-
-
Notifications
You must be signed in to change notification settings - Fork 403
/
alexandria.prm
509 lines (489 loc) · 30.8 KB
/
alexandria.prm
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
//
// Copyright (C) 2009 by Frank Peters <e.a.j.f.peters@tue.nl>
//
// This is a SMARTS template-file for GAFF-atom types
//
// It is attempted to obey the typing given in the "ATOMTYPE_GFF.DEF"
// file included with the antechamber package of amber10.
// There is no 1-to-1 correspondence between the ATD format and SMARTS.
// Therefore the current definitions need to be tested and possibly changed
//
//
//
// GAFF atomtypes defined using SMARTS
// [SMARTS] [atomtype id number] [description]
// must be sorted according to the ELEMENT and COMPLEXITY OF THE TYPERULE!
//
// Upadted (2016) by Mohammad Mehdi Ghahremanpour <mohammad.ghahremanpour@icm.uu.se>
// Updated (2019) by Mohammad Mehdi Ghahremanpour <mohammad.ghahremanpour@yale.edu>
// Updated (2021) by David van der Spoel <david.vanderspoel@icm.uu.se> for usage with alexandria
//
// Be careful lines do not exceed the maximum length of 150!
// SMARTS rules for hydrogens
atom [*] X
atom [#1] hc "other hydrogen e.g. on aromatic C"
atom [#1X1] ha "other hydrogen e.g. on aromatic C"
atom [#1X1]O ho "H on oxygen"
atom [#1X1][#9,#17,#35,#53] ho "H on halogen"
atom [#1X1][OD2]-[#1X1] hw "H on water"
atom [#1X1]N hn "H on nitrogen"
atom [#1X1]n hn "H on nitrogen"
atom [#1X1]S hs "H on sulphur"
atom [#1X1]P hp "H on phosphor"
atom [#1X1][CX4] hc "H on aliphatic C"
atom [#1X1][#6X4] hc "H on aliphatic C"
atom [#1X1][#6X3]=[#6] ha "H on conjugate carbon"
atom [#1X1][#6X3](=[#6])[#6] ha "H on conjugate carbon"
atom [#1X1][#6X3](=[#6])[#1] ha "H on conjugate carbon"
atom [#1X1][#6X2]#[#6] ha "H on carbon with a triple bond"
atom [#1X1][#6](-[#6]=[#7])(=[#6]) ha "H on conjugate carbon"
atom [#1X1][#6X4]([#6])([#6])[#1] hc "H on aliphatic C"
atom [#1X1][C][#7,#8,#9,#16,#17,#35,#53] h1 "H on carbon in a chain with 1 electron-withdrawal group"
atom [#1X1][C]=[#7,#8,#9,#16] h1 "H on carbon in a chain with 1 electron-withdrawal group"
atom [#1X1][C][F,Cl,Br,I] h1 "H on carbon in a chain with 1 electron-withdrawal group"
atom [#1X1][C]([#6])([F,Cl,Br,I])[#1] h1 "H on carbon in a chain with 1 electron-withdrawal group"
atom [#1X1][C](=[#6])[F,Cl,Br,I] h1 "H on carbon in a chain with 1 electron-withdrawal group"
atom [#1X1][C]([#7,#8,#9,#16,#17,#35,#53])[#7,#8,#9,#16,#17,#35,#53] h2 "H on carbon in a chain with 2 electron-withdrawal group"
atom [#1X1][C]([#6])([F,Cl,Br,I])[F,Cl,Br,I] h2 "H on carbon in a chain with 2 electron-withdrawal group"
atom [#1X1][C]([F,Cl,Br,I])[F,Cl,Br,I] h2 "H on carbon in a chain with 2 electron-withdrawal group"
