* TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN ATOMS: VERSION 19
* T. Lazaridis: here the ionic sidechains and termini are neutralized
* Also, a new atom type has been added, CR, for 4-bonded carbon in
* aromatics and Arginine. Modifications are marked by TL
*
   20    1                ! Version number
MASS     1 H      1.00800 ! hydrogen which can h-bond to neutral atom
MASS     2 HC     1.00800 !   -    "     -               charged atom
MASS     3 HA     1.00800 ! aliphatic hydrogen
MASS     4 HT     1.00800 ! TIPS3P WATER HYDROGEN
MASS     5 LP     0.0     ! ST2 LONE PAIR
MASS    10 CT    12.01100 ! aliphatic carbon
MASS    11 C     12.01100 ! carbonyl carbon
MASS    12 CH1E  13.01900 ! extended atom carbon w/ one hydrogen
MASS    13 CH2E  14.02700 !   -    "    -           two
MASS    14 CH3E  15.03500 !   -    "    -           three
MASS    15 CR1E  13.01900 !   -    "    -        in aromatic ring w/ one H
MASS    16 CM    12.01100 ! carbon in carbonmonoxide
MASS    31 N     14.00670 ! peptide nitrogen with no hydrogens attached
MASS    32 NR    14.00670 ! nitrogen in aromatic ring with no hydrogens
MASS    33 NP    14.00670 ! pyrole nitrogen
!MASS    34 NH1E  15.01470 ! extended atom peptide nitrogen with one hydrogen
!MASS    35 NH2E  16.02270 !  -       "        -                 two   -"-
!MASS    36 NH3E  17.03070 !  -       "        -                 three -"-
!MASS    37 NC2E  16.02270 ! extended atom charged guanidinium nitrogen w/ 2 H
MASS    38 NH1   14.00670 ! peptide nitrogen bound to one hydrogen
MASS    39 NH2   14.00670 !  -       "        -       two -"-
MASS    40 NH3   14.00670 ! nitrogen bound to three hydrogens
MASS    41 NC2   14.00670 ! charged guanidinuim nitrogen bound to two hydrogens
MASS    51 O     15.99940 ! carbonyl oxygen
MASS    52 OC    15.99940 ! carboxy oxygen
!MASS    53 OH1E  17.00740 ! extended atom hydroxy oxygen
!MASS    54 OH2E  18.01540 ! extended atom water
MASS    55 OH1   15.99940 ! hydroxy oxygen
MASS    56 OH2   15.99940 ! ST2 water oxygen
MASS    57 OM    15.99940 ! oxygen in carbonmonoxide
MASS    58 OT    15.99940 ! TIPS3P WATER OXYGEN
MASS    59 OS    15.99940 ! ester oxygen
MASS    81 S     32.06000 ! sulphur
MASS    82 SH1E  33.06800 ! extended atom sulphur with one hydrogen
MASS    91 FE    55.84700 ! iron
MASS    92 CR    12.01100 ! 4-bonded carbon in aromatics and Arginine

DECL -C
DECL -O
DECL +N
DECL +H
DECL +CA

AUTOGENERATE ANGLES
DEFA FIRS NTER LAST CTER

RESI ALA     0.00000
GROU
ATOM N    NH1    -0.35
ATOM H    H       0.25
ATOM CA   CH1E    0.10
GROU
ATOM CB   CH3E    0.00
GROU
ATOM C    C       0.55
ATOM O    O      -0.55
BOND N    CA        CA   C         C    +N        C    O         N    H
BOND CA   CB
DIHE -C   N    CA   C         N    CA   C    +N        CA   C    +N   +CA
IMPH N    -C   CA   H         C    CA   +N   O         CA   N    C    CB
DONO  H  N
ACCE O  C
IC   -C   CA   *N   H      0.0000    0.00  180.00    0.00   0.0000
IC   -C   N    CA   C      0.0000    0.00  180.00    0.00   0.0000
IC   N    CA   C    +N     0.0000    0.00  180.00    0.00   0.0000
IC   +N   CA   *C   O      0.0000    0.00  180.00    0.00   0.0000
IC   CA   C    +N   +CA    0.0000    0.00  180.00    0.00   0.0000
IC   N    C    *CA  CB     0.0000    0.00  120.00    0.00   0.0000

RESI ARG     0.00000        !TL
GROU
ATOM N    NH1    -0.35
ATOM H    H       0.25
ATOM CA   CH1E    0.10
GROU
ATOM CB   CH2E    0.00
ATOM CG   CH2E    0.00
GROU
ATOM CD   CH2E    0.10
ATOM NE   NH1    -0.40
ATOM HE   H       0.15
ATOM CZ   CR      0.25
GROU
ATOM NH1  NC2    -0.85
ATOM HH11 HC      0.40
ATOM HH12 HC      0.40
GROU
ATOM NH2  NC2    -0.85
ATOM HH21 HC      0.40
ATOM HH22 HC      0.40
GROU
ATOM C    C       0.55
ATOM O    O      -0.55
BOND N    CA        CA   C         C    +N        C    O         N    H
BOND CA   CB        CB   CG        CG   CD        CD   NE        NE   HE
BOND NE   CZ        CZ   NH1       CZ   NH2       NH1  HH11      NH1  HH12
BOND NH2  HH21      NH2  HH22
DIHE -C   N    CA   C         N    CA   C    +N        CA   C    +N   +CA
DIHE N    CA   CB   CG        CA   CB   CG   CD        CB   CG   CD   NE
DIHE CG   CD   NE   CZ        CD   NE   CZ   NH1       NE   CZ   NH1  HH11
DIHE NE   CZ   NH2  HH21      NE   CZ   NH1  HH12      NE   CZ   NH2  HH22
IMPH N    -C   CA   H         C    CA   +N   O         CA   N    C    CB
IMPH NE   CD   CZ   HE        CZ   NH1  NH2  NE
DONO  H N
DONO  HE NE
DONO  HH11 NH1
DONO  HH12 NH1
DONO  HH21 NH2
DONO  HH22 NH2
ACCE O C
IC   -C   CA   *N   H      0.0000    0.00  180.00    0.00   0.0000
IC   -C   N    CA   C      0.0000    0.00  180.00    0.00   0.0000
IC   N    CA   C    +N     0.0000    0.00  180.00    0.00   0.0000
IC   +N   CA   *C   O      0.0000    0.00  180.00    0.00   0.0000
IC   CA   C    +N   +CA    0.0000    0.00  180.00    0.00   0.0000
IC   N    C    *CA  CB     0.0000    0.00  120.00    0.00   0.0000
IC   N    CA   CB   CG     0.0000    0.00  180.00    0.00   0.0000
IC   CA   CB   CG   CD     0.0000    0.00  180.00    0.00   0.0000
IC   CB   CG   CD   NE     0.0000    0.00  180.00    0.00   0.0000
IC   CG   CD   NE   CZ     0.0000    0.00  180.00    0.00   0.0000
IC   CD   NE   CZ   NH1    0.0000    0.00  180.00    0.00   0.0000
IC   NH1  NE   *CZ  NH2    0.0000    0.00  180.00    0.00   0.0000
IC   CD   CZ   *NE  HE     0.0000    0.00  180.00    0.00   0.0000
IC   NE   CZ   NH1  HH11   0.0000    0.00  180.00    0.00   0.0000
IC   HH11 CZ   *NH1 HH12   0.0000    0.00  180.00    0.00   0.0000
IC   NE   CZ   NH2  HH21   0.0000    0.00  180.00    0.00   0.0000
IC   HH21 CZ   *NH2 HH22   0.0000    0.00  180.00    0.00   0.0000

