-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathtoppar_drude_master_example.str
7165 lines (6646 loc) · 352 KB
/
toppar_drude_master_example.str
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
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
* $Id: toppar_drude_master_protein.str 22 2014-08-12 22:16:31Z alex $
* DRUDE master topology and parameter stream file
* Includes water, ions and 2013 protein FF release
* October 2013
* Ions updated, June 2014
*
ioformat extended
!This file must be streamed prior to additional Drude FF toppar stream files
!and it includes parameters for the model compounds (toppar_drude_model*.str)
!references
!
!Proteins
!Lopes, P.E.M., Huang, J., Shim, J., Luo, Y., Li, H., Roux, B., and
!MacKerell, A.D., Jr., “Polarizable Force Field for Peptides and
!Proteins based on the Classical Drude Oscillator,” Journal of
!Chemical Theory and Computation, 9: 5430–5449, 2013 DOI:
!10.1021/ct400781b, NIHMS53671
!
!water
!SWM4-NDP, negative Drude (this will be the default model): Lamoureux,
!G., Harder, E., Vorobyov, I.V., Deng, Y., Roux, B. MacKerell, A.D.,
!Jr., A polarizable model of water for molecular dynamics simulations
!of biomolecules, Chemical Physics Letters, 2006, 418: 245-249.
!
!SWM6: Wenbo Yu, Pedro E. M. Lopes, Benoît Roux and Alexander
!D. MacKerell, Jr. "Six-site Polarizable Model of Water Based on the
!Classical Drude Oscillator" Journal of Chemical Physics, 138: 034508,
!2013
!atomic ions
!Yu, H., Whitfield, T.W., Harder, E., Lamoureux, G., Vorobyov, I.,
!Anisimov, V. M., MacKerell, A.D., Jr., and Roux, B. “Simulating
!Monovalent and Divalent Ions in Aqueous Solution Using a Drude
!Polarizable Force Field, “Journal of Chemical Theory and Computation,
!6: 774–786, 2010
!
!Luo, Y., Jiang, W., Yu, H., MacKerell, A.D., Jr., and Roux, B.,
!“Simulation study of ion pairing in concentrated aqueous salt
!solutions with a polarizable force field,” Faraday Discussions, 160,
!135–149, 2013, PMC3695446
! note use of D for second character to indicate Drude
! polarizable FF (be careful of Cadmium: use CDM)
! Parameter labeling after !
! RESName, generic compound name of model compound followed by additional comments
! for example ! BENZ, benzene, based on crystal survey data
!Formatting information
!RTF section: please use the following format for future residues, including the spacing
!(and please clean a few up of the residues not in this format if you so desire....)
!RESI ALA 0.000
!ATOM N ND2A2 -0.427 ALPHA -1.056 THOLE 0.711
!BOND A1 A2 A3 A4 A5 A6 A7 A8
!IMPR A1 A2 A3 A4
!CMAP A1 A2 A3 A4 A1 A2 A3 A4
!LONEPAIR relative A1 A2 A3 A4 distance 0.30 angle 91.00 dihe 180.00
!ANISOTROPY A1 A2 A3 A4 A11 0.6968 A22 1.2194
!IC A1 A2 A3 A4 1.3474 124.31 180.00 114.26 0.9979
!parameter section
!bond
!CD32E OD30A 360.00 1.415 ! comment
!angles
!HDA1A CD31A CD31A 34.50 110.10 ! comment
!HDA1A CD31A CD31A 34.50 110.10 22.53 2.1790 ! comment
!dihedrals
!CD2O1A ND2A2 CD31C CD2O2A 0.000 3 180.00 ! comment
!impropers
!CD2O1A CD31A ND2A2 OD2C1A 120.000 0 0.00 ! comment
!nonbond (LJ)
!HDW 0.0 -0.0000 0.0000 ! comment
!nbfix
!CD30A ODW -0.00500 4.04699 ! comment
!ioformat extended
read rtf card !append
* Topology for drude water, ions and proteins
*
38
MASS 1 HDP1A 1.00800 H ! polar H, general
MASS 2 HDP1B 1.00800 H ! polar H, ammonium cations
MASS 3 HDA1A 1.00800 H ! aliphatic, H, methyl (-CH), general
MASS 4 HDA1C 1.00800 H ! aliphatic, H, methyl (-CH), special case for ammonium cations
MASS 5 HDA1R5 1.00800 H ! aliphatic, H, methyl (-CH), 5-membered ring
MASS 6 HDA2A 1.00800 H ! aliphatic, H, methyl (-CH2), general
MASS 7 HDA2C 1.00800 H ! aliphatic, H, methyl (-CH2), special case for ammonium cations
MASS 8 HDA2E 1.00800 H ! aliphatic, H, methyl (-CH2), ethers
MASS 9 HDA2R5 1.00800 H ! aliphatic, H, methyl (-CH2), 5-membered ring
MASS 10 HDA3A 1.00800 H ! aliphatic, H, methyl (-CH3), general
MASS 11 HDA3B 1.00800 H ! aliphatic, H, methyl (-CH3), special case for methanol
MASS 12 HDA3C 1.00800 H ! aliphatic, H, methyl (-CH3), special case for ammonium cations
MASS 13 HDR5A 1.00800 H ! 5-membered ring, HG and HD2 in imidazole
MASS 14 HDR5B 1.00800 H ! 5-membered ring, HE1 in imidazole
MASS 15 HDR5C 1.00800 H ! 5-membered ring, H on carbon adjacent to N in pyrrole
