remark file topallhdg.hemes ! ! from http://www.postgenomicnmr.net/SW/PARArestraints.html ! set message off echo off end autogenerate angles=true dihedrals=false end mass CPA 12.011 mass CPB 12.011 mass CPM 12.011 mass CYC 12.011 mass NPH 14.007 mass CYN 14.007 mass FE 55.847 residue HEB ! Heme b group atom FE type=FE charge= 0.24 end atom NA type=NPH charge=-0.18 end atom NB type=NPH charge=-0.18 end atom NC type=NPH charge=-0.18 end atom ND type=NPH charge=-0.18 end group atom C1A type=CPA charge= 0.12 end atom CHA type=CPM charge=-0.10 end atom HA type=HA charge= 0.10 end atom C4D type=CPA charge= 0.12 end group atom C1B type=CPA charge= 0.12 end atom CHB type=CPM charge=-0.10 end atom HB type=HA charge= 0.10 end atom C4A type=CPA charge= 0.12 end group atom C1C type=CPA charge= 0.12 end atom CHC type=CPM charge=-0.10 end atom HC type=HA charge= 0.10 end atom C4B type=CPA charge= 0.12 end group atom C1D type=CPA charge= 0.12 end atom CHD type=CPM charge=-0.10 end atom HD type=HA charge= 0.10 end atom C4C type=CPA charge= 0.12 end group atom C2A type=CPB charge=-0.06 end atom CAA type=CT charge=-0.18 end atom HAA1 type=HA charge= 0.09 end atom HAA2 type=HA charge= 0.09 end group atom CBA type=CT charge=-0.28 end atom HBA1 type=HA charge= 0.09 end atom HBA2 type=HA charge= 0.09 end atom CGA type=C charge= 0.62 end atom O1A type=OC charge=-0.76 end atom O2A type=OC charge=-0.76 end group atom C3A type=CPB charge=-0.06 end atom CMA type=CT charge=-0.27 end atom HMA1 type=HA charge= 0.09 end atom HMA2 type=HA charge= 0.09 end atom HMA3 type=HA charge= 0.09 end group atom C2B type=CPB charge=-0.06 end atom CMB type=CT charge=-0.27 end atom HMB1 type=HA charge= 0.09 end atom HMB2 type=HA charge= 0.09 end atom HMB3 type=HA charge= 0.09 end group atom C3B type=CPB charge=-0.06 end atom CAB type=C charge=-0.20 end atom HAB type=HA charge= 0.20 end atom CBB type=C charge=-0.20 end atom HBB1 type=HA charge= 0.10 end atom HBB2 type=HA charge= 0.10 end group atom C2C type=CPB charge=-0.06 end atom CMC type=CT charge=-0.27 end atom HMC1 type=HA charge= 0.09 end atom HMC2 type=HA charge= 0.09 end atom HMC3 type=HA charge= 0.09 end group atom C3C type=CPB charge=-0.06 end atom CAC type=C charge=-0.20 end atom HAC type=HA charge= 0.20 end atom CBC type=C charge=-0.20 end atom HBC1 type=HA charge= 0.10 end atom HBC2 type=HA charge= 0.10 end group atom C2D type=CPB charge=-0.06 end atom CMD type=CT charge=-0.27 end atom HMD1 type=HA charge= 0.09 end atom HMD2 type=HA charge= 0.09 end atom HMD3 type=HA charge= 0.09 end group atom C3D type=CPB charge=-0.06 end atom CAD type=CT charge=-0.18 end atom HAD1 type=HA charge= 0.09 end atom HAD2 type=HA charge= 0.09 end group atom CBD type=CT charge=-0.28 end atom HBD1 type=HA charge= 0.09 end atom HBD2 type=HA charge= 0.09 end atom CGD type=C charge= 0.62 end atom O1D type=OC charge=-0.76 end atom O2D type=OC charge=-0.76 end bond FE NA bond FE NB bond FE NC bond FE ND bond NA C1A bond C1A C2A bond C2A C3A bond C3A C4A bond NA C4A bond C2A CAA bond CAA CBA bond CBA CGA bond CGA O1A bond CGA O2A bond C3A CMA bond CHB C4A bond CHB C1B bond NB C1B bond C1B C2B bond C2B C3B bond C3B C4B bond NB C4B bond C2B CMB bond C3B CAB bond CAB CBB bond CHC C4B bond CHC C1C bond NC C1C bond C1C C2C bond C2C C3C bond C3C C4C bond NC C4C bond C2C CMC