RESI ASN     0.00000
GROU
ATOM N    NH1    -0.35
ATOM H    H       0.25
ATOM CA   CH1E    0.10
GROU
ATOM CB   CH2E    0.00
GROU
ATOM CG   C       0.55
ATOM OD1  O      -0.55
GROU
ATOM ND2  NH2    -0.60
ATOM HD21 H       0.30
ATOM HD22 H       0.30
GROU
ATOM C    C       0.55
ATOM O    O      -0.55
BOND N    CA        CA   C         C    +N        C    O         N    H
BOND CA   CB        CB   CG        CG   OD1       CG   ND2       ND2  HD21
BOND ND2  HD22
DIHE -C   N    CA   C         N    CA   C    +N        CA   C    +N   +CA
DIHE N    CA   CB   CG        CA   CB   CG   OD1       CB   CG   ND2  HD21
IMPH N    -C   CA   H         C    CA   +N   O         CA   N    C    CB
IMPH CG   OD1  ND2  CB        ND2  HD21 HD22 CG
DONO  H N
DONO  HD21 ND2
DONO  HD22 ND2
ACCE OD1 CG
ACCE O C
IC   -C   CA   *N   H      0.0000    0.00  180.00    0.00   0.0000
IC   -C   N    CA   C      0.0000    0.00  180.00    0.00   0.0000
IC   N    CA   C    +N     0.0000    0.00  180.00    0.00   0.0000
IC   +N   CA   *C   O      0.0000    0.00  180.00    0.00   0.0000
IC   CA   C    +N   +CA    0.0000    0.00  180.00    0.00   0.0000
IC   N    C    *CA  CB     0.0000    0.00  120.00    0.00   0.0000
IC   N    CA   CB   CG     0.0000    0.00  180.00    0.00   0.0000
IC   CA   CB   CG   OD1    0.0000    0.00  180.00    0.00   0.0000
IC   OD1  CB   *CG  ND2    0.0000    0.00  180.00    0.00   0.0000
IC   OD1  CG   ND2  HD21   0.0000    0.00  180.00    0.00   0.0000
IC   HD21 CG   *ND2 HD22   0.0000    0.00  180.00    0.00   0.0000

RESI ASP     0.00000   ! TL
GROU
ATOM N    NH1    -0.35
ATOM H    H       0.25
ATOM CA   CH1E    0.10
GROU
ATOM CB   CH2E   -0.15
ATOM CG   C       1.35
ATOM OD1  OC     -0.60
ATOM OD2  OC     -0.60
GROU
ATOM C    C       0.55
ATOM O    O      -0.55
BOND N    CA        CA   C         C    +N        C    O         N    H
BOND CA   CB        CB   CG        CG   OD1       CG   OD2
DIHE -C   N    CA   C         N    CA   C    +N        CA   C    +N   +CA
DIHE N    CA   CB   CG        CA   CB   CG   OD1
IMPH N    -C   CA   H         C    CA   +N   O         CA   N    C    CB
IMPH CG   OD1  OD2  CB
DONO  H     N
ACCE OD1  CG
ACCE OD2  CG
ACCE O  C
IC   -C   CA   *N   H      0.0000    0.00  180.00    0.00   0.0000
IC   -C   N    CA   C      0.0000    0.00  180.00    0.00   0.0000
IC   N    CA   C    +N     0.0000    0.00  180.00    0.00   0.0000
IC   +N   CA   *C   O      0.0000    0.00  180.00    0.00   0.0000
IC   CA   C    +N   +CA    0.0000    0.00  180.00    0.00   0.0000
IC   N    C    *CA  CB     0.0000    0.00  120.00    0.00   0.0000
IC   N    CA   CB   CG     0.0000    0.00  180.00    0.00   0.0000
IC   CA   CB   CG   OD1    0.0000    0.00  180.00    0.00   0.0000
IC   OD1  CB   *CG  OD2    0.0000    0.00  180.00    0.00   0.0000

RESI CYS     0.00000
GROU
ATOM N    NH1    -0.35
ATOM H    H       0.25
ATOM CA   CH1E    0.10
GROU
ATOM CB   CH2E    0.19
ATOM SG   SH1E   -0.19
GROU
ATOM C    C       0.55
ATOM O    O      -0.55
BOND N    CA        CA   C         C    +N        C    O         N    H
BOND CA   CB        CB   SG
DIHE -C   N    CA   C         N    CA   C    +N        CA   C    +N   +CA
DIHE N    CA   CB   SG
IMPH N    -C   CA   H         C    CA   +N   O         CA   N    C    CB
DONO  H     N
ACCE O  C
IC   -C   CA   *N   H      0.0000    0.00  180.00    0.00   0.0000
IC   -C   N    CA   C      0.0000    0.00  180.00    0.00   0.0000
IC   N    CA   C    +N     0.0000    0.00  180.00    0.00   0.0000
IC   +N   CA   *C   O      0.0000    0.00  180.00    0.00   0.0000
IC   CA   C    +N   +CA    0.0000    0.00  180.00    0.00   0.0000
IC   N    C    *CA  CB     0.0000    0.00  120.00    0.00   0.0000
IC   N    CA   CB   SG     0.0000    0.00  180.00    0.00   0.0000

RESI GLN     0.00000
GROU
ATOM N    NH1    -0.35
ATOM H    H       0.25
ATOM CA   CH1E    0.10
GROU
ATOM CB   CH2E    0.00
ATOM CG   CH2E    0.00
GROU
ATOM CD   C       0.55
ATOM OE1  O      -0.55
GROU
ATOM NE2  NH2    -0.60
ATOM HE21 H       0.30
ATOM HE22 H       0.30
GROU
ATOM C    C       0.55
ATOM O    O      -0.55
BOND N    CA        CA   C         C    +N        C    O         N    H
BOND CA   CB        CB   CG        CG   CD        CD   OE1       CD   NE2
BOND NE2  HE21      NE2  HE22
DIHE -C   N    CA   C         N    CA   C    +N        CA   C    +N   +CA
DIHE N    CA   CB   CG        CA   CB   CG   CD        CB   CG   CD   OE1
DIHE CG   CD   NE2  HE21
IMPH N    -C   CA   H         C    CA   +N   O         CA   N    C    CB
IMPH CD   OE1  NE2  CG        NE2  HE21 HE22 CD
DONO  H     N
DONO  HE21  NE2
DONO  HE22  NE2
ACCE OE1  CD
ACCE O  C
IC   -C   CA   *N   H      0.0000    0.00  180.00    0.00   0.0000
IC   -C   N    CA   C      0.0000    0.00  180.00    0.00   0.0000
IC   N    CA   C    +N     0.0000    0.00  180.00    0.00   0.0000
IC   +N   CA   *C   O      0.0000    0.00  180.00    0.00   0.0000
IC   CA   C    +N   +CA    0.0000    0.00  180.00    0.00   0.0000
IC   N    C    *CA  CB     0.0000    0.00  120.00    0.00   0.0000
IC   N    CA   CB   CG     0.0000    0.00  180.00    0.00   0.0000
IC   CA   CB   CG   CD     0.0000    0.00  180.00    0.00   0.0000
IC   CB   CG   CD   OE1    0.0000    0.00  180.00    0.00   0.0000
IC   OE1  CG   *CD  NE2    0.0000    0.00  180.00    0.00   0.0000
IC   OE1  CD   NE2  HE21   0.0000    0.00  180.00    0.00   0.0000
IC   HE21 CD   *NE2 HE22   0.0000    0.00  180.00    0.00   0.0000

RESI GLU     0.00000 ! TL: as ASP
GROU
ATOM N    NH1    -0.35
ATOM H    H       0.25
ATOM CA   CH1E    0.10
GROU
ATOM CB   CH2E    0.00
GROU
ATOM CG   CH2E   -0.15
ATOM CD   C       1.35
ATOM OE1  OC     -0.60
ATOM OE2  OC     -0.60
GROU
ATOM C    C       0.55
ATOM O    O      -0.55
BOND N    CA        CA   C         C    +N        C    O         N    H
BOND CA   CB        CB   CG        CG   CD        CD   OE1       CD   OE2
DIHE -C   N    CA   C         N    CA   C    +N        CA   C    +N   +CA
DIHE N    CA   CB   CG        CA   CB   CG   CD        CB   CG   CD   OE1
IMPH N    -C   CA   H         C    CA   +N   O         CA   N    C    CB
IMPH CD   OE1  OE2  CG
DONO  H     N
ACCE OE1  CD
ACCE OE2  CD
ACCE O  C
IC   -C   CA   *N   H      0.0000    0.00  180.00    0.00   0.0000
IC   -C   N    CA   C      0.0000    0.00  180.00    0.00   0.0000
IC   N    CA   C    +N     0.0000    0.00  180.00    0.00   0.0000
IC   +N   CA   *C   O      0.0000    0.00  180.00    0.00   0.0000
IC   CA   C    +N   +CA    0.0000    0.00  180.00    0.00   0.0000
IC   N    C    *CA  CB     0.0000    0.00  120.00    0.00   0.0000
IC   N    CA   CB   CG     0.0000    0.00  180.00    0.00   0.0000
IC   CA   CB   CG   CD     0.0000    0.00  180.00    0.00   0.0000
IC   CB   CG   CD   OE1    0.0000    0.00  180.00    0.00   0.0000
IC   OE1  CG   *CD  OE2    0.0000    0.00  180.00    0.00   0.0000