atom [#1X1][C](=[#7,#8,#9,#16])([#7,#8,#9,#16]) h2 "H on carbon in a chain with 2 electron-withdrawal group"
atom [#1X1][C]([#7,#8,#16,#17,#35,#53])([#7,#8,#16,#17,#35,#53])[#7,#8] h3 "H on carbon in a chain with 3 electron-withdrawal group"
atom [#1X1][C]([#7,#8,#16,#17,#35,#53])([#7,#8,#16,#17,#35,#53])[#16,#17] h3 "H on carbon in a chain with 3 electron-withdrawal group"
atom [#1X1][C]([#7,#8,#16,#17,#35,#53])([#7,#8,#16,#17,#35,#53])[#35,#53] h3 "H on carbon in a chain with 3 electron-withdrawal group"
atom [#1X1][C]([F,Cl,Br,I])([F,Cl,Br,I])[F,Cl,Br,I] h3 "H on carbon in a chain with 3 electron-withdrawal group"
atom [#1X1][C]([F,Cl,Br,I])([F,Cl,Br,I])[O,F,Cl,Br,I] h3 "H on carbon in a chain with 3 electron-withdrawal group NEW"
atom [#1X1][c](=[#7,#8,#16]) h4 "H on carbon in a ring with 1 electron-withdrawal group"
atom [#1X1][c]([#7,#8,#16,#17,#35,#53])(=[#6]) h4 "H on carbon in a ring with 1 electron-withdrawal group"
atom [#1X1][c]([#7,#8,#16])(=[#6]) h4 "H on carbon in a ring with 1 electron-withdrawal group"
atom [#1X1][c][#7,#8,#16,#17,#35,#53] h4 "H on carbon in a ring with 1 electron-withdrawal group"
atom [#1X1][c][#7,#8,#16,#17,#35,#53] h4 "H on carbon in a ring with 1 electron-withdrawal group"
atom [#1X1][c]-[#15X3] h4 "H on carbon in a ring with 1 electron-withdrawal group"
atom [#1X1][c]([#7,#8,#9,#16,#17,#35,#53])(=[#7,#8,#16]) h5 "H on carbon in a ring with 2 electron-withdrawal group"
atom [#1X1][c](=[#7,#8,#16])([#7,#8,#9,#16,#17,#35,#53]) h5 "H on carbon in a ring with 2 electron-withdrawal group"
atom [#1X1][c]([#7,#8,#16,#17,#35,#53])[#7,#8,#16,#17,#35,#53] h5 "H on carbon in a ring with 2 electron-withdrawal group"
atom [#1X1][Ge] DU "H on Ge"
// SMARTS rules for carbons
atom [c] ca "sp2 C in aromatic ring"
atom [#6X1] c1 "sp C"
atom [#6X2] c1 "sp C"
atom [#6X2](#*)-*=* cg "sp C in conjugated system"
atom [#6X2](#*)-*#* cg "sp C in conjugated system"
atom [#6X2](#[#7])[#6X3] cg "sp C in conjugated system"
atom [#6X2](#[#6])[#1] c1 "sp C"
atom [#6X2](#[#6X2])(-[#7X3]) c1
atom [#6X3] c2 "sp2 C in aliphatic system"
//atom [#6X3](=[#7X3])(-[#8X1]) c "C-O- in resonance structure of amide"
atom [#6X3](=[#6X3])([#6X4])[#6X3] c2 "sp2 C in aliphatic system"
atom [#6X3;!R](=[#6])([#1])[#1] c2 "sp2 C in aliphatic system"
atom [#6X3;!R](=[#6])([#6])[#1] c2 "sp2 C in aliphatic system"
atom [#6X3;!R](=[#7X3])([#7X3])[#7X3] cz "guanidinium carbon"
atom [#6X3;!R](=[*&!O,S])-*=* ce "sp2 C conjugated chain"
atom [#6X3;!R](#*)-*=* ce "sp2 C conjugated chain"
atom [#6X3;!R](#*)-*#* ce "sp2 C conjugated chain"
atom [#6X3;!R](=*)-*#* ce "sp2 C conjugated chain"
atom [#6X3;H&!R](=*)-*~[R;a] ce "sp2 C conjugated chain"
