* CHARMM27 Custom Topology File * Heme for Cytochrome c * Felix Autenrieth, Emad Tajkhorshid, Jerome Baudry, Zan Luthey-Schulten; last update 12/19/2005 * Classical force field parameters for the heme prosthetic group of cytochrome c. * Journal of Computational Chemistry, 25, 1613-1622 (2004) * Journal of Physical Chemistry B, 108, 20376-20387 (2004) 31 1 ! HEMR contains reduced scaled Mulliken charge set and HEMO contains oxidized scaled Mulliken charge ! set. Note that these residues are only valid when used in conjunction with one of the patches ! below to covalently attach the heme to a Cytochrome c molecule. Note: fractional charges are due ! to charge distribution across the cytochrome covalent linkages. After application of a patch ! the net charge on the reduced heme/ligand system will be -2 and the next charge on the oxidized ! heme/ligand system will be -1. RESI HEMR -2.20 ! 6-liganded planar heme in reduced state. GROUP ATOM FE FE 1.20 ! O2A O1A O2D O1D ATOM NA NPH -0.76 ! \\ // \\ // ATOM NB NPH -0.76 ! CGA CGD ATOM NC NPH -0.76 ! | | ATOM ND NPH -0.76 ! HBA1--CBA--HBA2 HA HBD1--CBD--HBD2 ATOM C1A CPA 0.32 ! | | | ATOM C2A CPB 0.07 ! HAA1--CAA-HAA2 _CHA_ HAD1--CAD--HAD2 ATOM C3A CPB 0.07 ! | / \ | ATOM C4A CPA 0.32 ! C2A---C1A C4D---C3D ATOM C1B CPA 0.32 ! | | | | ATOM C2B CPB 0.07 !HMA1\ | | | | /HMD1 ATOM C3B CPB 0.07 !HMA2-CMA--C3A NA ND C2D--CMD-HMD2 ATOM C4B CPA 0.32 !HMA3/ \ / \ / \ / \HMD3 ATOM C1C CPA 0.32 ! C4A \ / C1D ATOM C2C CPB 0.07 ! / \ / \ ATOM C3C CPB 0.07 ! HB--CHB FE CHD--HD ATOM C4C CPA 0.32 ! \ / \ / ATOM C1D CPA 0.32 ! C1B / \ C4C HAC ATOM C2D CPB 0.07 !HMB1\ / \ / \ / \ / ATOM C3D CPB 0.07 !HMB2-CMB--C2B NB NC C3C--CAC ATOM C4D CPA 0.32 !HMB3/ | | | | \ /HBC1 GROUP ! | | | | CBC-HBC2 ATOM CHA CPM -0.31 ! C3B---C4B C1C---C2C \HBC3 ATOM HA HA 0.12 ! | \_CHC_/ | GROUP ! CAB | CMC--HMC3 ATOM CHB CPM -0.31 ! / \ HC / | ATOM HB HA 0.12 ! HBB3-CBB HAB HMC1 HMC2 GROUP ! / \ ATOM CHC CPM -0.31 ! HBB1 HBB2 ATOM HC HA 0.12 ! GROUP ATOM CHD CPM -0.31 ATOM HD HA 0.12 GROUP ATOM CMA CT3 -0.37 ATOM HMA1 HA 0.09 ATOM HMA2 HA 0.09 ATOM HMA3 HA 0.09 GROUP ATOM CAA CT2 -0.30 ATOM HAA1 HA 0.09 ATOM HAA2 HA 0.09 GROUP ATOM CBA CT2 -0.30 ATOM HBA1 HA 0.09 ATOM HBA2 HA 0.09 ATOM CGA CC 0.72 ATOM O1A OC -0.74 ATOM O2A OC -0.74 GROUP ATOM CMB CT3 -0.37 ATOM HMB1 HA 0.09 ATOM HMB2 HA 0.09 ATOM HMB3 HA 0.09 GROUP ATOM CAB CT1 -0.32 ATOM HAB HA 0.16 GROUP ATOM CBB CT3 -0.27 ATOM HBB1 HA 0.09 ATOM HBB2 HA 0.09 ATOM HBB3 HA 0.09 GROUP ATOM CMC CT3 -0.37 ATOM HMC1 HA 0.09 ATOM HMC2 HA 0.09 ATOM HMC3 HA 0.09 GROUP ATOM CAC CT1 -0.32 ATOM HAC HA 0.16 GROUP ATOM CBC CT3 -0.27 ATOM HBC1 HA 0.09 ATOM HBC2 HA 0.09 ATOM HBC3 