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| CPDI.frcmod- Shahrokh,K; Orendt,A; Yost, G.S; and Cheatham III, T.E. Jour Comp Chem (2011) | |
| MASS | |
| fe 55.85 | |
| oa 16.00 | |
| BOND | |
| fe-nc 114.00 2.029 | |
| fe-nd 114.00 2.029 | |
| fe-SH 39.00 2.565 | |
| cg-ha 341.50 1.089 # same as ce-ha 341.5 1.089 SOURCE3 | |
| fe-oa 572.00 1.639 | |
| ANGLE | |
| nc-fe-oa 65.000 92.406 # average angle | |
| nd-fe-oa 65.000 92.406 # average angle | |
| SH-fe-oa 0.000 174.087 # | |
| nc-fe-nd 239.000 89.900 # average angle | |
| fe-nc-cc 146.000 126.651 # average angle | |
| fe-nd-cd 146.000 126.651 # average angle | |
| nc-fe-nc 0.000 174.731 | |
| nd-fe-nd 0.000 175.636 | |
| SH-fe-nc 48.00 87.595 # average angle | |
| SH-fe-nd 48.00 87.595 # average angle | |
| CT-SH-fe 39.00 105.885 | |
| cc-cc-cg 65.6 124.539 # same as cc-cc-cf 65.6 123.92 SOURCE3 | |
| cd-cd-cg 65.6 124.539 # same as cc-cc-cf 65.6 123.92 SOURCE3 | |
| nc-cc-cg 68.5 125.044 # same as cf-cf-n2 68.5 123.00 SOURCE3 | |
| nd-cd-cg 68.5 125.044 # same as cf-cf-n2 68.5 123.00 SOURCE3 | |
| ha-cc-ha 38.0 117.65 # same as ha-c2-ha 38.0 117.65 SOURCE3 | |
| ha-cd-ha 38.0 117.65 # same as ha-c2-ha 38.0 117.65 SOURCE3 | |
| cc-cg-ha 46.6 116.969 # same as cd-cd-ha 46.6 123.74 SOURCE3 | |
| cd-cg-ha 46.6 116.969 # same as cd-cd-ha 46.6 123.74 SOURCE3 | |
| cd-cg-cc 63.8 126.057 # same as ce-ce-cf 63.8 130.92 SOURCE3 | |
| DIHEDRAL | |
| cd-nd-fe-oa 1 0.000 180.000 2.000 | |
| cc-nc-fe-oa 1 0.000 180.000 2.000 | |
| CT-SH-fe-nc 1 0.00 180.000 2.000 | |
| CT-SH-fe-nd 1 0.00 180.000 2.000 | |
| CT-SH-fe-oa 1 0.00 180.000 2.000 | |
| cc-cc-c3-c3 3 0.000 180.000 2.000 | |
| cc-cc-c3-hc 3 0.000 180.000 2.000 | |
| cd-cd-c3-c3 3 0.000 180.000 2.000 | |
| cd-cd-c3-hc 3 0.000 180.000 2.000 | |
| X -cg-cd-X 4 16.00 180.000 2.000 | |
| X -cg-cc-X 4 16.00 180.000 2.000 | |
| cg-cc-nc-fe 1 0.000 180.000 2.000 | |
| cg-cd-nd-fe 1 0.000 180.000 2.000 | |
| cc-cc-nc-fe 1 0.000 180.000 2.000 | |
| cd-cd-nd-fe 1 0.000 180.000 2.000 | |
| nd-fe-nc-cc 1 0.000 180.000 2.000 | |
| nc-fe-nd-cd 1 0.000 180.000 2.000 | |
| cc-nc-fe-nc 1 0.000 180.000 2.000 | |
| cd-nd-fe-nd 1 0.000 180.000 2.000 | |
| cc-nc-fe-SH 1 0.000 180.000 2.000 | |
| cd-nd-fe-sh 1 0.000 180.000 2.000 | |
| IMPROPER | |
| NONBON | |
| fe 1.3 0.01 | |
| oa 1.6612 0.21 |
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| # Shahrokh,K; Orendt,A; Yost, G.S; and Cheatham III, T.E. Jour Comp Chem (2011) | |
