* Topology and Parameter Stream File for heme and related
* ligands and patches.
*

!updated 2016/2, allow for use of AUTOGENERATE ANGLE DIHEDRAl PATCH

!Parent files that have to be read prior to streaming this file
!top_all36_prot.rtf
!par_all36_prot.prm

!Testcase
!test_all36_prot_heme.inp

read rtf card append
* Topology for heme and related compounds and patches
*
31  1

MASS  -1  CPA       12.01100 C ! heme alpha-C
MASS  -1  CPB       12.01100 C ! heme beta-C
MASS  -1  CPM       12.01100 C ! heme meso-C
MASS  -1  CM        12.01100 C ! heme CO carbon
MASS  -1  CST       12.01100 C ! CO2 carbon 
MASS  -1  NPH       14.00700 N ! heme pyrrole N
MASS  -1  OM        15.99900 O ! heme CO/O2 oxygen
MASS  -1  OST       15.99900 O ! CO2 oxygen
MASS  -1  FE        55.84700 Fe ! heme iron 56

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 HA3     0.09
ATOM HMA2 HA3     0.09
ATOM HMA3 HA3     0.09
GROUP   
ATOM CAA  CT2    -0.18
ATOM HAA1 HA2     0.09
ATOM HAA2 HA2     0.09
GROUP   
ATOM CBA  CT2    -0.28
ATOM HBA1 HA2     0.09
ATOM HBA2 HA2     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 HA3     0.09
ATOM HMB2 HA3     0.09
ATOM HMB3 HA3     0.09
GROUP   
ATOM CAB  CE1    -0.15 !vinyl parameters updated, adm jr., May 2002
ATOM HAB  HE1     0.15
GROUP
ATOM CBB  CE2    -0.42
ATOM HBB1 HE2     0.21
ATOM HBB2 HE2     0.21
GROUP   
ATOM CMC  CT3    -0.27
ATOM HMC1 HA3     0.09
ATOM HMC2 HA3     0.09
ATOM HMC3 HA3     0.09
GROUP   
ATOM CAC  CE1    -0.15
ATOM HAC  HE1     0.15
GROUP
ATOM CBC  CE2    -0.42
ATOM HBC1 HE2     0.21
ATOM HBC2 HE2     0.21
GROUP   
ATOM CMD  CT3    -0.27
ATOM HMD1 HA3     0.09
ATOM HMD2 HA3     0.09
ATOM HMD3 HA3     0.09
GROUP   
ATOM CAD  CT2    -0.18
ATOM HAD1 HA2     0.09
ATOM HAD2 HA2     0.09
GROUP   
ATOM CBD  CT2    -0.28
ATOM HBD1 HA2     0.09
ATOM HBD2 HA2     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   
!No vinyl impropers in update
!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   

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   

RESI CO2             0.00 ! Carbon Dioxide, John Straub
GROUP                     ! requires AUTOgenerate ANGLes
ATOM C      CST      0.596
ATOM OC1    OST     -0.298
ATOM OC2    OST     -0.298
BOND OC1 C   OC2 C
!ANGLE OC1 C OC2
PATCHING FIRS NONE LAST NONE

PRES FHEM         0.00 ! FIX UP THE HEME BY DELETING UNWANTED AUTOGENERATED ANGLES
                       ! unliganded heme patch
                       ! do NOT use AUTOgenerate ANGLes DIHEdrals after this 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.
                       ! do NOT use AUTOgenerate ANGLes DIHEdrals after this patch
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   
DIHE 1CD2  1NE2  2FE  2NA
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 PLOH         0.00 ! Patch residue for Heme ligand.  Residues must be
                       ! 1-Tyr , 2-HEME , and 3-HIS
                       ! OH of the Tyr is bonded to the iron.
                       ! do NOT use AUTOgenerate ANGLes DIHEdrals after this patch
BOND 1OH 2FE        
ANGLE 1HH 1OH 2FE
ANGLE 1OH 2FE 2NA  1OH 2FE 2NB !1CZ 1OH 2FE  
ANGLE 1OH 2FE 2NC  1OH 2FE 2ND 
!DIHE 1CZ 1OH 2FE 2NA   
IC 1CZ  1OH  2FE  2NA   0.0000  0.0000    0.0000  0.0000  0.0000
IC 1CZ  1OH  2FE  3NE2  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.
                       ! do NOT use AUTOgenerate ANGLes DIHEdrals after this patch
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
                       ! do NOT use AUTOgenerate ANGLes DIHEdrals after this patch
BOND 1C 2FE          
ANGLE 1C 2FE 3NE2    
ANGLE 1O 1C  2FE  
ANGLE 1C 2FE 2NA  1C 2FE 2NB   
ANGLE 1C 2FE 2NC  1C 2FE 2ND   
DIHE 1O  1C  2FE  2NA
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

