ATOM O32P ON3    -0.90 !      O33P (-2)
ATOM O33P ON3    -0.90
GROUP                 
ATOM C5'  CN8B   -0.18
ATOM H5'  HN8     0.09
ATOM H5'' HN8     0.09
GROUP                 
ATOM O5'  ON2    -0.40
ATOM P    P       1.10
ATOM O1P  ON3    -0.90
ATOM O2P  ON3    -0.90
ATOM O3P  ON3    -0.90

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C4'  C5'
BOND C1'  H1'  C1'  H1'' C2'  H2'  C2'  H2'' C3'  H3'  C3'  O3'
BOND C4'  H4'' C5'  H5'  C5'  H5'' C5'  O5'  O5'  P    P    O1P
BOND P    O2P  P    O3P  O3'  P3   P3   O31P P3   O32P P3   O33P 
IC   C4'     O4'     C1'     C2'    1.4416  109.61    0.45  106.74   1.5328
IC   O4'     C1'     C2'     C3'    1.4471  106.74  -21.92  103.38   1.5200
IC   C1'     C2'     C3'     C4'    1.5328  103.38   33.49  102.18   1.5321
IC   C2'     C3'     C4'     O4'    1.5200  102.18  -34.11  105.43   1.4416
IC   C3'     C4'     O4'     C1'    1.5321  105.43   21.23  109.61   1.4471
IC   H1'     C1'     C2'     C3'    1.1099  113.03 -141.96  103.38   1.5200
IC   H1''    C1'     C2'     C3'    1.1111  111.16   93.50  103.38   1.5200
IC   H2'     C2'     C3'     C4'    1.1135  109.13  -81.76  102.18   1.5321
IC   H2''    C2'     C3'     C4'    1.1076  113.49  155.97  102.18   1.5321
IC   H3'     C3'     C4'     O4'    1.1127  108.68   81.68  105.43   1.4416
IC   H4''    C4'     O4'     C1'    1.1127  106.71  -95.75  109.61   1.4471
IC   C5'     C4'     O4'     C1'    1.5325  108.43  144.82  109.61   1.4471
IC   H51'    C5'     C4'     O4'    1.1092  110.48  180.00  108.43   1.4416
IC   H52'    C5'     C4'     O4'    1.1104  110.01  -60.00  108.43   1.4416
IC   O4'     C4'     C5'     O5'    0.0       0.0    60.00    0.0    0.0   
IC   C4'     C5'     O5'     P      0.0       0.0   180.0     0.0    0.0 	
IC   C5'     O5'     P       O1P    0.0       0.0   -60.0     0.0    0.0
IC   C5'     O5'     P       O2P    0.0       0.0   180.0     0.0    0.0
IC   C5'     O5'     P       O3P    0.0       0.0   60.0      0.0    0.0 
IC   P3      C3'     C4'     O4'    1.5     112.41 -156.66  105.43   1.4416
IC   C5'     C4'     C3'     O3'    0.0       0.0   180.0     0.0    0.0
IC   C4'     C3'     O3'     P3     0.0       0.0   180.0     0.0    0.0
IC   C3'     O3'     P3      O31P   0.0       0.0   -60.0     0.0    0.0
IC   C3'     O3'     P3      O32P   0.0       0.0   180.0     0.0    0.0
IC   C3'     O3'     P3      O33P   0.0       0.0   60.0      0.0    0.0
PATC  FIRS NONE LAST NONE

RESI T2FU        -2.00 ! THF with PO3  on c3, F (alpha, down) on c2
                       ! Charge distribution is preliminary
GROUP
ATOM O4'  ON6    -0.50 !
ATOM C1'  CN7B    0.07 !     H41'   O4'  H11'
ATOM C4'  CN7     0.07 !        \  /  \  /
ATOM H11' HN7     0.09 !   H42'--C4'  C1'--H12'
ATOM H12' HN7     0.09 !          |    |
ATOM H41' HN7     0.09 !   H31'--C3'--C2'--F2' (alpha)
ATOM H42' HN7     0.09 !        /       \
GROUP                  !      O3'       H22'
ATOM C2'  CN7C    0.14 !       |
ATOM H22' HN7     0.09 !  O1P==P==O2P
ATOM F2'  FN1    -0.23 !       ||
GROUP                  !      O3P (-2)
ATOM C3'  CN7    -0.09 !        
ATOM H31' HN7     0.09
GROUP                 
ATOM O3'  ON2    -0.40
ATOM P    P       1.10
ATOM O1P  ON3    -0.90
ATOM O2P  ON3    -0.90
ATOM O3P  ON3    -0.90

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C3'  O3'
BOND C1'  H11' C1'  H12' C2'  F2'  C2'  H22' C3'  H31' C4'  H41'
BOND C4'  H42' O3'  P    P    O1P  P    O2P  P    O3P
IC   C4'     O4'     C1'     C2'    1.4055  108.09   23.45  106.18   1.5457
IC   O4'     C1'     C2'     C3'    1.4127  106.18    3.96  103.11   1.5346
IC   C1'     C2'     C3'     C4'    1.5457  103.11  -26.93  100.86   1.5211
IC   C2'     C3'     C4'     O4'    1.5346  100.86   41.73  103.15   1.4055
IC   C3'     C4'     O4'     C1'    1.5211  103.15  -41.62  108.09   1.4127
IC   H11'    C1'     C2'     C3'    1.0856  111.62  123.53  103.11   1.5346
IC   H12'    C1'     C2'     C3'    1.0818  113.32 -114.11  103.11   1.5346
IC   F2'     C2'     C3'     C4'    1.0846  110.65   91.68  100.86   1.5211
IC   H22'    C2'     C3'     C4'    1.0822  110.88 -148.45  100.86   1.5211
IC   H31'    C3'     C4'     O4'    1.0806  113.53  162.89  103.15   1.4055
IC   H41'    C4'     O4'     C1'    1.0891  110.89   77.76  108.09   1.4127
IC   H42'    C4'     O4'     C1'    1.0808  108.72 -162.12  108.09   1.4127
IC   O3'     C3'     C4'     O4'    1.4028  110.98  -77.39  103.15   1.4055
IC   P       O3'     C3'     C4'    0.0       0.0   180.00    0.0    0.0
IC   O1P     P       O3'     C3'    0.0       0.0   -60.0     0.0    0.0
IC   O2P     P       O3'     C3'    0.0       0.0   180.0     0.0    0.0
IC   O3P     P       O3'     C3'    0.0       0.0    60.0     0.0    0.0
PATC  FIRS NONE LAST NONE

RESI TMFU        -2.00 ! THF with ch3 on c4', opo3 on c3', F (beta, up) on c2' 
                       ! Caution: Charges are preliminary. Charge on fluorine was
                       ! taken from Daxu Yin's thesis (monofluoroethane).
GROUP
ATOM O4'  ON6    -0.50 !    H52' H53'
ATOM C1'  CN7B    0.07 !      \  /
ATOM H11' HN7     0.09 !  H51'-C5'  O4'  H11'
ATOM H12' HN7     0.09 !        \  /  \  /
ATOM C4'  CN7     0.16 !   H42'--C4'  C1'--H12'
ATOM H42' HN7     0.09 !          |    |
GROUP                  !   H31'--C3'--C2'--F2' (beta)
ATOM C2'  CN7C    0.19 !        /       \
ATOM H22' HN7     0.09 !      O3'       H22'
ATOM F2'  FN1    -0.28 !       |
GROUP                  !  O1P==P==O2P
ATOM C3'  CN7    -0.09 !       ||
ATOM H31' HN7     0.09 !      O3P (-2)
GROUP                 
ATOM O3'  ON2    -0.40
ATOM P    P       1.10
ATOM O1P  ON3    -0.90
ATOM O2P  ON3    -0.90
ATOM O3P  ON3    -0.90
GROUP
ATOM C5'  CN8B   -0.27
ATOM H51' HN8     0.09
ATOM H52' HN8     0.09
ATOM H53' HN8     0.09

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'
BOND C1'  H11' C1'  H12'
BOND C2'  H22' C2'  F2'
BOND C3'  O3'  C3'  H31'
BOND O3'  P    P    O1P  P    O2P   P   O3P
BOND C4'  C5'  C5'  H51' C5'  H52' C5'  H53' C4'  H42'
! The following IC table is a guess from thfohch3 (Nicolas):
IC 	C1'	C2'	C3'	C4'	0.0 0.0 330.81 0.0 0.0
IC	C2'	C3'	C4'	O4'	0.0 0.0  39.77 0.0 0.0
IC	H11'	C1'	C2'	C3'	0.0 0.0 129.38 0.0 0.0
IC	H12'	C1'	C2'	C3'	0.0 0.0 251.29 0.0 0.0
IC	F2'	C2'	C3'	C4'	0.0 0.0  89.74 0.0 0.0
IC	H22'	C2'	C3'	C4'	0.0 0.0 209.60 0.0 0.0
IC	H31'	C3'	C4'	O4'	0.0 0.0 161.48 0.0 0.0
IC	O3'	C3'	C4'	O4'	0.0 0.0 280.72 0.0 0.0
IC	P   	O3'	C3'	C4'	0.0 0.0 180.00 0.0 0.0
IC      O1P     P       O3'     C3'     0.0 0.0 180.00 0.0 0.0
IC      O2P     P       O3'     C3'     0.0 0.0  60.00 0.0 0.0
IC      O3P     P       O3'     C3'     0.0 0.0 -60.00 0.0 0.0
IC	C5' 	C4'	O4'	C1'	0.0 0.0  87.60 0.0 0.0 
IC 	H51'	C5'	C4'	O4'	0.0 0.0 176.37 0.0 0.0
IC	H52'	C5'	C4'	O4'	0.0 0.0  56.84 0.0 0.0
IC 	H53'	C5'	C4'	O4'	0.0 0.0 297.06 0.0 0.0
IC	H42'	C4'	O4'	C1'	0.0 0.0 207.55 0.0 0.0

PATC  FIRS NONE LAST NONE

RESI T2FD        -2.00 ! THF with methyl on c4', opo3 on c3, F (alpha, down) on c2 
                       ! Charge distribution is preliminary
GROUP
ATOM O4'  ON6    -0.50 !    
ATOM C1'  CN7B    0.07 !    
ATOM C4'  CN7     0.07 !     H41'   O4'  H11'
ATOM H11' HN7     0.09 !        \  /  \  /
ATOM H12' HN7     0.09 !   H42'--C4'  C1'--H12'
ATOM H41' HN7     0.09 !          |    |
ATOM H42' HN7     0.09 !   H31'--C3'--C2'--F2' (alpha)
GROUP                  !        /       \
ATOM C2'  CN7C    0.14 !      O3'       H22'
ATOM H21' HN7     0.09 !       |
ATOM F2'  FN1    -0.23 !  O1P==P==O2P
GROUP                  !       ||
ATOM C3'  CN7    -0.09 !      O3P (-2)
ATOM H31' HN7     0.09
GROUP                 
ATOM O3'  ON2    -0.40
ATOM P    P       1.10
ATOM O1P  ON3    -0.90
ATOM O2P  ON3    -0.90
ATOM O3P  ON3    -0.90

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C3'  O3'
BOND C1'  H11' C1'  H12' C2'  F2'  C2'  H21' C3'  H31' C4'  H41'
BOND C4'  H42' O3'  P    P    O1P  P    O2P  P    O3P
IC   C4'     O4'     C1'     C2'    1.4055  108.09   23.45  106.18   1.5457
IC   O4'     C1'     C2'     C3'    1.4127  106.18    3.96  103.11   1.5346
IC   C1'     C2'     C3'     C4'    1.5457  103.11  -26.93  100.86   1.5211
IC   C2'     C3'     C4'     O4'    1.5346  100.86   41.73  103.15   1.4055
IC   C3'     C4'     O4'     C1'    1.5211  103.15  -41.62  108.09   1.4127
IC   H11'    C1'     C2'     C3'    1.0856  111.62  123.53  103.11   1.5346
IC   H12'    C1'     C2'     C3'    1.0818  113.32 -114.11  103.11   1.5346
IC   F2'     C2'     C3'     C4'    1.0846  110.65 -148.45  100.86   1.5211
IC   H21'    C2'     C3'     C4'    1.0822  110.88   91.68  100.86   1.5211
IC   H31'    C3'     C4'     O4'    1.0806  113.53  162.89  103.15   1.4055
IC   H41'    C4'     O4'     C1'    1.0891  110.89   77.76  108.09   1.4127
IC   H42'    C4'     O4'     C1'    1.0808  108.72 -162.12  108.09   1.4127
IC   O3'     C3'     C4'     O4'    1.4028  110.98  -77.39  103.15   1.4055
IC   P       O3'     C3'     C4'    0.0       0.0   180.00    0.0    0.0 
IC   O1P     P       O3'     C3'    0.0       0.0   -60.0     0.0    0.0
IC   O2P     P       O3'     C3'    0.0       0.0   180.0     0.0    0.0
IC   O3P     P       O3'     C3'    0.0       0.0    60.0     0.0    0.0
PATC  FIRS NONE LAST NONE

RESI TMFD        -2.00 ! Flourine on C2' (alpha, down) with ch3 on c4', opo3 on c3', oh on c2' 
                       ! Charge distribution is preliminary
GROUP
ATOM O4'  ON6    -0.50 !    H52' H53'
ATOM C1'  CN7B    0.07 !      \  /
ATOM H11' HN7     0.09 !  H51'-C5'  O4'  H11'
ATOM H12' HN7     0.09 !        \  /  \  /
ATOM C4'  CN7     0.16 !   H42'--C4'  C1'--H12'
ATOM H42' HN7     0.09 !          |    |
GROUP                  !   H31'--C3'--C2'--F2' (alpha)
ATOM C2'  CN7D    0.19 !        /       \
ATOM H21' HN7     0.09 !      O3'       H22'
ATOM F2'  FN1    -0.28 !       |
GROUP                  !  O1P==P==O2P
ATOM C3'  CN7    -0.09 !       ||
ATOM H31' HN7     0.09 !      O3P (-2)
GROUP                 
ATOM O3'  ON2    -0.40
ATOM P    P       1.10
ATOM O1P  ON3    -0.90
ATOM O2P  ON3    -0.90
ATOM O3P  ON3    -0.90
GROUP                 
ATOM C5'  CN8B   -0.27
ATOM H51' HN8     0.09
ATOM H52' HN8     0.09
ATOM H53' HN8     0.09

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'
BOND C1'  H11' C1'  H12'
BOND C2'  F2'  C2'  H21' 
BOND C3'  O3'  C3'  H31'
BOND O3'  P    P    O1P  P    O2P   P   O3P
BOND C4'  C5'  C5'  H51' C5'  H52' C5'  H53' C4'  H42'
! The following IC table is a guess from thfohch3 (Nicolas):
IC 	C1'	C2'	C3'	C4'	0.0 0.0 330.81 0.0 0.0
IC	C2'	C3'	C4'	O4'	0.0 0.0  39.77 0.0 0.0
IC	H11'	C1'	C2'	C3'	0.0 0.0 129.38 0.0 0.0
IC	H12'	C1'	C2'	C3'	0.0 0.0 251.29 0.0 0.0
IC	H21'    C2'	C3'	C4'	0.0 0.0  89.74 0.0 0.0
IC	F2' 	C2'	C3'	C4'	0.0 0.0 209.60 0.0 0.0
IC	H31'	C3'	C4'	O4'	0.0 0.0 161.48 0.0 0.0
IC	O3'	C3'	C4'	O4'	0.0 0.0 280.72 0.0 0.0
IC	P   	O3'	C3'	C4'	0.0 0.0 180.00 0.0 0.0
IC      O1P     P       O3'     C3'     0.0 0.0 180.00 0.0 0.0
IC      O2P     P       O3'     C3'     0.0 0.0  60.00 0.0 0.0
IC      O3P     P       O3'     C3'     0.0 0.0 -60.00 0.0 0.0
IC	C5' 	C4'	O4'	C1'	0.0 0.0  87.60 0.0 0.0 
IC 	H51'	C5'	C4'	O4'	0.0 0.0 176.37 0.0 0.0
IC	H52'	C5'	C4'	O4'	0.0 0.0  56.84 0.0 0.0
IC 	H53'	C5'	C4'	O4'	0.0 0.0 297.06 0.0 0.0
IC	H42'	C4'	O4'	C1'	0.0 0.0 207.55 0.0 0.0
PATC  FIRS NONE LAST NONE

RESI ARMO         0.00 ! ribose, thfch3ohoh, with the c2' hydroxyl in the beta configuration
GROUP
ATOM O4'  ON6    -0.50 !    H52' H53'
ATOM C1'  CN8     0.07 !      \  /
ATOM H11' HN7     0.09 !  H51'-C5'  O4'  H11'
ATOM H12' HN7     0.09 !        \  /  \  /
ATOM C4'  CN7     0.16 !   H42'--C4'  C1'--H12'
ATOM H42' HN7     0.09 !          |    |
GROUP                  !   H31'--C3'--C2'--H21'
ATOM C2'  CN7     0.14 !        /       \
ATOM H22' HN7     0.09 !      O3'       O2'
ATOM O2'  ON5	 -0.66 !       |         |    (beta)
ATOM H21' HN5     0.43 !      H32'      H22'
GROUP                  !
ATOM C3'  CN7     0.14
ATOM H31' HN7     0.09 
ATOM O3'  ON5    -0.66 
ATOM H32' HN5     0.43 
GROUP                 
ATOM C5'  CN8B   -0.27
ATOM H51' HN8     0.09
ATOM H52' HN8     0.09
ATOM H53' HN8     0.09

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'
BOND C1'  H11' C1'  H12'
BOND C2'  O2'  C2'  H22' O2'  H21'
BOND C3'  O3'  O3'  H32' C3'  H31'
BOND C4'  C5'  C5'  H51' C5'  H52' C5'  H53' C4'  H42'