MASS 16 HDR5D 1.00800 H ! 5-membered ring, HG and HD2 in imidazolium
MASS 17 HDR5E 1.00800 H ! 5-membered ring, HE1 in imidazolium
MASS 18 HDR6A 1.00800 H ! aromatic H, 6-membered ring, general
MASS 19 HDR6B 1.00800 H ! aromatic H, 6-membered ring, adjacent to N (pyridine)
MASS 20 HDR6C 1.00800 H ! aromatic H, 6-membered ring, between 2 N's (pyrimidine)
MASS 41 CD2O1A 12.01100 C ! carbonyl C, neutral (amide)
MASS 42 CD2O2A 12.01100 C ! carboxylate C, anionic
MASS 43 CD2O3A 12.01100 C ! carboxylate C, neutral (esters, acids)
MASS 44 CD2O3B 12.01100 C ! ester carbonyl C, for lipids
MASS 45 CD2R5A 12.01100 C ! 5-membered ring, CG and CD2 in imidazole
MASS 46 CD2R5B 12.01100 C ! 5-membered ring, CE1 in imidazole
MASS 47 CD2R5C 12.01100 C ! 5-membered ring, pyrole, adjacent to N
MASS 48 CD2R5D 12.01100 C ! 5-membered ring, CG and CD2 in imidizolium
MASS 49 CD2R5E 12.01100 C ! 5-membered ring, CE1 in imidizolium
MASS 50 CD2R6A 12.01100 C ! aromatic C, 6-membered ring
MASS 51 CD2R6B 12.01100 C ! aromatic C, 6-membered ring, adjacent to N (pyridine)
MASS 52 CD2R6C 12.01100 C ! aromatic C, 6-membered ring, between 2 heteroatoms (pyrimidine)
MASS 53 CD2R6D 12.01100 C ! aromatic C, 6-membered ring, bridging far from N (indole)
MASS 54 CD2R6F 12.01100 C ! aromatic C, 6-membered ring, bridging adjacent to N7 (purine)
MASS 55 CD2R6H 12.01100 C ! aromatic C, 6-membered ring, cytosine cmb 01/09
MASS 60 CD2N1A 12.01100 C ! guanidinium C (EH)
MASS 61 CD30A 12.01100 C ! aliphatic sp3 C, 0 hydrogens
MASS 62 CD31A 12.01100 C ! aliphatic sp3 C, 1 hydrogen
MASS 63 CD31C 12.01100 C ! aliphatic sp3 C, 1 hydrogen, special case for carbons adjacent to esters/amides
MASS 64 CD31FA 12.01100 C ! aliphatic sp3 C, 1 hydrogen, furanoses, anomeric C1
MASS 65 CD31FB 12.01100 C ! aliphatic sp3 C, 1 hydrogen, furanoses, C2,C3
MASS 66 CD31FC 12.01100 C ! aliphatic sp3 C, 1 hydrogen, furanoses, C4
MASS 67 CD31G 12.01100 C ! aliphatic sp3 C, 1 hydrogen, glycerol, xhe
MASS 68 CD315A 12.01100 C ! aliphatic sp3 C, 1 hydrogen, ether, 5-memberd ring, CPNM
MASS 69 CD315B 12.01100 C ! aliphatic sp3 C, 1 hydrogen, ether, 5-memberd ring, TF2M
MASS 70 CD316A 12.01100 C ! aliphatic sp3 C, 1 hydrogens, 6-membered ring
MASS 71 CD32A 12.01100 C ! aliphatic sp3 C, 2 hydrogens
MASS 72 CD32AL 12.01100 C ! aliphatic sp3 C, 2 hydrogens, for lipids
MASS 73 CD32B 12.01100 C ! added for GLU, from CD32A
MASS 74 CD32C 12.01100 C ! aliphatic sp3 C, 2 hydrogens, special case for carbons adjacent to esters/amides (see
MASS 75 CD32E 12.01100 C ! aliphatic sp3 C, 2 hydrogens, ether, for CH2 adjacent to O in linear ethers
MASS 76 CD32F 12.01100 C ! aliphatic sp3 C, 2 hydrogens, ethylene glycol, glycerol, xhe
MASS 77 CD325A 12.01100 C ! aliphatic sp3 C, 2 hydrogens, 5-membered ring
MASS 78 CD325B 12.01100 C ! aliphatic sp3 C, 2 hydrogens, ether, 5-membered ring, THF
MASS 79 CD326A 12.01100 C ! aliphatic sp3 C, 2 hydrogens, 6-membered ring
MASS 80 CD326B 12.01100 C ! aliphatic sp3 C, 2 hydrogens, ether, 6-membered ring, THP
MASS 81 CD33A 12.01100 C ! aliphatic sp3 C, 3 hydrogens
MASS 82 CD33B 12.01100 C ! aliphatic sp3 C, 3 hydrogens: special case for methanol
MASS 83 CD33C 12.01100 C ! aliphatic sp3 C, 3 hydrogens: special case for carbons adjacent to esters/amides (see
MASS 84 CD33D 12.01100 C ! aliphatic sp3 C, 3 hydrogens: special methyl C for esters (MAS), neutral acids (ACEH)
MASS 85 CD33E 12.01100 C ! aliphatic sp3 C, 3 hydrogens: special case for CH3 adjacent to a O in linear ethers
MASS 86 CD31HA 12.01100 C ! anomeric carbon, Hexopyranose, dpatel
MASS 87 CD31HB 12.01100 C ! aliphatic sp3 C, 1 hydrogens, 6-membered ring, Hexopyranose
MASS 88 CD31HC 12.01100 C ! aliphatic sp3 C, 1 hydrogens, ether, 6-membered ring, Hexopyranose 1
MASS 131 ND2A1 14.00700 N ! amide, primary (ACEM)
MASS 132 ND2A2 14.00700 N ! amide, secondary (NMA, peptide bond)
MASS 133 ND2A3 14.00700 N ! amide, tertiary (DMA)
MASS 134 ND2B1 14.00700 N ! amine, primary (NA bases)
MASS 135 ND2R5A 14.00700 N ! neutral his protonated ring nitrogen
MASS 136 ND2R5B 14.00700 N ! neutral his unprotonated ring nitrogen
MASS 137 ND2R5C 14.00700 N ! positive his protonated ring nitrogen
MASS 138 ND2R5D 14.00700 N ! aromatic N, 5-membered, purine bases
MASS 139 ND2R5E 14.00700 N ! neutral unprotonated ring nitrogen from Gua/Ade