RESI GLY     0.00000
GROU
ATOM N    NH1    -0.35
ATOM H    H       0.25
ATOM CA   CH2E    0.10
GROU
ATOM C    C       0.55
ATOM O    O      -0.55
BOND N    CA        CA   C         C    +N        C    O         N    H
DIHE -C   N    CA   C         N    CA   C    +N        CA   C    +N   +CA
IMPH N    -C   CA   H         C    CA   +N   O
DONO  H     N
ACCE O  C
IC   -C   CA   *N   H      0.0000    0.00  180.00    0.00   0.0000
IC   -C   N    CA   C      0.0000    0.00  180.00    0.00   0.0000
IC   N    CA   C    +N     0.0000    0.00  180.00    0.00   0.0000
IC   +N   CA   *C   O      0.0000    0.00  180.00    0.00   0.0000
IC   CA   C    +N   +CA    0.0000    0.00  180.00    0.00   0.0000
PATC FIRS GLYP

RESI HIS     0.00000            ! Rings charges from Del Bene and Cohen
GROU                            ! JACS 100:5285 (1978) Imidazole sto-3g calc.
ATOM N    NH1    -0.35          ! Note that this residue has non-neutral groups.
ATOM H    H       0.25
ATOM CA   CH1E    0.10
GROU
ATOM CB   CH2E    0.00
GROUP
ATOM CG   CR      0.10
ATOM ND1  NH1    -0.40
ATOM HD1  H       0.30
GROU
ATOM CD2  CR1E    0.10
ATOM NE2  NR     -0.40
ATOM CE1  CR1E    0.30
GROU
ATOM C    C       0.55
ATOM O    O      -0.55
BOND N    CA        CA   C         C    +N        C    O         N    H
BOND CA   CB        CB   CG        CG   ND1       CG   CD2       ND1  HD1
BOND ND1  CE1       CD2  NE2       CE1  NE2
DIHE -C   N    CA   C         N    CA   C    +N        CA   C    +N   +CA
DIHE N    CA   CB   CG        CA   CB   CG   ND1
IMPH N    -C   CA   H         C    CA   +N   O         CA   N    C    CB
IMPH CG   ND1  CD2  CB        ND1  CG   CE1  HD1       CG   ND1  CE1  NE2
IMPH ND1  CE1  NE2  CD2       CE1  NE2  CD2  CG        NE2  CD2  CG   ND1
IMPH CD2  CG   ND1  CE1
DONO  H     N
DONO  HD1   ND1
ACCE NE2
ACCE O  C
IC   -C   CA   *N   H      0.0000    0.00  180.00    0.00   0.0000
IC   -C   N    CA   C      0.0000    0.00  180.00    0.00   0.0000
IC   N    CA   C    +N     0.0000    0.00  180.00    0.00   0.0000
IC   +N   CA   *C   O      0.0000    0.00  180.00    0.00   0.0000
IC   CA   C    +N   +CA    0.0000    0.00  180.00    0.00   0.0000
IC   N    C    *CA  CB     0.0000    0.00  120.00    0.00   0.0000
IC   N    CA   CB   CG     0.0000    0.00  180.00    0.00   0.0000
IC   CA   CB   CG   CD2    0.0000    0.00   90.00    0.00   0.0000
IC   CD2  CB   *CG  ND1    0.0000    0.00  180.00    0.00   0.0000
IC   CD2  CG   ND1  CE1    0.0000    0.00    0.00    0.00   0.0000
IC   ND1  CG   CD2  NE2    0.0000    0.00    0.00    0.00   0.0000
IC   CE1  CG   *ND1 HD1    0.0000    0.00  180.00    0.00   0.0000

RESI HSD     0.00000            ! see HIS above.
GROUP
ATOM N    NH1    -0.35
ATOM H    H       0.25
ATOM CA   CH1E    0.10
GROU
ATOM CB   CH2E    0.00
GROUP
ATOM CG   CR      0.10
ATOM ND1  NR     -0.40
ATOM CE1  CR1E    0.30
GROU
ATOM CD2  CR1E    0.10
ATOM NE2  NH1    -0.40
ATOM HE2  H       0.30
GROU
ATOM C    C       0.55
ATOM O    O      -0.55
BOND N    CA        CA   C         C    +N        C    O         N    H
BOND CA   CB        CB   CG        CG   ND1       CG   CD2       ND1  CE1
BOND CD2  NE2       CE1  NE2       NE2  HE2
DIHE -C   N    CA   C         N    CA   C    +N        CA   C    +N   +CA
DIHE N    CA   CB   CG        CA   CB   CG   ND1
IMPH N    -C   CA   H         C    CA   +N   O         CA   N    C    CB
IMPH CG   ND1  CD2  CB        NE2  CE1  CD2  HE2       CG   ND1  CE1  NE2
IMPH ND1  CE1  NE2  CD2       CE1  NE2  CD2  CG        NE2  CD2  CG   ND1
IMPH CD2  CG   ND1  CE1
DONO  H     N
DONO  HE2   NE2
ACCE ND1
ACCE O  C
IC   -C   CA   *N   H      0.0000    0.00  180.00    0.00   0.0000
IC   -C   N    CA   C      0.0000    0.00  180.00    0.00   0.0000
IC   N    CA   C    +N     0.0000    0.00  180.00    0.00   0.0000
IC   +N   CA   *C   O      0.0000    0.00  180.00    0.00   0.0000
IC   CA   C    +N   +CA    0.0000    0.00  180.00    0.00   0.0000
IC   N    C    *CA  CB     0.0000    0.00  120.00    0.00   0.0000
IC   N    CA   CB   CG     0.0000    0.00  180.00    0.00   0.0000
IC   CA   CB   CG   CD2    0.0000    0.00   90.00    0.00   0.0000
IC   CD2  CB   *CG  ND1    0.0000    0.00  180.00    0.00   0.0000
IC   CD2  CG   ND1  CE1    0.0000    0.00    0.00    0.00   0.0000
IC   ND1  CG   CD2  NE2    0.0000    0.00    0.00    0.00   0.0000
IC   CE1  CD2  *NE2 HE2    0.0000    0.00  180.00    0.00   0.0000

RESI HSC     1.00000            ! Doubly protonated histidine.  Ring charges
GROU
ATOM N    NH1    -0.35          ! Hayes and Kollman jacs 98:3335 (1976).
ATOM H    H       0.25
ATOM CA   CH1E    0.10
GROU
ATOM CB   CH2E    0.10
ATOM CG   CR      0.15
ATOM CD2  CR1E    0.20
GROU
ATOM ND1  NH1    -0.30
ATOM HD1  H       0.35
GROU
ATOM CE1  CR1E    0.45
GROU
ATOM NE2  NH1    -0.30
ATOM HE2  H       0.35
GROU
ATOM C    C       0.55
ATOM O    O      -0.55
BOND N    CA        CA   C         C    +N        C    O         N    H
BOND CA   CB        CB   CG        CG   ND1       CG   CD2       ND1  HD1
BOND ND1  CE1       CD2  NE2       CE1  NE2       NE2   HE2
DIHE -C   N    CA   C         N    CA   C    +N        CA   C    +N   +CA
DIHE N    CA   CB   CG        CA   CB   CG   ND1
IMPH N    -C   CA   H         C    CA   +N   O         CA   N    C    CB
IMPH CG   ND1  CD2  CB        ND1  CG   CE1  HD1       CG   ND1  CE1  NE2
IMPH ND1  CE1  NE2  CD2       CE1  NE2  CD2  CG        NE2  CD2  CG   ND1
IMPH CD2  CG   ND1  CE1       NE2  CD2  CE1  HE2
DONO  H     N
DONO  HD1   ND1
DONO  HE2   NE2
ACCE O  C
IC   -C   CA   *N   H      0.0000    0.00  180.00    0.00   0.0000
IC   -C   N    CA   C      0.0000    0.00  180.00    0.00   0.0000
IC   N    CA   C    +N     0.0000    0.00  180.00    0.00   0.0000
IC   +N   CA   *C   O      0.0000    0.00  180.00    0.00   0.0000
IC   CA   C    +N   +CA    0.0000    0.00  180.00    0.00   0.0000
IC   N    C    *CA  CB     0.0000    0.00  120.00    0.00   0.0000
IC   N    CA   CB   CG     0.0000    0.00  180.00    0.00   0.0000
IC   CA   CB   CG   CD2    0.0000    0.00   90.00    0.00   0.0000
IC   CD2  CB   *CG  ND1    0.0000    0.00  180.00    0.00   0.0000
IC   CD2  CG   ND1  CE1    0.0000    0.00    0.00    0.00   0.0000
IC   ND1  CG   CD2  NE2    0.0000    0.00    0.00    0.00   0.0000
IC   CE1  CG   *ND1 HD1    0.0000    0.00  180.00    0.00   0.0000
IC   CE1  CD2  *NE2 HE2    0.0000    0.00  180.00    0.00   0.0000