! The following IC table is a guess from thfohch3 (Nicolas):
IC 	C1'	C2'	C3'	C4'	0.0 0.0 330.81 0.0 0.0
IC	C2'	C3'	C4'	O4'	0.0 0.0  39.77 0.0 0.0
IC	H11'	C1'	C2'	C3'	0.0 0.0 129.38 0.0 0.0
IC	H12'	C1'	C2'	C3'	0.0 0.0 251.29 0.0 0.0
IC	O2'	C2'	C3'	C4'	0.0 0.0  89.74 0.0 0.0
IC      H21'    O2'	C2'	C3'	0.0 0.0  90.00 0.0 0.0 
IC	H22'	C2'	C3'	C4'	0.0 0.0 209.60 0.0 0.0
IC	H31'	C3'	C4'	O4'	0.0 0.0 161.48 0.0 0.0
IC	O3'	C3'	C4'	O4'	0.0 0.0 280.72 0.0 0.0
IC	H32'	O3'	C3'	C4'	0.0 0.0  44.72 0.0 0.0
IC	C5' 	C4'	O4'	C1'	0.0 0.0  87.60 0.0 0.0 
IC 	H51'	C5'	C4'	O4'	0.0 0.0 176.37 0.0 0.0
IC	H52'	C5'	C4'	O4'	0.0 0.0  56.84 0.0 0.0
IC 	H53'	C5'	C4'	O4'	0.0 0.0 297.06 0.0 0.0
IC	H42'	C4'	O4'	C1'	0.0 0.0 207.55 0.0 0.0
PATC  FIRS NONE LAST NONE

RESI THFA        0.00  ! THF-OH-CH3-IM  
GROUP
ATOM O4'  ON6    -0.50 !    H52' H53'
ATOM C4'  CN7     0.16 !      \  /
ATOM H42' HN7     0.09 !  H51'-C5'  O4'  Imidazole
ATOM C1'  CN7B    0.16 !        \  /  \  /
ATOM H12' HN7     0.09 !   H42'--C4'  C1'--H12'
GROUP                  !          |    |
ATOM C2'  CN8    -0.18 !   H31'--C3'--C2'--H21'
ATOM H21' HN8     0.09 !        /       \
ATOM H22' HN8     0.09 !      O3'       H22'
GROUP                  !       |
ATOM H31' HN7     0.09 !      H32'
ATOM C3'  CN7     0.14
ATOM O3'  ON5    -0.66
ATOM H32' HN5     0.43
GROUP                 
ATOM C5'  CN8B   -0.27
ATOM H51' HN8     0.09
ATOM H52' HN8     0.09
ATOM H53' HN8     0.09
GROUP	! Imidazole: transferred from isolated imidazole (IMIA)
ATOM CG   CPH1   -0.05 !     C1'       HE1
ATOM HG   HR3     0.09 !       \       /
ATOM CD2  CPH1    0.22 !       ND1---CE1
ATOM HD2  HR3     0.10 !      /       ||
ATOM ND1  NR1    -0.04 !  HG-CG       ||
ATOM CE1  CPH2    0.25 !      \\      ||
ATOM HE1  HR1     0.13 !       CD2---NE2
ATOM NE2  NR2    -0.70 !        |
                       !       HD2

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C4'  C5'
BOND C3'  O3'  C1'  H12' C2'  H21' C2'  H22' C3'  H31' C4'  H42'
BOND C5'  H51' C5'  H52' C5'  H53'
BOND O3'  H32'
BOND C1'  ND1  ND1  CE1  NE2  CD2  CG  ND1
BOND CE1  HE1  CD2  HD2  CG  HG
DOUBLE CG  CD2   CE1  NE2
! This IC table is only an initial guess:
IC 	C1'	C2'	C3'	C4' 	0.0 0.0 324.92 0.0 0.0
IC	C2'	C3'	C4' 	O4' 	0.0 0.0 33.390 0.0 0.0
IC 	H12'	C1'	C2'	C3' 	0.0 0.0 268.35 0.0 0.0
IC 	H21'	C2'	C3'	C4' 	0.0 0.0 82.530 0.0 0.0
IC 	H22'	C2'	C3'	C4' 	0.0 0.0 204.06 0.0 0.0
IC 	O3' 	C3'	C4'	O4' 	0.0 0.0 -93.14 0.0 0.0
IC	H32'	O3'	C3'	C2'	0.0 0.0 -60.00 0.0 0.0
IC 	H31'	C3'	C4'	O4' 	0.0 0.0 147.80 0.0 0.0
IC	H41'	C4'	O4'	C1' 	0.0 0.0 132.30 0.0 0.0
IC 	H42'	C4'	O4'	C1' 	0.0 0.0 220.70 0.0 0.0
IC	C4'	O4'	C1'	ND1 	0.0 0.0 256.98 0.0 0.0
IC 	O4'	C1'	ND1	CE1 	0.0 0.0 180.00 0.0 0.0
IC	C1'	ND1	CE1     NE2 	0.0 0.0 181.56 0.0 0.0
IC	ND1	CE1	NE2	CD2 	0.0 0.0   0.34 0.0 0.0
IC 	CE1	NE2	CD2	CG 	0.0 0.0   0.00 0.0 0.0 
IC 	HE1	CE1	NE2	CD2 	0.0 0.0 180.40 0.0 0.0
IC	CE1	NE2	CD2	HD2 	0.0 0.0 179.83 0.0 0.0
IC 	NE2 	CD2	CG 	HG 	0.0 0.0 178.45 0.0 0.0
IC      C5'     C4'     O4'     C1'     0.0 0.0 144.82 0.0 0.0   
IC      H51'    C5'     C4'     O4'     0.0 0.0 -179.98 0.0 0.0 
IC      H52'    C5'     C4'     O4'     0.0 0.0  -59.66 0.0 0.0
IC      H53'    C5'     C4'     O4'     0.0 0.0   59.68 0.0 0.0
PATC  FIRS NONE LAST NONE

RESI ARAO         0.00 ! arabinose sugar, oh alpha on c3', oh beta on c2' 
GROUP
ATOM O4'  ON6    -0.50 !
ATOM C1'  CN8     0.07 !
ATOM H11' HN8     0.09 !     H41'   O4'  H11'
ATOM H12' HN8     0.09 !        \  /  \  /
ATOM C4'  CN8B    0.07 !   H42'--C4'  C1'--H12'
ATOM H41' HN8     0.09 !          |    |
ATOM H42' HN8     0.09 !   H31'--C3'--C2'--H21'
GROUP                  !        /       \
ATOM C2'  CN7     0.14 !      O3'       O2'
ATOM H22' HN7     0.09 !       |         |    (beta)
ATOM O2'  ON5    -0.66 !      H32'      H22'
ATOM H21' HN5     0.43 !
GROUP                 
ATOM C3'  CN7     0.14
ATOM H31' HN7     0.09
ATOM O3'  ON5    -0.66 
ATOM H32' HN5     0.43

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C3'  O3'
BOND C1'  H11' C1'  H12' C2'  O2'  C2'  H22' C3'  H31' C4'  H41'  
BOND C4'  H42' O2'  H21' O3'  H32'
!Nicolas: the following IC are for thf-oh as optimized via ab initio calculations
IC   C4'     O4'     C1'     C2'    1.4055  108.09   23.45  106.18   1.5457
IC   O4'     C1'     C2'     C3'    1.4127  106.18    3.96  103.11   1.5346
IC   C1'     C2'     C3'     C4'    1.5457  103.11  -26.93  100.86   1.5211
IC   C2'     C3'     C4'     O4'    1.5346  100.86   41.73  103.15   1.4055
IC   C3'     C4'     O4'     C1'    1.5211  103.15  -41.62  108.09   1.4127
IC   H11'    C1'     C2'     C3'    1.0856  111.62  123.53  103.11   1.5346
IC   H12'    C1'     C2'     C3'    1.0818  113.32 -114.11  103.11   1.5346
IC   O2'     C2'     C3'     C4'    0.0000    0.00   91.68  0.0000   0.0000
IC   H21'    O2'     C2'     C3'    0.0       0.0   -60.0     0.0    0.0
IC   H22'    C2'     C3'     C4'    1.0822  110.88 -148.45  100.86   1.5211
IC   H31'    C3'     C4'     O4'    1.0806  113.53  162.89  103.15   1.4055
IC   H41'    C4'     O4'     C1'    1.0891  110.89   77.76  108.09   1.4127
IC   H42'    C4'     O4'     C1'    1.0808  108.72 -162.12  108.09   1.4127
IC   O3'     C3'     C4'     O4'    1.4028  110.98  -77.39  103.15   1.4055
IC   H32'    O3'     C3'     C4'    0.9492  108.72   44.80  110.98   1.5211
PATC  FIRS NONE LAST NONE

RESI ARIM         0.00 ! arabinose sugar with imidazole
                       ! transferred from thf
GROUP   
ATOM O4'  ON6    -0.50 !
ATOM C1'  CN7B    0.16 !     H41'   O4'  Imidazole
ATOM H12' HN7     0.09 !        \  /  \  /
ATOM C4'  CN8     0.07 !   H42'--C4'  C1'--H12'
ATOM H41' HN8     0.09 !          |    |
ATOM H42' HN8     0.09 !   H31'--C3'--C2'--H21'
GROUP                  !        /       \
ATOM C3'  CN8    -0.18 !      H32'      O2'
ATOM H31' HN8     0.09 !                 |    (beta)
ATOM H32' HN8     0.09 !                H22'
GROUP                 
ATOM C2'  CN7     0.14
ATOM H22' HN7     0.09
ATOM O2'  ON5    -0.66
ATOM H21' HN5     0.43 
GROUP	! Imidazole: transferred from isolated imidazole (IMIA)
ATOM CG   CPH1   -0.05 !     C1'       HE1
ATOM HG   HR3     0.09 !       \       /
ATOM CD2  CPH1    0.22 !       ND1---CE1
ATOM HD2  HR3     0.10 !      /       ||
ATOM ND1  NR1    -0.04 !  HG-CG       ||
ATOM CE1  CPH2    0.25 !      \\      ||
ATOM HE1  HR1     0.13 !       CD2---NE2
ATOM NE2  NR2    -0.70 !        |
                       !       HD2

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C1'  ND1
BOND C2'  O2'  C1'  H12' C2'  H22' C3'  H31' C3'  H32' O2'  H21'
BOND C4'  H41' C4'  H42'
BOND ND1  CE1  NE2  CD2  CG  ND1
BOND CE1  HE1  CD2  HD2  CG  HG
DOUBLE CG  CD2   CE1  NE2
! KEEPS HYDROGENS IN RING PLANE
IMPR ND1  CG   CE1  C1'       ND1  CE1  CG   C1'
IMPR CD2  CG   NE2  HD2       CD2  NE2  CG   HD2
IMPR CE1  ND1  NE2  HE1       CE1  NE2  ND1  HE1
IMPR CG   CD2  ND1  HG        CG   ND1  CD2  HG
! ic table for thfim, from Nicolas:
IC 	C1'	C2'	C3'	C4'    1.532 101.886 324.92 0.0 0.0
IC	C2'	C3'	C4' 	O4' 	0.0 0.0 33.390 0.0 0.0
IC 	H12'	C1'	C2'	C3' 	0.0 0.0 268.35 0.0 0.0
IC 	O2' 	C2'	C3'	C4' 	0.0 0.0 82.530 0.0 0.0
IC	H21'	O2'	C2'	C3'	0.0 0.0 -60.0  0.0 0.0
IC 	H22'	C2'	C3'	C4' 	0.0 0.0 204.06 0.0 0.0
IC 	H31'	C3'	C4'	O4' 	0.0 0.0 155.99 0.0 0.0
IC 	H32'	C3'	C4'	O4' 	0.0 0.0 276.70 0.0 0.0
IC	H41'	C4'	O4'	C1' 	0.0 0.0 132.30 0.0 0.0
IC 	H42'	C4'	O4'	C1' 	0.0 0.0 220.70 0.0 0.0
IC	C4'	O4'	C1'	ND1 	0.0 0.0 256.98 0.0 0.0
IC 	O4'	C1'	ND1	CE1 	0.0 0.0 180.00 0.0 0.0
IC	C1'	ND1	CE1     NE2 	0.0 0.0 181.56 0.0 0.0
IC	ND1	CE1	NE2	CD2 	0.0 0.0   0.34 0.0 0.0
IC 	CE1	NE2	CD2	CG 	0.0 0.0   0.00 0.0 0.0 
IC 	HE1	CE1	NE2	CD2 	0.0 0.0 180.40 0.0 0.0
IC	CE1	NE2	CD2	HD2 	0.0 0.0 179.83 0.0 0.0
IC 	NE2 	CD2	CG 	HG 	0.0 0.0 178.45 0.0 0.0
PATC  FIRS NONE LAST NONE

RESI AR3P        -2.00 ! arabinose sugar with phosphate on 3' (phosphate -2)
GROUP
ATOM O4'  ON6    -0.50 !      H41'  O4'  H11'
ATOM C1'  CN8     0.07 !        \  /  \  /
ATOM C4'  CN8B    0.07 !   H42'--C4'  C1'--H12'
ATOM H11' HN8     0.09 !          |    |
ATOM H12' HN8     0.09 !   H31'--C3'--C2'--H22' (alpha)
ATOM H41' HN8     0.09 !        /       \
ATOM H42' HN8     0.09 !      O3'       O2'
GROUP                  !       |         |
ATOM C2'  CN7     0.14 !  O1P==P==O2P   H21'
ATOM H22' HN7     0.09 !       ||
ATOM O2'  ON5    -0.66 !      O3P (-2)
ATOM H21' HN5     0.43
GROUP                 
ATOM C3'  CN7    -0.09
ATOM H31' HN7     0.09
GROUP                 
ATOM O3'  ON5    -0.40
ATOM P    P       1.10
ATOM O1P  ON3    -0.90
ATOM O2P  ON3    -0.90
ATOM O3P  ON3    -0.90

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C3'  O3'
BOND C1'  H11' C1'  H12' C2'  O2'  C2'  H22' C3'  H31' C4'  H41'
BOND C4'  H42' O2'  H21' O3'  P    P    O1P  P    O2P  P    O3P
IC   C4'     O4'     C1'     C2'    1.4055  108.09   23.45  106.18   1.5457
IC   O4'     C1'     C2'     C3'    1.4127  106.18    3.96  103.11   1.5346
IC   C1'     C2'     C3'     C4'    1.5457  103.11  -26.93  100.86   1.5211
IC   C2'     C3'     C4'     O4'    1.5346  100.86   41.73  103.15   1.4055
IC   C3'     C4'     O4'     C1'    1.5211  103.15  -41.62  108.09   1.4127
IC   H11'    C1'     C2'     C3'    1.0856  111.62  123.53  103.11   1.5346
IC   H12'    C1'     C2'     C3'    1.0818  113.32 -114.11  103.11   1.5346
IC   O2'     C2'     C3'     C4'    1.0846  110.65   91.68  100.86   1.5211
IC   H21'    O2'     C2'     C3'    0.0       0.0   -60.0     0.0    0.0
IC   H22'    C2'     C3'     C4'    1.0822  110.88 -148.45  100.86   1.5211
IC   H31'    C3'     C4'     O4'    1.0806  113.53  162.89  103.15   1.4055
IC   H41'    C4'     O4'     C1'    1.0891  110.89   77.76  108.09   1.4127
IC   H42'    C4'     O4'     C1'    1.0808  108.72 -162.12  108.09   1.4127
IC   O3'     C3'     C4'     O4'    1.4028  110.98  -77.39  103.15   1.4055
IC   P       O3'     C3'     C4'    0.0       0.0   180.00    0.0    0.0 
IC   O1P     P       O3'     C3'    0.0       0.0   -60.0     0.0    0.0
IC   O2P     P       O3'     C3'    0.0       0.0   180.0     0.0    0.0
IC   O3P     P       O3'     C3'    0.0       0.0    60.0     0.0    0.0
PATC  FIRS NONE LAST NONE

RESI RIBO         0.00 ! ribose, both c2' and c3' hydroxyls are alpha
GROUP
ATOM O4'  ON6    -0.50 !      H41'  O4'  H11'
ATOM C1'  CN8     0.07 !        \  /  \  /
ATOM C4'  CN8B    0.07 !   H42'--C4'  C1'--H12'
ATOM H11' HN8     0.09 !          |    |
ATOM H12' HN8     0.09 !   H31'--C3'--C2'--H22' 
ATOM H41' HN8     0.09 !        /       \
ATOM H42' HN8     0.09 !      O3'       O2'
GROUP                  !       |         |
ATOM C2'  CN7     0.14 !      H32'      H21'
ATOM H21' HN7     0.09 !
ATOM O2'  ON5    -0.66
ATOM H22' HN5     0.43
GROUP
ATOM C3'  CN7     0.14
ATOM H31' HN7     0.09
ATOM O3'  ON5    -0.66 
ATOM H32' HN5     0.43

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C3'  O3'
BOND C1'  H11' C1'  H12' C2'  O2'  C2'  H21' C3'  H31' C4'  H41'  
BOND C4'  H42' O2'  H22' O3'  H32'
!Nicolas: the following IC are for thf-oh as optimized via ab initio calculations
IC   C4'     O4'     C1'     C2'    1.4055  108.09   23.45  106.18   1.5457
IC   O4'     C1'     C2'     C3'    1.4127  106.18    3.96  103.11   1.5346
IC   C1'     C2'     C3'     C4'    1.5457  103.11  -26.93  100.86   1.5211
IC   C2'     C3'     C4'     O4'    1.5346  100.86   41.73  103.15   1.4055
IC   C3'     C4'     O4'     C1'    1.5211  103.15  -41.62  108.09   1.4127
IC   H11'    C1'     C2'     C3'    1.0856  111.62  123.53  103.11   1.5346
IC   H12'    C1'     C2'     C3'    1.0818  113.32 -114.11  103.11   1.5346
IC   H21'    C2'     C3'     C4'    1.0846  110.65   91.68  100.86   1.5211
IC   O2'     C2'     C3'     C4'    1.0822  110.88 -148.45  100.86   1.5211
IC   H22'    O2'     C2'     C3'    0.0       0.0   -60.0     0.0    0.0
IC   H31'    C3'     C4'     O4'    1.0806  113.53  162.89  103.15   1.4055
IC   H41'    C4'     O4'     C1'    1.0891  110.89   77.76  108.09   1.4127
IC   H42'    C4'     O4'     C1'    1.0808  108.72 -162.12  108.09   1.4127
IC   O3'     C3'     C4'     O4'    1.4028  110.98  -77.39  103.15   1.4055
IC   H32'    O3'     C3'     C4'    0.9492  108.72   44.80  110.98   1.5211
PATC  FIRS NONE LAST NONE

RESI TMPM        -1.00 ! 4'-methyl,3'-methylphosphate tetrahydrofuran (phosphate -1)
                        !charges corrected by adm jr. 9/98

