-
Notifications
You must be signed in to change notification settings - Fork 0
/
top_heme_b.inp
819 lines (804 loc) · 35.3 KB
/
top_heme_b.inp
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
* 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 -2.00 ! 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
ATOM HA HA 0.12 ! | \_CHC_/ |
GROUP ! CAB | CMC--HMC3
ATOM CHB CPM -0.31 ! // \ HC / |
ATOM HB HA 0.12 ! 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 CE1 -0.32 ! changed from -.32 so heme b has integral charge (JPB 9/19/08)
ATOM HAB HE1 0.16
GROUP
ATOM CBB CE2 -0.18
ATOM HBB1 HE2 0.09
ATOM HBB2 HE2 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 CE1 -0.32 ! -.32 for cytc only: set to -.31 for myoglobin, -.22 for hemoglobin? JPB 1/30/09
ATOM HAC HE1 0.16
GROUP
ATOM CBC CE2 -0.18
ATOM HBC1 HE2 0.09
ATOM HBC2 HE2 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
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
!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
PRES PHEM 0.00 ! Patch for HEME to His link.
! Patch residues must be 1-HIS, and 2-HEME.
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
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 HRCI -0.97 ! Patch for REDUCED HEME to Cytochrome c links in 1FI9
! Patch residues must be 1:CYS (N-terminal), 2:CYS (C-terminal), 3:HSD, 4:IMID
! and 5:HEMR.
! Modified by Elijah Roberts 12/9/2005 to include charge redistribution and
! to be a single patch.
! Modified by JPB 1/30/09 to include the imidazole linkage
! 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
! now Heme to imidazole portion of patch
ATOM 4H5 HR3 0.09 ! 4HN1 4H2 ! made 4H5 just like H4.
ATOM 4N1 NR1 -0.62 ! | /
ATOM 4HN1 H 0.42 ! 4N1----4C2
ATOM 4C5 CPH1 -0.02 ! / ||
GROUP ! 4H5--4C5 ||
ATOM 4C2 CPH2 0.23 ! \\ ||
ATOM 4H2 HR1 0.26 ! 4C4----4N3
ATOM 4N3 NR2 -0.49 ! | \
ATOM 4C4 CPH1 -0.05 ! 4H4 5FE-
ATOM 4H4 HR3 0.15 !
DELETE ANGLE 5NA 5FE 5NC 5NB 5FE 5ND
BOND 4N3 5FE
ANGLE 4C4 4N3 5FE 4C2 4N3 5FE 4N3 5FE 5NA 4N3 5FE 5NB
ANGLE 4N3 5FE 5NC 4N3 5FE 5ND
IMPR 4N3 4C4 4C2 5FE !add impr for heme/his planarity and heme/met planarity
IC 4C4 4N3 5FE 5NA 0.0000 0.0000 0.0000 0.0000 0.0000
IC 4C4 4N3 5FE 5NB 0.0000 0.0000 0.0000 0.0000 0.0000
IC 4C4 4N3 5FE 5NB 0.0000 0.0000 0.0000 0.0000 0.0000
IC 4C4 4N3 5FE 5NB 0.0000 0.0000 0.0000 0.0000 0.0000
IC 4C2 4N3 5FE 5NA 0.0000 0.0000 0.0000 0.0000 0.0000
PRES HIMD -0.97 ! Patch for REDUCED HEME to imidazole - cyto-c links.
! Patch residues must be 1:CYS (N-terminal), 2:CYS (C-terminal), 3:HSD, 4:IMD
! 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 imidazole portion of patch
GROUP ! !3HD1->4HN1
! 3HD1 3HE1 !3HE1->4H2
ATOM 4N1 NR1 -0.62 ! | / !3CG->4C5
ATOM 4HN1 H 0.42 ! 3HB1 3ND1--3CE1 !3CD2->4C4
ATOM 4C5 CPH1 0.32 ! | / || !3ND1->4N1
GROUP ! -3CB--3CG || !3CE1->4C2
ATOM 4C2 CPH2 0.23 ! | \\ || !3HD2->4H4
ATOM 4H2 HR1 0.26 ! 3HB2 3CD2--3NE2 !3NE2->4N3
ATOM 4N3 NR2 -0.53 ! | \
ATOM 4C4 CPH1 -0.05 ! 3HD2 5FE-
ATOM 4H4 HR3 0.15 !
DELETE ANGLE 5NA 5FE 5NC 5NB 5FE 5ND
BOND 4N3 5FE
ANGLE 4C4 4N3 5FE 4C2 4N3 5FE 4N3 5FE 5NA 4N3 5FE 5NB
ANGLE 4N3 5FE 5NC 4N3 5FE 5ND
IMPR 4N3 4C4 4C2 5FE !add impr for heme/his planarity and heme/met planarity
IC 4C4 4N3 5FE 5NA 0.0000 0.0000 0.0000 0.0000 0.0000
IC 4C4 4N3 5FE 5NB 0.0000 0.0000 0.0000 0.0000 0.0000
IC 4C4 4N3 5FE 5NB 0.0000 0.0000 0.0000 0.0000 0.0000
IC 4C4 4N3 5FE 5NB 0.0000 0.0000 0.0000 0.0000 0.0000
IC 4C2 4N3 5FE 5NA 0.0000 0.0000 0.0000 0.0000 0.0000
END