RESI ILE     0.00000
GROU
ATOM N    NH1    -0.35
ATOM H    H       0.25
ATOM CA   CH1E    0.10
GROU
ATOM CB   CH1E    0.00
ATOM CG2  CH3E    0.00
GROU
ATOM CG1  CH2E    0.00
ATOM CD   CH3E    0.00
GROU
ATOM C    C       0.55
ATOM O    O      -0.55
BOND N    CA        CA   C         C    +N        C    O         N    H
BOND CA   CB        CB   CG1       CB   CG2       CG1  CD
DIHE -C   N    CA   C         N    CA   C    +N        CA   C    +N   +CA
DIHE N    CA   CB   CG1       CA   CB   CG1  CD
IMPH N    -C   CA   H         C    CA   +N   O         CA   N    C    CB
IMPH CB   CG1  CG2  CA
DONO  H     N
ACCE O  C
IC   -C   CA   *N   H      0.0000    0.00  180.00    0.00   0.0000
IC   -C   N    CA   C      0.0000    0.00  180.00    0.00   0.0000
IC   N    CA   C    +N     0.0000    0.00  180.00    0.00   0.0000
IC   +N   CA   *C   O      0.0000    0.00  180.00    0.00   0.0000
IC   CA   C    +N   +CA    0.0000    0.00  180.00    0.00   0.0000
IC   N    C    *CA  CB     0.0000    0.00  120.00    0.00   0.0000
IC   N    CA   CB   CG1    0.0000    0.00  180.00    0.00   0.0000
IC   CA   CB   CG1  CD     0.0000    0.00  180.00    0.00   0.0000
IC   CG1  CA   *CB  CG2    0.0000    0.00 -120.00    0.00   0.0000

RESI LEU     0.00000
GROU
ATOM N    NH1    -0.35
ATOM H    H       0.25
ATOM CA   CH1E    0.10
GROU
ATOM CB   CH2E    0.00
ATOM CG   CH1E    0.00
ATOM CD1  CH3E    0.00
ATOM CD2  CH3E    0.00
GROU
ATOM C    C       0.55
ATOM O    O      -0.55
BOND N    CA        CA   C         C    +N        C    O         N    H
BOND CA   CB        CB   CG        CG   CD1       CG   CD2
DIHE -C   N    CA   C         N    CA   C    +N        CA   C    +N   +CA
DIHE N    CA   CB   CG        CA   CB   CG   CD2
IMPH N    -C   CA   H         C    CA   +N   O         CA   N    C    CB
IMPH CG   CD2  CD1  CB
DONO  H     N
ACCE O  C
IC   -C   CA   *N   H      0.0000    0.00  180.00    0.00   0.0000
IC   -C   N    CA   C      0.0000    0.00  180.00    0.00   0.0000
IC   N    CA   C    +N     0.0000    0.00  180.00    0.00   0.0000
IC   +N   CA   *C   O      0.0000    0.00  180.00    0.00   0.0000
IC   CA   C    +N   +CA    0.0000    0.00  180.00    0.00   0.0000
IC   N    C    *CA  CB     0.0000    0.00  120.00    0.00   0.0000
IC   N    CA   CB   CG     0.0000    0.00  180.00    0.00   0.0000
IC   CA   CB   CG   CD1    0.0000    0.00  180.00    0.00   0.0000
IC   CD1  CB   *CG  CD2    0.0000    0.00  120.00    0.00   0.0000

RESI LYS     0.00000   !TL
GROU
ATOM N    NH1    -0.35
ATOM H    H       0.25
ATOM CA   CH1E    0.10
GROU
ATOM CB   CH2E    0.00
ATOM CG   CH2E    0.00
ATOM CD   CH2E    0.00
GROU
ATOM CE   CH2E    0.00
ATOM NZ   NH3    -1.35
ATOM HZ1  HC      0.45
ATOM HZ2  HC      0.45
ATOM HZ3  HC      0.45
GROU
ATOM C    C       0.55
ATOM O    O      -0.55
BOND N    CA        CA   C         C    +N        C    O         N    H
BOND CA   CB        CB   CG        CG   CD        CD   CE        CE   NZ
BOND NZ   HZ1       NZ   HZ2       NZ   HZ3
DIHE -C   N    CA   C         N    CA   C    +N        CA   C    +N   +CA
DIHE N    CA   CB   CG        CA   CB   CG   CD        CB   CG   CD   CE
DIHE CG   CD   CE   NZ        CD   CE   NZ   HZ1       CD   CE   NZ   HZ2
DIHE CD   CE   NZ   HZ3
IMPH N    -C   CA   H         C    CA   +N   O         CA   N    C    CB
DONO  H     N
DONO  HZ1   NZ
DONO  HZ2   NZ
DONO  HZ3   NZ
ACCE O  C
IC   -C   CA   *N   H      0.0000    0.00  180.00    0.00   0.0000
IC   -C   N    CA   C      0.0000    0.00  180.00    0.00   0.0000
IC   N    CA   C    +N     0.0000    0.00  180.00    0.00   0.0000
IC   +N   CA   *C   O      0.0000    0.00  180.00    0.00   0.0000
IC   CA   C    +N   +CA    0.0000    0.00  180.00    0.00   0.0000
IC   N    C    *CA  CB     0.0000    0.00  120.00    0.00   0.0000
IC   N    CA   CB   CG     0.0000    0.00  180.00    0.00   0.0000
IC   CA   CB   CG   CD     0.0000    0.00  180.00    0.00   0.0000
IC   CB   CG   CD   CE     0.0000    0.00  180.00    0.00   0.0000
IC   CG   CD   CE   NZ     0.0000    0.00  180.00    0.00   0.0000
IC   CD   CE   NZ   HZ1    0.0000    0.00  180.00    0.00   0.0000
IC   HZ1  CE   *NZ  HZ2    0.0000    0.00  120.00    0.00   0.0000
IC   HZ2  CE   *NZ  HZ3    0.0000    0.00  120.00    0.00   0.0000

RESI MET     0.00000
GROU
ATOM N    NH1    -0.35
ATOM H    H       0.25
ATOM CA   CH1E    0.10
GROU
ATOM CB   CH2E    0.00
GROU
ATOM CG   CH2E    0.06
ATOM SD   S      -0.12
ATOM CE   CH3E    0.06
GROU
ATOM C    C       0.55
ATOM O    O      -0.55
BOND N    CA        CA   C         C    +N        C    O         N    H
BOND CA   CB        CB   CG        CG   SD        SD   CE
DIHE -C   N    CA   C         N    CA   C    +N        CA   C    +N   +CA
DIHE N    CA   CB   CG        CA   CB   CG   SD        CB   CG   SD   CE
IMPH N    -C   CA   H         C    CA   +N   O         CA   N    C    CB
DONO  H     N
ACCE O  C
IC   -C   CA   *N   H      0.0000    0.00  180.00    0.00   0.0000
IC   -C   N    CA   C      0.0000    0.00  180.00    0.00   0.0000
IC   N    CA   C    +N     0.0000    0.00  180.00    0.00   0.0000
IC   +N   CA   *C   O      0.0000    0.00  180.00    0.00   0.0000
IC   CA   C    +N   +CA    0.0000    0.00  180.00    0.00   0.0000
IC   N    C    *CA  CB     0.0000    0.00  120.00    0.00   0.0000
IC   N    CA   CB   CG     0.0000    0.00  180.00    0.00   0.0000
IC   CA   CB   CG   SD     0.0000    0.00  180.00    0.00   0.0000
IC   CB   CG   SD   CE     0.0000    0.00  180.00    0.00   0.0000