!added from top_all22_model_b5i.inp for heme-S-CH3 patch
RESI MES2       -1.00 ! methylthiolate, adm jr., was MES1
GROUP
ATOM S    SS    -0.80 !  H11
ATOM C1   CS    -0.47 !     \
ATOM H11  HA     0.09 ! H12--C1--S (-)
ATOM H12  HA     0.09 !     /
ATOM H13  HA     0.09 !  H13
                      !
BOND  S  C1  C1 H11 C1 H12 C1 H13
IC BLNK H11  C1   S     0.0000  0.0000  60.0000  0.0000  0.0000
IC S    H11 *C1   H12   0.0000  0.0000 120.0000  0.0000  0.0000
IC S    H11 *C1   H13   0.0000  0.0000 -120.0000  0.0000  0.0000
IC H12  H13 *C1   H11   0.0000  0.0000  120.0000  0.0000  0.0000
patch first none last none

PRES PSUL         0.00 ! Patch for HEME to thiolate (MES1) link
                       ! Patch residues must be 1-MES1, and 2-HEME.
                       ! do NOT use AUTOgenerate ANGLes DIHEdrals after this patch
DELETE ANGLE 2NA 2FE 2NC  2NB 2FE 2ND
BOND 1S 2FE
ANGLE 1C1 1S  2FE  1C1 1S  2FE  
ANGLE 1S  2FE 2NA  1S  2FE 2NB 1S  2FE  2NC  1S  2FE  2ND
IC 1C1 1S  2FE  2NA   0.0000  0.0000    0.0000  0.0000  0.0000
IC 1C1 1S  2FE  2NB   0.0000  0.0000    0.0000  0.0000  0.0000
IC 1C1 1S  2FE  2NB   0.0000  0.0000    0.0000  0.0000  0.0000
IC 1C1 1S  2FE  2NB   0.0000  0.0000    0.0000  0.0000  0.0000

end

read para card flex append
* additional parameters for heme
*

ATOMS
MASS  -1  CPA       12.01100 ! heme alpha-C
MASS  -1  CPB       12.01100 ! heme beta-C
MASS  -1  CPM       12.01100 ! heme meso-C
MASS  -1  CM        12.01100 ! heme CO carbon
MASS  -1  CST       12.01100 ! CO2 carbon 
MASS  -1  NPH       14.00700 ! heme pyrrole N
MASS  -1  OM        15.99900 ! heme CO/O2 oxygen
MASS  -1  OST       15.99900 ! CO2 oxygen
MASS  -1  FE        55.84700 ! heme iron 56

BONDS
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!
!atom type Kb          b0
!
C    C     600.000     1.3350 ! ALLOW ARO HEM???
                ! Heme vinyl substituent (KK, from propene (JCS))
!HA   C     330.000     1.1000 ! ALLOW ARO HEM???
                ! Heme vinyl substituent (KK, from propene (JCS))
!Carbon Dioxide
CST  OST   937.96      1.1600 ! JES
!Heme to Sulfate (PSUL) link
SS   FE    250.0       2.3200 !force constant a guess
           !equilbrium bond length optimized to reproduce 
           !CSD survey values of
           !2.341pm0.01 (mean, standard error)
           !adm jr., 7/01
CPB  CE1   450.000     1.3800 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
CPB  CPA   299.800     1.4432 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPB  CPB   340.700     1.3464 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPM  CPA   360.000     1.3716 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CT2  CPB   230.000     1.4900 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
CT3  CPB   230.000     1.4900 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
FE   CM    258.000     1.9000 ! ALLOW HEM
                ! Heme (6-liganded): CO ligand (KK 05/13/91)
FE   CPM     0.000     3.3814 ! ALLOW HEM
                ! Heme (6-liganded): for "ic para" only (KK 05/13/91)
HA   CPM   367.600     1.0900 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NPH  CPA   377.200     1.3757 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NPH  FE    270.200     1.9580 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NR2  FE     65.000     2.2000 ! ALLOW HEM
                ! Heme (6-liganded): His ligand (KK 05/13/91)
OM   CM   1115.000     1.1280 ! ALLOW HEM
                ! Heme (6-liganded): CO ligand (KK 05/13/91)
OM   FE    250.000     1.8000 ! ALLOW HEM
                ! Heme (6-liganded): O2 ligand (KK 05/13/91)
OM   OM    600.000     1.2300 ! ALLOW HEM
                ! Heme (6-liganded): O2 ligand (KK 05/13/91)
OH1  FE    250.000     2.0000 ! patch PLOH