bond C3C CAC bond CAC CBC bond CHD C4C bond CHD C1D bond ND C1D bond C1D C2D bond C2D C3D bond C3D C4D bond ND C4D bond C2D CMD bond C3D CAD bond CAD CBD bond CBD CGD bond CGD O1D bond CGD O2D bond CHA C4D bond CHA C1A bond CHA HA bond CHB HB bond CHC HC bond CHD HD bond CAA HAA1 bond CAA HAA2 bond CBA HBA1 bond CBA HBA2 bond CMA HMA1 bond CMA HMA2 bond CMA HMA3 bond CMB HMB1 bond CMB HMB2 bond CMB HMB3 bond CAB HAB bond CBB HBB1 bond CBB HBB2 bond CMC HMC1 bond CMC HMC2 bond CMC HMC3 bond CAC HAC bond CBC HBC1 bond CBC HBC2 bond CMD HMD1 bond CMD HMD2 bond CMD HMD3 bond CAD HAD1 bond CAD HAD2 bond CBD HBD1 bond CBD HBD2 omit angle NA FE NC omit angle NB FE ND improper C2A C1A C3A CAA improper C3A C2A C4A CMA improper C2B C1B C3B CMB improper C3B C2B C4B CAB improper C2C C1C C3C CMC improper C3C C2C C4C CAC improper C2D C1D C3D CMD improper C3D C2D C4D CAD improper CGA CBA O2A O1A improper CGD CBD O2D O1D improper C4A NA C1A C2A improper C1A NA C4A C3A improper C4B NB C1B C2B improper C1B NB C4B C3B improper C4C NC C1C C2C improper C1C NC C4C C3C improper C4D ND C1D C2D improper C1D ND C4D C3D improper NA C1A C2A C3A improper NA C4A C3A C2A improper NB C1B C2B C3B improper NB C4B C3B C2B improper NC C1C C2C C3C improper NC C4C C3C C2C improper ND C1D C2D C3D improper ND C4D C3D C2D improper NA C1A CHA C4D improper NA C4A CHB C1B improper NB C1B CHB C4A improper NB C4B CHC C1C improper NC C1C CHC C4B improper NC C4C CHD C1D improper ND C1D CHD C4C improper ND C4D CHA C1A improper CHA C1A C4D HA improper CHB C1B C4A HB improper CHC C1C C4B HC improper CHD C1D C4C HD improper C1A C2A CHA NA improper C4A C3A CHB NA improper C1B C2B CHB NB improper C4B C3B CHC NB improper C1C C2C CHC NC improper C4C C3C CHD NC improper C1D C2D CHD ND improper C4D C3D CHA ND improper NA C1A C4A FE improper NB C1B C4B FE improper NC C1C C4C FE improper ND C1D C4D FE improper CAB CBB C3B HAB improper HAB CAB CBB HBB2 improper CBB CAB HBB2 HBB1 improper CAC CBC C3C HAC improper HAC CAC CBC HBC2 improper CBC CAC HBC2 HBC1 dihedral C1A C2A CAA CBA dihedral C2A CAA CBA CGA dihedral CAA CBA CGA O1A dihedral C2D C3D CAD CBD dihedral C3D CAD CBD CGD dihedral CAD CBD CGD O1D dihedral C2B C3B CAB CBB dihedral C2C C3C CAC CBC dihedral C2A C3A CMA HMA1 dihedral C1B C2B CMB HMB1 dihedral C1C C2C CMC HMC1 dihedral C1D C2D CMD HMD1 ic FE NA C1A C2A 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 1 ic FE NA C4A C3A 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 1 ic C3A C4A NA C1A 0.0 0.0 0.0 0.0 0.0 ! 5-member ring 1 ic CHA C1A C2A CAA 0.0 0.0 0.0 0.0 0.0 ! 5-member ring 1 ic FE NB C1B C2B 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 2 ic FE NB C4B C3B 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 2 ic C2B C1B NB C4B 0.0 0.0 0.0 0.0 0.0 ! 5-member ring 2 ic CHB C1B C2B CMB 0.0 0.0 0.0 0.0 0.0 ! 5-member ring 2 ic FE NC C1C C2C 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 3 ic FE NC C4C C3C 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 3 ic C2C C1C NC C4C 0.0 0.0 0.0 0.0 0.0 ! 5-member ring 3 ic CHC C1C C2C CMC 0.0 0.0 0.0 0.0 0.0 ! 5-member ring 3 ic FE ND C1D C2D 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 4 ic FE ND C4D C3D 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 4 ic C2D C1D ND C4D 0.0 0.0 0.0 0.0 0.0 ! 