! Penicillamine
RESI PEN     0.00000
GROU
ATOM N    NH1    -0.35
ATOM H    H       0.25
ATOM CA   CH1E    0.10
GROU
ATOM CB   CT      0.19
ATOM CG1  CH3E    0.0
ATOM CG2  CH3E    0.0
ATOM SG   SH1E   -0.19
GROU
ATOM C    C       0.55
ATOM O    O      -0.55
BOND N    CA        CA   C         C    +N        C    O         N    H
BOND CA   CB        CB   SG        CB   CG1       CB   CG2
DIHE -C   N    CA   C         N    CA   C    +N        CA   C    +N   +CA
DIHE N    CA   CB   SG
IMPH N    -C   CA   H         C    CA   +N   O         CA   N    C    CB
DONO  H     N
ACCE O  C
IC   -C   CA   *N   H      0.0000    0.00  180.00    0.00   0.0000
IC   -C   N    CA   C      0.0000    0.00  180.00    0.00   0.0000
IC   N    CA   C    +N     0.0000    0.00  180.00    0.00   0.0000
IC   +N   CA   *C   O      0.0000    0.00  180.00    0.00   0.0000
IC   CA   C    +N   +CA    0.0000    0.00  180.00    0.00   0.0000
IC   N    C    *CA  CB     0.0000    0.00  120.00    0.00   0.0000
IC   N    CA   CB   SG     0.0000    0.00  180.00    0.00   0.0000
IC   SG   CA   *CB  CG1    0.0000    0.00  120.00    0.00   0.0000
IC   SG   CA   *CB  CG2    0.0000    0.00 -120.00    0.00   0.0000

RESI PHE     0.00000
GROU
ATOM N    NH1    -0.35
ATOM H    H       0.25
ATOM CA   CH1E    0.10
GROU
ATOM CB   CH2E    0.00
ATOM CG   CR      0.00    CZ
ATOM CD1  CR1E    0.00    CE2
ATOM CD2  CR1E    0.00    CE1
GROU
ATOM CE1  CR1E    0.00
ATOM CE2  CR1E    0.00
ATOM CZ   CR1E    0.00
GROU
ATOM C    C       0.55
ATOM O    O      -0.55
BOND N    CA        CA   C         C    +N        C    O         N    H
BOND CA   CB        CB   CG        CG   CD1       CG   CD2       CD1  CE1
BOND CD2  CE2       CE1  CZ        CE2  CZ
DIHE -C   N    CA   C         N    CA   C    +N        CA   C    +N   +CA
DIHE N    CA   CB   CG        CA   CB   CG   CD1
IMPH N    -C   CA   H         C    CA   +N   O         CA   N    C    CB
IMPH CG   CD1  CE1  CZ        CD1  CE1  CZ   CE2       CE1  CZ   CE2  CD2
IMPH CZ   CE2  CD2  CG        CE2  CD2  CG   CD1       CD2  CG   CD1  CE1
IMPH CG   CD1  CD2  CB
DONO  H     N
ACCE O  C
IC   -C   CA   *N   H      0.0000    0.00  180.00    0.00   0.0000
IC   -C   N    CA   C      0.0000    0.00  180.00    0.00   0.0000
IC   N    CA   C    +N     0.0000    0.00  180.00    0.00   0.0000
IC   +N   CA   *C   O      0.0000    0.00  180.00    0.00   0.0000
IC   CA   C    +N   +CA    0.0000    0.00  180.00    0.00   0.0000
IC   N    C    *CA  CB     0.0000    0.00  120.00    0.00   0.0000
IC   N    CA   CB   CG     0.0000    0.00  180.00    0.00   0.0000
IC   CA   CB   CG   CD1    0.0000    0.00   90.00    0.00   0.0000
IC   CD1  CB   *CG  CD2    0.0000  120.00  180.00  120.00   0.0000
IC   CD1  CG   CD2  CE2    0.0000  120.00    0.00  120.00   0.0000
IC   CD2  CG   CD1  CE1    0.0000  120.00    0.00  120.00   0.0000
IC   CG   CD1  CE1  CZ     0.0000  120.00    0.00  120.00   0.0000

RESI PRO     0.00000
GROU
ATOM N    N      -0.20
ATOM CD   CH2E    0.10
ATOM CA   CH1E    0.10
GROU
ATOM CB   CH2E    0.00
ATOM CG   CH2E    0.00
GROU
ATOM C    C       0.55
ATOM O    O      -0.55
BOND N    CA        CA   C         C    +N        C    O         N    CD
BOND CA   CB        CB   CG        CG   CD
DIHE -C   N    CA   C         N    CA   C    +N        CA   C    +N   +CA
DIHE N    CA   CB   CG        CA   CB   CG   CD        CB   CG   CD   N
DIHE CG   CD   N    CA
IMPH N    CA   CD   -C        C    CA   +N   O         CA   N    C    CB
ACCE O  C
IC   -C   CA   *N   CD     0.0000    0.00  180.00    0.00   0.0000
IC   -C   N    CA   C      0.0000    0.00  -60.00    0.00   0.0000
IC   N    CA   C    +N     0.0000    0.00  180.00    0.00   0.0000
IC   +N   CA   *C   O      0.0000    0.00  180.00    0.00   0.0000
IC   CA   C    +N   +CA    0.0000    0.00  180.00    0.00   0.0000
IC   C    N    *CA  CB     0.0000    0.00 -120.00    0.00   0.0000
IC   N    CA   CB   CG     0.0000    0.00    0.00  108.00   0.0000
PATC FIRS PROP

RESI SER     0.00000
GROU
ATOM N    NH1    -0.35
ATOM H    H       0.25
ATOM CA   CH1E    0.10
GROU
ATOM CB   CH2E    0.25
ATOM OG   OH1    -0.65
ATOM HG   H       0.40
GROU
ATOM C    C       0.55
ATOM O    O      -0.55
BOND N    CA        CA   C         C    +N        C    O         N    H
BOND CA   CB        CB   OG        OG   HG
DIHE -C   N    CA   C         N    CA   C    +N        CA   C    +N   +CA
DIHE N    CA   CB   OG        CA   CB   OG   HG
IMPH N    -C   CA   H         C    CA   +N   O         CA   N    C    CB
DONO  H     N
DONO  HG    OG
ACCE OG
ACCE O  C
IC   -C   CA   *N   H      0.0000    0.00  180.00    0.00   0.0000
IC   -C   N    CA   C      0.0000    0.00  180.00    0.00   0.0000
IC   N    CA   C    +N     0.0000    0.00  180.00    0.00   0.0000
IC   +N   CA   *C   O      0.0000    0.00  180.00    0.00   0.0000
IC   CA   C    +N   +CA    0.0000    0.00  180.00    0.00   0.0000
IC   N    C    *CA  CB     0.0000    0.00  120.00    0.00   0.0000
IC   N    CA   CB   OG     0.0000    0.00  180.00    0.00   0.0000
IC   CA   CB   OG   HG     0.0000    0.00  180.00    0.00   0.0000

RESI THR     0.00000
GROU
ATOM N    NH1    -0.35
ATOM H    H       0.25
ATOM CA   CH1E    0.10
GROU
ATOM CB   CH1E    0.25
ATOM OG1  OH1    -0.65
ATOM HG1  H       0.40
GROU
ATOM CG2  CH3E    0.00
GROU
ATOM C    C       0.55
ATOM O    O      -0.55
BOND N    CA        CA   C         C    +N        C    O         N    H
BOND CA   CB        CB   OG1       CB   CG2       OG1  HG1
DIHE -C   N    CA   C         N    CA   C    +N        CA   C    +N   +CA
DIHE N    CA   CB   OG1       CA   CB   OG1  HG1
IMPH N    -C   CA   H         C    CA   +N   O         CA   N    C    CB
IMPH CB   OG1  CG2  CA
DONO  H     N
DONO  HG1  OG1
ACCE OG1
ACCE O  C
IC   -C   CA   *N   H      0.0000    0.00  180.00    0.00   0.0000
IC   -C   N    CA   C      0.0000    0.00  180.00    0.00   0.0000
IC   N    CA   C    +N     0.0000    0.00  180.00    0.00   0.0000
IC   +N   CA   *C   O      0.0000    0.00  180.00    0.00   0.0000
IC   CA   C    +N   +CA    0.0000    0.00  180.00    0.00   0.0000
IC   N    C    *CA  CB     0.0000    0.00  120.00    0.00   0.0000
IC   N    CA   CB   OG1    0.0000    0.00  180.00    0.00   0.0000
IC   OG1  CA   *CB  CG2    0.0000    0.00 -120.00    0.00   0.0000
IC   CA   CB   OG1  HG1    0.0000    0.00  180.00    0.00   0.0000