ANGLES
!
!V(angle) = Ktheta(Theta - Theta0)**2
!
!V(Urey-Bradley) = Kub(S - S0)**2
!
!Ktheta: kcal/mole/rad**2
!Theta0: degrees
!Kub: kcal/mole/A**2 (Urey-Bradley)
!S0: A
!
!atom types     Ktheta    Theta0   Kub     S0
!
!HA   C    C      50.000   120.5000 ! ALLOW   PEP POL ARO???
                ! Heme vinyl substituent (KK from propene (JCS))
!HA   C    HA     50.000   118.0000 ! ALLOW   PEP POL ARO???
                ! Heme vinyl substituent (KK from propene (JCS))
!Carbon Dioxide, JES
OST  CST  OST    3000.00  180.0000 ! CO2, JES
!Heme to Sulfate (PSUL) link
CS   SS   FE    50.0      100.6    !force constant a guess
                !equilibrium angle optimized to reproduce
                !CSD survey values
                !107.5pm0.6 (mean, standard error)
                !adm jr., 7/01
SS   FE   NPH   100.0       90.0    !force constant a guess
                !adm jr., 7/01
CPA  CPB  CE1    70.000   126.7400 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
CPA  CPM  CPA    94.200   125.1200 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPA  NPH  CPA   139.300   103.9000 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPB  CE1  CE2    70.000   121.5000 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
CPB  CPB  CE1    70.000   126.7500 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
CPB  CPB  CPA    30.800   106.5100 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPM  CPA  CPB    61.600   124.0700 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CT2  CPB  CPA    65.000   126.7400 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
CT2  CPB  CPB    65.000   126.7500 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
CT2  CT2  CPB    70.000   113.0000 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
CT3  CPB  CPA    65.000   126.7400 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
CT3  CPB  CPB    65.000   126.7500 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
FE   NPH  CPA    96.150   128.0500 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
FE   NR2  CPH1   30.000   133.0000 ! ALLOW HEM
                ! Heme (6-liganded): ligand links (KK 05/13/91)
FE   NR2  CPH2   30.000   123.0000 ! ALLOW HEM
                ! Heme (6-liganded): ligand links (KK 05/13/91)
!HA   C    CPB    50.000   120.0000 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
HA   CPM  CPA    12.700   117.4400 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
HA   CPM  FE      0.000   180.0000 ! ALLOW HEM
                ! Heme (6-liganded): for "ic para" only (KK 05/13/91)
HA2  CT2  CPB    50.000   109.5000 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
HA3  CT3  CPB    50.000   109.5000 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
HE1  CE1  CPB    50.000   120.0000 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
NPH  CPA  CPB   122.000   111.5400 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NPH  CPA  CPM    88.000   124.3900 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NPH  FE   CM     50.000    90.0000 ! ALLOW HEM
                ! Heme (6-liganded): ligand links (KK 05/13/91)
NPH  FE   CPM     0.000    45.0000 ! ALLOW HEM
                ! Heme (6-liganded): for "ic para" only  (KK 05/13/91)
NPH  FE   NPH    14.390    90.0000 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NR2  FE   CM     50.000   180.0000 ! ALLOW HEM
                ! Heme (6-liganded): ligand links (KK 05/13/91)
NR2  FE   NPH    50.000    90.0000 ! ALLOW HEM
                ! Heme (6-liganded): ligand links (KK 05/13/91)
OM   CM   FE     35.000   180.0000 ! ALLOW HEM
                ! Heme (6-liganded): ligand links (KK 05/13/91)
OM   FE   NPH     5.000    90.0000 ! ALLOW HEM
                ! Heme (6-liganded): ligand links (KK 05/13/91)
OM   OM   FE      0.000   180.0000 ! ALLOW HEM
                ! Heme (6-liganded): ligand links (KK 05/13/91)
H    OH1  FE     65.000   108.0000 ! patch PLOH
OH1  FE   NPH     5.000    90.0000 ! patch PLOH