MASS 140 ND2R5F 14.00700 N ! N1 in THY, alexey
MASS 141 ND2R6A 14.00700 N ! aromatic N, 6-membered ring (pyridine)
MASS 142 ND2R6B 14.00700 N ! aromatic N, 6-membered ring (pyrimidine, N-C-N connectivity)
MASS 143 ND2R6C 14.00700 N ! aromatic N, 6-membered ring: protonated: NA bases
MASS 144 ND2R6D 14.00700 N ! N9 in GUA, alexey
MASS 145 ND2P1A 14.00700 N ! protonated sp2 nitrogen: guanidinium (EH)
MASS 146 ND3P2A 14.00700 N ! protonated sp3 nitrogen, 0, 1 or 3 hydrogens
MASS 147 ND3P3A 14.00700 N ! protonated sp3 nitrogen, 3 or 4 hydrogens (includes ammonia)
MASS 148 ND3A3 14.00700 N ! imino nitrogen as in proline
MASS 171 OD2C1A 15.99940 O ! carbonyl O, neutral (acetone, NMA, acetamide)
MASS 172 OD2C1B 15.99940 O ! carbonyl O, neutral (NA bases)
MASS 173 OD2C2A 15.99940 O ! carboxylate O, anionic (acetate)
MASS 174 OD2C2B 15.99940 O ! carboxylate O, anionic (phosphate), lipids
MASS 175 OD2C2C 15.99940 O ! carboxylate O, anionic (phosphate), nucleic acids
MASS 176 OD2C3A 15.99940 O ! carboxylate O, neutral (esters)
MASS 177 OD2C3B 15.99940 O ! carbonyl O for esters, for lipids
MASS 178 OD30A 15.99940 O ! ether oxygen
MASS 179 OD30B 15.99940 O ! ester oxygen (phosphate), lipid
MASS 180 OD30BN 15.99940 O ! ester oxygen (phosphate), nucleic acid
MASS 181 OD30C 15.99940 O ! ester oxygen (esters)
MASS 182 OD30CL 15.99940 O ! ester oxygen (esters), for lipids
MASS 183 OD30D 15.99900 O ! hydroxyl oxygen in acids
MASS 184 OD305A 15.99940 O ! ether oxygen, 5-membered ring (tetrahydrofuran)
MASS 185 OD306A 15.99940 O ! ether oxygen, 6-membered ring (tetrahydropyran)
MASS 186 OD31A 15.99900 O ! hydroxyl oxygen
MASS 187 OD31B 15.99900 O ! hydroxyl oxygen, special case for long, primary alcohols
MASS 188 OD31C 15.99900 O ! hydroxyl oxygen, phenol
MASS 189 OD31E 15.99900 O ! hydroxyl oxygen, ethylene glycol, glycerol, xhe
MASS 190 OD31F 15.99900 O ! hydroxyl oxygen, Carbohydrates, dpatel
! phosphorous
MASS 211 PD1A 30.974000 P ! phosphorus, (DMP)
MASS 212 PD1AN 30.974000 P ! phosphorus, (DMP), nucleic acids
! Rare gases, dummy atom, lone pair
MASS 221 DUM 0.00000 H ! dummy atom
MASS 222 XED 4.00260 He ! helium
MASS 223 NED 20.17970 Ne ! neon
MASS 224 DRUD 0.00000 H ! drude particle
! Sulfurs
MASS 226 SD31A 32.06000 S ! MESH
MASS 227 SD31B 32.06000 S ! ETSH
MASS 228 SD30A 32.06000 S ! EMS, DMS
MASS 229 SD30B 32.06000 S ! DMDS
! Lone pairs
MASS 231 LPD 0.00000 H ! general lone pair without LJ parameters, NBFIX or NBTHOLE
MASS 232 LPDW 0.00000 H ! lone pair for water: Note overlap of SWM4 and SWM6 LPs
MASS 233 LPDO1 0.00000 H ! lone pair, amide carbonyl oxygen, based on NMA
MASS 234 LPDNA1 0.00000 H ! lone pair, general nucleic acid
! SWM4 and SWM6 polarizable water models
MASS 241 ODW 15.99940 O ! water oxygen, SWM4
MASS 242 ODW6 15.99940 O ! water oxygen, SWM6
MASS 243 HDW 1.00800 H ! water hydrogen
MASS 244 DOH2 0.00000 H ! water Drude
!! Monovalent ions
MASS 251 LID 6.94120 Li ! Lithium
MASS 252 POTD 39.10200 K ! Potassium
MASS 253 SODD 23.00000 Na ! Sodium
MASS 254 RBD 85.46783 Rb ! Rubidium
MASS 255 CSD 132.90545 Cs ! Caesium
MASS 256 FAD 18.99840 F ! Fluoride
MASS 257 CLAD 35.45320 CL ! Chloride
MASS 258 BRAD 79.90410 Br ! Bromide
MASS 259 IAD 126.90447 I ! Iodide
! Divalent ions
MASS 271 MAGD 24.30000 Mg ! Magnesium
MASS 272 CALD 40.08000 CA ! calcium
MASS 273 SRD 87.62000 Sr ! Strontium
MASS 274 BAD 137.33000 Ba ! Barium
MASS 275 ZND 65.38400 Zn ! Zinc
! Halogens
MASS 282 CLDA1 35.45320 CL ! aliphatic chlorine
MASS 283 CLDR1 35.45320 CL ! CHLB, chlorobenzene
DECL -CA
DECL -C
DECL -O
DECL +N
DECL +HN
DECL +CA
!DEFA FIRS NTER LAST CTER
!reset default patches
DEFA FIRS NONE LAST NONE
AUTOGENERATE ANGLES DIHEDRALS DRUDE !note use of DRUDE
! SWM4-NDP water
RESI SWM4 0.000
GROUP
ATOM OH2 ODW 0.00000 TYPE DOH2 ALPHA -0.97825258 THOLE 1.3
ATOM OM LPDW -1.11466
ATOM H1 HDW 0.55733
ATOM H2 HDW 0.55733
BOND OH2 H1
BOND OH2 H2
BOND OH2 OM
BOND H1 H2 ! for SHAKE
ANGLE H1 OH2 H2
ACCEPTOR OH2
LONEPAIR bisector OM OH2 H1 H2 distance 0.24034492 angle 0.0 dihe 0.0
IC H1 OH2 H2 H1 0.9572 104.52 0.00 37.74 1.5139
IC H1 OM *OH2 H2 0.9572 52.26 180.00 52.26 0.9572
IC H2 H1 OH2 OM 1.5139 37.74 0.01 52.26 0.24034492
PATCH FIRST NONE LAST NONE
! SWM6-NDP water
RESI SWM6 0.0000 !