RESI TRP     0.00000
GROU
ATOM N    NH1    -0.35
ATOM H    H       0.25
ATOM CA   CH1E    0.10
GROU
ATOM CB   CH2E    0.00
GROU
ATOM CG   CR     -0.03     CD1  CD2  NE1  CE2  CE3  CZ2  CZ3  CH2
ATOM CD2  CR      0.10     NE1  CE2  CE3  CZ2  CZ3  CH2
ATOM CE2  CR     -0.04     CE3  CZ2  CZ3  CH2
ATOM CE3  CR1E   -0.03     CZ2  CZ3  CH2
GROU
ATOM CD1  CR1E    0.06     CD2  NE1  CE2  CE3  CZ2  CZ3  CH2
ATOM NE1  NH1    -0.36     CE2  CE3  CZ2  CZ3  CH2
ATOM HE1  H       0.30
GROU
ATOM CZ2  CR1E    0.00     CZ3  CH2
ATOM CZ3  CR1E    0.00     CH2
ATOM CH2  CR1E    0.00
GROU
ATOM C    C       0.55
ATOM O    O      -0.55
BOND N    CA        CA   C         C    +N        C    O         N    H
BOND CA   CB        CB   CG        CG   CD1       CG   CD2       CD1  NE1
BOND CD2  CE2       NE1  HE1       NE1  CE2       CD2  CE3       CE2  CZ2
BOND CE3  CZ3       CZ2  CH2       CZ3  CH2
! The ring angles are only assigned for the five and six member rings.
! The angles CG CD2 CE3  and NE1 CE2 CZ2 are left out to avoid conflicts
! with the histidine angle parameters and to preserve symmetry.
DIHE -C   N    CA   C         N    CA   C    +N        CA   C    +N   +CA
DIHE N    CA   CB   CG        CA   CB   CG   CD1
! The following dihedrals span the rings and keep them parallel.
DIHE CD1  CE2  CD2  CZ3       CD1  CD2  CE2  CH2
DIHE CZ2  CE2  CD2  CG        CE3  CD2  CE2  NE1
IMPH N    -C   CA   H         C    CA   +N   O         CA   N    C    CB
IMPH CG   CD1  CD2  CB        NE1  CD1  CE2  HE1       CD2  CE2  CZ2  CH2
IMPH CE2  CZ2  CH2  CZ3       CZ2  CH2  CZ3  CE3       CH2  CZ3  CE3  CD2
IMPH CZ3  CE3  CD2  CE2       CE3  CD2  CE2  CZ2       CG   CD1  NE1  CE2
IMPH CD1  NE1  CE2  CD2       NE1  CE2  CD2  CG        CE2  CD2  CG   CD1
IMPH CD2  CG   CD1  NE1
! These impropers are skipped IMPH CD2  CG   CE3  CE2       CE2  CZ2  NE1  CD2
! because the rings are kept flat by the proper dihedrals noted above.
DONO  H     N
DONO  HE1   NE1
ACCE O  C
IC   -C   CA   *N   H      0.0000    0.00  180.00    0.00   0.0000
IC   -C   N    CA   C      0.0000    0.00  180.00    0.00   0.0000
IC   N    CA   C    +N     0.0000    0.00  180.00    0.00   0.0000
IC   +N   CA   *C   O      0.0000    0.00  180.00    0.00   0.0000
IC   CA   C    +N   +CA    0.0000    0.00  180.00    0.00   0.0000
IC   N    C    *CA  CB     0.0000    0.00  120.00    0.00   0.0000
IC   N    CA   CB   CG     0.0000    0.00  180.00    0.00   0.0000
IC   CA   CB   CG   CD2    0.0000    0.00   90.00  127.45   1.3673
IC   CD2  CB   *CG  CD1    1.3673  127.45  180.00  121.78   1.3815
IC   CD1  CG   CD2  CE2    1.3815  110.77    0.00  102.51   1.3551
IC   CD2  CG   CD1  NE1    1.3673  110.77    0.00  106.30   1.3203
IC   CE2  CD1  *NE1 HE1    1.3374  108.05  180.00  125.46   0.9802
IC   CE2  CG   *CD2 CE3    1.3551  102.51  180.00  134.73   1.3728
IC   CE2  CD2  CE3  CZ3    1.3551  122.76    0.00  115.22   1.3882
IC   CE3  CD2  CE2  CZ2    1.3728  122.76    0.00  123.56   1.3712
IC   CD2  CE2  CZ2  CH2    1.3551  123.56    0.00  114.96   1.3877

RESI TYR     0.00000
GROU
ATOM N    NH1    -0.35
ATOM H    H       0.25
ATOM CA   CH1E    0.10
GROU
ATOM CB   CH2E    0.00
ATOM CG   CR      0.00    CZ
GROU
ATOM CD1  CR1E    0.00    CE2
ATOM CE1  CR1E    0.00    CD2
GROU
ATOM CD2  CR1E    0.00
ATOM CE2  CR1E    0.00
GROU
ATOM CZ   C       0.25
ATOM OH   OH1    -0.65
ATOM HH   H       0.40
GROU
ATOM C    C       0.55
ATOM O    O      -0.55
BOND N    CA        CA   C         C    +N        C    O         N    H
BOND CA   CB        CB   CG        CG   CD1       CG   CD2       CD1  CE1
BOND CD2  CE2       CE1  CZ        CE2  CZ        CZ   OH        OH   HH
DIHE -C   N    CA   C         N    CA   C    +N        CA   C    +N   +CA
DIHE N    CA   CB   CG        CA   CB   CG   CD1       CE2  CZ   OH   HH
IMPH N    -C   CA   H         C    CA   +N   O         CA   N    C    CB
IMPH CG   CD1  CD2  CB        CZ   CE1  CE2  OH        CG   CD1  CE1  CZ
IMPH CD1  CE1  CZ   CE2       CE1  CZ   CE2  CD2       CZ   CE2  CD2  CG
IMPH CE2  CD2  CG   CD1       CD2  CG   CD1  CE1
DONO  H     N
DONO  HH    OH
ACCE OH
ACCE O  C
IC   -C   CA   *N   H      0.0000    0.00  180.00    0.00   0.0000
IC   -C   N    CA   C      0.0000    0.00  180.00    0.00   0.0000
IC   N    CA   C    +N     0.0000    0.00  180.00    0.00   0.0000
IC   +N   CA   *C   O      0.0000    0.00  180.00    0.00   0.0000
IC   CA   C    +N   +CA    0.0000    0.00  180.00    0.00   0.0000
IC   N    C    *CA  CB     0.0000    0.00  120.00    0.00   0.0000
IC   N    CA   CB   CG     0.0000    0.00  180.00    0.00   0.0000
IC   CA   CB   CG   CD1    0.0000    0.00   90.00    0.00   0.0000
IC   CD1  CB   *CG  CD2    0.0000  120.00  180.00  120.00   0.0000
IC   CD2  CG   CD1  CE1    0.0000  120.00    0.00  120.00   0.0000
IC   CD1  CG   CD2  CE2    0.0000  120.00    0.00  120.00   0.0000
IC   CG   CD1  CE1  CZ     0.0000  120.00    0.00  120.00   0.0000
IC   CE2  CE1  *CZ  OH     0.0000  120.00  180.00  120.00   0.0000
IC   CE1  CZ   OH   HH     0.0000  120.00  180.00    0.00   0.0000