GROUP
ATOM O4'  ON6    -0.50 !    H52' H53'
ATOM C1'  CN8     0.07 !      \  /
ATOM H11' HN8     0.09 !  H51'-C5'  O4'  H11'
ATOM H12' HN8     0.09 !        \  /  \  /
ATOM C4'  CN7     0.16 !   H42'--C4'  C1'--H12'
ATOM H42' HN7     0.09 !          |    |
GROUP                  !   H31'--C3'--C2'--H21'
ATOM C2'  CN8    -0.18 !        /       \
ATOM H21' HN8     0.09 !      O3'       H22'
ATOM H22' HN8     0.09 !       |
GROUP                  !  O1P==P==O2P
ATOM C3'  CN7     0.01 !       |
ATOM H31' HN7     0.09 !      O3P  (-1)
GROUP                  !        \
ATOM O3'  ON2    -0.57 !        C3T--H3T3
ATOM P    P       1.50 !       /  \
ATOM O1P  ON3    -0.78 !    H3T1 H3T2
ATOM O2P  ON3    -0.78 !
ATOM O3P  ON2    -0.57
ATOM C3T  CN9    -0.17
ATOM H3T1 HN9     0.09
ATOM H3T2 HN9     0.09
ATOM H3T3 HN9     0.09
GROUP
ATOM C5'  CN8B   -0.27
ATOM H51' HN8     0.09
ATOM H52' HN8     0.09
ATOM H53' HN8     0.09

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C3'  O3'
BOND C1'  H11' C1'  H12' C2'  H21' C2'  H22' C3'  H31' C4'  H42' 
BOND O3'  P    P    O1P  P    O2P  P    O3P  
BOND O3P  C3T  C3T  H3T1 C3T  H3T2 C3T  H3T3
BOND C4'  C5'  C5'  H51' C5'  H52' C5'  H53'
IC   C4'     O4'     C1'     C2'    1.4055  108.09   23.45  106.18   1.5457
IC   O4'     C1'     C2'     C3'    1.4127  106.18    3.96  103.11   1.5346
IC   C1'     C2'     C3'     C4'    1.5457  103.11  -26.93  100.86   1.5211
IC   C2'     C3'     C4'     O4'    1.5346  100.86   41.73  103.15   1.4055
IC   C3'     C4'     O4'     C1'    1.5211  103.15  -41.62  108.09   1.4127
IC   H11'    C1'     C2'     C3'    1.0856  111.62  123.53  103.11   1.5346
IC   H12'    C1'     C2'     C3'    1.0818  113.32 -114.11  103.11   1.5346
IC   H21'    C2'     C3'     C4'    1.0846  110.65   91.68  100.86   1.5211
IC   H22'    C2'     C3'     C4'    1.0822  110.88 -148.45  100.86   1.5211
IC   H31'    C3'     C4'     O4'    1.0806  113.53  162.89  103.15   1.4055
IC   C5'     C4'     O4'     C1'    0.0000  000.00   77.76  108.09   1.4127
IC   H51'    C5'     C4'     O4'    0.0     0.0     180.0     0.0    0.0
IC   H52'    C5'     C4'     O4'    0.0     0.0      -60.0    0.0    0.0
IC   H53'    C5'     C4'     O4'    0.0     0.0       60.0    0.0    0.0
IC   H42'    C4'     O4'     C1'    1.0808  108.72 -162.12  108.09   1.4127
IC   O3'     C3'     C4'     O4'    1.4028  110.98  -77.39  103.15   1.4055
IC   P       O3'     C3'     C4'    0.0       0.0   180.00    0.0    0.0
IC   O1P     P       O3'     C3'    0.0       0.0   -60.0     0.0    0.0
IC   O2P     P       O3'     C3'    0.0       0.0    60.0     0.0    0.0
IC   O3P     P       O3'     C3'    0.0       0.0   180.0     0.0    0.0
IC   C3T     O3P     P       O3'    0.0       0.0   180.0     0.0    0.0 
IC   H3T1    C3T     O3P     P	    0.0       0.0    60.0     0.0    0.0
IC   H3T2    C3T     O3P     P	    0.0       0.0   -60.0     0.0    0.0
IC   H3T3    C3T     O3P     P	    0.0       0.0   180.0     0.0    0.0
PATC  FIRS NONE LAST NONE

RESI TADE         0.00 ! thf with adenine
                       ! Atom types for aliphatic atoms based on nucleotide
                       ! atom order consistent with 9-m-ade
GROUP                  
ATOM C5   CN5     0.28 !             H61  H62!
ATOM N7   NN4    -0.71 !               \  /
ATOM C8   CN4     0.34 !                N6
ATOM H8   HN3     0.12 !                |
ATOM N9   NN2    -0.05 !                C6
ATOM C1'  CN7B    0.16 !              //  \
ATOM N1   NN3A   -0.74 !              N1   C5--N7\\
ATOM C2   CN4     0.50 !              |    ||     C8-H8
ATOM H2   HN3     0.13 !              C2   C4--N9/
ATOM N3   NN3A   -0.75 !             / \\ /     \
ATOM C4   CN5     0.43 !           H2   N3       \
ATOM C6   CN2     0.46 !                          \
ATOM N6   NN1    -0.77 !                           \
ATOM H61  HN1     0.38 !                            \
ATOM H62  HN1     0.38 !                  H42'  O4'  \
ATOM O4'  ON6    -0.50 !                     \ /   \  \
ATOM H12' HN7     0.09 !                H41'-C4'    C1'
ATOM C4'  CN7     0.07 !                      \     / \
ATOM H41' HN7     0.09 !                H31'--C3'--C2' H12'
ATOM H42' HN7     0.09 !                     /    /  \
GROUP                  !                 H32'   H21' H22'
ATOM C2'  CN8    -0.18 !
ATOM H21' HN8     0.09
ATOM H22' HN8     0.09
GROUP
ATOM C3'  CN7    -0.18
ATOM H31' HN7     0.09
ATOM H32' HN7     0.09

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4' 
BOND C1'  H12' C2'  H21' C2'  H22' C3'  H31' C3'  H32'
BOND C4'  H41' C4'  H42'
BOND C1'  N9   
BOND N9   C4    N9   C8   C4   N3    C2   N1    C6   N6
BOND N6   H61   N6   H62  C6   C5    C5   N7    C8   H8    C2   H2
DOUBLE  N1  C6    C2   N3     C4   C5     N7   C8
IMPR N6   C6   H61  H62       C6   N1   C5   N6
! ic table for thfim, from Nicolas:
IC 	C1'	C2'	C3'	C4' 	0.0 0.0 324.92 0.0 0.0
IC	C2'	C3'	C4' 	O4' 	0.0 0.0 33.390 0.0 0.0
IC 	H12'	C1'	C2'	C3' 	0.0 0.0 268.35 0.0 0.0
IC 	H21'	C2'	C3'	C4' 	0.0 0.0 82.530 0.0 0.0
IC 	H22'	C2'	C3'	C4' 	0.0 0.0 204.06 0.0 0.0
IC 	H31'	C3'	C4'	O4' 	0.0 0.0 155.99 0.0 0.0
IC 	H32'	C3'	C4'	O4' 	0.0 0.0 276.70 0.0 0.0
IC	H41'	C4'	O4'	C1' 	0.0 0.0 132.30 0.0 0.0
IC 	H42'	C4'	O4'	C1' 	0.0 0.0 220.70 0.0 0.0
IC C3'  C2'  C1'  N9     1.5284  101.97  147.80  113.71   1.4896
IC O4'  C1'  N9   C4     1.5251  113.71  180.2   125.59   1.3783 !chi
IC C1'  C4   *N9  C8     1.4896  125.97 -180.00  106.0    1.367
IC C4   N9   C8   N7     1.376   106.0     0.0   113.6    1.312
IC C8   N9   C4   C5     1.367   106.0     0.0   105.6    1.382
IC C8   N7   C5   C6     0.0       0.0   180.0     0.0    0.0
IC N7   C5   C6   N1     0.0       0.0   180.0     0.0    0.0
IC C5   C6   N1   C2     0.0       0.0     0.0     0.0    0.0
IC N9   C5   *C4  N3     1.376   105.6  -180.0   126.9    1.342
IC C5   N1   *C6  N6     1.409   117.6  -180.0   121.2    1.337
IC N1   C6   N6   H61    1.337   121.2     0.0   119.0    1.01
IC H61  C6   *N6  H62    1.01    119.0   180.0   119.00   1.01
IC C5   N1   *C6  N6     1.409   117.6  -180.0   119.0    1.337
IC N1   C6   N6   H61    1.337   119.0     0.0   119.0    1.01
IC H61  C6   *N6  H62    1.01    119.0   180.0   121.00   1.01
IC N9   N7   *C8   H8    0.0       0.0   180.0     0.0    0.0
IC N1   N3   *C2   H2    0.0       0.0   180.0     0.0    0.0
PATC  FIRS NONE LAST NONE

RESI TCYT         0.00  ! THF with cytosine
                        ! Atom types for aliphatic atoms based on nucleotide
                        !atom order to be consistent with 1-m-cyt
GROUP                   
ATOM N1   NN2    -0.13  !
ATOM C1'  CN7B    0.16  !                      H42  H41
ATOM C6   CN3     0.05  !                        \  /    
ATOM H6   HN3     0.17  !                         N4
ATOM C2   CN1     0.52  !                         |
ATOM O2   ON1C   -0.49  !                         C4
ATOM N3   NN3    -0.66  !                        /  \\
ATOM C4   CN2     0.65  !                    H5-C5   N3
ATOM N4   NN1    -0.75  !                       ||   |
ATOM H41  HN1     0.37  !                    H6-C6   C2
ATOM H42  HN1     0.33  !                        \  / \\
ATOM C5   CN3    -0.13  !                         N1   O2
ATOM H5   HN3     0.07  !                          \
ATOM O4'  ON6    -0.50  !                           \
ATOM H12' HN7     0.09  !                            \ 
ATOM C4'  CN7     0.07  !                  H42'  O4'  \
ATOM H41' HN7     0.09  !                     \ /   \  \
ATOM H42' HN7     0.09  !                H41'-C4'    C1'
GROUP                   !                      \     / \
ATOM C2'  CN8    -0.18  !                H31'--C3'--C2' H12'
ATOM H21' HN8     0.09  !                     /    /  \
ATOM H22' HN8     0.09  !                 H32'   H21' H22'
GROUP                 
ATOM C3'  CN7    -0.18
ATOM H31' HN7     0.09
ATOM H32' HN7     0.09

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4' 
BOND C1'  H12' C2'  H21' C2'  H22' C3'  H31' C3'  H32'
BOND C4'  H41' C4'  H42'
BOND C1'  N1        
BOND N1   C2    N1   C6    C4   N4    N4   H41   N4   H42
BOND C2   N3    C4   C5    C5   H5    C6   H6
DOUBLE   C2   O2    C5   C6       N3   C4
IMPR C2   N1   N3   O2        C4   N3   C5   N4
IMPR N4   C4   H41  H42
BILD C3'  C2'  C1'  N1     1.5284  101.97  147.89  113.71   1.4896
BILD O4'  C1'  N1   C2     1.5251  113.71  -97.2   125.59   1.3783 !chi
BILD C1'  C2   *N1  C6     1.4896  117.79 -180.00  120.6    1.364   
BILD C2   N1   C6   C5     1.399   120.6     0.0   121.0    1.337   
BILD C6   N1   C2   N3     1.364   120.6     0.0   118.9    1.356   
BILD N1   N3   *C2  O2     1.399   118.9   180.0   121.9    1.237   
BILD N1   C2   N3   C4     1.399   118.9     0.0   120.0    1.334   
BILD C5   N3   *C4  N4     1.426   121.8   180.00  118.9    1.337   
BILD N3   C4   N4   H41    1.337   117.9     0.00  118.9    1.01    
BILD H41  C4   *N4  H42    1.01    118.9   180.00  120.7    1.01    
BILD C6   C4   *C5  H5     0.0       0.0   180.0     0.0    0.0
BILD N1   C5   *C6  H6     0.0       0.0   180.0     0.0    0.0
! ic table for thfim, from Nicolas:
IC 	C1'	C2'	C3'	C4' 	0.0 0.0 324.92 0.0 0.0
IC	C2'	C3'	C4' 	O4' 	0.0 0.0 33.390 0.0 0.0
IC 	H12'	C1'	C2'	C3' 	0.0 0.0 268.35 0.0 0.0
IC 	H21'	C2'	C3'	C4' 	0.0 0.0 82.530 0.0 0.0
IC 	H22'	C2'	C3'	C4' 	0.0 0.0 204.06 0.0 0.0
IC 	H31'	C3'	C4'	O4' 	0.0 0.0 155.99 0.0 0.0
IC 	H32'	C3'	C4'	O4' 	0.0 0.0 276.70 0.0 0.0
IC	H41'	C4'	O4'	C1' 	0.0 0.0 132.30 0.0 0.0
IC 	H42'	C4'	O4'	C1' 	0.0 0.0 220.70 0.0 0.0
IC C3'  C2'  C1'  N1     1.5284  101.97  147.89  113.71   1.4896
IC O4'  C1'  N1   C2     1.5251  113.71  -97.2   125.59   1.3783 !chi
IC C1'  C2   *N1  C6     1.4896  117.79 -180.00  120.6    1.364
IC C2   N1   C6   C5     1.399   120.6     0.0   121.0    1.337
IC C6   N1   C2   N3     1.364   120.6     0.0   118.9    1.356
IC N1   N3   *C2  O2     1.399   118.9   180.0   121.9    1.237
IC N1   C2   N3   C4     1.399   118.9     0.0   120.0    1.334
IC C5   N3   *C4  N4     1.426   121.8   180.00  118.9    1.337
IC N3   C4   N4   H41    1.337   117.9     0.00  118.9    1.01
IC H41  C4   *N4  H42    1.01    118.9   180.00  120.7    1.01
IC C6   C4   *C5  H5     0.0       0.0   180.0     0.0    0.0
IC N1   C5   *C6  H6     0.0       0.0   180.0     0.0    0.0
PATC  FIRS NONE LAST NONE

RESI TGUA         0.00  ! thf with guanine 
                        ! Atom types for aliphatic atoms based on nucleotide
                        ! atom order consistent with 9-m-gua
GROUP                   
ATOM N9   NN2B   -0.02  !               O6                
ATOM C4   CN5     0.26  !               ||   
ATOM C1'  CN7B    0.16  !               C6    
ATOM N3   NN3G   -0.74  !              /  \  
ATOM C2   CN2     0.75  !          H1-N1   C5--N7\\
ATOM N1   NN2G   -0.34  !             |    ||     C8-H8
ATOM H1   HN2     0.26  !             C2   C4--N9/
ATOM N2   NN1    -0.68  !            / \\ /      \
ATOM H21  HN1     0.32  !      H21-N2   N3        \
ATOM H22  HN1     0.35  !          |               \
ATOM C6   CN1     0.54  !         H22               \
ATOM O6   ON1    -0.51  !                            \
ATOM C5   CN5G    0.00  !                  H42'  O4'  \
ATOM N7   NN4    -0.60  !                     \ /   \  \
ATOM C8   CN4     0.25  !                H41'-C4'    C1'
ATOM H8   HN3     0.16  !                      \     / \
ATOM O4'  ON6    -0.50  !                H31'--C3'--C2' H12'
ATOM H12' HN7     0.09  !                     /    /  \
ATOM C4'  CN7     0.07  !                 H32'   H21' H22'
ATOM H41' HN7     0.09
ATOM H42' HN7     0.09
GROUP                 
ATOM C2'  CN8    -0.18
ATOM H21' HN8     0.09
ATOM H22' HN8     0.09
GROUP
ATOM C3'  CN7    -0.18
ATOM H31' HN7     0.09
ATOM H32' HN7     0.09

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4' 
BOND C1'  H12' C2'  H21' C2'  H22' C3'  H31' C3'  H32'
BOND C4'  H41' C4'  H42'
BOND C1'  N9
BOND N9   C4     N9   C8    C4   N3    C2   N2   C2   N1    N2   H21
BOND N2   H22    N1   H1    N1   C6    C6   C5   C5   N7    C8   H8
DOUBLE  C2   N3    C4   C5    N7   C8   C6   O6
IMPR C2   N3   N1   N2        C6   N1   C5   O6        N2   H21  C2   H22
! ic table for thfim, from Nicolas:
IC 	C1'	C2'	C3'	C4' 	0.0 0.0 324.92 0.0 0.0
IC	C2'	C3'	C4' 	O4' 	0.0 0.0 33.390 0.0 0.0
IC 	H12'	C1'	C2'	C3' 	0.0 0.0 268.35 0.0 0.0
IC 	H21'	C2'	C3'	C4' 	0.0 0.0 82.530 0.0 0.0
IC 	H22'	C2'	C3'	C4' 	0.0 0.0 204.06 0.0 0.0
IC 	H31'	C3'	C4'	O4' 	0.0 0.0 155.99 0.0 0.0
IC 	H32'	C3'	C4'	O4' 	0.0 0.0 276.70 0.0 0.0
IC	H41'	C4'	O4'	C1' 	0.0 0.0 132.30 0.0 0.0
IC 	H42'	C4'	O4'	C1' 	0.0 0.0 220.70 0.0 0.0
IC C3'  C2'  C1'  N9     1.5284  101.97  147.80  113.71   1.4896
IC O4'  C1'  N9   C4     1.5251  113.71  -97.2   125.59   1.3783 !chi
IC C1'  C4   *N9  C8     1.4896  125.59 -179.99  106.0    1.374
IC C4   N9   C8   N7     1.377   106.0     0.0   113.5    1.304
IC C8   N9   C4   C5     1.374   106.0     0.0   105.6    1.377
IC N9   C5   *C4  N3     1.377   105.6   180.0   128.4    1.355
IC C5   C4   N3   C2     1.377   128.4     0.0   111.8    1.327
IC C4   N3   C2   N1     1.355   111.8     0.0   124.0    1.375
IC N1   N3   *C2  N2     1.375   124.0   180.0   119.7    1.341
IC N3   C2   N2   H21    1.327   119.7   180.0   127.0    1.01
IC H21  C2   *N2  H22    1.01    127.0  -180.0   116.5    1.01
IC N3   C2   N1   C6     1.327   124.0     0.0   124.9    1.393
IC C6   C2   *N1  H1     1.393   124.9  180.00   117.4    1.03
IC C5   N1   *C6  O6     1.415   111.7  180.0    120.0    1.239
IC N9   N7   *C8  H8     0.0       0.0   180.0     0.0    0.0
PATC  FIRS NONE LAST NONE