| # Compound I cysteine coordinates and atomic charges | |
| @<TRIPOS>MOLECULE | |
| CYP-CPDI | |
| 10 9 1 0 0 | |
| SMALL | |
| USER_CHARGES | |
| @<TRIPOS>ATOM | |
| 1 N -2.6330 -1.3520 2.7840 N 1 CYP -0.4157 | |
| 2 H -2.8330 -2.0920 3.4500 H 1 CYP 0.2719 | |
| 3 CA -1.2870 -1.4470 2.2240 CT 1 CYP 0.0725 | |
| 4 HA -1.3570 -1.6240 1.1450 H1 1 CYP -0.0095 | |
| 5 CB -0.4780 -0.1320 2.4210 CT 1 CYP 0.0020 | |
| 6 HB2 -0.4010 0.0680 3.4970 H1 1 CYP 0.0508 | |
| 7 HB3 -1.0820 0.6620 1.9770 H1 1 CYP 0.0508 | |
| 8 SG 1.2250 -0.0810 1.7090 SH 1 CYP -0.4381 | |
| 9 C -0.6660 -2.7000 2.8810 C 1 CYP 0.5973 | |
| 10 O -1.2840 -3.3630 3.7280 O 1 CYP -0.5679 | |
| @<TRIPOS>BOND | |
| 1 1 3 1 | |
| 2 1 2 1 | |
| 3 3 4 1 | |
| 4 3 5 1 | |
| 5 3 9 1 | |
| 6 5 6 1 | |
| 7 5 7 1 | |
| 8 5 8 1 | |
| 9 9 10 2 | |
| @<TRIPOS>SUBSTRUCTURE | |
| 1 CYP 1 RESIDUE 4 A CYP 0 ROOT |
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| # Shahrokh,K; Orendt,A; Yost, G.S; and Cheatham III, T.E. Jour Comp Chem (2011) | |
| # Coumpound I High-spin heme coordinates and atomic charges | |
| @<TRIPOS>MOLECULE | |
| HEM-CPDI | |
| 74 81 1 0 1 | |
| SMALL | |
| USER_CHARGES | |
| @<TRIPOS>ATOM | |
| 1 NC 2.870000 -0.982000 -0.754000 nc 1 HEM -0.0333 **** | |
| 2 C1C 4.206000 -0.781000 -0.528000 cc 1 HEM -0.0836 **** | |
| 3 C4C 2.714000 -2.307000 -1.022000 cc 1 HEM -0.0148 **** | |
| 4 C2C 4.934000 -2.026000 -0.645000 cc 1 HEM -0.0025 **** | |
| 5 C3C 3.998000 -2.997000 -0.943000 cc 1 HEM -0.1636 **** | |
| 6 CHD 1.504000 -2.923000 -1.333000 cg 1 HEM 0.0470 **** | |
| 7 HHD 1.518000 -3.994000 -1.504000 ha 1 HEM 0.0773 **** | |
| 8 C1D 0.275000 -2.292000 -1.459000 cd 1 HEM -0.1256 **** | |
| 9 ND 0.033000 -0.964000 -1.253000 nd 1 HEM 0.0685 **** | |
| 10 C4D -1.296000 -0.768000 -1.518000 cd 1 HEM -0.0340 **** | |
| 11 C3D -1.935000 -2.029000 -1.895000 cd 1 HEM -0.0325 **** | |
| 12 C2D -0.948000 -2.976000 -1.850000 cd 1 HEM 0.0288 **** | |
| 13 CHA -1.955000 0.450000 -1.421000 cg 1 HEM -0.0124 **** | |
| 14 HHA -3.015000 0.459000 -1.641000 ha 1 HEM 0.1920 **** | |
| 15 C1A -1.380000 1.648000 -1.011000 cc 1 HEM -0.0365 **** | |
| 16 C2A -2.100000 2.914000 -0.894000 cc 1 HEM -0.0626 **** | |
| 17 C4A 0.084000 3.125000 -0.329000 cc 1 HEM -0.0543 **** | |
| 18 NA -0.069000 1.806000 -0.659000 nc 1 HEM -0.0015 **** | |
| 19 C3A -1.181000 3.829000 -0.460000 cc 1 HEM 0.0097 **** | |
| 20 CHB 1.271000 3.739000 0.037000 cg 1 HEM 0.0210 **** | |