5-member ring 4 ic CHD C1D C2D CMD 0.0 0.0 0.0 0.0 0.0 ! 5-member ring 4 ic C4A NA FE NB 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 1 ic NA FE NB C1B 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 1 ic FE NA C4A CHB 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 1 ic NA C4A CHB C1B 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 1 ic C4A CHB C1B NB 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 1 ic C4B NB FE NC 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 2 ic NB FE NC C1C 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 2 ic FE NB C4B CHC 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 2 ic NB C4B CHC C1C 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 2 ic C4B CHC C1C NC 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 2 ic C4C NC FE ND 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 3 ic NC FE ND C1D 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 3 ic FE NC C4C CHD 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 3 ic NC C4C CHD C1D 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 3 ic C4C CHD C1D ND 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 3 ic C4A NA FE CHB 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 4 ic NA FE CHB HB 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 4 ic FE ND C4D CHA 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 4 ic ND C4D CHA C1A 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 4 ic C4D CHA C1A NA 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 4 ic C4A C2A *C3A CMA 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 1 chiralities ic C3A C1A *C2A CAA 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 1 chiralities ic C3B C1B *C2B CMB 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 2 chiralities ic C4B C2B *C3B CAB 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 2 chiralities ic C3C C1C *C2C CMC 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 3 chiralities ic C4C C2C *C3C CAC 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 3 chiralities ic C3D C1D *C2D CMD 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 4 chiralities ic C4D C2D *C3D CAD 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 4 chiralities ic CHB NB *C1B C2B 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 1 chiralities ic CHB NA *C4A C3A 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 1 chiralities ic FE C1B *NB C4B 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 1 chiralities ic C4A C1B *CHB HB 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 1 chiralities ic CHC NC *C1C C2C 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 2 chiralities ic CHC NB *C4B C3B 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 2 chiralities ic FE C1C *NC C4C 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 2 chiralities ic C4B C1C *CHC HC 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 2 chiralities ic CHD ND *C1D C2D 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 3 chiralities ic CHD NC *C4C C3C 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 3 chiralities ic FE C1D *ND C4D 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 3 chiralities ic C4C C1D *CHD HD 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 3 chiralities ic CHA NA *C1A C2A 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 