HA 0.09 GROUP ATOM CMD CT3 -0.37 ATOM HMD1 HA 0.09 ATOM HMD2 HA 0.09 ATOM HMD3 HA 0.09 GROUP ATOM CAD CT2 -0.30 ATOM HAD1 HA 0.09 ATOM HAD2 HA 0.09 GROUP ATOM CBD CT2 -0.30 ATOM HBD1 HA 0.09 ATOM HBD2 HA 0.09 ATOM CGD CC 0.72 ATOM O1D OC -0.74 ATOM O2D OC -0.74 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 CBB HBB3 BOND CMC HMC1 CMC HMC2 CMC HMC3 BOND CAC HAC CBC HBC1 CBC HBC2 CBC HBC3 BOND CMD HMD1 CMD HMD2 CMD HMD3 BOND CAD HAD1 CAD HAD2 CBD HBD1 CBD HBD2 IMPR C2A C1A C3A CAA C3A C2A C4A CMA C2B C1B C3B CMB IMPR C3B C2B C4B CAB C2C C1C C3C CMC C3C C2C C4C CAC IMPR C2D C1D C3D CMD C3D C2D C4D CAD IMPR CGA CBA O2A O1A CGD CBD O2D O1D IMPR C4A NA C1A C2A C1A NA C4A C3A IMPR C4B NB C1B C2B C1B NB C4B C3B IMPR C4C NC C1C C2C C1C NC C4C C3C IMPR C4D ND C1D C2D C1D ND C4D C3D IMPR NA C1A C2A C3A NA C4A C3A C2A IMPR NB C1B C2B C3B NB C4B C3B C2B IMPR NC C1C C2C C3C NC C4C C3C C2C IMPR ND C1D C2D C3D ND C4D C3D C2D IMPR NA C1A CHA C4D NA C4A CHB C1B IMPR NB C1B CHB C4A NB C4B CHC C1C IMPR NC C1C CHC C4B NC C4C CHD C1D IMPR ND C1D CHD C4C ND C4D CHA C1A IMPR CHA C1A C4D HA IMPR CHB C1B C4A HB IMPR CHC C1C C4B HC IMPR CHD C1D C4C HD IMPR C1A C2A CHA NA C4A C3A CHB NA IMPR C1B C2B CHB NB C4B C3B CHC NB IMPR C1C C2C CHC NC C4C C3C CHD NC IMPR C1D C2D CHD ND C4D C3D CHA ND IMPR NA C1A C4A FE IMPR NB C1B C4B FE IMPR NC C1C C4C FE IMPR ND C1D C4D FE !IMPR CAB CBB C3B HAB HAB CAB CBB HBB2 CAB CBB HBB2 HBB1 !IMPR CAC CBC C3C HAC HAC CAC CBC HBC2 CAC CBC HBC2 HBC1 ACCEPTOR NA ACCEPTOR O1A ! CGA ACCEPTOR O2A ! CGA ACCEPTOR NB ACCEPTOR NC ACCEPTOR ND ACCEPTOR O1D ! CGD ACCEPTOR O2D ! CGD IC FE NA C4A C3A 0.0000 0.0000 180.0000 0.0000 0.0000 IC C3A C4A NA C1A 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE NA C1A C2A 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4A NA FE NB 0.0000 0.0000 0.0000 0.0000 0.0000 IC NA FE NB C1B 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE NB C1B C2B 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2B C1B NB C4B 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE NB C4B C3B 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4B NB FE NC 0.0000 0.0000 0.0000 0.0000 0.0000 IC NB FE NC C1C 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE NC C1C C2C 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2C C1C NC C4C 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE NC C4C C3C 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4C NC FE ND 0.0000 0.0000 0.0000 0.0000 0.0000 IC NC FE ND C1D 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE ND C1D C2D 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2D C1D ND C4D 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE ND C4D C3D 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4A NA FE CHB 0.0000 0.0000 0.0000 0.0000 0.0000 IC NA FE CHB HB 0.0000 0.0000 0.0000 0.0000 0.0000 IC C4B NB FE CHC 0.0000 0.0000 0.0000 0.0000 0.0000 IC NB FE CHC HC 0.0000 0.0000 0.0000 0.0000 0.0000 IC C4C NC FE CHD 0.0000 0.0000 0.0000 0.0000 0.0000 IC NC FE CHD HD 0.0000 0.0000 0.0000 0.0000 0.0000 IC C4D ND FE CHA 0.0000 0.0000 0.0000 0.0000 0.0000 IC ND FE CHA HA 0.0000 0.0000 0.0000 0.0000 0.0000 IC C3B C1B *C2B CMB 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4B C2B *C3B CAB 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2B C3B CAB CBB 0.0000 0.0000 -45.0000 0.0000 0.0000 ! PREVENTS VINYL COLLISION IC CHC C1C C2C CMC 0.0000 0.0000 0.0000 0.0000 0.0000 IC C4C C2C *C3C CAC 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2C C3C CAC CBC 0.0000 0.0000 -45.0000 0.0000 0.0000 ! PREVENTS VINYL COLLISION IC C4D C2D *C3D CAD 0.0000 0.0000 180.0000 0.0000 0.0000 IC C3D C1D *C2D CMD 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2D C3D CAD CBD 0.0000 0.0000 -120.0000 0.0000 0.0000 IC C3D CAD CBD CGD 0.0000 0.0000 180.0000 0.0000 0.0000 IC CAD CBD CGD O1D 0.0000 0.0000 0.0000 0.0000 0.0000 IC CAD CBD CGD O2D 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4A C2A *C3A CMA 0.0000 0.0000 180.0000 0.0000 0.0000 IC C3A C1A *C2A CAA 0.0000 0.0000 180.0000 0.0000 0.0000 IC C1A C2A CAA CBA 0.0000 0.0000 120.0000 0.0000 0.0000 IC C2A CAA CBA CGA 0.0000 0.0000 180.0000 0.0000 0.0000 IC CAA CBA CGA O1A 0.0000 0.0000 0.0000 0.0000 0.0000 IC CAA CBA CGA O2A 0.0000 0.0000 180.0000 0.0000 0.0000 IC C3C C1C *C2C CMC 0.0000 0.0000 180.0000 0.0000 0.0000 IC CBA O1A *CGA O2A 0.0000 0.0000 180.0000 0.0000 0.0000 IC CBD O1D *CGD O2D 0.0000 0.0000 180.0000 0.0000 0.0000 IC HMA1 CMA C2A C1A 1.1000 109.5 0.0 124.64 1.58 IC HMA2 CMA C2A C1A 1.1000 109.5 120.0 124.64 1.58 IC HMA3 CMA C2A C1A 1.1000 109.5 240.0 124.64 1.58 IC HMB1 CMB C2B C1B 1.1000 109.5 0.0 124.64 1.58 IC HMB2 CMB C2B C1B 1.1000 109.5 120.0 124.64 1.58 IC HMB3 CMB C2B C1B 1.1000 109.5 240.0 124.64 1.58 IC HMC1 CMC C2C C1C 1.1000 109.5 0.0 124.64 1.58 IC HMC2 CMC C2C C1C 1.1000 109.5 120.0 124.64 1.58 IC HMC3 CMC C2C C1C 1.1000 109.5 240.0 124.64 1.58 IC HMD1 CMD C2D C1D 1.1000 109.5 0.0 124.64 1.58 IC HMD2 CMD C2D C1D 1.1000 109.5 120.0 124.64 1.58 IC HMD3 CMD C2D C1D 1.1000 109.5 240.0 124.64 1.58 IC HAA1 CAA C2A C3A 1.1000 109.5 0.0 127.34 1.58 IC HAA2 CAA C2A C3A 1.1000 109.5 180.0 127.34 1.58 IC HBA1 CBA CAA C2A 1.1000 109.5 0.0 116.64 1.58 IC HBA2 CBA CAA C2A 1.1000 109.5 180.0 116.64 1.58 IC HAD1 CAD C2D C3D 1.1000 109.5 0.0 127.34 1.58 IC HAD2 CAD C2D C3D 1.1000 109.5 180.0 