| 21 HHB 1.216000 4.793000 0.285000 ha 1 HEM 0.1004 **** | |
| 22 C1B 2.526000 3.138000 0.092000 cd 1 HEM -0.1156 **** | |
| 23 C2B 3.750000 3.834000 0.427000 cd 1 HEM 0.0805 **** | |
| 24 NB 2.778000 1.824000 -0.184000 nd 1 HEM 0.0339 **** | |
| 25 C4B 4.122000 1.646000 -0.047000 cd 1 HEM -0.0866 **** | |
| 26 CHC 4.792000 0.439000 -0.209000 cg 1 HEM 0.0569 **** | |
| 27 HHC 5.861000 0.438000 -0.029000 ha 1 HEM 0.0740 **** | |
| 28 FE 1.406000 0.441000 -0.796000 fe 1 HEM 0.2620 **** | |
| 29 C3B 4.763000 2.899000 0.343000 cd 1 HEM -0.0237 **** | |
| 30 CAB 6.194000 3.060000 0.540000 cc 1 HEM -0.0963 **** | |
| 31 HAB 6.817000 2.326000 0.027000 ha 1 HEM 0.1169 **** | |
| 32 CBB 6.836000 3.995000 1.265000 cd 1 HEM -0.3967 **** | |
| 33 HBB1 6.314000 4.743000 1.853000 ha 1 HEM 0.1410 **** | |
| 34 HBB2 7.922000 4.014000 1.310000 ha 1 HEM 0.1410 **** | |
| 35 CAC 4.181000 -4.419000 -1.186000 cd 1 HEM 0.0915 **** | |
| 36 HAC 3.404000 -4.891000 -1.788000 ha 1 HEM 0.0767 **** | |
| 37 CBC 5.182000 -5.213000 -0.760000 cc 1 HEM -0.4715 **** | |
| 38 HBC1 5.981000 -4.859000 -0.117000 ha 1 HEM 0.1517 **** | |
| 39 HBC2 5.207000 -6.266000 -1.032000 ha 1 HEM 0.1517 **** | |
| 40 CMB 3.863000 5.294000 0.744000 c3 1 HEM -0.1258 **** | |
| 41 HMB1 3.798000 5.494000 1.824000 hc 1 HEM 0.0397 **** | |
| 42 HMB2 4.826000 5.693000 0.402000 hc 1 HEM 0.0397 **** | |
| 43 HMB3 3.069000 5.874000 0.261000 hc 1 HEM 0.0397 **** | |
| 44 CMC 6.418000 -2.183000 -0.508000 c3 1 HEM 0.0353 **** | |
| 45 HMC1 6.720000 -2.440000 0.518000 hc 1 HEM 0.0049 **** | |
| 46 HMC2 6.786000 -2.983000 -1.160000 hc 1 HEM 0.0049 **** | |
| 47 HMC3 6.946000 -1.261000 -0.777000 hc 1 HEM 0.0049 **** | |
| 48 CMD -1.057000 -4.446000 -2.127000 c3 1 HEM -0.2123 **** | |
| 49 HMD1 -0.334000 -4.774000 -2.886000 hc 1 HEM 0.0653 **** | |
| 50 HMD2 -0.870000 -5.047000 -1.226000 hc 1 HEM 0.0653 **** | |
| 51 HMD3 -2.057000 -4.704000 -2.489000 hc 1 HEM 0.0653 **** | |
| 52 CMA -1.392000 5.286000 -0.173000 c3 1 HEM -0.0747 **** | |
| 53 HMA1 -1.304000 5.510000 0.900000 hc 1 HEM 0.0306 **** | |
| 54 HMA2 -0.657000 5.915000 -0.693000 hc 1 HEM 0.0306 **** | |
| 55 HMA3 -2.388000 5.608000 -0.491000 hc 1 HEM 0.0306 **** | |
| 56 CAA -3.554000 3.168000 -1.187000 c3 1 HEM -0.0115 **** | |
| 57 HAA1 -3.660000 4.127000 -1.709000 hc 1 HEM 0.0253 **** | |
| 58 HAA2 -3.949000 2.419000 -1.880000 hc 1 HEM 0.0253 **** | |
| 59 CAD -3.395000 -2.247000 -2.184000 c3 1 HEM -0.0659 **** | |