RESI TTHY         0.00  ! THF with thymine on C1' 
                        ! Atom type for N1 changed from NN2 to NN2B, to adjust
                        ! chi in thymine independantly of cytosine.
                        ! Atom types for aliphatic atoms based on nucleotide
                        ! atom order consistent with 1-m-thy
GROUP                 
ATOM N1   NN2B   -0.34  !                  H51    O4                               
ATOM C1'  CN7B    0.16  !                   |     ||
ATOM C6   CN3     0.17  !               H52-C5M   C4    H3
ATOM H6   HN3     0.17  !                   |  \ /  \  /
ATOM C2   CN1T    0.51  !                  H53  C5   N3
ATOM O2   ON1    -0.41  !                       ||   |
ATOM N3   NN2U   -0.46  !                    H6-C6   C2
ATOM H3   HN2     0.36  !                        \  / \\  
ATOM C4   CN1     0.50  !                         N1   O2
ATOM O4   ON1    -0.45  !                          \
ATOM C5   CN3T   -0.15  !                           \
ATOM C5M  CN9    -0.11  !                            \ 
ATOM H51  HN9     0.07  !                  H42'  O4'  \
ATOM H52  HN9     0.07  !                     \ /   \  \
ATOM H53  HN9     0.07  !                H41'-C4'    C1'
ATOM O4'  ON6    -0.50  !                      \     / \
ATOM H12' HN7     0.09  !                H31'--C3'--C2' H12'
ATOM C4'  CN7     0.07  !                     /    /  \
ATOM H41' HN7     0.09  !                 H32'   H21' H22'
ATOM H42' HN7     0.09
GROUP                 
ATOM C2'  CN8    -0.18
ATOM H21' HN8     0.09
ATOM H22' HN8     0.09
GROUP                 
ATOM C3'  CN7    -0.18
ATOM H31' HN7     0.09
ATOM H32' HN7     0.09

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4' 
BOND C1'  H12' C2'  H21' C2'  H22' C3'  H31' C3'  H32'
BOND C4'  H41' C4'  H42'
BOND C1'  N1   
BOND N1   C2   N1   C6   C2   N3   N3   H3   N3   C4   C4   C5
BOND C5   C5M  C6   H6   C5M  H51  C5M  H52  C5M  H53
DOUBLE  C2   O2    C4   O4     C5   C6
IMPR C2   N1   N3   O2        C4   N3   C5   O4        C5   C4   C6   C5M
! ic table for thfim, from Nicolas:
IC 	C1'	C2'	C3'	C4' 	0.0 0.0 324.92 0.0 0.0
IC	C2'	C3'	C4' 	O4' 	0.0 0.0 33.390 0.0 0.0
IC 	H12'	C1'	C2'	C3' 	0.0 0.0 268.35 0.0 0.0
IC 	H21'	C2'	C3'	C4' 	0.0 0.0 82.530 0.0 0.0
IC 	H22'	C2'	C3'	C4' 	0.0 0.0 204.06 0.0 0.0
IC 	H31'	C3'	C4'	O4' 	0.0 0.0 155.99 0.0 0.0
IC 	H32'	C3'	C4'	O4' 	0.0 0.0 276.70 0.0 0.0
IC	H41'	C4'	O4'	C1' 	0.0 0.0 132.30 0.0 0.0
IC 	H42'	C4'	O4'	C1' 	0.0 0.0 220.70 0.0 0.0
IC C3'  C2'  C1'  N1     1.5284  101.97  147.89  113.71   1.4896
IC C3'  C2'  C1'  N1     1.5284  101.97  147.89  113.71   1.4896
IC O4'  C1'  N1   C2     1.5251  113.71  180.0   125.59   1.3783 !chi
IC C1'  C2   *N1  C6     1.4896  117.06 -179.96  122.08   1.3704
IC C2   N1   C6   C5     1.3746  122.08   -0.02  121.23   1.3432
IC C6   N1   C2   N3     1.3704  122.08    0.06  115.38   1.3813
IC N1   N3   *C2  O2     1.3746  115.38 -179.95  121.70   1.2191
IC N1   C2   N3   C4     1.3746  115.38   -0.07  126.46   1.3795
IC C5   N3   *C4  O4     1.4439  114.07  179.98  120.59   1.2327
IC C2   C4   *N3  H3     1.3813  126.46  180.00  116.77   1.0900
IC C4   C6   *C5  C5M    1.4439  120.78 -179.94  121.63   1.5000
IC N1   C5   *C6  H6     0.0       0.0   180.0     0.0    0.0
IC C6   C5   C5M  H51    0.0       0.0     0.0     0.0    0.0
IC C5   H51  *C5M H52    0.0       0.0   115.0     0.0    0.0
IC H51  H52  *C5M H53    0.0       0.0  -115.0     0.0    0.0
PATC  FIRS NONE LAST NONE

RESI TURA         0.00  ! THF with uracil on C1' 
                        ! Atom type for N1 changed from NN2 to NN2B, in order to adjust
                        ! chi in uracil/thymine independantly of cytosine.
                        ! Atom types for aliphatic atoms based on nucleotide
                        ! atom order consistent with 1-m-thy
GROUP                 
ATOM N1   NN2B   -0.34  !                         O4                               
ATOM C1'  CN7B    0.16  !                         ||
ATOM C6   CN3     0.20  !                         C4    H3
ATOM H6   HN3     0.14  !                        /  \  /
ATOM C2   CN1T    0.55  !                    H5-C5   N3
ATOM O2   ON1    -0.45  !                       ||   |
ATOM N3   NN2U   -0.46  !                    H6-C6   C2
ATOM H3   HN2     0.36  !                        \  / \\    
ATOM C4   CN1     0.53  !                         N1   O2
ATOM O4   ON1    -0.48  !                          \
ATOM C5   CN3    -0.15  !                           \
ATOM H5   HN3     0.10  !                            \ 
ATOM O4'  ON6    -0.50  !                  H42'  O4'  \
ATOM H12' HN7     0.09  !                     \ /   \  \
ATOM C4'  CN7     0.07  !                H41'-C4'    C1'
ATOM H41' HN7     0.09  !                      \     / \
ATOM H42' HN7     0.09  !                H31'--C3'--C2' H12'
GROUP                   !                     /    /  \
ATOM C2'  CN8    -0.18  !                 H32'   H21' H22'
ATOM H21' HN8     0.09
ATOM H22' HN8     0.09
GROUP                 
ATOM C3'  CN7    -0.18
ATOM H31' HN7     0.09
ATOM H32' HN7     0.09

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4' 
BOND C1'  H12' C2'  H21' C2'  H22' C3'  H31' C3'  H32'
BOND C4'  H41' C4'  H42'
BOND C1'  N1   
BOND N1   C2   N1   C6 
BOND C2   N3   N3   H3   N3   C4    C4   C5
BOND C5   H5   C6   H6
DOUBLE  C2   O2     C4   O4      C5   C6
IMPR C2   N1   N3   O2        C4   N3   C5   O4
! ic table for thfim, from Nicolas:
IC 	C1'	C2'	C3'	C4' 	0.0 0.0 324.92 0.0 0.0
IC	C2'	C3'	C4' 	O4' 	0.0 0.0 33.390 0.0 0.0
IC 	H12'	C1'	C2'	C3' 	0.0 0.0 268.35 0.0 0.0
IC 	H21'	C2'	C3'	C4' 	0.0 0.0 82.530 0.0 0.0
IC 	H22'	C2'	C3'	C4' 	0.0 0.0 204.06 0.0 0.0
IC 	H31'	C3'	C4'	O4' 	0.0 0.0 155.99 0.0 0.0
IC 	H32'	C3'	C4'	O4' 	0.0 0.0 276.70 0.0 0.0
IC	H41'	C4'	O4'	C1' 	0.0 0.0 132.30 0.0 0.0
IC 	H42'	C4'	O4'	C1' 	0.0 0.0 220.70 0.0 0.0
IC C3'  C2'  C1'  N1     1.5284  101.97  147.89  113.71   1.4896
IC C3'  C2'  C1'  N1     1.5284  101.97  147.89  113.71   1.4896
IC O4'  C1'  N1   C2     1.5251  113.71  180.0   125.59   1.3783 !chi
IC C1'  C2   *N1  C6     1.4896  117.06 -179.96  122.08   1.3704
IC C2   N1   C6   C5     1.3746  122.08   -0.02  121.23   1.3432
IC C6   N1   C2   N3     1.3704  122.08    0.06  115.38   1.3813
IC N1   N3   *C2  O2     1.3746  115.38 -179.95  121.70   1.2191
IC N1   C2   N3   C4     1.3746  115.38   -0.07  126.46   1.3795
IC C5   N3   *C4  O4     1.4439  114.07  179.98  120.59   1.2327
IC C2   C4   *N3  H3     1.3813  126.46  180.00  116.77   1.0900
IC C4   C6   *C5  C5M    1.4439  120.78 -179.94  121.63   1.5000
IC N1   C5   *C6  H6     0.0       0.0   180.0     0.0    0.0
IC C6   C5   C5M  H51    0.0       0.0     0.0     0.0    0.0
IC C5   H51  *C5M H52    0.0       0.0   115.0     0.0    0.0
IC H51  H52  *C5M H53    0.0       0.0  -115.0     0.0    0.0
PATC  FIRS NONE LAST NONE

RESI THAO         0.00 ! Nucleoside analogue with imidazole 
GROUP
ATOM O4'  ON6    -0.50 !          H5T
ATOM C4'  CN7     0.16 !         /
ATOM H42' HN7     0.09 !  H51' O5'
ATOM C1'  CN7B    0.16 !     \ |
ATOM H12' HN7     0.09 !H52'--C5'   O4'  Imidazole
GROUP                  !        \  /  \  /
ATOM C2'  CN8    -0.18 !   H42'--C4'  C1'--H12'
ATOM H21' HN8     0.09 !          |    |
ATOM H22' HN8     0.09 !   H31'--C3'--C2'--H21'
GROUP                  !        /       \
ATOM H31' HN7     0.09 !      O3'       H22'
ATOM C3'  CN7     0.14 !       |
ATOM O3'  ON5    -0.66 !     H32'
ATOM H32' HN5     0.43 !
GROUP                 
ATOM C5'  CN8B    0.05
ATOM H51' HN8     0.09
ATOM H52' HN8     0.09
ATOM O5'  ON5    -0.66
ATOM H5T  HN5     0.43
GROUP	! Imidazole: transferred from isolated imidazole (IMIA)
ATOM CG   CPH1   -0.05 !     C1'       HE1
ATOM HG   HR3     0.09 !       \       /
ATOM CD2  CPH1    0.22 !       ND1---CE1
ATOM HD2  HR3     0.10 !      /       ||
ATOM ND1  NR1    -0.04 !  HG-CG       ||
ATOM CE1  CPH2    0.25 !      \\      ||
ATOM HE1  HR1     0.13 !       CD2---NE2
ATOM NE2  NR2    -0.70 !        |
                       !       HD2

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C4'  C5'
BOND C3'  O3'  C1'  H12' C2'  H21' C2'  H22' C3'  H31' C4'  H42'
BOND C5'  H51' C5'  H52' C5'  O5'  O5'  H5T
BOND O3'  H32'
BOND C1'  ND1  
BOND ND1  CE1  NE2  CD2  CG  ND1
BOND CE1  HE1  CD2  HD2  CG  HG
DOUBLE CG  CD2   CE1  NE2
! KEEPS HYDROGENS IN RING PLANE
IMPR ND1  CG   CE1  C1'       ND1  CE1  CG   C1'
IMPR CD2  CG   NE2  HD2       CD2  NE2  CG   HD2
IMPR CE1  ND1  NE2  HE1       CE1  NE2  ND1  HE1
IMPR CG   CD2  ND1  HG        CG   ND1  CD2  HG
! This IC table is only an initial guess:
IC 	C1'	C2'	C3'	C4' 	0.0 0.0 324.92 0.0 0.0
IC	C2'	C3'	C4' 	O4' 	0.0 0.0 33.390 0.0 0.0
IC 	H12'	C1'	C2'	C3' 	0.0 0.0 268.35 0.0 0.0
IC 	H21'	C2'	C3'	C4' 	0.0 0.0 82.530 0.0 0.0
IC 	H22'	C2'	C3'	C4' 	0.0 0.0 204.06 0.0 0.0
IC 	O3' 	C3'	C4'	O4' 	0.0 0.0 -93.14 0.0 0.0
IC	H32'	O3'	C3'	C2'	0.0 0.0 -60.00 0.0 0.0
IC 	H31'	C3'	C4'	O4' 	0.0 0.0 147.80 0.0 0.0
IC	H41'	C4'	O4'	C1' 	0.0 0.0 132.30 0.0 0.0
IC 	H42'	C4'	O4'	C1' 	0.0 0.0 220.70 0.0 0.0
IC	C4'	O4'	C1'	ND1 	0.0 0.0 256.98 0.0 0.0
IC 	O4'	C1'	ND1	CG  	0.0 0.0  90.00 0.0 0.0
IC	C1'	ND1	CE1     NE2 	0.0 0.0 181.56 0.0 0.0
IC	ND1	CE1	NE2	CD2 	0.0 0.0   0.34 0.0 0.0
IC 	CE1	NE2	CD2	CG 	0.0 0.0   0.00 0.0 0.0 
IC 	HE1	CE1	NE2	CD2 	0.0 0.0 180.40 0.0 0.0
IC	CE1	NE2	CD2	HD2 	0.0 0.0 179.83 0.0 0.0
IC 	NE2 	CD2	CG 	HG 	0.0 0.0 178.45 0.0 0.0
IC      C5'     C4'     O4'     C1'     0.0 0.0 144.82 0.0 0.0   
IC      H51'    C5'     C4'     O4'     0.0 0.0 -179.98 0.0 0.0 
IC      H52'    C5'     C4'     O4'     0.0 0.0   59.66 0.0 0.0
IC      O5'     C5'     C4'     O4'     0.0 0.0  -59.68 0.0 0.0
IC      H5T     O5'     C5'     C4'     0.0 0.0  180.0 0.0 0.0
PATC  FIRS NONE LAST NONE

RESI NUSA         0.00 ! deoxy-nucleoside with adenine 
GROUP
ATOM O4'  ON6    -0.50 !          H5T
ATOM C4'  CN7     0.16 !         /
ATOM H42' HN7     0.09 !  H51' O5'
ATOM C1'  CN7B    0.16 !     \ |
ATOM H12' HN7     0.09 !H52'--C5'   O4'  Adenine
GROUP                  !        \  /  \  /
ATOM C2'  CN8    -0.18 !   H42'--C4'  C1'--H12'
ATOM H21' HN8     0.09 !          |    |
ATOM H22' HN8     0.09 !   H31'--C3'--C2'--H21'
! Adenine atoms        !        /       \
GROUP                  !      O3'       H22'
ATOM C5   CN5     0.28 !       |
ATOM N7   NN4    -0.71 !     H32'
ATOM C8   CN4     0.34  
ATOM H8   HN3     0.12  
ATOM N9   NN2    -0.05  
ATOM N1   NN3A   -0.74  
ATOM C2   CN4     0.50  
ATOM H2   HN3     0.13  
ATOM N3   NN3A   -0.75
ATOM C4   CN5     0.43
ATOM C6   CN2     0.46
ATOM N6   NN1    -0.77
ATOM H61  HN1     0.38
ATOM H62  HN1     0.38
GROUP ! Hydroxyl group on C3'
ATOM H31' HN7     0.09
ATOM C3'  CN7     0.14
ATOM O3'  ON5    -0.66
ATOM H32' HN5     0.43
GROUP ! Methyl group on C4'
ATOM C5'  CN8B    0.05
ATOM H51' HN8     0.09
ATOM H52' HN8     0.09
ATOM O5'  ON5    -0.66
ATOM H5T  HN5     0.43

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C4'  C5'
BOND C3'  O3'  C1'  H12' C2'  H21' C2'  H22' C3'  H31' C4'  H42'
BOND C5'  H51' C5'  H52' C5'  O5'  O5'  H5T
BOND O3'  H32'
BOND C1'  N9
BOND N9   C4    N9   C8   C4   N3    C2   N1    C6   N6
BOND N6   H61   N6   H62  C6   C5    C5   N7    C8   H8    C2   H2
DOUBLE  N1  C6    C2   N3     C4   C5     N7   C8
IMPR N6   C6   H61  H62       C6   N1   C5   N6       
! This IC table is only an initial guess:
IC 	C1'	C2'	C3'	C4' 	0.0 0.0 324.92 0.0 0.0
IC	C2'	C3'	C4' 	O4' 	0.0 0.0 33.390 0.0 0.0
IC 	H12'	C1'	C2'	C3' 	0.0 0.0 268.35 0.0 0.0
IC 	H21'	C2'	C3'	C4' 	0.0 0.0 82.530 0.0 0.0
IC 	H22'	C2'	C3'	C4' 	0.0 0.0 204.06 0.0 0.0
IC 	O3' 	C3'	C4'	O4' 	0.0 0.0 -93.14 0.0 0.0
IC	H32'	O3'	C3'	C2'	0.0 0.0 -60.00 0.0 0.0
IC 	H31'	C3'	C4'	O4' 	0.0 0.0 147.80 0.0 0.0
IC	H41'	C4'	O4'	C1' 	0.0 0.0 132.30 0.0 0.0
IC 	H42'	C4'	O4'	C1' 	0.0 0.0 220.70 0.0 0.0
IC C3'  C2'  C1'  N9     1.5284  101.97  147.80  113.71   1.4896
IC O4'  C1'  N9   C4     1.5251  113.71  -97.2   125.59   1.3783 !chi
IC C1'  C4   *N9  C8     1.4896  125.97 -179.94  106.0    1.367
IC C4   N9   C8   N7     1.376   106.0     0.0   113.6    1.312
IC C8   N9   C4   C5     1.367   106.0     0.0   105.6    1.382
IC C8   N7   C5   C6     0.0       0.0   180.0     0.0    0.0
IC N7   C5   C6   N1     0.0       0.0   180.0     0.0    0.0
IC C5   C6   N1   C2     0.0       0.0     0.0     0.0    0.0
IC N9   C5   *C4  N3     1.376   105.6  -180.0   126.9    1.342
IC C5   N1   *C6  N6     1.409   117.6  -180.0   121.2    1.337
IC N1   C6   N6   H61    1.337   121.2     0.0   119.0    1.01
IC H61  C6   *N6  H62    1.01    119.0   180.0   119.00   1.01
IC C5   N1   *C6  N6     1.409   117.6  -180.0   119.0    1.337
IC N1   C6   N6   H61    1.337   119.0     0.0   119.0    1.01
IC H61  C6   *N6  H62    1.01    119.0   180.0   121.00   1.01
IC N9   N7   *C8   H8    0.0       0.0   180.0     0.0    0.0
IC N1   N3   *C2   H2    0.0       0.0   180.0     0.0    0.0
IC      C5'     C4'     O4'     C1'     0.0 0.0 144.82 0.0 0.0   
IC      H51'    C5'     C4'     O4'     0.0 0.0 -179.98 0.0 0.0 
IC      H52'    C5'     C4'     O4'     0.0 0.0   59.66 0.0 0.0
IC      O5'     C5'     C4'     O4'     0.0 0.0  -59.68 0.0 0.0
IC      H5T     O5'     C5'     C4'     0.0 0.0  180.0 0.0 0.0
PATC  FIRS NONE LAST NONE