127.34 1.58 IC HBD1 CBD CAD C2D 1.1000 109.5 0.0 116.64 1.58 IC HBD2 CBD CAD C2D 1.1000 109.5 180.0 116.64 1.58 IC HAC CAC C3C C4C 1.1000 109.5 0.0 122.90 1.58 IC HBC1 CBC CAC C3C 1.1000 109.5 0.0 125.00 1.58 IC HBC2 CBC CAC C3C 1.1000 109.5 120.0 125.00 1.58 IC HBC3 CBC CAC C3C 1.1000 109.5 240.0 125.00 1.58 IC CBC HBC2 *CBC HBC1 1.1000 109.5 0.0 125.00 1.58 IC HAB CAB C3B C4B 1.1000 109.5 0.0 122.90 1.58 IC HBB1 CBB CAB C3B 1.1100 109.5 0.0 118.00 1.58 IC HBB2 CBB CAB C3B 1.1100 109.5 120.0 118.00 1.58 IC HBB3 CBB CAB C3B 1.1100 109.5 240.0 118.00 1.58 IC CAB HBB2 *CBB HBB1 1.1000 109.5 180.0 120.00 1.58 RESI HEMO -1.44 ! 6-liganded planar heme in oxidized state. GROUP ATOM FE FE 1.34 ! O2A O1A O2D O1D ATOM NA NPH -0.76 ! \\ // \\ // ATOM NB NPH -0.76 ! CGA CGD ATOM NC NPH -0.76 ! | | ATOM ND NPH -0.76 ! HBA1--CBA--HBA2 HA HBD1--CBD--HBD2 ATOM C1A CPA 0.32 ! | | | ATOM C2A CPB 0.07 ! HAA1--CAA-HAA2 _CHA_ HAD1--CAD--HAD2 ATOM C3A CPB 0.07 ! | / \ | ATOM C4A CPA 0.32 ! C2A---C1A C4D---C3D ATOM C1B CPA 0.32 ! | | | | ATOM C2B CPB 0.07 !HMA1\ | | | | /HMD1 ATOM C3B CPB 0.07 !HMA2-CMA--C3A NA ND C2D--CMD-HMD2 ATOM C4B CPA 0.32 !HMA3/ \ / \ / \ / \HMD3 ATOM C1C CPA 0.32 ! C4A \ / C1D ATOM C2C CPB 0.07 ! / \ / \ ATOM C3C CPB 0.07 ! HB--CHB FE CHD--HD ATOM C4C CPA 0.32 ! \ / \ / ATOM C1D CPA 0.32 ! C1B / \ C4C HAC ATOM C2D CPB 0.07 !HMB1\ / \ / \ / \ / ATOM C3D CPB 0.07 !HMB2-CMB--C2B NB NC C3C--CAC ATOM C4D CPA 0.32 !HMB3/ | | | | \ /HBC1 GROUP ! | | | | CBC-HBC2 ATOM CHA CPM -0.29 ! C3B---C4B C1C---C2C \HBC3 ATOM HA HA 0.13 ! | \_CHC_/ | GROUP ! CAB | CMC--HMC3 ATOM CHB CPM -0.29 ! / \ HC / | ATOM HB HA 0.13 ! HBB3-CBB HAB HMC1 HMC2 GROUP ! / \ ATOM CHC CPM -0.29 ! HBB1 HBB2 ATOM HC HA 0.13 ! GROUP ATOM CHD CPM -0.29 ATOM HD HA 0.13 GROUP ATOM CMA CT3 -0.34 ATOM HMA1 HA 0.09 ATOM HMA2 HA 0.09 ATOM HMA3 HA 0.09 GROUP ATOM CAA CT2 -0.27 ATOM HAA1 HA 0.09 ATOM HAA2 HA 0.09 GROUP ATOM CBA CT2 -0.25 ATOM HBA1 HA 0.09 ATOM HBA2 HA 0.09 ATOM CGA CC 0.63 ATOM O1A OC -0.64 ATOM O2A OC -0.64 GROUP ATOM CMB CT3 -0.34 ATOM HMB1 HA 0.09 ATOM HMB2 HA 0.09 ATOM HMB3 HA 0.09 GROUP ATOM CAB CT1 -0.34 ATOM HAB HA 0.16 GROUP ATOM CBB CT3 -0.25 ATOM HBB1 HA 0.09 ATOM HBB2 HA 0.09 ATOM HBB3 HA 0.09 GROUP ATOM CMC CT3 -0.34 ATOM HMC1 HA 0.09 ATOM HMC2 HA 0.09 ATOM HMC3 HA 0.09 GROUP ATOM CAC CT1 -0.34 ATOM HAC HA 0.16 GROUP ATOM CBC CT3 -0.25 ATOM HBC1 HA 0.09 ATOM HBC2 HA 0.09 ATOM HBC3 HA 0.09 GROUP ATOM CMD CT3 -0.34 ATOM HMD1 HA 0.09 ATOM HMD2 HA 0.09 ATOM HMD3 HA 0.09 GROUP ATOM CAD CT2 -0.27 ATOM HAD1 HA 0.09 ATOM HAD2 HA 0.09 GROUP ATOM CBD CT2 -0.25 ATOM HBD1 HA 0.09 ATOM HBD2 HA 0.09 ATOM CGD CC 0.63 ATOM O1D OC -0.64 ATOM O2D OC -0.64 