RESI VAL     0.00000
GROU
ATOM N    NH1    -0.35
ATOM H    H       0.25
ATOM CA   CH1E    0.10
GROU
ATOM CB   CH1E    0.00
ATOM CG1  CH3E    0.00
ATOM CG2  CH3E    0.00
GROU
ATOM C    C       0.55
ATOM O    O      -0.55
BOND N    CA        CA   C         C    +N        C    O         N    H
BOND CA   CB        CB   CG1       CB   CG2
DIHE -C   N    CA   C         N    CA   C    +N        CA   C    +N   +CA
DIHE N    CA   CB   CG1
IMPH N    -C   CA   H         C    CA   +N   O         CA   N    C    CB
IMPH CB   CG2  CG1  CA
DONO  H     N
ACCE O C
IC   -C   CA   *N   H      0.0000    0.00  180.00    0.00   0.0000
IC   -C   N    CA   C      0.0000    0.00  180.00    0.00   0.0000
IC   N    CA   C    +N     0.0000    0.00  180.00    0.00   0.0000
IC   +N   CA   *C   O      0.0000    0.00  180.00    0.00   0.0000
IC   CA   C    +N   +CA    0.0000    0.00  180.00    0.00   0.0000
IC   N    C    *CA  CB     0.0000    0.00  120.00    0.00   0.0000
IC   N    CA   CB   CG1    0.0000    0.00  180.00    0.00   0.0000
IC   CG1  CA   *CB  CG2    0.0000    0.00  120.00    0.00   0.0000


RESI HEME   -2.00000
GROU
ATOM FE   FE      0.24
ATOM NA   NP     -0.18
ATOM NB   NP     -0.18
ATOM NC   NP     -0.18
ATOM ND   NP     -0.18
GROU
ATOM C1A  C       0.03
ATOM CHA  CR1E    0.04
ATOM C4D  C       0.02
GROU
ATOM C1B  C       0.03
ATOM CHB  CR1E    0.04
ATOM C4A  C       0.02
GROU
ATOM C1C  C       0.03
ATOM CHC  CR1E    0.04
ATOM C4B  C       0.02
GROU
ATOM C1D  C       0.03
ATOM CHD  CR1E    0.04
ATOM C4C  C       0.02
GROU
ATOM C2A  C      -0.02
ATOM CAA  CH2E    0.04
GROU
ATOM C3A  C       0.02
ATOM CMA  CH3E   -0.04
GROU
ATOM CBA  CH2E   -0.10
ATOM CGA  C       0.30
ATOM O1A  OC     -0.50
ATOM O2A  OC     -0.50
GROU
ATOM C2B  C       0.02
ATOM CMB  CH3E   -0.04
GROU
ATOM C3B  C      -0.05
ATOM CAB  CR1E    0.03
ATOM CBB  CH2E   -0.10
GROU
ATOM C2C  C       0.02
ATOM CMC  CH3E   -0.04
GROU
ATOM C3C  C      -0.05
ATOM CAC  CR1E    0.03
ATOM CBC  CH2E   -0.10
GROU
ATOM C2D  C       0.02
ATOM CMD  CH3E   -0.04
GROU
ATOM C3D  C      -0.02
ATOM CAD  CH2E    0.04
GROU
ATOM CBD  CH2E   -0.10
ATOM CGD  C       0.30
ATOM O1D  OC     -0.50
ATOM O2D  OC     -0.50
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
DIHE NA   C4A  CHB  C1B       C4A  CHB  C1B  NB        NB   C4B  CHC  C1C
DIHE C4B  CHC  C1C  NC        NC   C4C  CHD  C1D       C4C  CHD  C1D  ND
DIHE ND   C4D  CHA  C1A       C4D  CHA  C1A  NA        C1A  C2A  CAA  CBA
DIHE C2A  CAA  CBA  CGA       CAA  CBA  CGA  O1A       C2B  C3B  CAB  CBB
DIHE C2C  C3C  CAC  CBC       C2D  C3D  CAD  CBD       C3D  CAD  CBD  CGD
DIHE CAD  CBD  CGD  O1D
IMPH FE   C1A  C4A  NA        FE   C1B  C4B  NB        FE   C1C  C4C  NC
IMPH FE   C1D  C4D  ND        CHA  NA   C2A  C1A       CHB  NA   C3A  C4A
IMPH CHB  NB   C2B  C1B       CHC  NB   C3B  C4B       CHC  NC   C2C  C1C
IMPH CHD  NC   C3C  C4C       CHD  ND   C2D  C1D       CHA  ND   C3D  C4D
IMPH C2A  C1A  C3A  CAA       C3A  C2A  C4A  CMA       C2B  C1B  C3B  CMB
IMPH C3B  C2B  C4B  CAB       C2C  C1C  C3C  CMC       C3C  C2C  C4C  CAC
IMPH C2D  C1D  C3D  CMD       C3D  C2D  C4D  CAD       CBA  O1A  O2A  CGA
IMPH CBD  O1D  O2D  CGD
ACCE NA
ACCE O1A CGA
ACCE O2A CGA
ACCE NB
ACCE NC
ACCE ND
ACCE O1D CGD
ACCE O2D CGD
PATC  FIRS NONE LAST NONE

RESI ACE     0.00000 ! Acetyl blocking group with standard naming.
GROU
ATOM CH3  CH3E    0.00
GROU
ATOM C    C       0.55
ATOM O    O      -0.55
BOND CH3  C         C    +N        C    O
DIHE CH3  C    +N   +CA
IMPH C    CH3  +N   O
ACCE O C
IC   +N   CH3  *C   O      0.0000    0.00  180.00    0.00   0.0000
IC   CH3  C    +N   +CA    0.0000    0.00  180.00    0.00   0.0000
PATC  FIRS NONE LAST NONE

!
! formamide. Charges according to Reiher (from States?)
RESI FORM    0.00000
GROU
ATOM HA   HA      0.00
GROU
ATOM C    C       0.55
ATOM O    O      -0.55
GROU
ATOM N    NH2    -0.60
ATOM H1   H       0.30
ATOM H2   H       0.30
BOND HA   C         C     N        C    O
BOND N    H2        N    H1
DIHE HA   C     N    H2
IMPH C    HA    N   O
IMPH N     C   H2   H1
ACCE O  C
DONO  H1   N
IC    N   HA   *C   O      0.0000    0.00  180.00    0.00   0.0000
IC   HA   C     N    H2    0.0000    0.00  180.00    0.00   0.0000
IC    C   H2   *N   H1     0.0000    0.00  180.00    0.00   0.0000
PATC  FIRS NONE LAST NONE

RESI AMN     0.00000
GROU
ATOM CL   CH3E    0.00
GROU
ATOM C    C       0.55
ATOM O    O      -0.55
BOND CL   C         C    +N        C    O
DIHE CL   C    +N   +CA
IMPH C    CL   +N   O
ACCE O C
IC   +N   CL   *C   O      0.0000    0.00  180.00    0.00   0.0000
IC   CL   C    +N   +CA    0.0000    0.00  180.00    0.00   0.0000
PATC  FIRS NONE LAST NONE

RESI CBX     0.00000
GROU
ATOM N    NH1    -0.35
ATOM H    H       0.25
ATOM CA   CH3E    0.10
BOND N    CA        N    H
IMPH N    -C   CA   H
DONO  H    N
IC   -C   CA   *N   H      0.0000    0.00  180.00    0.00   0.0000
PATC  FIRS NONE LAST NONE

PRES NTER    0.00000          !TL
GROU
ATOM HT1  HC      0.45
ATOM HT2  HC      0.45
ATOM N    NH3    -1.35
ATOM HT3  HC      0.45
DELETE ATOM H
ATOM CA   CH1E    0.00
BOND HT1  N         HT2  N    HT3  N
DIHE HT2  N    CA   C         HT1  N    CA   C         HT3  N    CA   C
DONO  HT1   N
DONO  HT2   N
DONO  HT3   N
IC   HT1  N    CA   C      0.0000    0.00  180.00    0.00   0.0000
IC   HT2  CA   *N   HT1    0.0000    0.00  120.00    0.00   0.0000
IC   HT3  CA   *N   HT2    0.0000    0.00  120.00    0.00   0.0000