atom [#6X3;!R](=[#7X3])([#7X3])[#7X2](=[#6X3;!R]) cz "guanidinium carbon"
atom [#6X3;R](=[#6,#7,#8])(-[#6,#7,#8])(-[#1]) ca "sp2 C in aromatic ring"
atom [#6X3;R]([#6]=[#6]-[#6]) cc "sp2 C in conjugated ring NEW"
atom [#6X3;R](:[#6])[#6] ca "sp2 C in aromatic ring"
atom [#6X3;R](=[#6])([#6])[#1] ca "sp2 C in aromatic ring"
//atom [#6X3;R](=*)-*=* ca "sp2 C in aromatic ring"
atom [#6X3;R](=[#6X3])([#6])[#1] ca "sp2 C in aromatic ring"
atom [#6X3;R](=[#6])([#6])[F,Cl,Br,I] c2 "sp2 C in a ring with 1 electron-withdrawal group"
atom [#6X3;R](=[#6X3])([#6X4])[#6] c2 "sp2 C in a ring"
atom [#6X3;R](=*)-*#* cc "sp2 C in a conjugated ring"
atom [#6X3;R](#*)-*#* cc "sp2 C in a conjugated ring"
atom [#6X3;R]:[#7,#8,#16] cc "sp2 C in a ring with 1 electron-withdrawal group"
atom [#6X3;R]([#7,#8,#16])[#1] cc "sp2 C in a ring with 1 electron-withdrawal group"
atom [#6X3;R](=[#7])(-[#6,#7])[#1] cc "sp2 C in a ring"
atom [#6X3;R](=[#6])([#8X2,#16X2])[#6] cc "sp2 C in a ring"
atom [#6X3;R]([#7,#8,#16])[#7,#8,#16] cc "sp2 C in a ring with 2 electron-withdrawal group"
atom [#6X3]=[O,S] c "C=O or C=S"
atom [#6X3](=[#7X3])(-[#8X1]) c "C-O- in resonance structure of amide"
atom [#6X3](-[OD1])=[O] cm "COO- NEW"
atom [#6X3;R]([#7,#8,#16])([#7,#8,#16])[#1] cc "sp2 C in a ring with 2 electron-withdrawal group"
atom [#6X3;R](=[#6])([#7,#8,#16])[#1] cc "sp2 C in a ring with 1 electron-withdrawal group"
atom [#6X3;R](=[#6,#7])(@[#7,#8,#16]) cc "sp2 C in a ring with 2 electron-withdrawal group"
atom [#6X3;R](=[#7])(@[#6,#7,#8,#16]) cc "sp2 C in a ring with 2 electron-withdrawal group"
atom [#6X3;R](=[#6,#7])(@[#7,#8,#16])[#1] cc "sp2 C in a ring with 2 electron-withdrawal group"
atom [#6X3;R](=[#7])(@[#6,#7,#8,#16])[#1] cc "sp2 C in a ring with 2 electron-withdrawal group"
atom [#6X3;R](=[#6X3])(-[#6X3]=[#8X1])[#1] cc "sp2 C in a conjugated ring"
atom [#6X3;R](:[#6][#8X2])[#6]=[#16X1] cc
atom [#6X3r3] cu "sp2 C 3-membered ring"
atom [#6X3r3]=O c "sp2 C 3-membered ring"
atom [#6X3r4] cv "sp2 C 4-membered ring"
atom [#6X3r4]=*-*=* cc "NEW"
atom [#6X3r4]-*=*-* cc "NEW"
atom [#6X3r4]=O c
atom [#6X3r5](:[#6][#7,#8,#16])[#6] cd "CHANGED"
atom [cr5]o cc
atom [cr5]n cc
atom [cr5]([nX2]) cd
atom [cr5]([nX3]) cc
atom [cX3r5](=[O])([nX3])[nX3] c
atom [#6X3r5](-[#6]=[#6]-[#6]) cc "sp2 C fulvene"
atom [#6X3r5](=[#6])([#6])[#1] c2 "sp2 C in aliphatic ring of size 5 with 1 electron-withdrawal group"
atom [#6X3r5](=[#6X3])(-[#6X3]=[#8X1])[#1] cc "sp2 C in a conjugated ring of size 5"
atom [#6X3r5](:[#6X3])(-[#16X2])[#1] cc "sp2 C in a conjugated ring of size 5"
atom [#6X3r5](:[#6X3]-[#16X2])([#6X3])[#1] cd "sp2 C in a conjugated ring of size 5"
atom [#6X3r5](=[#6X3][#6X3])[#6X3]=[#8X1] cc
atom [#6X3r5](=[#6X3][#6X3]=[#8X1])[#6X3] cc