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 CBB HBB3 BOND CMC HMC1 CMC HMC2 CMC HMC3 BOND CAC HAC CBC HBC1 CBC HBC2 CBC HBC3 BOND CMD HMD1 CMD HMD2 CMD HMD3 BOND CAD HAD1 CAD HAD2 CBD HBD1 CBD HBD2 IMPR C2A C1A C3A CAA C3A C2A C4A CMA C2B C1B C3B CMB IMPR C3B C2B C4B CAB C2C C1C C3C CMC C3C C2C C4C CAC IMPR C2D C1D C3D CMD C3D C2D C4D CAD IMPR CGA CBA O2A O1A CGD CBD O2D O1D IMPR C4A NA C1A C2A C1A NA C4A C3A IMPR C4B NB C1B C2B C1B NB C4B C3B IMPR C4C NC C1C C2C C1C NC C4C C3C IMPR C4D ND C1D C2D C1D ND C4D C3D IMPR NA C1A C2A C3A NA C4A C3A C2A IMPR NB C1B C2B C3B NB C4B C3B C2B IMPR NC C1C C2C C3C NC C4C C3C C2C IMPR ND C1D C2D C3D ND C4D C3D C2D IMPR NA C1A CHA C4D NA C4A CHB C1B IMPR NB C1B CHB C4A NB C4B CHC C1C IMPR NC C1C CHC C4B NC C4C CHD C1D IMPR ND C1D CHD C4C ND C4D CHA C1A IMPR CHA C1A C4D HA IMPR CHB C1B C4A HB IMPR CHC C1C C4B HC IMPR CHD C1D C4C HD IMPR C1A C2A CHA NA C4A C3A CHB NA IMPR C1B C2B CHB NB C4B C3B CHC NB IMPR C1C C2C CHC NC C4C C3C CHD NC IMPR C1D C2D CHD ND C4D C3D CHA ND IMPR NA C1A C4A FE IMPR NB C1B C4B FE IMPR NC C1C C4C FE IMPR ND C1D C4D FE !IMPR CAB CBB C3B HAB HAB CAB CBB HBB2 CAB CBB HBB2 HBB1 !IMPR CAC CBC C3C HAC HAC CAC CBC HBC2 CAC CBC HBC2 HBC1 ACCEPTOR NA ACCEPTOR O1A ! CGA ACCEPTOR O2A ! CGA ACCEPTOR NB ACCEPTOR NC ACCEPTOR ND ACCEPTOR O1D ! CGD ACCEPTOR O2D ! CGD IC FE NA C4A C3A 0.0000 0.0000 180.0000 0.0000 0.0000 IC C3A C4A NA C1A 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE NA C1A C2A 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4A NA FE NB 0.0000 0.0000 0.0000 0.0000 0.0000 IC NA FE NB C1B 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE NB C1B C2B 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2B C1B NB C4B 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE NB C4B C3B 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4B NB FE NC 0.0000 0.0000 0.0000 0.0000 0.0000 IC NB FE NC C1C 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE NC C1C C2C 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2C C1C NC C4C 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE NC C4C C3C 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4C NC FE ND 0.0000 0.0000 0.0000 0.0000 0.0000 IC NC FE ND C1D 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE ND C1D C2D 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2D C1D ND C4D 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE ND C4D C3D 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4A NA FE CHB 0.0000 0.0000 0.0000 0.0000 0.0000 IC NA FE CHB HB 0.0000 0.0000 0.0000 0.0000 0.0000 IC C4B NB FE CHC 0.0000 0.0000 0.0000 0.0000 0.0000 IC NB FE CHC HC 0.0000 0.0000 0.0000 