GROUP ! OL1 H1
ATOM OH2 ODW6 0.2880 TYPE DOH2 ALPHA -0.88 THOLE 1.3 ! \ /
ATOM OL1 LPDW -0.1080 ! DOH2~OH2-OM
ATOM OL2 LPDW -0.1080 ! / \
ATOM H1 HDW 0.5307 ! OL2 H2
ATOM H2 HDW 0.5307 !
ATOM OM LPDW -1.1334 !
BOND OH2 H1
BOND OH2 H2
BOND OH2 OL1
BOND OH2 OL2
BOND OH2 OM
BOND H1 H2 ! for SHAKE
ANGLE H1 OH2 H2
ACCEPTOR OH2
LONEPAIR bisector OL1 OH2 H1 H2 distance 0.315 angle 129.451 dihe 90.0
LONEPAIR bisector OL2 OH2 H1 H2 distance 0.315 angle 129.451 dihe 270.0
LONEPAIR bisector OM OH2 H1 H2 distance 0.247 angle 0.000 dihe 0.0
IC H1 OH2 H2 H1 0.9572 104.520 0.000 37.740 1.5139
IC H2 H1 OH2 OL1 1.5139 37.740 123.054 112.888 0.3150
IC H1 H2 OH2 OL2 1.5139 37.740 123.054 112.888 0.3150
IC H1 OL1 *OH2 H2 0.9572 112.888 118.270 112.888 0.9572
IC H2 OL2 *OH2 H1 0.9572 112.888 118.270 112.888 0.9572
IC H2 H1 OH2 OM 1.5139 37.740 0.000 52.260 0.2470
PATCH FIRST NONE LAST NONE
!! Monovalent Ions
RESI LI 1.000 ! Lithium Ion
GROUP
ATOM LI LID 1.000 ALPHA -0.032
PATCHING FIRST NONE LAST NONE
RESI POT 1.000 ! Potassium Ion
GROUP
ATOM POT POTD 1.000 ALPHA -0.830
PATCHING FIRST NONE LAST NONE
RESI SOD 1.000 ! Sodium Ion
GROUP
ATOM SOD SODD 1.000 ALPHA -0.157
PATCHING FIRST NONE LAST NONE
RESI RB 1.000 ! Rubidium Ion
GROUP
ATOM RB RBD 1.000 ALPHA -1.370
PATCHING FIRST NONE LAST NONE
RESI CS 1.000 ! Caesium Ion
GROUP
ATOM CS CSD 1.000 ALPHA -2.360
PATCHING FIRST NONE LAST NONE
RESI F -1.000 ! Fluoride Ion
GROUP
ATOM F FAD -1.000 ALPHA -1.786
PATCHING FIRST NONE LAST NONE
RESI CLA -1.000 ! Chloride Ion
GROUP
ATOM CLA CLAD -1.000 ALPHA -3.969
PATCHING FIRST NONE LAST NONE
RESI BR -1.000 ! Bromide Ion
GROUP
ATOM BR BRAD -1.000 ALPHA -5.262
PATCHING FIRST NONE LAST NONE
RESI I -1.000 ! Iodide Ion
GROUP
ATOM I IAD -1.000 ALPHA -7.439
PATCHING FIRST NONE LAST NONE
!! Divalent Ions
! Yu et al. JCTC 2010, 6, 774-786
RESI ZN 2.000 ! Zinc Ion
GROUP
ATOM ZN ZND 2.000 ALPHA -0.420
PATCHING FIRST NONE LAST NONE
!
RESI MAG 2.000 ! Magnesium Ion
GROUP
ATOM MAG MAGD 2.000 ALPHA -0.075
PATCHING FIRST NONE LAST NONE
!
RESI CAL 2.000 ! Calcium Ion
GROUP
ATOM CAL CALD 2.000 ALPHA -0.490
PATCHING FIRST NONE LAST NONE
!
RESI SR 2.000 ! Strontium Ion
GROUP
ATOM SR SRD 2.000 ALPHA -0.870
PATCHING FIRST NONE LAST NONE
!
RESI BA 2.000 ! Barium Ion
GROUP
ATOM BA BAD 2.000 ALPHA -1.560
PATCHING FIRST NONE LAST NONE
!
!! Dummy atom and rare gases
RESI DUM 0.000 ! DUMMY ATOM
GROUP
ATOM DUM DUM 0.000
PATCHING FIRST NONE LAST NONE
RESI HE 0.000 ! helium
GROUP
ATOM HE XED 0.000 ALPHA -0.205
PATCHING FIRST NONE LAST NONE
RESI NE 0.000 ! neon
GROUP
ATOM NE NED 0.000 ALPHA -0.396
PATCHING FIRST NONE LAST NONE
RESI HE1 0.000 ! helium
GROUP
ATOM HE01 XED 0.000 ALPHA -0.205
PATCHING FIRST NONE LAST NONE
RESI NE1 0.000 ! neon
GROUP
ATOM NE01 NED 0.000 ALPHA -0.396
PATCHING FIRST NONE LAST NONE
RESI ALAD 0.000 ! Alanine dipeptide
!
! HY1 OY O HT1
! \ || HN HA || HNT /
! \ || | | || | /
! HY2--CAY--CY---N---CA--C----NT---CAT--HT2
! / | \
! / HB1--CB--HB3 \
! HY3 | HT3
! HB2
!