4 chiralities ic CHA ND *C4D C3D 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 4 chiralities ic FE C1A *NA C4A 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 4 chiralities ic C4D C1A *CHA HA 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 4 chiralities ic C1A C2A CAA CBA 0.0 0.0 120.0 0.0 0.0 ! Glutamate 1 ic C2A CAA CBA CGA 0.0 0.0 180.0 0.0 0.0 ! Glutamate 1 ic CAA CBA CGA O1A 0.0 0.0 0.0 0.0 0.0 ! Glutamate 1 ic CAA CBA CGA O2A 0.0 0.0 180.0 0.0 0.0 ! Glutamate 1 ic CBA O1A *CGA O2A 0.0 0.0 180.0 0.0 0.0 ! Glutamate 1 chiralities ic C2D C3D CAD CBD 0.0 0.0 -120.0 0.0 0.0 ! Glutamate 2 ic C3D CAD CBD CGD 0.0 0.0 180.0 0.0 0.0 ! Glutamate 2 ic CAD CBD CGD O1D 0.0 0.0 0.0 0.0 0.0 ! Glutamate 2 ic CAD CBD CGD O2D 0.0 0.0 180.0 0.0 0.0 ! Glutamate 2 ic CBD O1D *CGD O2D 0.0 0.0 180.0 0.0 0.0 ! Glutamate 2 chiralities ic C2B C3B CAB CBB 0.0 0.0 -45.0 0.0 0.0 ! Prevents vinyl collision ic C2C C3C CAC CBC 0.0 0.0 -45.0 0.0 0.0 ! Prevents vinyl collision ic NA ND *FE NB 0.0 0.0 180.0 0.0 0.0 ! Iron site ic NB NA *FE NC 0.0 0.0 180.0 0.0 0.0 ! Iron site ic NC NB *FE ND 0.0 0.0 180.0 0.0 0.0 ! Iron site ic ND NC *FE NA 0.0 0.0 180.0 0.0 0.0 ! Iron site end residue HEC ! Heme c group atom FE type=FE charge= 0.24 end atom NA type=NPH charge=-0.18 end atom NB type=NPH charge=-0.18 end atom NC type=NPH charge=-0.18 end atom ND type=NPH charge=-0.18 end group atom C1A type=CPA charge= 0.12 end atom CHA type=CPM charge=-0.10 end atom HA type=HA charge= 0.10 end atom C4D type=CPA charge= 0.12 end group atom C1B type=CPA charge= 0.12 end atom CHB type=CPM charge=-0.10 end atom HB type=HA charge= 0.10 end atom C4A type=CPA charge= 0.12 end group atom C1C type=CPA charge= 0.12 end atom CHC type=CPM charge=-0.10 end atom HC type=HA charge= 0.10 end atom C4B type=CPA charge= 0.12 end group atom C1D type=CPA charge= 0.12 end atom CHD type=CPM charge=-0.10 end atom HD type=HA charge= 0.10 end atom C4C type=CPA charge= 0.12 end group atom C2A type=CPB charge=-0.06 end atom CAA type=CT charge=-0.18 end atom HAA1 type=HA charge= 0.09 end atom HAA2 type=HA charge= 0.09 end group atom CBA type=CT charge=-0.28 end atom HBA1 type=HA charge= 0.09 end atom HBA2 type=HA charge= 0.09 end atom CGA type=C charge= 0.62 end atom O1A type=OC charge=-0.76 end atom O2A type=OC charge=-0.76 end group atom C3A type=CPB charge=-0.06 end atom CMA type=CT charge=-0.27 end atom HMA1 type=HA charge= 0.09 end atom HMA2 type=HA charge= 0.09 end atom HMA3 type=HA charge= 0.09 end group atom C2B type=CPB charge=-0.06 end atom CMB type=CT charge=-0.27 end atom HMB1 type=HA charge= 0.09 end atom HMB2 type=HA charge= 0.09 end atom HMB3 type=HA charge= 0.09 end group atom C3B type=CPB charge=-0.06 end atom CAB type=CT charge=-0.20 end atom HAB type=HA charge= 0.20 end group atom CBB type=CT charge=-0.27 end atom HBB1 type=HA charge= 0.09 end atom HBB2 type=HA charge= 0.09 end atom HBB3 type=HA charge= 0.09 end group atom C2C type=CPB charge=-0.06 end atom CMC type=CT charge=-0.27 end atom HMC1 type=HA charge= 0.09 end atom HMC2 type=HA charge= 0.09 end atom HMC3 type=HA charge= 0.09 end group atom C3C type=CPB charge=-0.06 end atom CAC type=CT charge=-0.20 end atom HAC type=HA charge= 0.20 end group atom CBC type=CT charge=-0.27 end atom HBC1 type=HA charge= 0.09 end atom HBC2 type=HA