0.0000 0.0000 IC C4C NC FE CHD 0.0000 0.0000 0.0000 0.0000 0.0000 IC NC FE CHD HD 0.0000 0.0000 0.0000 0.0000 0.0000 IC C4D ND FE CHA 0.0000 0.0000 0.0000 0.0000 0.0000 IC ND FE CHA HA 0.0000 0.0000 0.0000 0.0000 0.0000 IC C3B C1B *C2B CMB 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4B C2B *C3B CAB 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2B C3B CAB CBB 0.0000 0.0000 -45.0000 0.0000 0.0000 ! PREVENTS VINYL COLLISION IC CHC C1C C2C CMC 0.0000 0.0000 0.0000 0.0000 0.0000 IC C4C C2C *C3C CAC 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2C C3C CAC CBC 0.0000 0.0000 -45.0000 0.0000 0.0000 ! PREVENTS VINYL COLLISION IC C4D C2D *C3D CAD 0.0000 0.0000 180.0000 0.0000 0.0000 IC C3D C1D *C2D CMD 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2D C3D CAD CBD 0.0000 0.0000 -120.0000 0.0000 0.0000 IC C3D CAD CBD CGD 0.0000 0.0000 180.0000 0.0000 0.0000 IC CAD CBD CGD O1D 0.0000 0.0000 0.0000 0.0000 0.0000 IC CAD CBD CGD O2D 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4A C2A *C3A CMA 0.0000 0.0000 180.0000 0.0000 0.0000 IC C3A C1A *C2A CAA 0.0000 0.0000 180.0000 0.0000 0.0000 IC C1A C2A CAA CBA 0.0000 0.0000 120.0000 0.0000 0.0000 IC C2A CAA CBA CGA 0.0000 0.0000 180.0000 0.0000 0.0000 IC CAA CBA CGA O1A 0.0000 0.0000 0.0000 0.0000 0.0000 IC CAA CBA CGA O2A 0.0000 0.0000 180.0000 0.0000 0.0000 IC C3C C1C *C2C CMC 0.0000 0.0000 180.0000 0.0000 0.0000 IC CBA O1A *CGA O2A 0.0000 0.0000 180.0000 0.0000 0.0000 IC CBD O1D *CGD O2D 0.0000 0.0000 180.0000 0.0000 0.0000 IC HMA1 CMA C2A C1A 1.1000 109.5 0.0 124.64 1.58 IC HMA2 CMA C2A C1A 1.1000 109.5 120.0 124.64 1.58 IC HMA3 CMA C2A C1A 1.1000 109.5 240.0 124.64 1.58 IC HMB1 CMB C2B C1B 1.1000 109.5 0.0 124.64 1.58 IC HMB2 CMB C2B C1B 1.1000 109.5 120.0 124.64 1.58 IC HMB3 CMB C2B C1B 1.1000 109.5 240.0 124.64 1.58 IC HMC1 CMC C2C C1C 1.1000 109.5 0.0 124.64 1.58 IC HMC2 CMC C2C C1C 1.1000 109.5 120.0 124.64 1.58 IC HMC3 CMC C2C C1C 1.1000 109.5 240.0 124.64 1.58 IC HMD1 CMD C2D C1D 1.1000 109.5 0.0 124.64 1.58 IC HMD2 CMD C2D C1D 1.1000 109.5 120.0 124.64 1.58 IC HMD3 CMD C2D C1D 1.1000 109.5 240.0 124.64 1.58 IC HAA1 CAA C2A C3A 1.1000 109.5 0.0 127.34 1.58 IC HAA2 CAA C2A C3A 1.1000 109.5 180.0 127.34 1.58 IC HBA1 CBA CAA C2A 1.1000 109.5 0.0 116.64 1.58 IC HBA2 CBA CAA C2A 1.1000 109.5 180.0 116.64 1.58 IC HAD1 CAD C2D C3D 1.1000 109.5 0.0 127.34 1.58 IC HAD2 CAD C2D C3D 1.1000 109.5 180.0 127.34 1.58 IC HBD1 CBD CAD C2D 1.1000 109.5 0.0 116.64 1.58 IC HBD2 CBD CAD C2D 1.1000 109.5 180.0 116.64 1.58 IC HAC CAC C3C C4C 1.1000 109.5 0.0 122.90 1.58 IC HBC1 CBC CAC C3C 1.1000 109.5 0.0 125.00 1.58 IC HBC2 CBC CAC C3C 1.1000 109.5 120.0 125.00 1.58 IC