GROUP
ATOM CAY CD33C -0.102 ALPHA -1.894 THOLE 2.122
ATOM HY1 HDA3A 0.048
ATOM HY2 HDA3A 0.048
ATOM HY3 HDA3A 0.048
ATOM CY CD2O1A 0.497 ALPHA -0.675 THOLE 0.295
ATOM OY OD2C1A 0.000 ALPHA -0.651 THOLE 0.310
ATOM LPY1 LPDO1 -0.312
ATOM LPY2 LPDO1 -0.227
ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250
ATOM HN HDP1A 0.272
ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078
ATOM HA HDA1A -0.017
ATOM CB CD33A -0.099 ALPHA -1.804 THOLE 2.080
ATOM HB1 HDA3A 0.033
ATOM HB2 HDA3A 0.033
ATOM HB3 HDA3A 0.033
ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295
ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310
ATOM LPOA LPDO1 -0.312
ATOM LPOB LPDO1 -0.227
ATOM NT ND2A2 -0.382 ALPHA -1.942 THOLE 0.250
ATOM HNT HDP1A 0.272
ATOM CAT CD33C -0.055 ALPHA -1.639 THOLE 2.122
ATOM HTC1 HDA3A 0.055
ATOM HTC2 HDA3A 0.055
ATOM HTC3 HDA3A 0.055
BOND CAY CY CY N N CA
BOND CA C C NT NT CAT
BOND CY OY C O
BOND N HN NT HNT
BOND CA HA CA CB CB HB1 CB HB2 CB HB3
BOND CAY HY1 CAY HY2 CAY HY3
BOND CAT HTC1 CAT HTC2 CAT HTC3
BOND OY LPY1 OY LPY2
BOND O LPOA O LPOB
IMPR CY CAY N OY N CY CA HN
IMPR C CA NT O NT C CAT HNT
!2D correction surface
CMAP CY N CA C N CA C NT
LONEPAIR relative LPY1 OY CY CAY distance 0.30 angle 91.0 dihe 0.0
LONEPAIR relative LPY2 OY CY CAY distance 0.30 angle 91.0 dihe 180.0
LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0
LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0
ANISOTROPY OY CY LPY1 LPY2 A11 0.82322 A22 1.14332
ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332
IC CY N CA C 0.00 0.00 -86.00 0.00 0.00 !phi C7eq=-86,C7ax=76
IC N CA C NT 0.00 0.00 79.00 0.00 0.00 !psi C7eq= 79,C7ax=-55
IC CAY CY N CA 0.00 0.00 180.00 0.00 0.00 !omega left
IC CA C NT CAT 0.00 0.00 180.00 0.00 0.00 !omega right
IC N CAY *CY OY 0.00 0.00 144.00 0.00 0.00
IC CA CY *N HN 0.00 0.00 180.00 0.00 0.00
IC NT CA *C O 0.00 0.00 120.00 0.00 0.00
IC CAT C *NT HNT 0.00 0.00 180.00 0.00 0.00
IC C N *CA CB 0.00 0.00 -120.00 0.00 0.00 !define L sugar
IC C N *CA HA 0.00 0.00 120.00 0.00 0.00 !
IC N CA CB HB1 0.00 0.00 180.00 0.00 0.00
IC HB1 CA *CB HB2 0.00 0.00 120.00 0.00 0.00
IC HB1 CA *CB HB3 0.00 0.00 -120.00 0.00 0.00
IC N CY CAY HY1 0.00 0.00 180.00 0.00 0.00
IC HY1 CY *CAY HY2 0.00 0.00 120.00 0.00 0.00
IC HY1 CY *CAY HY3 0.00 0.00 -120.00 0.00 0.00
IC C NT CAT HTC1 0.00 0.00 180.00 0.00 0.00
IC HTC1 NT *CAT HTC2 0.00 0.00 120.00 0.00 0.00
IC HTC1 NT *CAT HTC3 0.00 0.00 -120.00 0.00 0.00
patch first none last none
RESI ALA 0.000
!
! |
! HN-N
! | HB1
! | /
! HA-CA--CB-HB2
! | \
! | HB3
! O=C
! |
!
GROUP
ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250
ATOM HN HDP1A 0.272
ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078
ATOM HA HDA1A -0.017
ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295
ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310
ATOM LPOA LPDO1 -0.312
ATOM LPOB LPDO1 -0.227
GROUP
ATOM CB CD33A -0.099 ALPHA -1.804 THOLE 2.080
ATOM HB1 HDA3A 0.033
ATOM HB2 HDA3A 0.033
ATOM HB3 HDA3A 0.033
BOND N CA CA C C +N CA HA
BOND N HN C O
BOND CA CB CB HB1 CB HB2 CB HB3
BOND O LPOA O LPOB
IMPR C CA +N O N -C CA HN
CMAP -C N CA C N CA C +N
LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0
LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0
ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332
DONOR HN N
ACCEPTOR O C
!C22 IC Table
IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996
IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390 !phi, -60. for a-helix
IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558 !psi, -45. for a-helix
IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297
IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613
IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461
IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840
IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109
IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119
IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114
RESI ARG 1.000 ! arginine
!
! | HH11
! HN-N |
! | HB1 HG1 HD1 HE NH1-HH12
! | | | | | //(+)
! HA-CA--CB--CG--CD--NE--CZ
! | | | | \
! | HB2 HG2 HD2 NH2-HH22
! O=C |
! | HH21
!