charge= 0.09 end atom HBC3 type=HA charge= 0.09 end group atom C2D type=CPB charge=-0.06 end atom CMD type=CT charge=-0.27 end atom HMD1 type=HA charge= 0.09 end atom HMD2 type=HA charge= 0.09 end atom HMD3 type=HA charge= 0.09 end group atom C3D type=CPB charge=-0.06 end atom CAD type=CT charge=-0.18 end atom HAD1 type=HA charge= 0.09 end atom HAD2 type=HA charge= 0.09 end group atom CBD type=CT charge=-0.28 end atom HBD1 type=HA charge= 0.09 end atom HBD2 type=HA charge= 0.09 end atom CGD type=C charge= 0.62 end atom O1D type=OC charge=-0.76 end atom O2D type=OC charge=-0.76 end bond FE NA bond FE NB bond FE NC bond FE ND bond NA C1A bond C1A C2A bond C2A C3A bond C3A C4A bond NA C4A bond C2A CAA bond CAA CBA bond CBA CGA bond CGA O1A bond CGA O2A bond C3A CMA bond CHB C4A bond CHB C1B bond NB C1B bond C1B C2B bond C2B C3B bond C3B C4B bond NB C4B bond C2B CMB bond C3B CAB bond CAB CBB bond CHC C4B bond CHC C1C bond NC C1C bond C1C C2C bond C2C C3C bond C3C C4C bond NC C4C bond C2C CMC bond C3C CAC bond CAC CBC bond CHD C4C bond CHD C1D bond ND C1D bond C1D C2D bond C2D C3D bond C3D C4D bond ND C4D bond C2D CMD bond C3D CAD bond CAD CBD bond CBD CGD bond CGD O1D bond CGD O2D bond CHA C4D bond CHA C1A bond CHA HA bond CHB HB bond CHC HC bond CHD HD bond CAA HAA1 bond CAA HAA2 bond CBA HBA1 bond CBA HBA2 bond CMA HMA1 bond CMA HMA2 bond CMA HMA3 bond CMB HMB1 bond CMB HMB2 bond CMB HMB3 bond CAB HAB bond CBB HBB1 bond CBB HBB2 bond CBB HBB3 bond CMC HMC1 bond CMC HMC2 bond CMC HMC3 bond CAC HAC bond CBC HBC1 bond CBC HBC2 bond CBC HBC3 bond CMD HMD1 bond CMD HMD2 bond CMD HMD3 bond CAD HAD1 bond CAD HAD2 bond CBD HBD1 bond CBD HBD2 omit angle NA FE NC omit angle NB FE ND improper C2A C1A C3A CAA improper C3A C2A C4A CMA improper C2B C1B C3B CMB improper C3B C2B C4B CAB improper C2C C1C C3C CMC improper C3C C2C C4C CAC improper C2D C1D C3D CMD improper C3D C2D C4D CAD improper CGA CBA O2A O1A improper CGD CBD O2D O1D improper C4A NA C1A C2A improper C1A NA C4A C3A improper C4B NB C1B C2B improper C1B NB C4B C3B improper C4C NC C1C C2C improper C1C NC C4C C3C improper C4D ND C1D C2D improper C1D ND C4D C3D improper NA C1A C2A C3A improper NA C4A C3A C2A improper NB C1B C2B C3B improper NB C4B C3B C2B improper NC C1C C2C C3C improper NC C4C C3C C2C improper ND C1D C2D C3D improper ND C4D C3D C2D improper NA C1A CHA C4D improper NA C4A CHB C1B improper NB C1B CHB C4A improper NB C4B CHC C1C improper NC C1C CHC C4B improper NC C4C CHD C1D improper ND C1D CHD C4C improper ND C4D CHA C1A improper CHA C1A C4D HA improper CHB C1B C4A HB improper CHC C1C C4B HC improper CHD C1D C4C HD improper C1A C2A CHA NA improper C4A C3A CHB NA improper C1B C2B CHB NB improper C4B C3B CHC NB improper C1C C2C CHC NC improper C4C C3C CHD NC improper C1D C2D CHD ND improper C4D C3D CHA ND improper NA C1A C4A FE improper NB C1B C4B FE improper NC C1C C4C FE improper ND C1D C4D FE dihedral C1A C2A CAA CBA dihedral C2A CAA CBA CGA dihedral CAA CBA CGA O1A dihedral C2D C3D CAD CBD dihedral C3D CAD CBD CGD dihedral CAD CBD CGD O1D dihedral C2B C3B CAB CBB dihedral C3B CAB CBB HBB1 dihedral C2C C3C CAC CBC dihedral C3C CAC CBC HBC1 dihedral C2A C3A CMA HMA1 dihedral C1B C2B CMB HMB1 dihedral C1C C2C CMC HMC1 dihedral C1D C2D CMD HMD1 ic FE NA C1A C2A 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 1 ic FE NA C4A C3A 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 1 ic C3A C4A NA C1A 0.0 0.0 0.0 0.0 0.0 ! 