atom [#6X3r5](=[#6X3]-[#6X3])[#6X3]=[#8X1] cc
atom [#6X3r5](-[#6X3])(=[#6X3]-[#6X4])[#1] cc
atom [#6X3r5](-[#6X4])(=[#6X3]-[#6X3])[#1] cc
atom [#6X3r5](=[#6X3][#8X2])([#6X3])[#1] cc
atom [#6X3r5](=[#6X3])(-[#6X4]-[#8])[#1] c2
atom [#6X3r5](=[#6X3])(-[#6X4]-[#8])[#1] c2
atom [#6X3r5]([#6X4])(=[#6X3]-[#8])[#1] c2
atom [#6X3r5](=[#6])([#7,#8,#16])[#1] c2 "sp2 C in aliphatic ring of size 5"
atom [#6X3r5](-[#6X3]=[#6X3])(=[#6X3]-[#6X4])[#1] cd
atom [#6X3r5](=[#6X3][#8X2])([#6X4]-[#6X3])[#1] c2
atom [#6X3r5](=[#6X3]-[#6X4])([#6X4]-[#6X4])[#1] c2
atom [#6X3r5](=[#6X3]-[#6X3])(@[#8]@[#6X3]([#1]))[#1] cc
atom [#6X3r5](=[#6X3]-[#16X2])(-[#6X4]-[#6X4])[#1] c2
atom [#6X3r5]=[O,S] c
atom c-c cp "bridge aromatic c"
atom [#6X3r6](=[#6])([#6X4])[#1] c2 "sp2 C in aliphatic ring of size 6"
atom [#6X3r6](=[#6X3])([#6X4])[#6X4] c2 "sp2 C in a ring of size 6"
atom [#6X3r6](=[#6X3])([#6X3])[Br] ca
atom [#6X3r6](=[#6X3])([#6X3])[Cl] ca
atom [#6X3r6](=[#6X3])([#6X3])[F] ca
atom [#6X3r6](:[#6])([#6]@[#7])[#1] cc
atom [#6X3r6](=[#6X3]-[#6X3]=[#8X1])([#6X3])[#1] cd "sp2 C in a conjugated ring of size 6"
atom [#6X3r6](=[#6]@[#7,#8,#16])[#6] cd "CHANGED"
atom [#6X3r6](=[#6]-[#6X4])([#8]-[#6X4])[#1] c2
atom [#6X3r6](=[#6X3]-[#6X4])([#8]-[#6X3])[#1] c2
atom [#6X3r6](=[#6X3]-[#6X4])([#6X3]=[#8])[#1] c2
atom [#6X3r6]([#6X4])(=[#6X3]-[#6X3])[#1] c2
atom [#6X3r6](=[#6X3]@[#6X4])([#6X3])[#1] c2
atom [#6X3r6](=[#6X3]-[F])([#6X4]-[#6X4])[#1] c2
atom [#6X3r6](-[#6X4]-[#6X4])(=[#6X3]-[#8])[#1] c2
atom [#6X3r6]([#6X4]-[#6X3])(=[#6X3]-[#8])[#1] c2
atom [#6X3r6](=[#6X3][#7])([#6X3]=[#7])[#1] cc
atom [#6X3r6](=[#6X3])([#6X3](=[O])[O])[#6X3]=[O] cc
atom [#6X3r6](=[#6X3][#6X3](=[O])[O])([#6X3]=[O])[#1] cc
atom [cr6]n ca
atom [cr6]([c][n]) ca
atom [cX3r6]=O c
atom [cX3r6](:[n][c]=[O])([NX3])[c] cd "SP2 carbon in cytosine-like rings"
atom [cX3r6](:[c][nX3])([c][NX3]) cd "SP2 carbon in cytosine-like rings"
atom [cX3r6](:[c][cX3][NX3])([nX3]) cc "SP2 carbon in cytosine-like rings"
atom [cX3r6]([cX3]=O) cd
atom [cX3r6]([nX3])([cX3][cX3]=O) cc
atom [#6X3r7](=[#6])([#6])[#1] c2
atom [#6X3r7][#6]=[#6]-[#15] cc
atom [#6X3r7](=[#6][#15])([#6])[#1] cc
atom [#6X3r7](=[#6X3])([#15X3])[#1] cc "sp2 C in a conjugated ring of size 7"
atom [#6X3r7](!:[#6])([#6]=[#6]) cc "sp2 C in a non-aromatic conjugated ring of size 7"
atom [#6X3r7](=[#6][#15])([#6])[#1] cc
atom [#6X3r7](:[#6X3])([#6X3]=[O])[#1] cc
atom [#6X3r7](:[#6X3][#6X3]=[O])[#6X3][#1] cc
atom [#6X3r7]([#6X3]:[#6X3][#6X3]=[O])[#6X3][#1] cc
atom [#6X3r8](=[#6]-*)(-[#6]=*)[#1] cc
atom [#6X3r8](=[#6])([#6])[#1] c2 "sp2 C in a ring of size 8"
atom [#6X3r8]=*-*=* cc "sp2 C in a ring of size 8"
atom [#6X4] c3 "other sp3 C"
atom [#6X4](-*)(-*)(-*)-* c3 "other sp3 C"