GROUP
ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250
ATOM HN HDP1A 0.272
ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078
ATOM HA HDA1A -0.017
ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295
ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310
ATOM LPOA LPDO1 -0.312
ATOM LPOB LPDO1 -0.227
GROUP
ATOM CB CD32A -0.066 ALPHA -1.804 THOLE 2.080
ATOM HB1 HDA2A 0.033
ATOM HB2 HDA2A 0.033
GROUP
ATOM CG CD32A -0.156 ALPHA -1.660 THOLE 1.3
ATOM HG1 HDA2A 0.078
ATOM HG2 HDA2A 0.078
GROUP
ATOM CD CD32A 0.227 ALPHA -1.788 THOLE 0.342
ATOM HD1 HDA2A 0.078
ATOM HD2 HDA2A 0.078
ATOM NE ND2P1A -0.748 ALPHA -1.550 THOLE 1.538
ATOM HE HDP1B 0.378
ATOM CZ CD2N1A 1.129 ALPHA -1.096 THOLE 0.262
ATOM NH1 ND2P1A -0.809 ALPHA -1.403 THOLE 1.538
ATOM HH11 HDP1B 0.369
ATOM HH12 HDP1B 0.369
ATOM NH2 ND2P1A -0.809 ALPHA -1.403 THOLE 1.538
ATOM HH21 HDP1B 0.369
ATOM HH22 HDP1B 0.369
BOND N CA CA C C +N CA HA
BOND N HN C O
BOND CA CB CB HB1 CB HB2
BOND CB CG CG HG1 CG HG2
BOND CG CD CD HD1 CD HD2
BOND CD NE NE HE NE CZ
BOND CZ NH1 NH1 HH11 NH1 HH12
BOND CZ NH2 NH2 HH21 NH2 HH22
BOND O LPOA O LPOB
IMPR CZ NH1 NH2 NE
IMPR C CA +N O N -C CA HN
CMAP -C N CA C N CA C +N
LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0
LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0
ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332
DONOR HN N
DONOR HE NE
DONOR HH11 NH1
DONOR HH12 NH1
DONOR HH21 NH2
DONOR HH22 NH2
ACCEPTOR O C
!C22 IC Table
IC -C CA *N HN 1.3496 122.4500 180.0000 116.6700 0.9973
IC -C N CA C 1.3496 122.4500 180.0000 109.8600 1.5227
IC N CA C +N 1.4544 109.8600 180.0000 117.1200 1.3511
IC +N CA *C O 1.3511 117.1200 180.0000 121.4000 1.2271
IC CA C +N +CA 1.5227 117.1200 180.0000 124.6700 1.4565
IC N C *CA CB 1.4544 109.8600 123.6400 112.2600 1.5552
IC N C *CA HA 1.4544 109.8600 -117.9300 106.6100 1.0836
IC N CA CB CG 1.4544 110.7000 180.0000 115.9500 1.5475
IC CG CA *CB HB1 1.5475 115.9500 120.0500 106.4000 1.1163
IC CG CA *CB HB2 1.5475 115.9500 -125.8100 109.5500 1.1124
IC CA CB CG CD 1.5552 115.9500 180.0000 114.0100 1.5384
IC CD CB *CG HG1 1.5384 114.0100 125.2000 108.5500 1.1121
IC CD CB *CG HG2 1.5384 114.0100 -120.3000 108.9600 1.1143
IC CB CG CD NE 1.5475 114.0100 180.0000 107.0900 1.5034
IC NE CG *CD HD1 1.5034 107.0900 120.6900 109.4100 1.1143
IC NE CG *CD HD2 1.5034 107.0900 -119.0400 111.5200 1.1150
IC CG CD NE CZ 1.5384 107.0900 180.0000 123.0500 1.3401
IC CZ CD *NE HE 1.3401 123.0500 180.0000 113.1400 1.0065
IC CD NE CZ NH1 1.5034 123.0500 180.0000 118.0600 1.3311
IC NE CZ NH1 HH11 1.3401 118.0600 -178.2800 120.6100 0.9903
IC HH11 CZ *NH1 HH12 0.9903 120.6100 171.1900 116.2900 1.0023
IC NH1 NE *CZ NH2 1.3311 118.0600 178.6400 122.1400 1.3292
IC NE CZ NH2 HH21 1.3401 122.1400 -174.1400 119.9100 0.9899
IC HH21 CZ *NH2 HH22 0.9899 119.9100 166.1600 116.8800 0.9914
RESI ASN 0.000
!
! |
! HN-N
! | HB1 OD1 HD21 (cis to OD1)
! | | || /
! HA-CA--CB--CG--ND2
! | | \
! | HB2 HD22 (trans to OD1)
! O=C
! |
!
GROUP
ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250
ATOM HN HDP1A 0.272
ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078
ATOM HA HDA1A -0.017
ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295
ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310
ATOM LPOA LPDO1 -0.312
ATOM LPOB LPDO1 -0.227
GROUP
ATOM CB CD32C -0.302 ALPHA -1.417 THOLE 1.130
ATOM HB1 HDA2A 0.082
ATOM HB2 HDA2A 0.082
ATOM CG CD2O1A 0.906 ALPHA -1.583 THOLE 1.095
ATOM OD1 OD2C1A 0.035 ALPHA -0.885 THOLE 1.227
ATOM ND2 ND2A1 -0.782 ALPHA -1.717 THOLE 1.132
ATOM HD21 HDP1A 0.303
ATOM HD22 HDP1A 0.351
ATOM LPDA LPD -0.411
ATOM LPDB LPD -0.264
BOND N CA CA C C +N CA HA
BOND N HN C O
BOND CA CB CB HB1 CB HB2
BOND CB CG CG OD1
BOND CG ND2 ND2 HD21 ND2 HD22
BOND O LPOA O LPOB
BOND OD1 LPDA OD1 LPDB
IMPR CG CB ND2 OD1 ND2 HD21 HD22 CG
IMPR C CA +N O N -C CA HN
CMAP -C N CA C N CA C +N
LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0
LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0
ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332
LONEPAIR relative LPDA OD1 CG CB distance 0.30 angle 91.0 dihe 0.0
LONEPAIR relative LPDB OD1 CG CB distance 0.30 angle 91.0 dihe 180.0
ANISOTROPY OD1 CG LPDA LPDB A11 0.88 A22 1.32
DONOR HN N
DONOR HD21 ND2
DONOR HD22 ND2
ACCEPTOR OD1 CG
ACCEPTOR O C
!C22 IC Table
IC -C CA *N HN 1.3480 124.0500 180.0000 114.4900 0.9992
IC -C N CA C 1.3480 124.0500 180.0000 105.2300 1.5245
IC N CA C +N 1.4510 105.2300 180.0000 117.3800 1.3467
IC +N CA *C O 1.3467 117.3800 180.0000 120.3200 1.2282
IC CA C +N +CA 1.5245 117.3800 180.0000 124.8800 1.4528
IC N C *CA CB 1.4510 105.2300 121.1800 113.0400 1.5627
IC N C *CA HA 1.4510 105.2300 -115.5200 107.6300 1.0848
IC N CA CB CG 1.4510 110.9100 180.0000 114.3000 1.5319
IC CG CA *CB HB1 1.5319 114.3000 119.1700 107.8200 1.1120
IC CG CA *CB HB2 1.5319 114.3000 -123.7400 110.3400 1.1091
IC CA CB CG OD1 1.5627 114.3000 180.0000 122.5600 1.2323
IC OD1 CB *CG ND2 1.2323 122.5600 -179.1900 116.1500 1.3521
IC CB CG ND2 HD21 1.5319 116.1500 -179.2600 117.3500 0.9963
IC HD21 CG *ND2 HD22 0.9963 117.3500 178.0200 120.0500 0.9951
RESI ASP -1.000
!
! |
! HN-N
! | HB1 OD1
! | | //
! HA-CA--CB--CG
! | | \
! | HB2 OD2(-)
! O=C
! |
!