5-member ring 1 ic CHA C1A C2A CAA 0.0 0.0 0.0 0.0 0.0 ! 5-member ring 1 ic FE NB C1B C2B 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 2 ic FE NB C4B C3B 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 2 ic C2B C1B NB C4B 0.0 0.0 0.0 0.0 0.0 ! 5-member ring 2 ic CHB C1B C2B CMB 0.0 0.0 0.0 0.0 0.0 ! 5-member ring 2 ic FE NC C1C C2C 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 3 ic FE NC C4C C3C 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 3 ic C2C C1C NC C4C 0.0 0.0 0.0 0.0 0.0 ! 5-member ring 3 ic CHC C1C C2C CMC 0.0 0.0 0.0 0.0 0.0 ! 5-member ring 3 ic FE ND C1D C2D 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 4 ic FE ND C4D C3D 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 4 ic C2D C1D ND C4D 0.0 0.0 0.0 0.0 0.0 ! 5-member ring 4 ic CHD C1D C2D CMD 0.0 0.0 0.0 0.0 0.0 ! 5-member ring 4 ic C4A NA FE NB 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 1 ic NA FE NB C1B 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 1 ic FE NA C4A CHB 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 1 ic NA C4A CHB C1B 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 1 ic C4A CHB C1B NB 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 1 ic C4B NB FE NC 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 2 ic NB FE NC C1C 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 2 ic FE NB C4B CHC 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 2 ic NB C4B CHC C1C 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 2 ic C4B CHC C1C NC 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 2 ic C4C NC FE ND 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 3 ic NC FE ND C1D 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 3 ic FE NC C4C CHD 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 3 ic NC C4C CHD C1D 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 3 ic C4C CHD C1D ND 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 3 ic C4A NA FE CHB 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 4 ic NA FE CHB HB 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 4 ic FE ND C4D CHA 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 4 ic ND C4D CHA C1A 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 4 ic C4D CHA C1A NA 0.0 0.0 0.0 0.0 0.0 ! 6-member ring 4 ic C4A C2A *C3A CMA 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 1 chiralities ic C3A C1A *C2A CAA 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 1 chiralities ic C3B C1B *C2B CMB 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 2 chiralities ic C4B C2B *C3B CAB 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 2 chiralities ic C3C C1C *C2C CMC 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 3 chiralities ic C4C C2C *C3C CAC 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 3 chiralities ic C3D C1D *C2D CMD 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 4 chiralities ic C4D C2D *C3D CAD 0.0 0.0 180.0 0.0 0.0 ! 