atom [#6X4]([#6])([#6])([#1])[#1] c3 "sp3 carbon"
atom [#6X4]([#6X3])([#6X3])([#1])[#1] c3
atom [#6X4]([#6X4])([#6X4])([#1])[#1] c3
atom [#6X4]([#6X3])([#8X2])([#1])[#1] c3
atom [#6X4]([#6])([#6])([#6])[#6] c3
atom [#6X4;R]([#6])([#6])([#1])[#1] c3 "sp3 carbon in aliphatic ring"
atom [#6X4;R]([#6])([#6])([#6])[#6] c3
atom [#6X4;R]([#6])([#6])([#6])[#8] c3
atom [#6X4;R]([#6])([#6])([#6])[F] c3
atom [#6X4;R]([#6])([#6])([F])[F] c3
atom [#6X4&H;R] cc
atom [#6X4&H0;R][#7] cc
atom [#6X4r3] cx "3-membered ring atom"
atom [#6X4r4] cy "4-membered ring atom"
atom [#6X4r5] c3
atom [#6X4r5]([#7])([#6])[#6] cc
atom [cX3r5] ca
atom [cX3r6] ca
atom [#6X4r5] c3
atom [#6X4r5]([#6X4])([#6X4r5])([#6X3r5])[#1] c3
atom [#6X4r5]([#6X3]=[#8X1])([#6X3])([#6X4])[#1] c3
atom [#6X4r5]([#6X4])([#6X3]=[#8])([#7X3])[#1] c3
atom [#6X4r5]([#6X4])([#6X3])([#6X3])[#1] c3
atom [#6X4r6] c3
atom [#6X4r6]([#6X3])([#6X3])[#6X4] cc
atom [#6X4r6]([#6X4])([#8X2])([#6X2])[#1] c3
atom [#6X4r6]([#6X4][#8X2])([#7])([#1])[#1] c3
atom [#6X4r7] c3
atom [#6X4r8] c3
atom [CX3r5]1=[CX3r5][CX3r5]=[CX3r5][NX3r5]1 ca "sp2 N pyrrole"
// SMARTS rules for halogens
atom [#9]~* f (-*) "general fluorine"
atom [#17]~* cl (-*) "general chlorine"
atom [#35]~* br (-*) "general bromine"
atom [#53]~* i (-*) "general iodine"
// SMARTS rules for phosphorous
atom [#15X1] p2 "other sp2 P"
atom [#15X1]#[#6,#7,#8,#16,#15] p1 "sp P"
atom [#15X2] p2 "other sp2 P"
atom [#15X2;R](=*)-*=* pc "sp2 P of conjugated ring"
atom [#15X2;R](=*)-*#* pc "sp2 P of conjugated ring"
atom [#15X2;R](=[#6])[#8] pc "sp2 P of conjugated ring"
atom [#15X2;R](#*)-*#* pc "sp2 P of conjugated ring"
atom [#15X2;!R](=*)-*=* pe "sp2 P of conjugated chain"
atom [#15X2;!R](=*)-*#* pe "sp2 P of conjugated chain"
atom [#15X2;!R](#*)-*#* pe "sp2 P of conjugated chain"
atom [#15;a] pb "aromatic P"
atom [#15X3] p3 "other sp3 P"
atom [#15X3](=[#8])(=[#8])[#8] p4 ""
atom [#15X3]=[O,S] p4 "hypervalent P"
atom [#15X3](=*)-*=* px "sp2 P of conjugated system"
atom [#15X3](=*)-*#* px "sp2 P of conjugated system"
atom [#15X4] p5 "hypervalent P"
atom [#15X4](=*)-*=* py "P of conjugated system"
atom [#15X4](=*)-*#* py "P of conjugated system"
atom [#15X5] p6 "sp3d P, hypervalent P"
atom [#15X6] p7 "sp3d2 P, hypervalent P"
// SMARTS rules for nitrogens
atom [#7X1;!R] n1 "sp1 N"
atom [#7X1]=[#8] n1 "sp1 N"
atom [#7X2] n2 "sp2 N"
atom [#7X2](=[#6])[#1] n2 "sp2 N"
atom [#7X2](=[#8])[F,Cl,Br,I] n2 "sp2 N"
atom [#7X2](=[#7X2]=[#7X2]) n1 "sp1 N"
atom [#7X2](=[#7X2])(=[#7X2]) n1 "sp1 N"
atom [#7X2](=[#8X1])(=[#8X1]) n1 "sp1 N in NO2^+"
atom [#7X2](#*)-* n1 "sp1 N"
atom [#7X2](=[#7X2])-* n2 "sp1 N"
atom [nX2] nb "aromatic N"
#atom [#7X2;R](=*)=* nb "aromatic N; MMW: Aromatic?"