GROUP
ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250
ATOM HN HDP1A 0.272
ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078
ATOM HA HDA1A -0.017
ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295
ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310
ATOM LPOA LPDO1 -0.312
ATOM LPOB LPDO1 -0.227
GROUP
ATOM CB CD32A -0.190 ALPHA -2.528 THOLE 1.414 ! charge adjusted
ATOM HB1 HDA2A 0.004
ATOM HB2 HDA2A 0.004
ATOM CG CD2O2A 0.708 ALPHA -1.016 THOLE 0.899
ATOM OD1 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399
ATOM OD2 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399
ATOM LP1A LPD -0.383
ATOM LP1B LPD -0.383
ATOM LP2A LPD -0.383
ATOM LP2B LPD -0.383
BOND N CA CA C C +N CA HA
BOND N HN C O
BOND CA CB CB HB1 CB HB2
BOND CB CG CG OD1 CG OD2
BOND O LPOA O LPOB
BOND OD1 LP1A OD1 LP1B
BOND OD2 LP2A OD2 LP2B
IMPH OD1 CB OD2 CG
IMPR C CA +N O N -C CA HN
CMAP -C N CA C N CA C +N
LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0
LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0
ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332
LONEPAIR relative LP1A OD1 CG CB distance 0.35 angle 110.0 dihe 0.0
LONEPAIR relative LP1B OD1 CG CB distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP2A OD2 CG CB distance 0.35 angle 110.0 dihe 0.0
LONEPAIR relative LP2B OD2 CG CB distance 0.35 angle 110.0 dihe 180.0
ANISOTROPY OD1 CG LP1A LP1B A11 0.7229 A22 1.265
ANISOTROPY OD2 CG LP2A LP2B A11 0.7229 A22 1.265
DONOR HN N
ACCEPTOR OD1 CG
ACCEPTOR OD2 CG
ACCEPTOR O C
!C22 IC Table
IC -C CA *N HN 1.3465 125.3100 180.0000 112.9400 0.9966
IC -C N CA C 1.3465 125.3100 180.0000 105.6300 1.5315
IC N CA C +N 1.4490 105.6300 180.0000 117.0600 1.3478
IC +N CA *C O 1.3478 117.0600 180.0000 120.7100 1.2330
IC CA C +N +CA 1.5315 117.0600 180.0000 125.3900 1.4484
IC N C *CA CB 1.4490 105.6300 122.3300 114.1000 1.5619
IC N C *CA HA 1.4490 105.6300 -116.4000 106.7700 1.0841
IC N CA CB CG 1.4490 111.1000 180.0000 112.6000 1.5218
IC CG CA *CB HB1 1.5218 112.6000 119.2200 109.2300 1.1086
IC CG CA *CB HB2 1.5218 112.6000 -121.6100 110.6400 1.1080
IC CA CB CG OD1 1.5619 112.6000 180.0000 117.9900 1.2565
IC OD1 CB *CG OD2 1.2565 117.9900 -170.2300 117.7000 1.2541
RESI CYS 0.000 ! cystiene
!
! |
! HN-N
! | HB1
! | |
! HA-CA--CB--SG
! | | \
! | HB2 HG1
! O=C
! |
!
GROUP
ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250
ATOM HN HDP1A 0.272
ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078
ATOM HA HDA1A -0.017
ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295
ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310
ATOM LPOA LPDO1 -0.312
ATOM LPOB LPDO1 -0.227
GROUP
ATOM CB CD32A 0.106 ALPHA -1.273 THOLE 0.716
ATOM HB1 HDA2A 0.013
ATOM HB2 HDA2A 0.013
ATOM SG SD31B 0.050 ALPHA -2.180 THOLE 1.612
ATOM HG1 HDP1A 0.148
ATOM LPGA LPD -0.165
ATOM LPGB LPD -0.165
BOND N CA CA C C +N CA HA
BOND N HN C O
BOND CA CB CB HB1 CB HB2
BOND CB SG SG HG1
BOND SG LPGA SG LPGB
BOND O LPOA O LPOB
IMPR C CA +N O N -C CA HN
CMAP -C N CA C N CA C +N
LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0
LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0
ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332
LONEPAIR relative LPGA SG CB HG1 distance 0.75 angle 95.0 dihe 100.0
LONEPAIR relative LPGB SG CB HG1 distance 0.75 angle 95.0 dihe 260.0
ANISOTROPY SG CB LPGA LPGB A11 0.8800 A22 1.3200
DONOR HN N
DONOR HG1 SG
ACCEPTOR SG
ACCEPTOR O C
!C22 IC table
IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982
IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202
IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498
IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306
IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548
IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584
IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837
IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359
IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134
IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124
IC CA CB SG HG1 1.5584 113.8700 176.9600 97.1500 1.3341
RESI GLN 0.000
!
! |
! HN-N
! | HB1 HG1 OE1 HE21 (cis to OE1)
! | | | || /
! HA-CA--CB--CG--CD--NE2
! | | | \
! | HB2 HG2 HE22 (trans to OE1)
! O=C
! |
!