RESI NUSG         0.00 ! nucleoside with guanine 
GROUP
ATOM O4'  ON6    -0.50 !          H5T
ATOM C4'  CN7     0.16 !         /
ATOM H42' HN7     0.09 !  H51' O5'
ATOM C1'  CN7B    0.16 !     \ |
ATOM H12' HN7     0.09 !H52'--C5'   O4'  Guanine
GROUP                  !        \  /  \  /
ATOM C2'  CN8    -0.18 !   H42'--C4'  C1'--H12'
ATOM H21' HN8     0.09 !          |    |
ATOM H22' HN8     0.09 !   H31'--C3'--C2'--H21'
! Guanine atoms        !        /       \
GROUP                  !      O3'       H22'
ATOM N9   NN2B   -0.02 !       |
ATOM C4   CN5     0.26 !     H32'
ATOM N3   NN3G   -0.74  
ATOM C2   CN2     0.75  
ATOM N1   NN2G   -0.34  
ATOM H1   HN2     0.26  
ATOM N2   NN1    -0.68
ATOM H21  HN1     0.32
ATOM H22  HN1     0.35
ATOM C6   CN1     0.54
ATOM O6   ON1    -0.51
ATOM C5   CN5G    0.00
ATOM N7   NN4    -0.60
ATOM C8   CN4     0.25
ATOM H8   HN3     0.16
GROUP ! Hydroxyl group on C3'
ATOM H31' HN7     0.09
ATOM C3'  CN7     0.14
ATOM O3'  ON5    -0.66
ATOM H32' HN5     0.43
GROUP ! C5' hydroxyl
ATOM C5'  CN8B    0.05
ATOM H51' HN8     0.09
ATOM H52' HN8     0.09
ATOM O5'  ON5    -0.66
ATOM H5T  HN5     0.43

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C4'  C5'
BOND C3'  O3'  C1'  H12' C2'  H21' C2'  H22' C3'  H31' C4'  H42'
BOND C5'  H51' C5'  H52' C5'  O5'  O5'  H5T
BOND O3'  H32'
BOND C1'  N9
BOND N9   C4     N9   C8    C4   N3    C2   N2   C2   N1    N2   H21
BOND N2   H22    N1   H1    N1   C6    C6   C5   C5   N7    C8   H8
DOUBLE  C2   N3    C4   C5    N7   C8   C6   O6
IMPR C2   N3   N1   N2        C6   N1   C5   O6        N2  H21  C2   H22
! This IC table is only an initial guess:
IC 	C1'	C2'	C3'	C4' 	0.0 0.0 324.92 0.0 0.0
IC	C2'	C3'	C4' 	O4' 	0.0 0.0 33.390 0.0 0.0
IC 	H12'	C1'	C2'	C3' 	0.0 0.0 268.35 0.0 0.0
IC 	H21'	C2'	C3'	C4' 	0.0 0.0 82.530 0.0 0.0
IC 	H22'	C2'	C3'	C4' 	0.0 0.0 204.06 0.0 0.0
IC 	O3' 	C3'	C4'	O4' 	0.0 0.0 -93.14 0.0 0.0
IC	H32'	O3'	C3'	C2'	0.0 0.0 -60.00 0.0 0.0
IC 	H31'	C3'	C4'	O4' 	0.0 0.0 147.80 0.0 0.0
IC	H41'	C4'	O4'	C1' 	0.0 0.0 132.30 0.0 0.0
IC 	H42'	C4'	O4'	C1' 	0.0 0.0 220.70 0.0 0.0
IC C3'  C2'  C1'  N9     1.5284  101.97  147.80  113.71   1.4896
IC O4'  C1'  N9   C4     1.5251  113.71  -97.2   125.59   1.3783 !chi
IC C1'  C4   *N9  C8     1.4896  125.59 -179.99  106.0    1.374
IC C4   N9   C8   N7     1.377   106.0     0.0   113.5    1.304
IC C8   N9   C4   C5     1.374   106.0     0.0   105.6    1.377
IC N9   C5   *C4  N3     1.377   105.6   180.0   128.4    1.355
IC C5   C4   N3   C2     1.377   128.4     0.0   111.8    1.327
IC C4   N3   C2   N1     1.355   111.8     0.0   124.0    1.375
IC N1   N3   *C2  N2     1.375   124.0   180.0   119.7    1.341
IC N3   C2   N2   H21    1.327   119.7   180.0   127.0    1.01
IC H21  C2   *N2  H22    1.01    127.0  -180.0   116.5    1.01
IC N3   C2   N1   C6     1.327   124.0     0.0   124.9    1.393
IC C6   C2   *N1  H1     1.393   124.9  180.00   117.4    1.03
IC C5   N1   *C6  O6     1.415   111.7  180.0    120.0    1.239
IC N9   N7   *C8  H8     0.0       0.0   180.0     0.0    0.0
IC      C5'     C4'     O4'     C1'     0.0 0.0 144.82 0.0 0.0   
IC      H51'    C5'     C4'     O4'     0.0 0.0 -179.98 0.0 0.0 
IC      H52'    C5'     C4'     O4'     0.0 0.0   59.66 0.0 0.0
IC      O5'     C5'     C4'     O4'     0.0 0.0  -59.68 0.0 0.0
IC      H5T     O5'     C5'     C4'     0.0 0.0  180.0 0.0 0.0
PATC  FIRS NONE LAST NONE

RESI NUSC         0.00 ! nucleoside with cytosine 
GROUP
ATOM O4'  ON6    -0.50 !          H5T
ATOM C4'  CN7     0.16 !         /
ATOM H42' HN7     0.09 !  H51' O5'
ATOM C1'  CN7B    0.16 !     \ |
ATOM H12' HN7     0.09 !H52'--C5'   O4'  Cytosine
GROUP                  !        \  /  \  /
ATOM C2'  CN8    -0.18 !   H42'--C4'  C1'--H12'
ATOM H21' HN8     0.09 !          |    |
ATOM H22' HN8     0.09 !   H31'--C3'--C2'--H21'
! Cytosine atoms       !        /       \
GROUP                  !      O3'       H22'
ATOM N1   NN2    -0.13 !       |
ATOM C6   CN3     0.05 !     H32'
ATOM H6   HN3     0.17  
ATOM C2   CN1     0.52  
ATOM O2   ON1C   -0.49  
ATOM N3   NN3    -0.66  
ATOM C4   CN2     0.65  
ATOM N4   NN1    -0.75  
ATOM H41  HN1     0.37  
ATOM H42  HN1     0.33  
ATOM C5   CN3    -0.13  
ATOM H5   HN3     0.07  
GROUP ! Hydroxyl group on C3'
ATOM H31' HN7     0.09
ATOM C3'  CN7     0.14
ATOM O3'  ON5    -0.66
ATOM H32' HN5     0.43
GROUP ! C5' hydroxyl
ATOM C5'  CN8B    0.05
ATOM H51' HN8     0.09
ATOM H52' HN8     0.09
ATOM O5'  ON5    -0.66
ATOM H5T  HN5     0.43

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C4'  C5'
BOND C3'  O3'  C1'  H12' C2'  H21' C2'  H22' C3'  H31' C4'  H42'
BOND C5'  H51' C5'  H52' C5'  O5'  O5'  H5T
BOND O3'  H32'
BOND C1'  N1
BOND N1   C2    N1   C6    C4   N4    N4   H41   N4   H42
BOND C2   N3    C4   C5    C5   H5    C6   H6
DOUBLE   C2   O2    C5   C6       N3   C4
IMPR N4   C4   H41  H42       C2   N1   N3   O2        C4   N3   C5   N4
! This IC table is only an initial guess:
IC 	C1'	C2'	C3'	C4' 	0.0 0.0 324.92 0.0 0.0
IC	C2'	C3'	C4' 	O4' 	0.0 0.0 33.390 0.0 0.0
IC 	H12'	C1'	C2'	C3' 	0.0 0.0 268.35 0.0 0.0
IC 	H21'	C2'	C3'	C4' 	0.0 0.0 82.530 0.0 0.0
IC 	H22'	C2'	C3'	C4' 	0.0 0.0 204.06 0.0 0.0
IC 	O3' 	C3'	C4'	O4' 	0.0 0.0 -93.14 0.0 0.0
IC	H32'	O3'	C3'	C2'	0.0 0.0 -60.00 0.0 0.0
IC 	H31'	C3'	C4'	O4' 	0.0 0.0 147.80 0.0 0.0
IC	H41'	C4'	O4'	C1' 	0.0 0.0 132.30 0.0 0.0
IC 	H42'	C4'	O4'	C1' 	0.0 0.0 220.70 0.0 0.0
IC C3'  C2'  C1'  N1     1.5284  101.97  147.89  113.71   1.4896
IC O4'  C1'  N1   C2     1.5251  113.71  -97.2   125.59   1.3783 !chi
IC C1'  C2   *N1  C6     1.4896  117.79 -180.00  120.6    1.364   
IC C2   N1   C6   C5     1.399   120.6     0.0   121.0    1.337   
IC C6   N1   C2   N3     1.364   120.6     0.0   118.9    1.356   
IC N1   N3   *C2  O2     1.399   118.9   180.0   121.9    1.237   
IC N1   C2   N3   C4     1.399   118.9     0.0   120.0    1.334   
IC C5   N3   *C4  N4     1.426   121.8   180.00  118.9    1.337   
IC N3   C4   N4   H41    1.337   117.9     0.00  118.9    1.01    
IC H41  C4   *N4  H42    1.01    118.9   180.00  120.7    1.01    
IC C6   C4   *C5  H5     0.0       0.0   180.0     0.0    0.0
IC N1   C5   *C6  H6     0.0       0.0   180.0     0.0    0.0
IC      C5'     C4'     O4'     C1'     0.0 0.0 144.82 0.0 0.0   
IC      H51'    C5'     C4'     O4'     0.0 0.0 -179.98 0.0 0.0 
IC      H52'    C5'     C4'     O4'     0.0 0.0   59.66 0.0 0.0
IC      O5'     C5'     C4'     O4'     0.0 0.0  -59.68 0.0 0.0
IC      H5T     O5'     C5'     C4'     0.0 0.0  180.0 0.0 0.0
PATC  FIRS NONE LAST NONE

RESI NUST         0.00 ! nucleoside with thymine
GROUP
ATOM O4'  ON6    -0.50 !          H5T
ATOM C4'  CN7     0.16 !         /
ATOM H42' HN7     0.09 !  H51' O5'
ATOM C1'  CN7B    0.16 !     \ |
ATOM H12' HN7     0.09 !H52'--C5'   O4'  Thymine
GROUP                  !        \  /  \  /
ATOM C2'  CN8    -0.18 !   H42'--C4'  C1'--H12'
ATOM H21' HN8     0.09 !          |    |
ATOM H22' HN8     0.09 !   H31'--C3'--C2'--H21'
! Atoms for thymine    !        /       \
GROUP                  !      O3'       H22'
ATOM N1   NN2B   -0.34 !       |
ATOM C6   CN3     0.17 !     H32'
ATOM H6   HN3     0.17
ATOM C2   CN1T    0.51 
ATOM O2   ON1    -0.41
ATOM N3   NN2U   -0.46 
ATOM H3   HN2     0.36 
ATOM C4   CN1     0.50
ATOM O4   ON1    -0.45
ATOM C5   CN3T   -0.15
ATOM C5M  CN9    -0.11
ATOM H51  HN9     0.07
ATOM H52  HN9     0.07
ATOM H53  HN9     0.07
GROUP ! Hydroxyl group on C3'
ATOM H31' HN7     0.09
ATOM C3'  CN7     0.14
ATOM O3'  ON5    -0.66
ATOM H32' HN5     0.43
GROUP ! C5' hydroxyl
ATOM C5'  CN8B    0.05
ATOM H51' HN8     0.09
ATOM H52' HN8     0.09
ATOM O5'  ON5    -0.66
ATOM H5T  HN5     0.43

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C4'  C5'
BOND C3'  O3'  C1'  H12' C2'  H21' C2'  H22' C3'  H31' C4'  H42'
BOND C5'  H51' C5'  H52' C5'  O5'  O5'  H5T
BOND O3'  H32'
BOND C1'  N1
BOND N1   C2   N1   C6   C2   N3   N3   H3   N3   C4   C4   C5
BOND C5   C5M  C6   H6   C5M  H51  C5M  H52  C5M  H53
DOUBLE  C2   O2    C4   O4     C5   C6
IMPR C2   N1   N3   O2        C4   N3   C5   O4        C5   C4   C6   C5M
! This IC table is only an initial guess:
IC 	C1'	C2'	C3'	C4' 	0.0 0.0 324.92 0.0 0.0
IC	C2'	C3'	C4' 	O4' 	0.0 0.0 33.390 0.0 0.0
IC 	H12'	C1'	C2'	C3' 	0.0 0.0 268.35 0.0 0.0
IC 	H21'	C2'	C3'	C4' 	0.0 0.0 82.530 0.0 0.0
IC 	H22'	C2'	C3'	C4' 	0.0 0.0 204.06 0.0 0.0
IC 	O3' 	C3'	C4'	O4' 	0.0 0.0 -93.14 0.0 0.0
IC	H32'	O3'	C3'	C2'	0.0 0.0 -60.00 0.0 0.0
IC 	H31'	C3'	C4'	O4' 	0.0 0.0 147.80 0.0 0.0
IC	H41'	C4'	O4'	C1' 	0.0 0.0 132.30 0.0 0.0
IC 	H42'	C4'	O4'	C1' 	0.0 0.0 220.70 0.0 0.0
IC C3'  C2'  C1'  N1     1.5284  101.97  147.89  113.71   1.4896
IC O4'  C1'  N1   C2     1.5251  113.71  -97.2   125.59   1.3783 !chi
IC C1'  C2   *N1  C6     1.4896  117.06 -179.96  122.08   1.3704
IC C2   N1   C6   C5     1.3746  122.08   -0.02  121.23   1.3432
IC C6   N1   C2   N3     1.3704  122.08    0.06  115.38   1.3813
IC N1   N3   *C2  O2     1.3746  115.38 -179.95  121.70   1.2191
IC N1   C2   N3   C4     1.3746  115.38   -0.07  126.46   1.3795
IC C5   N3   *C4  O4     1.4439  114.07  179.98  120.59   1.2327
IC C2   C4   *N3  H3     1.3813  126.46  180.00  116.77   1.0900
IC C4   C6   *C5  C5M    1.4439  120.78 -179.94  121.63   1.5000
IC N1   C5   *C6  H6     0.0       0.0   180.0     0.0    0.0
IC C6   C5   C5M  H51    0.0       0.0     0.0     0.0    0.0
IC C5   H51  *C5M H52    0.0       0.0   115.0     0.0    0.0
IC H51  H52  *C5M H53    0.0       0.0  -115.0     0.0    0.0
IC      C5'     C4'     O4'     C1'     0.0 0.0 144.82 0.0 0.0   
IC      H51'    C5'     C4'     O4'     0.0 0.0 -179.98 0.0 0.0 
IC      H52'    C5'     C4'     O4'     0.0 0.0   59.66 0.0 0.0
IC      O5'     C5'     C4'     O4'     0.0 0.0  -59.68 0.0 0.0
IC      H5T     O5'     C5'     C4'     0.0 0.0  180.0 0.0 0.0
PATC  FIRS NONE LAST NONE

RESI NUSU         0.00  ! nucleoside with uracil
GROUP
ATOM O4'  ON6    -0.50 !          H5T
ATOM C4'  CN7     0.16 !         /
ATOM H42' HN7     0.09 !  H51' O5'
ATOM C1'  CN7B    0.16 !     \ |
ATOM H12' HN7     0.09 !H52'--C5'   O4'  Uracil
GROUP                  !        \  /  \  /
ATOM C2'  CN8    -0.18 !   H42'--C4'  C1'--H12'
ATOM H21' HN8     0.09 !          |    |
ATOM H22' HN8     0.09 !   H31'--C3'--C2'--H21'
! Atoms for uracil     !        /       \
GROUP                  !      O3'       H22'
ATOM N1   NN2B   -0.34 !       |
ATOM C6   CN3     0.20 !     H32'
ATOM H6   HN3     0.14
ATOM C2   CN1T    0.55
ATOM O2   ON1    -0.45
ATOM N3   NN2U   -0.46
ATOM H3   HN2     0.36
ATOM C4   CN1     0.53
ATOM O4   ON1    -0.48
ATOM C5   CN3    -0.15 
ATOM H5   HN3     0.10  
GROUP ! Hydroxyl group on C3'
ATOM H31' HN7     0.09
ATOM C3'  CN7     0.14
ATOM O3'  ON5    -0.66
ATOM H32' HN5     0.43
GROUP ! C5' hydroxyl
ATOM C5'  CN8B    0.05
ATOM H51' HN8     0.09
ATOM H52' HN8     0.09
ATOM O5'  ON5    -0.66
ATOM H5T  HN5     0.43