HBC3 CBC CAC C3C 1.1000 109.5 240.0 125.00 1.58 IC CBC HBC2 *CBC HBC1 1.1000 109.5 0.0 125.00 1.58 IC HAB CAB C3B C4B 1.1000 109.5 0.0 122.90 1.58 IC HBB1 CBB CAB C3B 1.1100 109.5 0.0 118.00 1.58 IC HBB2 CBB CAB C3B 1.1100 109.5 120.0 118.00 1.58 IC HBB3 CBB CAB C3B 1.1100 109.5 240.0 118.00 1.58 IC CAB HBB2 *CBB HBB1 1.1000 109.5 180.0 120.00 1.58 PRES HRCY -0.97 ! Patch for REDUCED HEME to Cytochrome c links. ! Patch residues must be 1:CYS (N-terminal), 2:CYS (C-terminal), 3:HSD, 4:MET ! and 5:HEMR. ! Modified by Elijah Roberts 12/9/2005 to include charge redistribution and ! to be a single patch. ! ! First (N-terminal) Heme to Cysteine (Thioether bond) portion of patch GROUP ! ATOM 1CB CT2 0.07 ! -1CB--1SG--5CAB- ATOM 1SG S -0.27 ! DELETE ATOM 1HG1 BOND 1SG 5CAB ANGLE 1CB 1SG 5CAB ANGLE 1SG 5CAB 5C3B ANGLE 1SG 5CAB 5CBB ANGLE 1SG 5CAB 5HAB DIHEDRAL 1CB 1SG 5CAB 5C3B DIHEDRAL 1CB 1SG 5CAB 5CBB DIHEDRAL 1CB 1SG 5CAB 5HAB DIHEDRAL 1CA 1CB 1SG 5CAB DIHEDRAL 1HB1 1CB 1SG 5CAB DIHEDRAL 1HB2 1CB 1SG 5CAB ! ! Second (C-terminal) Heme to Cysteine (Thioether bond) portion of patch GROUP ! ATOM 2CB CT2 0.07 ! -2CB--2SG--5CAC- ATOM 2SG S -0.27 ! DELETE ATOM 2HG1 BOND 2SG 5CAC ANGLE 2CB 2SG 5CAC ANGLE 2SG 5CAC 5C3C ANGLE 2SG 5CAC 5CBC ANGLE 2SG 5CAC 5HAC DIHEDRAL 2CB 2SG 5CAC 5C3C DIHEDRAL 2CB 2SG 5CAC 5CBC DIHEDRAL 2CB 2SG 5CAC 5HAC DIHEDRAL 2CA 2CB 2SG 5CAC DIHEDRAL 2HB1 2CB 2SG 5CAC DIHEDRAL 2HB2 2CB 2SG 5CAC ! ! Heme to Histidine portion of patch GROUP ! ATOM 3CB CT2 -0.25 ! 3HD1 3HE1 ATOM 3ND1 NR1 -0.62 ! | / ATOM 3HD1 H 0.42 ! 3HB1 3ND1--3CE1 ATOM 3CG CPH1 0.32 ! | / || GROUP ! -3CB--3CG || ATOM 3CE1 CPH2 0.23 ! | \\ || ATOM 3HE1 HR1 0.26 ! 3HB2 3CD2--3NE2 ATOM 3NE2 NR2 -0.49 ! | \ ATOM 3CD2 CPH1 -0.05 ! 3HD2 5FE- ATOM 3HD2 HR3 0.15 ! DELETE ANGLE 5NA 5FE 5NC 5NB 5FE 5ND BOND 3NE2 5FE ANGLE 3CD2 3NE2 5FE 3CE1 3NE2 5FE 3NE2 5FE 5NA 3NE2 5FE 5NB ANGLE 3NE2 5FE 5NC 3NE2 5FE 5ND IMPR 3NE2 3CD2 3CE1 5FE !add impr for heme/his planarity and heme/met planarity IC 3CD2 3NE2 5FE 5NA 0.0000 0.0000 0.0000 0.0000 0.0000 IC 3CD2 3NE2 5FE 5NB 0.0000 0.0000 0.0000 0.0000 0.0000 IC 3CD2 3NE2 5FE 5NB 0.0000 0.0000 0.0000 0.0000 0.0000 IC 3CD2 3NE2 5FE 5NB 0.0000 0.0000 0.0000 0.0000 0.0000 IC 3CE1 3NE2 5FE 5NA 0.0000 0.0000 0.0000 0.0000 0.0000 ! ! Heme to Methionine (Iron-sulfur bond) portion of patch GROUP ! ATOM 4CB CT2 -0.18 ! -4CB--4CG--4SD--4CE ATOM 4CG CT2 -0.23 ! | ATOM 4SD S 0.22 ! 