GROUP
ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250
ATOM HN HDP1A 0.272
ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078
ATOM HA HDA1A -0.017
ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295
ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310
ATOM LPOA LPDO1 -0.312
ATOM LPOB LPDO1 -0.227
GROUP
ATOM CB CD32A -0.066 ALPHA -1.804 THOLE 2.080
ATOM HB1 HDA2A 0.033
ATOM HB2 HDA2A 0.033
GROUP
ATOM CG CD32C -0.302 ALPHA -1.417 THOLE 1.130
ATOM HG1 HDA2A 0.082
ATOM HG2 HDA2A 0.082
ATOM CD CD2O1A 0.906 ALPHA -1.583 THOLE 1.095
ATOM OE1 OD2C1A 0.035 ALPHA -0.885 THOLE 1.227
ATOM NE2 ND2A1 -0.782 ALPHA -1.717 THOLE 1.132
ATOM HE21 HDP1A 0.303
ATOM HE22 HDP1A 0.351
ATOM LPEA LPD -0.411
ATOM LPEB LPD -0.264
BOND N CA CA C C +N CA HA
BOND N HN C O
BOND CA CB CB HB1 CB HB2
BOND CB CG CG HG1 CG HG2
BOND CG CD CD OE1
BOND CD NE2 NE2 HE21 NE2 HE22
BOND O LPOA O LPOB
BOND OE1 LPEA OE1 LPEB
IMPR CD CG NE2 OE1 NE2 HE21 HE22 CD
IMPR C CA +N O N -C CA HN
CMAP -C N CA C N CA C +N
LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0
LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0
ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332
LONEPAIR relative LPEA OE1 CD CG distance 0.30 angle 91.0 dihe 0.0
LONEPAIR relative LPEB OE1 CD CG distance 0.30 angle 91.0 dihe 180.0
ANISOTROPY OE1 CD LPEA LPEB A11 0.82322 A22 1.14332
DONOR HN N
DONOR HE21 NE2
DONOR HE22 NE2
ACCEPTOR OE1 CD
ACCEPTOR O C
!C22 IC Table
IC -C CA *N HN 1.3477 123.9300 180.0000 114.4500 0.9984
IC -C N CA C 1.3477 123.9300 180.0000 106.5700 1.5180
IC N CA C +N 1.4506 106.5700 180.0000 117.7200 1.3463
IC +N CA *C O 1.3463 117.7200 180.0000 120.5900 1.2291
IC CA C +N +CA 1.5180 117.7200 180.0000 124.3500 1.4461
IC N C *CA CB 1.4506 106.5700 121.9100 111.6800 1.5538
IC N C *CA HA 1.4506 106.5700 -116.8200 107.5300 1.0832
IC N CA CB CG 1.4506 111.4400 180.0000 115.5200 1.5534
IC CG CA *CB HB1 1.5534 115.5200 120.9300 106.8000 1.1147
IC CG CA *CB HB2 1.5534 115.5200 -124.5800 109.3400 1.1140
IC CA CB CG CD 1.5538 115.5200 180.0000 112.5000 1.5320
IC CD CB *CG HG1 1.5320 112.5000 118.6900 110.4100 1.1112
IC CD CB *CG HG2 1.5320 112.5000 -121.9100 110.7400 1.1094
IC CB CG CD OE1 1.5534 112.5000 180.0000 121.5200 1.2294
IC OE1 CG *CD NE2 1.2294 121.5200 179.5700 116.8400 1.3530
IC CG CD NE2 HE21 1.5320 116.8400 -179.7200 116.8600 0.9959
IC HE21 CD *NE2 HE22 0.9959 116.8600 -178.9100 119.8300 0.9943
RESI GLU -1.000 ! glutamate
!
! |
! HN-N
! | HB1 HG1 OE1
! | | | //
! HA-CA--CB--CG--CD
! | | | \
! | HB2 HG2 OE2(-)
! O=C
! |
!
GROUP
ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250
ATOM HN HDP1A 0.272
ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078
ATOM HA HDA1A -0.017
ATOM C CD2O1A 0.497 ALPHA -0.675 THOLE 0.295
ATOM O OD2C1A 0.000 ALPHA -0.651 THOLE 0.310
ATOM LPOA LPDO1 -0.312
ATOM LPOB LPDO1 -0.227
GROUP
ATOM CB CD32B -0.066 ALPHA -1.804 THOLE 2.080
ATOM HB1 HDA2A 0.033
ATOM HB2 HDA2A 0.033
GROUP
ATOM CG CD32A -0.190 ALPHA -2.528 THOLE 1.414
ATOM HG1 HDA2A 0.004
ATOM HG2 HDA2A 0.004
ATOM CD CD2O2A 0.708 ALPHA -1.016 THOLE 0.899
ATOM OE1 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399
ATOM OE2 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399
ATOM LP1A LPD -0.383
ATOM LP1B LPD -0.383
ATOM LP2A LPD -0.383
ATOM LP2B LPD -0.383
BOND N CA CA C C +N CA HA
BOND N HN C O
BOND CA CB CB HB1 CB HB2
BOND CB CG CG HG1 CG HG2
BOND CG CD CD OE1 CD OE2
BOND O LPOA O LPOB
BOND OE1 LP1A OE1 LP1B
BOND OE2 LP2A OE2 LP2B
IMPH OE1 CG OE2 CD
IMPR C CA +N O N -C CA HN
CMAP -C N CA C N CA C +N
LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0
LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0
ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332
LONEPAIR relative LP1A OE1 CD CG distance 0.35 angle 110.0 dihe 0.0
LONEPAIR relative LP1B OE1 CD CG distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP2A OE2 CD CG distance 0.35 angle 110.0 dihe 0.0
LONEPAIR relative LP2B OE2 CD CG distance 0.35 angle 110.0 dihe 180.0
ANISOTROPY OE1 CD LP1A LP1B A11 0.7229 A22 1.265
ANISOTROPY OE2 CD LP2A LP2B A11 0.7229 A22 1.265
DONOR HN N
ACCEPTOR OE1 CD
ACCEPTOR OE2 CD
ACCEPTOR O C
!C22 IC Table
IC -C CA *N HN 1.3471 124.4500 180.0000 113.9900 0.9961
IC -C N CA C 1.3471 124.4500 180.0000 107.2700 1.5216
IC N CA C +N 1.4512 107.2700 180.0000 117.2500 1.3501
IC +N CA *C O 1.3501 117.2500 180.0000 121.0700 1.2306
IC CA C +N +CA 1.5216 117.2500 180.0000 124.3000 1.4530
IC N C *CA CB 1.4512 107.2700 121.9000 111.7100 1.5516
IC N C *CA HA 1.4512 107.2700 -118.0600 107.2600 1.0828
IC N CA CB CG 1.4512 111.0400 180.0000 115.6900 1.5557
IC CG CA *CB HB1 1.5557 115.6900 121.2200 108.1600 1.1145
IC CG CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131
IC CA CB CG CD 1.5516 115.6900 180.0000 115.7300 1.5307
IC CD CB *CG HG1 1.5307 115.7300 117.3800 109.5000 1.1053
IC CD CB *CG HG2 1.5307 115.7300 -121.9600 111.0000 1.1081
IC CB CG CD OE1 1.5557 115.7300 180.0000 114.9900 1.2590
IC OE1 CG *CD OE2 1.2590 114.9900 -179.1000 120.0800 1.2532
RESI GLY 0.000
!