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C4'  C5'
BOND C3'  O3'  C1'  H12' C2'  H21' C2'  H22' C3'  H31' C4'  H42'
BOND C5'  H51' C5'  H52' C5'  O5'  O5'  H5T
BOND O3'  H32'
BOND C1'  N1        N1   C2        N1   C6        C2   O2
BOND C2   N3        N3   H3        N3   C4        C4   O4        C4   C5
BOND C5   C6        C5   H5        C6   H6
IMPR C2   N1   N3   O2        C4   N3   C5   O4
! This IC table is only an initial guess:
IC 	C1'	C2'	C3'	C4' 	0.0 0.0 324.92 0.0 0.0
IC	C2'	C3'	C4' 	O4' 	0.0 0.0 33.390 0.0 0.0
IC 	H12'	C1'	C2'	C3' 	0.0 0.0 268.35 0.0 0.0
IC 	H21'	C2'	C3'	C4' 	0.0 0.0 82.530 0.0 0.0
IC 	H22'	C2'	C3'	C4' 	0.0 0.0 204.06 0.0 0.0
IC 	O3' 	C3'	C4'	O4' 	0.0 0.0 -93.14 0.0 0.0
IC	H32'	O3'	C3'	C2'	0.0 0.0 -60.00 0.0 0.0
IC 	H31'	C3'	C4'	O4' 	0.0 0.0 147.80 0.0 0.0
IC	H41'	C4'	O4'	C1' 	0.0 0.0 132.30 0.0 0.0
IC 	H42'	C4'	O4'	C1' 	0.0 0.0 220.70 0.0 0.0
BILD C3'  C2'  C1'  N1     1.5284  101.97  144.39  113.71   1.4896
BILD O4'  C1'  N1   C2     1.5251  113.71  -96.0   117.06   1.3746
BILD C1'  C2   *N1  C6     1.4896  117.06 -180.0   121.3    1.379
BILD C2   N1   C6   C5     1.379   121.3     0.0   122.8    1.338
BILD C6   N1   C2   N3     1.380   121.3     0.0   114.8    1.373
BILD N1   N3   *C2  O2     1.379   114.8  -180.0   122.0    1.218
BILD N1   C2   N3   C4     1.379   114.8     0.0   127.0    1.383
BILD C5   N3   *C4  O4     1.440   114.7   180.0   119.8    1.227
BILD C2   C4   *N3  H3     1.373   127.0   180.0   116.5    1.03
BILD C6   C4   *C5  H5     0.0       0.0   180.0     0.0    0.0
BILD N1   C5   *C6  H6     0.0       0.0   180.0     0.0    0.0
IC      C5'     C4'     O4'     C1'     0.0 0.0 144.82 0.0 0.0   
IC      H51'    C5'     C4'     O4'     0.0 0.0 -179.98 0.0 0.0 
IC      H52'    C5'     C4'     O4'     0.0 0.0   59.66 0.0 0.0
IC      O5'     C5'     C4'     O4'     0.0 0.0  -59.68 0.0 0.0
IC      H5T     O5'     C5'     C4'     0.0 0.0  180.0 0.0 0.0
PATC  FIRS NONE LAST NONE

RESI RNUS         0.00 ! Ribonucleoside analogue with imidazole 
GROUP
ATOM O4'  ON6B   -0.50 !          H5T
ATOM C4'  CN7     0.16 !         /
ATOM H42' HN7     0.09 !  H51' O5'
ATOM C1'  CN7B    0.16 !     \ |
ATOM H12' HN7     0.09 !H52'--C5'   O4'  Imidazole
GROUP                  !        \  /  \  /
ATOM C2'  CN7B    0.14 !   H42'--C4'  C1'--H12'
ATOM H21' HN7     0.09 !          |    |
ATOM O2'  ON5    -0.66 !   H31'--C3'--C2'--H21'
ATOM H22' HN5     0.43 !        /       \
GROUP                  !      O3'       O2'
ATOM H31' HN7     0.09 !       |         |
ATOM C3'  CN7     0.14 !      H32'      H22'
ATOM O3'  ON5    -0.66
ATOM H32' HN5     0.43
GROUP                 
ATOM C5'  CN8B    0.05
ATOM H51' HN8     0.09
ATOM H52' HN8     0.09
ATOM O5'  ON5    -0.66
ATOM H5T  HN5     0.43
GROUP	! Imidazole: transferred from isolated imidazole (IMIA)
ATOM CG   CPH1   -0.05 !     C1'       HE1
ATOM HG   HR3     0.09 !       \       /
ATOM CD2  CPH1    0.22 !       ND1---CE1
ATOM HD2  HR3     0.10 !      /       ||
ATOM ND1  NR1    -0.04 !  HG-CG       ||
ATOM CE1  CPH2    0.25 !      \\      ||
ATOM HE1  HR1     0.13 !       CD2---NE2
ATOM NE2  NR2    -0.70 !        |
                       !       HD2

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C4'  C5'
BOND C3'  O3'  C1'  H12' C2'  H21' C2'  O2'  O2'  H22' C3'  H31' 
BOND C4'  H42' C5'  H51' C5'  H52' C5'  O5'  O5'  H5T
BOND O3'  H32'
BOND C1'  ND1  
BOND ND1  CE1  NE2  CD2  CG  ND1
BOND CE1  HE1  CD2  HD2  CG  HG
DOUBLE CG  CD2   CE1  NE2
! KEEPS HYDROGENS IN RING PLANE
IMPR ND1  CG   CE1  C1'       ND1  CE1  CG   C1'
IMPR CD2  CG   NE2  HD2       CD2  NE2  CG   HD2
IMPR CE1  ND1  NE2  HE1       CE1  NE2  ND1  HE1
IMPR CG   CD2  ND1  HG        CG   ND1  CD2  HG
! This IC table is only an initial guess:
IC 	C1'	C2'	C3'	C4' 	0.0 0.0 324.92 0.0 0.0
IC	C2'	C3'	C4' 	O4' 	0.0 0.0 33.390 0.0 0.0
IC 	H12'	C1'	C2'	C3' 	0.0 0.0 268.35 0.0 0.0
IC 	H21'	C2'	C3'	C4' 	0.0 0.0 82.530 0.0 0.0
IC 	O2' 	C2'	C3'	C4' 	0.0 0.0 204.06 0.0 0.0
IC 	H22'	O2'	C2'	C3' 	0.0 0.0 -60.00 0.0 0.0
IC 	O3' 	C3'	C4'	O4' 	0.0 0.0 -93.14 0.0 0.0
IC	H32'	O3'	C3'	C2'	0.0 0.0 -60.00 0.0 0.0
IC 	H31'	C3'	C4'	O4' 	0.0 0.0 147.80 0.0 0.0
IC	H41'	C4'	O4'	C1' 	0.0 0.0 132.30 0.0 0.0
IC 	H42'	C4'	O4'	C1' 	0.0 0.0 220.70 0.0 0.0
IC	C4'	O4'	C1'	ND1 	0.0 0.0 256.98 0.0 0.0
IC 	O4'	C1'	ND1	CE1 	0.0 0.0 180.00 0.0 0.0
IC	C1'	ND1	CE1     NE2 	0.0 0.0 181.56 0.0 0.0
IC	ND1	CE1	NE2	CD2 	0.0 0.0   0.34 0.0 0.0
IC 	CE1	NE2	CD2	CG 	0.0 0.0   0.00 0.0 0.0 
IC 	HE1	CE1	NE2	CD2 	0.0 0.0 180.40 0.0 0.0
IC	CE1	NE2	CD2	HD2 	0.0 0.0 179.83 0.0 0.0
IC 	NE2 	CD2	CG 	HG 	0.0 0.0 178.45 0.0 0.0
IC      C5'     C4'     O4'     C1'     0.0 0.0 144.82 0.0 0.0   
IC      H51'    C5'     C4'     O4'     0.0 0.0 -179.98 0.0 0.0 
IC      H52'    C5'     C4'     O4'     0.0 0.0   59.66 0.0 0.0
IC      O5'     C5'     C4'     O4'     0.0 0.0  -59.68 0.0 0.0
IC      H5T     O5'     C5'     C4'     0.0 0.0  180.0 0.0 0.0
PATC  FIRS NONE LAST NONE

RESI RNUA         0.00 ! ribo-nucleoside with adenine 
GROUP
ATOM O4'  ON6B   -0.50 !          H5T
ATOM C4'  CN7     0.16 !         /
ATOM H42' HN7     0.09 !  H51' O5'
ATOM C1'  CN7B    0.16 !     \ |
ATOM H12' HN7     0.09 !H52'--C5'   O4'  Adenine
GROUP                  !        \  /  \  /
ATOM H21' HN7     0.09 !   H42'--C4'  C1'--H12'
ATOM C2'  CN7B    0.14 !          |    |
ATOM O2'  ON5    -0.66 !   H31'--C3'--C2'--H21'
ATOM H22' HN5     0.43 !        /       \
! Adenine atoms        !      O3'       O2'
GROUP                  !       |         |
ATOM C5   CN5     0.28 !      H32'      H22'
ATOM N7   NN4    -0.71  
ATOM C8   CN4     0.34  
ATOM H8   HN3     0.12  
ATOM N9   NN2    -0.05  
ATOM N1   NN3A   -0.74  
ATOM C2   CN4     0.50  
ATOM H2   HN3     0.13  
ATOM N3   NN3A   -0.75
ATOM C4   CN5     0.43
ATOM C6   CN2     0.46
ATOM N6   NN1    -0.77
ATOM H61  HN1     0.38
ATOM H62  HN1     0.38
GROUP ! Hydroxyl group on C3'
ATOM H31' HN7     0.09
ATOM C3'  CN7     0.14
ATOM O3'  ON5    -0.66
ATOM H32' HN5     0.43
GROUP ! C5' hydroxyl
ATOM C5'  CN8B    0.05
ATOM H51' HN8     0.09
ATOM H52' HN8     0.09
ATOM O5'  ON5    -0.66
ATOM H5T  HN5     0.43

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C4'  C5'
BOND C3'  O3'  C1'  H12' C2'  H21' C2'  O2'  C3'  H31' C4'  H42'
BOND C5'  H51' C5'  H52' C5'  O5'  O5'  H5T
BOND O2'  H22' O3'  H32'
BOND C1'  N9
BOND N9   C4    N9   C8   C4   N3    C2   N1    C6   N6
BOND N6   H61   N6   H62  C6   C5    C5   N7    C8   H8    C2   H2
DOUBLE  N1  C6    C2   N3     C4   C5     N7   C8
IMPR N6   C6   H61  H62       C6   N1   C5   N6       
! This IC table is only an initial guess:
IC 	C1'	C2'	C3'	C4' 	0.0 0.0 324.92 0.0 0.0
IC	C2'	C3'	C4' 	O4' 	0.0 0.0 33.390 0.0 0.0
IC 	H12'	C1'	C2'	C3' 	0.0 0.0 268.35 0.0 0.0
IC 	H21'	C2'	C3'	C4' 	0.0 0.0 82.530 0.0 0.0
IC 	O2' 	C2'	C3'	C4' 	1.42 109.06 283.42 0.0 0.0
IC      H22'    O2'     C2'     C3'     0.98 109.05 283.42 0.0 0.0
IC 	O3' 	C3'	C4'	O4' 	0.0 0.0 324.95 0.0 0.0
IC	H32'	O3'	C3'	C2'	0.0 0.0 -60.00 0.0 0.0
IC 	H31'	C3'	C4'	O4' 	0.0 0.0 147.80 0.0 0.0
IC	H41'	C4'	O4'	C1' 	0.0 0.0 132.30 0.0 0.0
IC 	H42'	C4'	O4'	C1' 	0.0 0.0 220.70 0.0 0.0
IC C3'  C2'  C1'  N9     1.5284  101.97  150.8   113.71   1.4896
IC O4'  C1'  N9   C4     1.5251  108.6   229.5   125.5    1.3783 !chi
IC C1'  C4   *N9  C8     1.4896  125.97 -179.94  106.0    1.367
IC C4   N9   C8   N7     1.376   106.0     0.0   113.6    1.312
IC C8   N9   C4   C5     1.367   106.0     0.0   105.6    1.382
IC C8   N7   C5   C6     0.0       0.0   180.0     0.0    0.0
IC N7   C5   C6   N1     0.0       0.0   180.0     0.0    0.0
IC C5   C6   N1   C2     0.0       0.0     0.0     0.0    0.0
IC N9   C5   *C4  N3     1.376   105.6  -180.0   126.9    1.342
IC C5   N1   *C6  N6     1.409   117.6  -180.0   121.2    1.337
IC N1   C6   N6   H61    1.337   121.2     0.0   119.0    1.01
IC H61  C6   *N6  H62    1.01    119.0   180.0   119.00   1.01
IC C5   N1   *C6  N6     1.409   117.6  -180.0   119.0    1.337
IC N1   C6   N6   H61    1.337   119.0     0.0   119.0    1.01
IC H61  C6   *N6  H62    1.01    119.0   180.0   121.00   1.01
IC N9   N7   *C8   H8    0.0       0.0   180.0     0.0    0.0
IC N1   N3   *C2   H2    0.0       0.0   180.0     0.0    0.0
IC      C5'     C4'     O4'     C1'     0.0 0.0 144.82 0.0 0.0   
IC      H51'    C5'     C4'     O4'     0.0 0.0 -179.98 0.0 0.0 
IC      H52'    C5'     C4'     O4'     0.0 0.0   59.66 0.0 0.0
IC      O5'     C5'     C4'     O4'     0.0 0.0  -59.68 0.0 0.0
IC      H5T     O5'     C5'     C4'     0.0 0.0  180.0 0.0 0.0
PATC  FIRS NONE LAST NONE

RESI RNUG         0.00 ! ribo-nucleoside with guanine
GROUP
ATOM O4'  ON6B   -0.50 !          H5T
ATOM C4'  CN7     0.16 !         /
ATOM H42' HN7     0.09 !  H51' O5'
ATOM C1'  CN7B    0.16 !     \ |
ATOM H12' HN7     0.09 !H52'--C5'   O4'  Guanine
GROUP                  !        \  /  \  /
ATOM H21' HN7     0.09 !   H42'--C4'  C1'--H12'
ATOM C2'  CN7B    0.14 !          |    |
ATOM O2'  ON5    -0.66 !   H31'--C3'--C2'--H21'
ATOM H22' HN5     0.43 !        /       \
! Guanine atoms        !      O3'       O2'
GROUP                  !       |         |
ATOM N9   NN2B   -0.02 !      H32'      H22'
ATOM C4   CN5     0.26 
ATOM N3   NN3G   -0.74 
ATOM C2   CN2     0.75
ATOM N1   NN2G   -0.34 
ATOM H1   HN2     0.26
ATOM N2   NN1    -0.68
ATOM H21  HN1     0.32
ATOM H22  HN1     0.35
ATOM C6   CN1     0.54 
ATOM O6   ON1    -0.51
ATOM C5   CN5G    0.00
ATOM N7   NN4    -0.60
ATOM C8   CN4     0.25
ATOM H8   HN3     0.16
GROUP ! Hydroxyl group on C3'
ATOM H31' HN7     0.09
ATOM C3'  CN7     0.14
ATOM O3'  ON5    -0.66
ATOM H32' HN5     0.43
GROUP ! C5' hydroxyl
ATOM C5'  CN8B    0.05
ATOM H51' HN8     0.09
ATOM H52' HN8     0.09
ATOM O5'  ON5    -0.66
ATOM H5T  HN5     0.43

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C4'  C5'
BOND C3'  O3'  C1'  H12' C2'  H21' C2'  O2'  C3'  H31' C4'  H42'
BOND C5'  H51' C5'  H52' C5'  O5'  O5'  H5T
BOND O2'  H22' O3'  H32'
BOND C1'  N9
BOND N9   C4     N9   C8    C4   N3    C2   N2   C2   N1    N2   H21
BOND N2   H22    N1   H1    N1   C6    C6   C5   C5   N7    C8   H8
DOUBLE  C2   N3    C4   C5    N7   C8   C6   O6
IMPR C2   N3   N1   N2        C6   N1   C5   O6        N2   H21  C2   H22
! This IC table is only an initial guess:
IC 	C1'	C2'	C3'	C4' 	0.0 0.0 324.92 0.0 0.0
IC	C2'	C3'	C4' 	O4' 	0.0 0.0 33.390 0.0 0.0
IC 	H12'	C1'	C2'	C3' 	0.0 0.0 268.35 0.0 0.0
IC 	H21'	C2'	C3'	C4' 	0.0 0.0 82.530 0.0 0.0
IC 	O2' 	C2'	C3'	C4' 	1.42 109.06 283.42 0.0 0.0
IC      H22'    O2'     C2'     C3'     0.98 109.05 283.42 0.0 0.0
IC 	O3' 	C3'	C4'	O4' 	0.0 0.0 324.95 0.0 0.0
IC	H32'	O3'	C3'	C2'	0.0 0.0 -60.00 0.0 0.0
IC 	H31'	C3'	C4'	O4' 	0.0 0.0 147.80 0.0 0.0
IC	H41'	C4'	O4'	C1' 	0.0 0.0 132.30 0.0 0.0
IC 	H42'	C4'	O4'	C1' 	0.0 0.0 220.70 0.0 0.0
BILD C3'  C2'  C1'  N9     1.5284  101.97  147.80  113.71   1.4896
BILD O4'  C1'  N9   C4     1.5251  113.71  -97.2   125.59   1.3783 !chi
BILD C1'  C4   *N9  C8     1.4896  125.59 -179.99  106.0    1.374
BILD C4   N9   C8   N7     1.377   106.0     0.0   113.5    1.304
BILD C8   N9   C4   C5     1.374   106.0     0.0   105.6    1.377
BILD N9   C5   *C4  N3     1.377   105.6   180.0   128.4    1.355
BILD C5   C4   N3   C2     1.377   128.4     0.0   111.8    1.327
BILD C4   N3   C2   N1     1.355   111.8     0.0   124.0    1.375
BILD N1   N3   *C2  N2     1.375   124.0   180.0   119.7    1.341
BILD N3   C2   N2   H21    1.327   119.7   180.0   127.0    1.01
BILD H21  C2   *N2  H22    1.01    127.0  -180.0   116.5    1.01
BILD N3   C2   N1   C6     1.327   124.0     0.0   124.9    1.393
BILD C6   C2   *N1  H1     1.393   124.9   180.0   117.4    1.03
BILD C5   N1   *C6  O6     1.415   111.7   180.0   120.0    1.239
BILD N9   N7   *C8  H8     0.0       0.0   180.0     0.0    0.0
IC      C5'     C4'     O4'     C1'     0.0 0.0 144.82 0.0 0.0   
IC      H51'    C5'     C4'     O4'     0.0 0.0 -179.98 0.0 0.0 
IC      H52'    C5'     C4'     O4'     0.0 0.0   59.66 0.0 0.0
IC      O5'     C5'     C4'     O4'     0.0 0.0  -59.68 0.0 0.0
IC      H5T     O5'     C5'     C4'     0.0 0.0  180.0 0.0 0.0
PATC  FIRS NONE LAST NONE