5-member ring 4 chiralities ic CHB NB *C1B C2B 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 1 chiralities ic CHB NA *C4A C3A 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 1 chiralities ic FE C1B *NB C4B 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 1 chiralities ic C4A C1B *CHB HB 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 1 chiralities ic CHC NC *C1C C2C 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 2 chiralities ic CHC NB *C4B C3B 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 2 chiralities ic FE C1C *NC C4C 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 2 chiralities ic C4B C1C *CHC HC 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 2 chiralities ic CHD ND *C1D C2D 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 3 chiralities ic CHD NC *C4C C3C 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 3 chiralities ic FE C1D *ND C4D 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 3 chiralities ic C4C C1D *CHD HD 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 3 chiralities ic CHA NA *C1A C2A 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 4 chiralities ic CHA ND *C4D C3D 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 4 chiralities ic FE C1A *NA C4A 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 4 chiralities ic C4D C1A *CHA HA 0.0 0.0 180.0 0.0 0.0 ! 6-member ring 4 chiralities ic C1A C2A CAA CBA 0.0 0.0 120.0 0.0 0.0 ! Glutamate 1 ic C2A CAA CBA CGA 0.0 0.0 180.0 0.0 0.0 ! Glutamate 1 ic CAA CBA CGA O1A 0.0 0.0 0.0 0.0 0.0 ! Glutamate 1 ic CAA CBA CGA O2A 0.0 0.0 180.0 0.0 0.0 ! Glutamate 1 ic CBA O1A *CGA O2A 0.0 0.0 180.0 0.0 0.0 ! Glutamate 1 chiralities ic C2D C3D CAD CBD 0.0 0.0 -120.0 0.0 0.0 ! Glutamate 2 ic C3D CAD CBD CGD 0.0 0.0 180.0 0.0 0.0 ! Glutamate 2 ic CAD CBD CGD O1D 0.0 0.0 0.0 0.0 0.0 ! Glutamate 2 ic CAD CBD CGD O2D 0.0 0.0 180.0 0.0 0.0 ! Glutamate 2 ic CBD O1D *CGD O2D 0.0 0.0 180.0 0.0 0.0 ! Glutamate 2 chiralities ic C2B C3B CAB CBB 0.0 0.0 -45.0 0.0 0.0 ! Prevents vinyl collision ic C2C C3C CAC CBC 0.0 0.0 -45.0 0.0 0.0 ! Prevents vinyl collision ic NA ND *FE NB 0.0 0.0 180.0 0.0 0.0 ! Iron site ic NB NA *FE NC 0.0 0.0 180.0 0.0 0.0 ! Iron site ic NC NB *FE ND 0.0 0.0 180.0 0.0 0.0 ! Iron site ic ND NC *FE NA 0.0 0.0 180.0 0.0 0.0 ! Iron site end residue CYA ! Cyanide ion group atom C type=CYC charge= 0.00 end atom N type=CYN charge= 0.00 end bond C N end presidue PCYA ! Patch residue for 1=CYA and 2=HEC add bond 1C 2FE add angle 1N 1C 2FE add angle 1C 2FE 2NA add angle 1C 2FE 2NB add angle 1C 2FE 2NC add angle 1C 2FE 2ND end presidue PHEM ! Patch residue for 1=HIS and 2=HEB, or 2=HEC add bond 1NE2 2FE add angle 1CD2 1NE2 2FE add angle 1CE1 1NE2 2FE add angle 1NE2 2FE 2NA add angle 1NE2 2FE 2NB add angle 1NE2 2FE 2NC add angle 1NE2 2FE 2ND end presidue PHCB ! Patch residue for 1=CYS and 2=HEC (CAB carbon) delete atom 1HG end modify atom 1SG charge= 0.00 end add bond 1SG 2CAB add angle 1CB 1SG 2CAB add angle 1SG 2CAB 2C3B add angle 1SG 2CAB 2HAB add angle 1SG 2CAB 2CBB add dihedral 1CA 1CB 1SG 2CAB add dihedral 1CB 1SG 2CAB 2C3B add dihedral 1SG 2CAB 2C3B 2C2B add improper 1SG 2CBB 2C3B 2HAB end presidue PHCC ! Patch residue for 1=CYS and 2=HEC (CAC carbon) delete atom 1HG end modify atom 1SG charge= 0.00 end add bond 1SG 2CAC add angle 1CB 1SG 2CAC add angle 1SG 2CAC 2C3C add angle 1SG 2CAC 2HAC add angle 1SG 2CAC 2CBC add dihedral 1CA 1CB 1SG 2CAC add dihedral 1CB 1SG 2CAC 2C3C add dihedral 1SG 2CAC 2C3C 2C2C add improper 1SG 2CBC 2C3C 2HAC end set message on echo on end