PRES GLYP    0.00000          !TL
GROUP
ATOM HT1  HC      0.45
ATOM HT2  HC      0.45
ATOM N    NH3    -1.35
ATOM HT3  HC      0.45
DELETE ATOM H
ATOM CA   CH2E    0.00
BOND HT1  N         HT2  N    HT3  N
DIHE HT2  N    CA   C         HT1  N    CA   C         HT3  N    CA   C
DONO  HT1   N
DONO  HT2   N
DONO  HT3   N
IC   HT1  N    CA   C      0.0000    0.00  180.00    0.00   0.0000
IC   HT2  CA   *N   HT1    0.0000    0.00  120.00    0.00   0.0000
IC   HT3  CA   *N   HT2    0.0000    0.00  120.00    0.00   0.0000

PRES PROP    0.00000          !TL
GROUP
ATOM HT1  HC      0.45
ATOM HT2  HC      0.45
ATOM N    NH3    -1.40
ATOM CD   CH2E    0.25
ATOM CA   CH1E    0.25
BOND HT1  N         HT2  N
DIHE HT2  N    CA   C         HT1  N    CA   C
DONO  HT1   N
DONO  HT2   N
IC   HT1  CA   *N   CD     0.0000    0.00  120.00    0.00   0.0000
IC   HT2  CA   *N   HT1    0.0000    0.00  120.00    0.00   0.0000

PRES CTER   0.00000           !TL
GROU
ATOM C    C       1.20
ATOM OT1  OC     -0.60
ATOM OT2  OC     -0.60
DELETE ATOM O
BOND C    OT1       C    OT2
DIHE N    CA    C    OT2
IMPH C    CA    OT2  OT1
ACCE OT1 C
ACCE OT2 C
IC   N    CA    C    OT2    0.0  0.0  180.0  0.0  0.0
IC   OT2  CA    *C   OT1    0.0  0.0  180.0  0.0  0.0

PRES LINK  0.0  ! linkage for IMAGES or for joining segments
!       1 refers to previous (N terminal), 2 refers to next (C terminal)
BOND 1C   2N
THET 1C   2N   2CA            1CA  1C   2N
THET 1O   1C   2N             1C   2N   2H
DIHE 1C   2N   2CA  2C        1N   1CA  1C   2N        1CA  1C   2N   2CA
IMPH 2N   1C   2CA  2H        1C   1CA  2N   1O
IC   1N   1CA  1C   2N     0.0000    0.00  180.00    0.00   0.0000
IC   2N   1CA  *1C  1O     0.0000    0.00  180.00    0.00   0.0000
IC   1CA  1C   2N   2CA    0.0000    0.00  180.00    0.00   0.0000
IC   1C   2N   2CA  2C     0.0000    0.00  180.00    0.00   0.0000
IC   1C   2CA  *2N  2H     0.0000    0.00  180.00    0.00   0.0000

RESI O2      0.00000
GROUP
ATOM O1    OM      0.021
ATOM O2    OM     -0.021
BOND O1    O2
PATC  FIRS NONE LAST NONE

RESI CO2P    0.00000
GROUP
ATOM C    CM      0.021
ATOM O    OM     -0.021
BOND C    O
PATC  FIRS NONE LAST NONE

RESI CO      0.00000
GROUP
ATOM C    CM      0.021
ATOM O    OM     -0.021
BOND C    O
PATC  FIRS NONE LAST NONE

RESI ETH     0.00000
GROU
ATOM C2   CH3E    0.00
GROU
ATOM C1   CH2E    0.25
ATOM O    OH1    -0.65
ATOM H    H       0.40
BOND C2   C1        C1   O         O    H
DIHE C2   C1   O    H
DONO  H     O
ACCE O
IC   C2   C1   O    H      0.0000    0.00  180.00    0.00   0.0000
IC   C1   O    H    BLNK   0.0000    0.00    0.00    0.00   0.0000
PATC  FIRS NONE LAST NONE

RESI ST2     .000   ! NOW INCLUDES THE LONE PAIRS GIVING 5 ATOMS FOR ST2
GROUP
ATOM OX2  OH2     .00
ATOM HX1  H       .24
ATOM HX2  H       .24
ATOM LX1  LP     -.24
ATOM LX2  LP     -.24
BOND OX2  HX1       OX2  HX2
BOND OX2  LX1       OX2  LX2
!                          NOTE: NO DONORS OR ACCEPTORS FOR ST2
PATC  FIRS NONE LAST NONE

RESI TIP3    .000   ! TIPS3P WATER MODEL
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
ACCE OH2
PATC  FIRS NONE LAST NONE

RESI OH2    .000   ! TIPS3P WATER MODEL
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
ACCE OH2
PATC  FIRS NONE LAST NONE

RESI SO4  -2.0
GROUP
ATOM S    S     0.0
ATOM O1   OC   -0.5
ATOM O2   OC   -0.5
ATOM O3   OC   -0.5
ATOM O4   OC   -0.5
BOND S O1    S O2    S O3    S O4
ACCE O1  S
ACCE O2  S
ACCE O3  S
ACCE O4  S
PATC FIRS NONE LAST NONE

RESI COH     0.00000
GROU
ATOM C    CH3E    0.25
ATOM O    OH1    -0.65
ATOM H    H       0.40
BOND  C    O         O    H
DONO  H    O
ACCE O
IC   C    O    H    BLNK   0.0000    0.00    0.00    0.00   0.0000
PATC  FIRS NONE LAST NONE

PRES DISU 0.000  ! PATCH FOR DISULFIDES. Patch must be 1-CYS and 2-CYS.
GROUP
ATOM 1CB  CH2E  0.19
ATOM 1SG  S    -0.19
GROUP
ATOM 2SG  S    -0.19
ATOM 2CB  CH2E  0.19
BOND 1SG 2SG
ANGLE  1CB 1SG 2SG      1SG 2SG 2CB
DIHE   1CA 1CB 1SG 2SG      1CB 1SG 2SG 2CB    1SG 2SG 2CB 2CA
IC     1CA 1CB 1SG 2SG    0.0  0.0  180.0  0.0  0.0
IC     1CB 1SG 2SG 2CB    0.0  0.0  180.0  0.0  0.0
IC     1SG 2SG 2CB 2CA    0.0  0.0  180.0  0.0  0.0

PRES FHEM 0.0   ! FIX UP THE HEME BY DELETING UNWANTED ANGLES
DELETE ANGLE 2NA 2FE 2NC  2NB 2FE 2ND

PRES PHEM  0.0  ! Patch for HEME. Patch residues must be 1-HIS, and 2-HEME.
BOND 1NE2 2FE
ANGL 1CD2  1NE2  2FE    1CE1  1NE2  2FE    1NE2  2FE  2NA    1NE2  2FE  2NB
ANGL 1NE2  2FE   2NC    1NE2  2FE   2ND
DELETE ANGLE 2NA 2FE 2NC  2NB 2FE 2ND
DIHE 1CD2  1NE2  2FE  2NA

PRES PLO2 0.0 ! 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
!ANGL 1O1  2FE  3NE2
ANGL 1O2  1O1  2FE    1O1  2FE  2NA    1O1  2FE  2NB
ANGL 1O1  2FE  2NC     1O1  2FE 2ND
DIHE 1O2  1O1  2FE  2NA

PRES PLIG 0.0 ! Patch residue for Heme ligand. Residues must be,
!                           1-CO , 2-HEME , and 3-HIS
BOND 1C  2FE
!ANGL 1C  2FE  3NE2
ANGL 1O  1C  2FE    1C  2FE  2NA    1C  2FE  2NB
ANGL 1C  2FE  2NC     1C  2FE 2ND
DIHE 1O  1C  2FE  2NA

PRES LTOD 0.0
DELE IMPR 1CA 1N 1C 1CB
IMPR 1CA 1C 1N 1CB

PRES HS2          0.00 ! Patch for neutral His, move proton from ND1 to NE2
!
!
!          ND1--CE1
!         /      |
!  -CB--CG       |
!         \      |
!          CD2--NE2
!                 \
!                 HE2
GROUP
ATOM CG   C       0.10
ATOM ND1  NR     -0.40
ATOM CE1  CR1E    0.30
GROU
ATOM CD2  CR1E    0.10
ATOM NE2  NH1    -0.40
ATOM HE2  H       0.30
DELETE ATOM HD1
DELETE ACCE NE2
BOND NE2 HE2
ANGLE  CE1 NE2 HE2 CD2 NE2 HE2
IMPR NE2 CE1 CD2 HE2
DONOR HE2 NE2
ACCEPTOR ND1
IC CE1  CD2  *NE2 HE2   0.0000  0.0000  180.0000  0.0000  0.0000


END