RESI RNUC        0.00  ! ribo-nucleoside with cytosine
GROUP
ATOM O4'  ON6B   -0.50 !          H5T
ATOM C4'  CN7     0.16 !         /
ATOM H42' HN7     0.09 !  H51' O5'
ATOM C1'  CN7B    0.16 !     \ |
ATOM H12' HN7     0.09 !H52'--C5'   O4'  Cytosine
GROUP                  !        \  /  \  /
ATOM H21' HN7     0.09 !   H42'--C4'  C1'--H12'
ATOM C2'  CN7B    0.14 !          |    |
ATOM O2'  ON5    -0.66 !   H31'--C3'--C2'--H21'
ATOM H22' HN5     0.43 !        /       \
! Cytosine atoms       !      O3'       O2'
GROUP                  !       |         |
ATOM N1   NN2    -0.13 !      H32'      H22'
ATOM C6   CN3     0.05  
ATOM H6   HN3     0.17  
ATOM C2   CN1     0.52  
ATOM O2   ON1C   -0.49  
ATOM N3   NN3    -0.66  
ATOM C4   CN2     0.65  
ATOM N4   NN1    -0.75  
ATOM H41  HN1     0.37  
ATOM H42  HN1     0.33  
ATOM C5   CN3    -0.13  
ATOM H5   HN3     0.07  
GROUP ! Hydroxyl group on C3'
ATOM H31' HN7     0.09
ATOM C3'  CN7     0.14
ATOM O3'  ON5    -0.66
ATOM H32' HN5     0.43
GROUP ! Methyl group on C4'
ATOM C5'  CN8B    0.05
ATOM H51' HN8     0.09
ATOM H52' HN8     0.09
ATOM O5'  ON5    -0.66
ATOM H5T  HN5     0.43

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C4'  C5'
BOND C3'  O3'  C1'  H12' C2'  H21' C2'  O2'  C3'  H31' C4'  H42'
BOND C5'  H51' C5'  H52' C5'  O5'  O5'  H5T
BOND O2'  H22' O3'  H32'
BOND C1'  N1        
BOND N1   C2        N1   C6
BOND C2   N3        C4   N4        N4   H41       N4   H42
BOND C4   C5        C5   H5        C6   H6
DOUBLE   C2   O2    C5   C6        N3   C4
IMPR N4   C4   H41  H42       C2   N1   N3   O2        C4   N3   C5   N4
! This IC table is only an initial guess:
IC 	C1'	C2'	C3'	C4' 	0.0 0.0 324.92 0.0 0.0
IC	C2'	C3'	C4' 	O4' 	0.0 0.0 33.390 0.0 0.0
IC 	H12'	C1'	C2'	C3' 	0.0 0.0 268.35 0.0 0.0
IC 	H21'	C2'	C3'	C4' 	0.0 0.0 82.530 0.0 0.0
IC 	O2' 	C2'	C3'	C4' 	1.42 109.06 283.42 0.0 0.0
IC      H22'    O2'     C2'     C3'     0.98 109.05 283.42 0.0 0.0
IC 	O3' 	C3'	C4'	O4' 	0.0 0.0 324.95 0.0 0.0
IC	H32'	O3'	C3'	C2'	0.0 0.0 -60.00 0.0 0.0
IC 	H31'	C3'	C4'	O4' 	0.0 0.0 147.80 0.0 0.0
IC	H41'	C4'	O4'	C1' 	0.0 0.0 132.30 0.0 0.0
IC 	H42'	C4'	O4'	C1' 	0.0 0.0 220.70 0.0 0.0
IC C3'  C2'  C1'  N1     1.5284  101.97  147.89  113.71   1.4896
IC O4'  C1'  N1   C2     1.5251  113.71  -97.2   125.59   1.3783 !chi
IC C1'  C2   *N1  C6     1.4896  117.79 -180.00  120.6    1.364   
IC C2   N1   C6   C5     1.399   120.6     0.0   121.0    1.337   
IC C6   N1   C2   N3     1.364   120.6     0.0   118.9    1.356   
IC N1   N3   *C2  O2     1.399   118.9   180.0   121.9    1.237   
IC N1   C2   N3   C4     1.399   118.9     0.0   120.0    1.334   
IC C5   N3   *C4  N4     1.426   121.8   180.00  118.9    1.337   
IC N3   C4   N4   H41    1.337   117.9     0.00  118.9    1.01    
IC H41  C4   *N4  H42    1.01    118.9   180.00  120.7    1.01    
IC C6   C4   *C5  H5     0.0       0.0   180.0     0.0    0.0
IC N1   C5   *C6  H6     0.0       0.0   180.0     0.0    0.0
IC      C5'     C4'     O4'     C1'     0.0 0.0 144.82 0.0 0.0   
IC      H51'    C5'     C4'     O4'     0.0 0.0 -179.98 0.0 0.0 
IC      H52'    C5'     C4'     O4'     0.0 0.0   59.66 0.0 0.0
IC      O5'     C5'     C4'     O4'     0.0 0.0  -59.68 0.0 0.0
IC      H5T     O5'     C5'     C4'     0.0 0.0  180.0 0.0 0.0
PATC  FIRS NONE LAST NONE

RESI NUCL        -1.00 ! 
!WARNING: - The charge distribution on the imidazole is identical
! to the charge distribution on the imidazole in THFI, which is
! different from the charge distribution on the equivalent moiety 
! in adenine.
!	- The charge distribution on the sugar is identical to what 
! it is in the DNA.
!	- The charge' on the 3' end of the "backbone" is identical to
! what it is in the DNA, except for the terminal methyl group for which
! there is no DNA equivalent.
! 	- The charges on the 5' extremity of the backbone is as in the 
! 5TER patch used for the DNA. An alternative to that would be to use
! charges more similar to what is in non-terminal residues in DNA.
GROUP
ATOM O4'  ON6    -0.50
ATOM C1'  CN7B    0.16
ATOM H12' HN7     0.09
ATOM C4'  CN7     0.16
ATOM H42' HN7     0.09
GROUP	! Imidazole: transferred from isolated imidazole (IMIA)
! The following atom types use the parameters specifically developed
! for the imidazole
! Atom types for aliphatic atoms based on nucleotide
ATOM CG   CPH1   -0.05 !     C1'       HE1
ATOM HG   HR3     0.09 !       \       /
ATOM CD2  CPH1    0.22 !       ND1---CE1
ATOM HD2  HR3     0.10 !      /       ||
ATOM ND1  NR1    -0.04 !  HG-CG       ||
ATOM CE1  CPH2    0.25 !      \\      ||
ATOM HE1  HR1     0.13 !       CD2---NE2
ATOM NE2  NR2    -0.70 !        |
                       !       HD2
GROUP                  !
ATOM C2'  CN8    -0.18 !
ATOM H21' HN8     0.09 !         H5T
ATOM H22' HN8     0.09 !          |
GROUP                  !    H52' O5'
ATOM C3'  CN7     0.01 !      \ / 
ATOM H31' HN7     0.09 !  H51'-C5'  O4'  Imidazole
ATOM O3'  ON2    -0.57 !        \  /  \  /
ATOM P    P       1.50 !   H42'--C4'  C1'--H12'
ATOM O1P  ON3    -0.78 !          |    |
ATOM O2P  ON3    -0.78 !   H31'--C3'--C2'--H21'
ATOM O3P  ON2    -0.57 !        /       \
ATOM C3T  CN8B   -0.17 !      O3'       H22'
ATOM H3T1 HN8     0.09 !       |
ATOM H3T2 HN8     0.09 !  O1P==P==O2P
ATOM H3T3 HN8     0.09 !       |
GROUP                  !      O3P  (-1)
ATOM C5'  CN8B    0.05 !        \
ATOM H51' HN8     0.09 !        C3T--H3T3
ATOM H52' HN8     0.09 !       /  \
ATOM H5T  HN5     0.43 !    H3T1 H3T2
ATOM O5'  ON5    -0.66

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C3'  O3'
BOND C1'  H12' C2'  H21' C2'  H22' C3'  H31' C4'  H42' 
BOND O3'  P    P    O1P  P    O2P  P    O3P  
BOND O3P  C3T  C3T  H3T1 C3T  H3T2 C3T  H3T3
BOND C4'  C5'  C5'  H51' C5'  H52' 
BOND C5'  O5'  O5'  H5T
BOND C1'  ND1 
BOND ND1  CE1  NE2  CD2  CG  ND1
BOND CE1  HE1  CD2  HD2  CG  HG
DOUBLE CG  CD2   CE1  NE2
! KEEPS HYDROGENS IN RING PLANE
IMPR ND1  CG   CE1  C1'       ND1  CE1  CG   C1'
IMPR CD2  CG   NE2  HD2       CD2  NE2  CG   HD2
IMPR CE1  ND1  NE2  HE1       CE1  NE2  ND1  HE1
IMPR CG   CD2  ND1  HG        CG   ND1  CD2  HG
IC   C4'     O4'     C1'     C2'    1.4055  108.09   23.45  106.18   1.5457
IC   O4'     C1'     C2'     C3'    1.4127  106.18    3.96  103.11   1.5346
IC   C1'     C2'     C3'     C4'    1.5457  103.11  -26.93  100.86   1.5211
IC   C2'     C3'     C4'     O4'    1.5346  100.86   41.73  103.15   1.4055
IC   C3'     C4'     O4'     C1'    1.5211  103.15  -41.62  108.09   1.4127
IC   H12'    C1'     C2'     C3'    1.0818  113.32 -114.11  103.11   1.5346
IC   H21'    C2'     C3'     C4'    1.0846  110.65   91.68  100.86   1.5211
IC   H22'    C2'     C3'     C4'    1.0822  110.88 -148.45  100.86   1.5211
IC   H31'    C3'     C4'     O4'    1.0806  113.53  162.89  103.15   1.4055
IC   C5'     C4'     O4'     C1'    0.0000  000.00   77.76  108.09   1.4127
IC   H51'    C5'     C4'     O4'    0.0     0.0     180.0     0.0    0.0
IC   H52'    C5'     C4'     O4'    0.0     0.0      -60.0    0.0    0.0
IC   H42'    C4'     O4'     C1'    1.0808  108.72 -162.12  108.09   1.4127
IC   O3'     C3'     C4'     O4'    1.4028  110.98  -77.39  103.15   1.4055
IC   P       O3'     C3'     C4'    0.0       0.0   180.00    0.0    0.0
IC   O1P     P       O3'     C3'    0.0       0.0   -60.0     0.0    0.0
IC   O2P     P       O3'     C3'    0.0       0.0    60.0     0.0    0.0
IC   O3P     P       O3'     C3'    0.0       0.0   180.0     0.0    0.0
IC   C3T     O3P     P       O3'    0.0       0.0   180.0     0.0    0.0 
IC   H3T1    C3T     O3P     P	    0.0       0.0    60.0     0.0    0.0
IC   H3T2    C3T     O3P     P	    0.0       0.0   -60.0     0.0    0.0
IC   H3T3    C3T     O3P     P	    0.0       0.0   180.0     0.0    0.0
IC      C4'	O4'	C1'	ND1 	0.0 0.0 256.98 0.0 0.0
IC 	O4'	C1'	ND1	CE1 	0.0 0.0  90.00 0.0 0.0
IC	C1'	ND1	CE1     NE2 	0.0 0.0 181.56 0.0 0.0
IC	ND1	CE1	NE2	CD2 	0.0 0.0   0.34 0.0 0.0
IC 	CE1	NE2	CD2	CG 	0.0 0.0   0.00 0.0 0.0 
IC 	HE1	CE1	NE2	CD2 	0.0 0.0 180.40 0.0 0.0
IC	CE1	NE2	CD2	HD2 	0.0 0.0 179.83 0.0 0.0
IC 	NE2 	CD2	CG 	HG 	0.0 0.0 178.45 0.0 0.0
IC      C3'     C4'     C5'     O5'     0.0 0.0 60.0   0.0 0.0
IC      H5T     O5'     C5'     C4'   0.0000    0.00  180.00    0.00   0.0000
PATC  FIRS NONE LAST NONE

RESI NADE        -1.00 ! 
! NADE is a nucleotide analogue similar to NUCL, except that the imidazole
! has been replaced by an adenine
!	- The charge distribution on the sugar is identical to what 
! it is in the DNA.
!	- The charge' on the 3' end of the "backbone" is identical to
! what it is in the DNA, except for the terminal methyl group for which
! there is no DNA equivalent.
! 	- The charges on the 5' extremity of the backbone is as in the 
! 5TER patch used for the DNA. An alternative to that would be to use
! charges more similar to what is actuallly in non-terminal residues in the 
! DNA.
GROUP
ATOM O4'  ON6    -0.50 !         H5T
ATOM C1'  CN7B    0.16 !          |
ATOM H12' HN7     0.09 !    H52' O5'
ATOM C4'  CN7     0.16 !      \ / 
ATOM H42' HN7     0.09 !  H51'-C5'  O4'  Adenine
GROUP                  !        \  /  \  /
ATOM C5   CN5     0.30 !   H42'--C4'  C1'--H12'
ATOM N7   NN4    -0.69 !          |    |
ATOM C8   CN4     0.34 !   H31'--C3'--C2'--H21'
ATOM H8   HN3     0.10 !        /       \
ATOM N9   NN2    -0.06 !      O3'       H22'
ATOM N1   NN3A   -0.74 !       |
ATOM C2   CN4     0.50 !  O1P==P==O2P
ATOM H2   HN3     0.13 !       |
ATOM N3   NN3A   -0.75 !      O3P  (-1)
ATOM C4   CN5     0.43 !        \
ATOM C6   CN2     0.44 !        C3T--H3T3
ATOM N6   NN1    -0.75 !       /  \
ATOM H61  HN1     0.38 !    H3T1 H3T2
ATOM H62  HN1     0.37
GROUP                 
ATOM C2'  CN8    -0.18
ATOM H21' HN8     0.09
ATOM H22' HN8     0.09
GROUP                 
ATOM C3'  CN7     0.01
ATOM H31' HN7     0.09
ATOM O3'  ON2    -0.57
ATOM P    P       1.50
ATOM O1P  ON3    -0.78
ATOM O2P  ON3    -0.78
ATOM O3P  ON2    -0.57
ATOM C3T  CN8B   -0.17
ATOM H3T1 HN7     0.09
ATOM H3T2 HN7     0.09
ATOM H3T3 HN7     0.09
GROUP
ATOM C5'  CN8B    0.05
ATOM H51' HN8     0.09
ATOM H52' HN8     0.09
ATOM H5T  HN5     0.43
ATOM O5'  ON5    -0.66

BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C3'  O3'
BOND C1'  H12' C2'  H21' C2'  H22' C3'  H31' C4'  H42' 
BOND O3'  P    P    O1P  P    O2P  P    O3P  
BOND O3P  C3T  C3T  H3T1 C3T  H3T2 C3T  H3T3
BOND C4'  C5'  C5'  H51' C5'  H52' 
BOND C5'  O5'  O5'  H5T
BOND C1'  N9
BOND N9   C4    N9   C8   C4   N3    C2   N1    C6   N6
BOND N6   H61   N6   H62  C6   C5    C5   N7    C8   H8    C2   H2
DOUBLE  N1  C6    C2   N3     C4   C5     N7   C8
IMPR N6   C6   H61  H62        C6   N1   C5   N6        
IC   C4'     O4'     C1'     C2'    1.4055  108.09   23.45  106.18   1.5457
IC   O4'     C1'     C2'     C3'    1.4127  106.18    3.96  103.11   1.5346
IC   C1'     C2'     C3'     C4'    1.5457  103.11  -26.93  100.86   1.5211
IC   C2'     C3'     C4'     O4'    1.5346  100.86   41.73  103.15   1.4055
IC   C3'     C4'     O4'     C1'    1.5211  103.15  -41.62  108.09   1.4127
IC   H12'    C1'     C2'     C3'    1.0818  113.32 -114.11  103.11   1.5346
IC   H21'    C2'     C3'     C4'    1.0846  110.65   91.68  100.86   1.5211
IC   H22'    C2'     C3'     C4'    1.0822  110.88 -148.45  100.86   1.5211
IC   H31'    C3'     C4'     O4'    1.0806  113.53  162.89  103.15   1.4055
IC   C5'     C4'     O4'     C1'    0.0000  000.00   77.76  108.09   1.4127
IC   H51'    C5'     C4'     O4'    0.0     0.0     180.0     0.0    0.0
IC   H52'    C5'     C4'     O4'    0.0     0.0      -60.0    0.0    0.0
IC   H42'    C4'     O4'     C1'    1.0808  108.72 -162.12  108.09   1.4127
IC   O3'     C3'     C4'     O4'    1.4028  110.98  -77.39  103.15   1.4055
IC   P       O3'     C3'     C4'    0.0       0.0   180.00    0.0    0.0
IC   O1P     P       O3'     C3'    0.0       0.0   -60.0     0.0    0.0
IC   O2P     P       O3'     C3'    0.0       0.0    60.0     0.0    0.0
IC   O3P     P       O3'     C3'    0.0       0.0   180.0     0.0    0.0
IC   C3T     O3P     P       O3'    0.0       0.0   180.0     0.0    0.0 
IC   H3T1    C3T     O3P     P	    0.0       0.0    60.0     0.0    0.0
IC   H3T2    C3T     O3P     P	    0.0       0.0   -60.0     0.0    0.0
IC   H3T3    C3T     O3P     P	    0.0       0.0   180.0     0.0    0.0
IC C3'  C2'  C1'  N9     1.5284  101.97  147.80  113.71   1.4896
IC O4'  C1'  N9   C4     1.5251  113.71  180.2   125.59   1.3783 !chi
IC C1'  C4   *N9  C8     1.4896  125.97 -180.00  106.0    1.367
IC C4   N9   C8   N7     1.376   106.0     0.0   113.6    1.312
IC C8   N9   C4   C5     1.367   106.0     0.0   105.6    1.382
IC C8   N7   C5   C6     0.0       0.0   180.0     0.0    0.0
IC N7   C5   C6   N1     0.0       0.0   180.0     0.0    0.0
IC C5   C6   N1   C2     0.0       0.0     0.0     0.0    0.0
IC N9   C5   *C4  N3     1.376   105.6  -180.0   126.9    1.342
IC C5   N1   *C6  N6     1.409   117.6  -180.0   121.2    1.337
IC N1   C6   N6   H61    1.337   121.2     0.0   119.0    1.01
IC H61  C6   *N6  H62    1.01    119.0   180.0   119.00   1.01
IC C5   N1   *C6  N6     1.409   117.6  -180.0   119.0    1.337
IC N1   C6   N6   H61    1.337   119.0     0.0   119.0    1.01
IC H61  C6   *N6  H62    1.01    119.0   180.0   121.00   1.01
IC N9   N7   *C8  H8     0.0       0.0   180.0     0.0    0.0
IC N1   N3   *C2  H2     0.0       0.0   180.0     0.0    0.0
IC C3'  C4'   C5' O5'    0.0       0.0    60.0     0.0    0.0
IC H5T  O5'   C5' C4'    0.0       0.0   180.0     0.0    0.0
PATC  FIRS NONE LAST NONE