5FE- ATOM 4CE CT3 -0.35 ! DELE ANGLE 5NA 5FE 5NC 5NB 5FE 5ND BOND 4SD 5FE ANGLE 4CE 4SD 5FE 4CG 4SD 5FE 4SD 5FE 5NA ANGLE 4SD 5FE 5NB 4SD 5FE 5NC 4SD 5FE 5ND IC 4CE 4SD 5FE 5NA 0.0000 0.0000 0.0000 0.0000 0.0000 IC 4CE 4SD 5FE 5NB 0.0000 0.0000 0.0000 0.0000 0.0000 IC 4CE 4SD 5FE 5NB 0.0000 0.0000 0.0000 0.0000 0.0000 IC 4CE 4SD 5FE 5NB 0.0000 0.0000 0.0000 0.0000 0.0000 IC 4CG 4SD 5FE 5NA 0.0000 0.0000 0.0000 0.0000 0.0000 PRES HOCY -0.73 ! Patch for OXIDIZED HEME to Cytochrome c links. ! Patch residues must be 1:CYS (N-terminal), 2:CYS (C-terminal), 3:HSD, 4:MET ! and 5:HEMO. ! Modified by Elijah Roberts 12/9/2005 to include charge redistribution and ! to be a single patch. ! ! First (N-terminal) Heme to Cysteine (Thioether bond) portion of patch GROUP ! ATOM 1CB CT2 0.07 ! -1CB--1SG--5CAB- ATOM 1SG S -0.23 ! DELETE ATOM 1HG1 BOND 1SG 5CAB ANGLE 1CB 1SG 5CAB ANGLE 1SG 5CAB 5C3B ANGLE 1SG 5CAB 5CBB ANGLE 1SG 5CAB 5HAB DIHEDRAL 1CB 1SG 5CAB 5C3B DIHEDRAL 1CB 1SG 5CAB 5CBB DIHEDRAL 1CB 1SG 5CAB 5HAB DIHEDRAL 1CA 1CB 1SG 5CAB DIHEDRAL 1HB1 1CB 1SG 5CAB DIHEDRAL 1HB2 1CB 1SG 5CAB ! ! Second (C-terminal) Heme to Cysteine (Thioether bond) portion of patch GROUP ! ATOM 2CB CT2 0.07 ! -2CB--2SG--5CAC- ATOM 2SG S -0.23 ! DELETE ATOM 2HG1 BOND 2SG 5CAC ANGLE 2CB 2SG 5CAC ANGLE 2SG 5CAC 5C3C ANGLE 2SG 5CAC 5CBC ANGLE 2SG 5CAC 5HAC DIHEDRAL 2CB 2SG 5CAC 5C3C DIHEDRAL 2CB 2SG 5CAC 5CBC DIHEDRAL 2CB 2SG 5CAC 5HAC DIHEDRAL 2CA 2CB 2SG 5CAC DIHEDRAL 2HB1 2CB 2SG 5CAC DIHEDRAL 2HB2 2CB 2SG 5CAC ! ! Heme to Histidine portion of patch GROUP ! ATOM 3CB CT2 -0.22 ! 3HD1 3HE1 ATOM 3ND1 NR1 -0.61 ! | / ATOM 3HD1 H 0.45 ! 3HB1 3ND1--3CE1 ATOM 3CG CPH1 0.32 ! | / || GROUP ! -3CB--3CG || ATOM 3CE1 CPH2 0.24 ! | \\ || ATOM 3HE1 HR1 0.27 ! 3HB2 3CD2--3NE2 ATOM 3NE2 NR2 -0.51 ! | \ ATOM 3CD2 CPH1 -0.04 ! 3HD2 5FE- ATOM 3HD2 HR3 0.16 ! DELETE ANGLE 5NA 5FE 5NC 5NB 5FE 5ND BOND 3NE2 5FE ANGLE 3CD2 3NE2 5FE 3CE1 3NE2 5FE 3NE2 5FE 5NA 3NE2 5FE 5NB ANGLE 3NE2 5FE 5NC 3NE2 5FE 5ND IMPR 3NE2 3CD2 3CE1 5FE !add impr for heme/his planarity and heme/met planarity IC 3CD2 3NE2 5FE 5NA 0.0000 0.0000 0.0000 0.0000 0.0000 IC 3CD2 3NE2 5FE 5NB 0.0000 0.0000 0.0000 0.0000 0.0000 IC 3CD2 3NE2 5FE 5NB 0.0000 0.0000 0.0000 0.0000 0.0000 IC 3CD2 3NE2 5FE 5NB 0.0000 0.0000 0.0000 0.0000 0.0000 IC 3CE1 3NE2 5FE 5NA 0.0000 0.0000 0.0000 0.0000 0.0000 ! ! Heme to Methionine (Iron-sulfur bond) portion of patch GROUP ! ATOM 4CB CT2 -0.14 ! -4CB--4CG--4SD--4CE ATOM 4CG CT2 -0.25 ! | ATOM 4SD S 0.23 ! 5FE- ATOM 4CE CT3 -0.31 ! DELE ANGLE 5NA 5FE 5NC 5NB 5FE 5ND BOND 4SD 5FE ANGLE 4CE 4SD 5FE 4CG 4SD 5FE 4SD 5FE 5NA ANGLE 4SD 5FE 5NB 4SD 5FE 5NC 4SD 5FE 5ND IC 4CE 4SD 5FE 5NA 0.0000 0.0000 0.0000 0.0000 0.0000 IC 4CE 4SD 5FE 5NB 0.0000 0.0000 0.0000 0.0000 0.0000 IC 4CE 4SD 5FE 5NB 0.0000 0.0000 0.0000 0.0000 0.0000 IC 4CE 4SD 5FE 5NB 0.0000 0.0000 0.0000 0.0000 0.0000 IC 4CG 4SD 5FE 5NA 0.0000 0.0000 0.0000 0.0000 0.0000 END