DIHEDRALS
!
!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
!
!Kchi: kcal/mole
!n: multiplicity
!delta: degrees
!
!atom types             Kchi    n   delta
!
!HA   C    C    HA     20.0000         0      0.0000 ! ALLOW   PEP POL ARO???
                ! Heme vinyl substituent (KK, from propene (JCS))
!HA   HA   C    C      20.0000         0    180.0000 ! ALLOW   PEP POL ARO???
                ! Heme vinyl substituent (KK, from propene (JCS))
HE2  CE2  CE1  CPB      5.2000  2   180.00 !
                ! for vinyl, from butene, yin/adm jr., 12/95
!Heme to Sulfate (PSUL) link
X    FE   SS   X        0.0000  4     0.00 ! guess
                !adm jr., 7/01
!X    CS   SS   X        0.0000  3     0.20 ! guess
                !from methanethiol, HS S CT3 HA
                !adm jr., 7/01
!X    C    C    X        4.0000  2   180.00 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
X    CPA  CPB  X        0.0000  2     0.00 ! ALLOW HEM
                ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91)
X    CPA  CPM  X        0.0000  2     0.00 ! ALLOW HEM
                ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91)
X    CPB  CE1  X        3.0000  2   180.00 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
X    CPB  CPB  X        0.0000  2     0.00 ! ALLOW HEM
                ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91)
X    CPB  CT2  X        0.0000  6     0.00 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
X    CPB  CT3  X        0.0000  6     0.00 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
X    FE   CM   X        0.0500  4     0.00 ! ALLOW HEM
                ! Heme (6-liganded): ligands (KK 05/13/91)
X    FE   NPH  X        0.0000  2     0.00 ! ALLOW HEM
                ! Heme (6-liganded): for "ic para" only (KK 05/13/91)
X    FE   NR2  X        0.0500  4     0.00 ! ALLOW HEM
                ! Heme (6-liganded): from param19.inp
X    FE   OM   X        0.0000  4     0.00 ! ALLOW HEM
                ! Heme (6-liganded): ligands (KK 05/13/91)
X    NPH  CPA  X        0.0000  2     0.00 ! ALLOW HEM
                ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91)

IMPROPER
!
!V(improper) = Kpsi(psi - psi0)**2
!
!Kpsi: kcal/mole/rad**2
!psi0: degrees
!note that the second column of numbers (0) is ignored
!
!atom types           Kpsi                   psi0
!
CPB  CPA  NPH  CPA    20.8000         0      0.0000 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPB  X    X    CE1    90.0000         0      0.0000 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
CT2  X    X    CPB    90.0000         0      0.0000 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
CT3  X    X    CPB    90.0000         0      0.0000 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
HA   CPA  CPA  CPM    29.4000         0      0.0000 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
!HA   CPB  C    C      20.0000         0      0.0000 ! ALLOW HEM ARO
                ! Heme (6-liganded): substituents (KK 05/13/91)
NPH  CPA  CPA  FE    137.4000         0      0.0000 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NPH  CPA  CPB  CPB    40.6000         0      0.0000 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NPH  CPA  CPM  CPA    18.3000         0      0.0000 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NPH  CPM  CPB  CPA    32.7000         0      0.0000 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)

NONBONDED nbxmod  5 atom cdiel fshift vatom vdistance vfswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
                !adm jr., 5/08/91, suggested cutoff scheme
!
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
!
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
!
!atom  ignored    epsilon      Rmin/2   ignored   eps,1-4       Rmin/2,1-4
!
CPA    0.000000  -0.090000     1.800000 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPB    0.000000  -0.090000     1.800000 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPM    0.000000  -0.090000     1.800000 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CM     0.000000  -0.110000     2.100000 ! ALLOW HEM
                ! Heme (6-liganded): CO ligand carbon (KK 05/13/91)
CST    0.000000  -0.058000     1.563000 ! 
                ! carbon dioxide, JES
NPH    0.000000  -0.200000     1.850000 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
OM     0.000000  -0.120000     1.700000 ! ALLOW HEM
                ! Heme (6-liganded): CO ligand oxygen (KK 05/13/91)
OST    0.000000  -0.165000     1.692000 ! 
                ! carbon dioxide, JES
FE     0.010000   0.000000     0.650000 ! ALLOW HEM
                ! Heme (6-liganded): Iron atom (KK 05/13/91)

end

return