RESI NTHY        -1.00 ! 
! NTHY is a nucleotide analogue similar to NUCL, except that the imidazole
! has been replaced by a thymine
!	- The charge distribution on the sugar is identical to what 
! it is in the DNA.
!	- The charge' on the 3' end of the "backbone" is identical to
! what it is in the DNA, except for the terminal methyl group for which
! there is no DNA equivalent.
! 	- The charges on the 5' extremity of the backbone is as in the 
! 5TER patch used for the DNA. An alternative to that would be to use
! charges more similar to what is actuallly in non-terminal residues in the 
! DNA.
GROUP
ATOM O4'  ON6    -0.50 !         H5T
ATOM C1'  CN7B    0.16 !          |
ATOM H12' HN7     0.09 !    H52' O5'
ATOM C4'  CN7     0.16 !      \ / 
ATOM H42' HN7     0.09 !  H51'-C5'  O4'  Thymine
GROUP                  !        \  /  \  /
ATOM N1   NN2B   -0.34 !   H42'--C4'  C1'--H12'
ATOM C6   CN3     0.17 !          |    |
ATOM H6   HN3     0.17 !   H31'--C3'--C2'--H21'
ATOM C2   CN1T    0.51 !        /       \
ATOM O2   ON1    -0.41 !      O3'       H22'
ATOM N3   NN2U   -0.46 !       |
ATOM H3   HN2     0.36 !  O1P==P==O2P
ATOM C4   CN1     0.50 !       |
ATOM O4   ON1    -0.45 !      O3P  (-1)
ATOM C5   CN3T   -0.15 !        \
ATOM C5M  CN9    -0.11 !        C3T--H3T3
ATOM H51  HN9     0.07 !       /  \
ATOM H52  HN9     0.07 !    H3T1 H3T2
ATOM H53  HN9     0.07
GROUP                 
ATOM C2'  CN8    -0.18
ATOM H21' HN8     0.09
ATOM H22' HN8     0.09
GROUP                 
ATOM C3'  CN7     0.01
ATOM H31' HN7     0.09
ATOM O3'  ON2    -0.57
ATOM P    P       1.50
ATOM O1P  ON3    -0.78
ATOM O2P  ON3    -0.78
ATOM O3P  ON2    -0.57
ATOM C3T  CN8B   -0.17
ATOM H3T1 HN7     0.09
ATOM H3T2 HN7     0.09
ATOM H3T3 HN7     0.09
GROUP
ATOM C5'  CN8B    0.05
ATOM H51' HN8     0.09
ATOM H52' HN8     0.09
ATOM H5T  HN5     0.43
ATOM O5'  ON5    -0.66
BOND C1'  O4'  C1'  C2'  C2'  C3'  C3'  C4'  C4'  O4'  C3'  O3'
BOND C1'  H12' C2'  H21' C2'  H22' C3'  H31' C4'  H42' 
BOND O3'  P    P    O1P  P    O2P  P    O3P  
BOND O3P  C3T  C3T  H3T1 C3T  H3T2 C3T  H3T3
BOND C4'  C5'  C5'  H51' C5'  H52' 
BOND C5'  O5'  O5'  H5T
BOND C1'  N1
BOND N1   C2   N1   C6   C2   N3   N3   H3   N3   C4   C4   C5
BOND C5   C5M  C6   H6   C5M  H51  C5M  H52  C5M  H53
DOUBLE  C2   O2    C4   O4     C5   C6
IMPR C2   N1   N3   O2        C4   N3   C5   O4        C5   C4   C6   C5M
IC   C4'     O4'     C1'     C2'    1.4055  108.09   23.45  106.18   1.5457
IC   O4'     C1'     C2'     C3'    1.4127  106.18    3.96  103.11   1.5346
IC   C1'     C2'     C3'     C4'    1.5457  103.11  -26.93  100.86   1.5211
IC   C2'     C3'     C4'     O4'    1.5346  100.86   41.73  103.15   1.4055
IC   C3'     C4'     O4'     C1'    1.5211  103.15  -41.62  108.09   1.4127
IC   H12'    C1'     C2'     C3'    1.0818  113.32 -114.11  103.11   1.5346
IC   H21'    C2'     C3'     C4'    1.0846  110.65   91.68  100.86   1.5211
IC   H22'    C2'     C3'     C4'    1.0822  110.88 -148.45  100.86   1.5211
IC   H31'    C3'     C4'     O4'    1.0806  113.53  162.89  103.15   1.4055
IC   C5'     C4'     O4'     C1'    0.0000  000.00   77.76  108.09   1.4127
IC   H51'    C5'     C4'     O4'    0.0     0.0     180.0     0.0    0.0
IC   H52'    C5'     C4'     O4'    0.0     0.0      -60.0    0.0    0.0
IC   H42'    C4'     O4'     C1'    1.0808  108.72 -162.12  108.09   1.4127
IC   O3'     C3'     C4'     O4'    1.4028  110.98  -77.39  103.15   1.4055
IC   P       O3'     C3'     C4'    0.0       0.0   180.00    0.0    0.0
IC   O1P     P       O3'     C3'    0.0       0.0   -60.0     0.0    0.0
IC   O2P     P       O3'     C3'    0.0       0.0    60.0     0.0    0.0
IC   O3P     P       O3'     C3'    0.0       0.0   180.0     0.0    0.0
IC   C3T     O3P     P       O3'    0.0       0.0   180.0     0.0    0.0 
IC   H3T1    C3T     O3P     P	    0.0       0.0    60.0     0.0    0.0
IC   H3T2    C3T     O3P     P	    0.0       0.0   -60.0     0.0    0.0
IC   H3T3    C3T     O3P     P	    0.0       0.0   180.0     0.0    0.0
IC      C3'     C4'     C5'     O5'     0.0 0.0 60.0   0.0 0.0
IC      H5T     O5'     C5'     C4'   0.0000    0.00  180.00    0.00   0.0000
IC C3'  C2'  C1'  N1     1.5284  101.97  147.89  113.71   1.4896
IC C3'  C2'  C1'  N1     1.5284  101.97  147.89  113.71   1.4896
IC O4'  C1'  N1   C2     1.5251  113.71  180.0   125.59   1.3783 !chi
IC C1'  C2   *N1  C6     1.4896  117.06 -179.96  122.08   1.3704
IC C2   N1   C6   C5     1.3746  122.08   -0.02  121.23   1.3432
IC C6   N1   C2   N3     1.3704  122.08    0.06  115.38   1.3813
IC N1   N3   *C2  O2     1.3746  115.38 -179.95  121.70   1.2191
IC N1   C2   N3   C4     1.3746  115.38   -0.07  126.46   1.3795
IC C5   N3   *C4  O4     1.4439  114.07  179.98  120.59   1.2327
IC C2   C4   *N3  H3     1.3813  126.46  180.00  116.77   1.0900
IC C4   C6   *C5  C5M    1.4439  120.78 -179.94  121.63   1.5000
IC N1   C5   *C6  H6     0.0       0.0   180.0     0.0    0.0
IC C6   C5   C5M  H51    0.0       0.0     0.0     0.0    0.0
IC C5   H51  *C5M H52    0.0       0.0   115.0     0.0    0.0
IC H51  H52  *C5M H53    0.0       0.0  -115.0     0.0    0.0
PATC  FIRS NONE LAST NONE

PRES 5TER         0.00  ! 5'-terminal HYDROXYL patch, from MeOH
                        ! use in generate statement
GROUP
ATOM H5T  HN5     0.43
ATOM O5'  ON5    -0.66
ATOM C5'  CN8B    0.05
ATOM H5'  HN8     0.09 
ATOM H5'' HN8     0.09 
!
DELETE ATOM P
DELETE ATOM O1P
DELETE ATOM O2P
!
BOND H5T   O5'        
DONO H5T   O5'
BILD H5T  O5'   C5'  C4'   0.0000    0.00  180.00    0.00   0.0000
 
PRES 5MET         0.00  ! 5'-ribose METHYL patch
                        ! use in generate statement
GROUP
ATOM C5'  CN9    -0.27
ATOM H5'  HN9     0.09 
ATOM H5'' HN9     0.09 
ATOM H53' HN9     0.09  ! Can't use ''' and avoid conflict with THY
!              
DELETE ATOM O5'
DELETE ATOM P
DELETE ATOM O1P
DELETE ATOM O2P
!
BOND C5' H53'
 
PRES 5PHO        -1.00  ! 5'terminal PHOSPHATE patch
                        ! use in generate statement
GROUP
ATOM C5'  CN8B   -0.08
ATOM H5'  HN8     0.09 
ATOM H5'' HN8     0.09 
ATOM P    P       1.50
ATOM O1P  ON3    -0.82
ATOM O2P  ON3    -0.82
ATOM O5'  ON2    -0.62
ATOM O5T  ON4    -0.68
ATOM H5T  HN4     0.34
BOND O5T  P     H5T  O5T      
DONO H5T  O5T
! Built in B-DNA-like conformation (NF)
BILD C4'   C5'  O5' P      0.0000  000.00 -146.00   000.00   0.0000
BILD C5'   O5'  P   O5T    0.0000  000.00  -46.90   000.00   0.0000
BILD O5T   O5'  *P  O1P    0.0000  000.00 -115.82   000.00   0.0000
BILD O5T   O5'  *P  O2P    0.0000  000.00  115.90   000.00   0.0000
BILD H5T   O5T  P   O5'    0.0000  000.00  -95.20   000.00   0.0000
                           
PRES 5POM        -1.00  ! 5'terminal Methyl-Phosphate patch
                        ! use in generate statement
GROUP
ATOM C5'  CN8B   -0.08
ATOM H5'  HN8     0.09
ATOM H5'' HN8     0.09
ATOM P    P       1.50
ATOM O1P  ON3    -0.78
ATOM O2P  ON3    -0.78
ATOM O5'  ON2    -0.57
ATOM O5T  ON2    -0.57
ATOM C5T  CN9    -0.17
ATOM H5T1 HN9     0.09
ATOM H5T2 HN9     0.09
ATOM H5T3 HN9     0.09

BOND O5T  P     O5T	C5T	C5T 	H5T1	C5T     H5T2	
BOND C5T     H5T3
!DONO H5T  O5T
! Built in B-DNA-like conformation (NF)
BILD C4'   C5'  O5' P      0.0000  000.00 -146.00   000.00   0.0000
BILD C5'   O5'  P   O5T    0.0000  000.00  -46.90   000.00   0.0000
BILD O5T   O5'  *P  O1P    0.0000  000.00 -115.82   000.00   0.0000
BILD O5T   O5'  *P  O2P    0.0000  000.00  115.90   000.00   0.0000
BILD C5T   O5T  P   O5'    0.0000  000.00  -95.20   000.00   0.0000
BILD H5T1  C5T   O5T  P    0.0000  000.00  180.20   000.00   0.0000
BILD H5T2  C5T   O5T  P    0.0000  000.00   60.00   000.00   0.0000
BILD H5T3  C5T   O5T  P    0.0000  000.00  -60.00   000.00   0.0000

PRES 3TER         0.00  ! 3'terminal HYDROXYL patch, from MeOH
                        ! use in generate statement
GROUP
ATOM C3'  CN7     0.14 
ATOM H3'  HN7     0.09 
ATOM O3'  ON5    -0.66
ATOM H3T  HN5     0.43
BOND O3'  H3T
DONO H3T  O3'
BILD H3T  O3'   C3'  C4'   0.9600  114.97  148.63  111.92   1.5284
             
PRES 3PHO        -1.00  ! 3'terminal PHOSPHATE patch
                        ! use in generate statement
GROUP                   
ATOM C3'  CN7     0.01
ATOM H3'  HN7     0.09 
ATOM P3   P       1.50
ATOM O1P3 ON3    -0.82
ATOM O2P3 ON3    -0.82
ATOM O3'  ON2    -0.62
ATOM O3T  ON4    -0.68
ATOM H3T  HN4     0.34
BOND O3'  P3     P3  O1P3   P3  O2P3   P3  O3T  O3T  H3T  
DONO H3T  O3T                                            
ACCE O3T
ACCE O1P2
ACCE O1P3
! Build in B-DNA-like conformation (NF)
BILD C4'   C3'  O3' P3     0.0000  000.00  155.00   000.00   0.0000
BILD C3'   O3'  P3  O3T    0.0000  000.00  -95.20   000.00   0.0000
BILD O3T   O3' *P3  O1P3   0.0000  000.00 -115.82   000.00   0.0000
BILD O3T   O3' *P3  O2P3   0.0000  000.00  115.90   000.00   0.0000
BILD H3T   O3T  P3  O3'    0.0000  000.00  -46.90   000.00   0.0000

PRES 3POM        -1.00  ! 3'terminal Methyl Phosphate patch
                        ! use in generate statement
! To build model compound with OPO3-CH3 at the 3' end (nicolas)
GROUP
ATOM C3'  CN7     0.01
ATOM H3'  HN7     0.09
ATOM P3   P       1.50
ATOM O1P3 ON3    -0.78
ATOM O2P3 ON3    -0.78
ATOM O3'  ON2    -0.57
ATOM O3T  ON2    -0.57
ATOM C3T  CN9    -0.17
ATOM H3T1 HN9     0.09
ATOM H3T2 HN9     0.09
ATOM H3T3 HN9     0.09

BOND O3'  P3     P3   O1P3  P3   O2P3   P3  O3T  O3T C3T 
BOND C3T  H3T1   C3T  H3T2  C3T  H3T3
ACCE O3'
ACCE O5'
ACCE O1P2
ACCE O1P3
BILD C4'   C3'  O3' P3     0.0000  000.00  155.00   000.00   0.0000
BILD C3'   O3'  P3  O3T    0.0000  000.00  -95.22   000.00   0.0000
BILD O3T   O3' *P3  O1P3   0.0000  000.00 -115.82   000.00   0.0000
BILD O3T   O3' *P3  O2P3   0.0000  000.00  115.90   000.00   0.0000
BILD C3T   O3T  P3  O3'    0.0000  000.00  -46.90   000.00   0.0000
BILD H3T1  C3T  O3T P3     0.0000  000.00  180.00   000.00   0.0000
BILD H3T2  C3T  O3T P3     0.0000  000.00   60.00   000.00   0.0000
BILD H3T3  C3T  O3T P3     0.0000  000.00  -60.00   000.00   0.0000

PRES 3PO3        -2.00  ! 3'terminal PHOSPHATE patch
                        ! use in generate statement
			! Added by Nicolas, to be consistent with model componds
GROUP
ATOM C3'  CN7    -0.09
ATOM H3'  HN7     0.09
ATOM P3   P       1.10
ATOM O3'  ON2    -0.40
ATOM O1P3 ON3    -0.90
ATOM O2P3 ON3    -0.90
ATOM O3P3 ON3    -0.90
BOND O3'  P3     P3  O1P3   P3  O2P3   P3  O3P3
ACCE O1P2
ACCE O1P3
BILD C4'  C3'  O3'  P3     0.0000  000.00  180.00   000.00   0.0000
BILD C3'  O3'  P3   O3P3   0.0000  000.00  -39.52   000.00   0.0000
BILD O3P3 O3'  *P3  O1P3   0.0000  000.00 -115.82   000.00   0.0000
BILD O3P3 O3'  *P3  O2P3   0.0000  000.00  115.90   000.00   0.0000
BILD O3'  P3   O3P3 O3T    0.0000  000.00  180.00   000.00   0.0000
BILD P3   O3P3 O3T  H3T    0.0000  000.00  180.00   000.00   0.0000

PRES DEO1         0.000 ! Patch to make DEOXYribose in PYRIMIDINES
DELETE ATOM O2'         ! necessary due to auto-generate dihedrals

GROUP ! To correct O4' atom type in DNA (NF)
ATOM C4'  CN7     0.16  !
ATOM H4'  HN7     0.09  !
ATOM O4'  ON6    -0.50  !
ATOM C1'  CN7B    0.16  !
ATOM H1'  HN7     0.09  !
GROUP
ATOM C2'  CN8    -0.18
ATOM H2'  HN8     0.09
ATOM H2'' HN8     0.09

BOND C2'  H2'
!removed by adm jr.
!BOND O4'  C1'  O4'   C4'
THET C1'  C2'  H2'   C3'  C2'  H2'   H2'  C2'  H2''
DIHE H2'  C2'  C1'  O4'   H2'  C2'  C1'  N1    H2'  C2'  C1'  H1'
DIHE H2'  C2'  C3'  C4'   H2'  C2'  C3'  O3'   H2'  C2'  C3'  H3'
BILD C1'  C3'  *C2' H2' 0.0 0.0 -115.0 0.0 0.0

PRES DEO2         0.000 ! Patch to make DEOXYribose in PURINES
DELETE ATOM O2'         ! necessary due to auto-generate dihedrals

GROUP ! To correct O4' atom type in DNA (NF) 
ATOM C4'  CN7     0.16  !
ATOM H4'  HN7     0.09  !
ATOM O4'  ON6    -0.50  !
ATOM C1'  CN7B    0.16  !
ATOM H1'  HN7     0.09  ! 
GROUP
ATOM C2'  CN8    -0.18
ATOM H2'  HN8     0.09
ATOM H2'' HN8     0.09

BOND C2'  H2'
THET C1'  C2'  H2'   C3'  C2'  H2'   H2'  C2'  H2''
DIHE H2'  C2'  C1'  O4'   H2'  C2'  C1'  N9    H2'  C2'  C1'  H1'
DIHE H2'  C2'  C3'  C4'   H2'  C2'  C3'  O3'   H2'  C2'  C3'  H3'
BILD C1'  C3'  *C2' H2' 0.0 0.0 -115.0 0.0 0.0


END