| 60 HAD1 -3.818000 -1.387000 -2.716000 hc 1 HEM 0.0364 **** | |
| 61 HAD2 -3.526000 -3.100000 -2.860000 hc 1 HEM 0.0364 **** | |
| 62 CBA -4.444000 3.191000 0.074000 c3 1 HEM -0.0304 **** | |
| 63 HBA1 -4.048000 3.901000 0.813000 h1 1 HEM -0.0023 **** | |
| 64 HBA2 -4.428000 2.209000 0.564000 h1 1 HEM -0.0023 **** | |
| 65 CBD -4.217000 -2.482000 -0.900000 c3 1 HEM -0.0022 **** | |
| 66 HBD1 -4.053000 -1.651000 -0.207000 h1 1 HEM 0.0140 **** | |
| 67 HBD2 -3.864000 -3.386000 -0.384000 h1 1 HEM 0.0140 **** | |
| 68 CGD -5.729000 -2.615000 -1.120000 c 1 HEM 0.5749 **** | |
| 69 CGA -5.891000 3.581000 -0.216000 c 1 HEM 0.6402 **** | |
| 70 O1A -6.681000 3.739000 0.763000 o 1 HEM -0.6508 ***** | |
| 71 O1D -6.463000 -2.631000 -0.087000 o 1 HEM -0.6552 ***** | |
| 72 O2A -6.295000 3.767000 -1.392000 o 1 HEM -0.6508 ***** | |
| 73 O2D -6.192000 -2.733000 -2.281000 o 1 HEM -0.6552 ***** | |
| 74 O1 1.689000 0.783000 -2.374000 oa 1 HEM -0.3729 **** | |
| @<TRIPOS>BOND | |
| 1 1 2 1 | |
| 2 1 3 1 | |
| 3 1 28 1 | |
| 4 2 4 1 | |
| 5 2 26 1 | |
| 6 3 5 1 | |
| 7 3 6 1 | |
| 8 4 5 1 | |
| 9 4 44 1 | |
| 10 5 35 1 | |
| 11 6 7 1 | |
| 12 6 8 1 | |
| 13 8 9 1 | |
| 14 8 12 1 | |
| 15 9 10 1 | |
| 16 9 28 1 | |
| 17 10 11 1 | |
| 18 10 13 1 | |
| 19 11 12 1 | |
| 20 11 59 1 | |
| 21 12 48 1 | |
| 22 13 14 1 | |
| 23 13 15 1 | |
| 24 15 16 1 | |
| 25 15 18 1 | |
| 26 16 19 1 | |
| 27 16 56 1 | |
| 28 17 18 1 | |
| 29 17 19 1 | |
| 30 17 20 1 | |
| 31 18 28 1 | |
| 32 19 52 1 | |
| 33 20 21 1 | |
| 34 20 22 1 | |
| 35 22 23 1 | |
| 36 22 24 1 | |
| 37 23 29 1 | |
| 38 23 40 1 | |
| 39 24 25 1 | |
| 40 24 28 1 | |
| 41 25 26 1 | |
| 42 25 29 1 | |
| 43 26 27 1 | |
| 44 28 74 1 | |
| 45 29 30 1 | |
| 46 30 31 1 | |
| 47 30 32 1 | |
| 48 32 33 1 | |
| 49 32 34 1 | |
| 50 35 36 1 | |
| 51 35 37 1 | |
| 52 37 38 1 | |
| 53 37 39 1 | |
| 54 40 41 1 | |
| 55 40 42 1 | |
| 56 40 43 1 | |
| 57 44 45 1 | |
| 58 44 46 1 | |
| 59 44 47 1 | |
| 60 48 49 1 | |
| 61 48 50 1 | |
| 62 48 51 1 | |
| 63 52 53 1 | |
| 64 52 54 1 | |
| 65 52 55 1 | |
| 66 56 57 1 | |
| 67 56 58 1 | |
| 68 56 62 1 | |
| 69 59 60 1 | |
| 70 59 61 1 | |
| 71 59 65 1 | |
| 72 62 63 1 | |
| 73 62 64 1 | |
| 74 62 69 1 | |
| 75 65 66 1 | |
| 76 65 67 1 | |
| 77 65 68 1 | |
| 78 68 71 1 | |
| 79 68 73 1 | |
| 80 69 70 1 | |
| 81 69 72 1 | |
| @<TRIPOS>SUBSTRUCTURE | |
| 1 HEM 1 **** 0 **** **** |
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