#atom [#7X2;R](=*)(-*) nb "aromatic N; MMW: Aromatic?"
atom [#7X2;R](=[#7])[#16] nd "sp2 N of conjugated ring"
atom [#7X2;R](:[#6])[#7] nd "sp2 N of conjugated ring"
atom [#7X2;R]=[#6][#7] nd "sp2 N of conjugated ring"
atom [#7X2;R]=[#6][#8] nd "sp2 N of conjugated ring"
atom [#7X2;R]=[#6][#16] nd "sp2 N of conjugated ring"
atom [#7X2r5](:[#6])[#6] nb "N in aromatic ring due to lone pairs of size 5"
atom [nX2r6](:[#6X3][NX3])([#6X3]=[O]) nd "N in Cytosine"
atom [nX2r5]([#6])[#8,#16] nc "N in aromatic ring due to lone pairs of size 5"
atom [#7X2;R](-[#7X3]-[#6X3])=[#6X3] nc "sp2 N of conjugated ring"
atom [#7X2;R](=*)-*=* nc "sp2 N of conjugated ring"
atom [#7X2;R](=*)-*#* nc "sp2 N of conjugated ring"
atom [#7X2;R](#*)-*#* nc "sp2 N of conjugated ring"
atom [#7X2;R](:[#7])[#7] nc "sp2 N of conjugated ring"
atom [#7X2;R](:[#7])[#16X2] nc "sp2 N of conjugated ring"
atom [#7X2;R]([#7])[#7] nc "sp2 N of conjugated ring"
atom [#7X2;R]=[#6]([#7])[#7] nc "sp2 N of conjugated ring"
atom [#7X2;!R](=*)-*=* ne "sp2 N of conjugated chain"
atom [#7X2;!R](=*)-*#* ne "sp2 N of conjugated chain"
atom [#7X2;!R](#*)-*#* ne "sp2 N of conjugated chain"
atom [#7X3] n3 "sp3 N"
atom [#7X3&H0](=[#7])[F,Cl,Br,I] n2 "sp2 N"
atom [#7X3]([#7])([F,Cl,Br,I])[F,Cl,Br,I] n3 "sp3 N"
atom [#7X3;R](-*)=*-* na "sp2 N with 3 subst"
atom [#7X3;R](=[#6])([#6])[#6] na "sp2 N with 3 subst"
atom [#7X3r6]([#6])([#6])[#6] n3 "sp3 N"
atom [#7X3r6]([#6])([#6])[#1] n3 "sp3 N"
atom [#7X3r5]([#6])([#6])[#6] n3 "sp3 N"
atom [#7X3r5]([#6])([#6])[#1] n3 "sp3 N"
atom [nX3;R]([#6])([#6])[#6] na "sp2 N with 3 subst"
atom [nX3&H;R] na "sp2 N with 3 subst"
atom [nX3] nb "sp2 N with 3 subst"
atom [nX3](=[#6])([#6])[#1] na "sp2 N with 3 subst"
atom [#7X3](=[#6])([#6])[#1] na "sp2 N with 3 subst"
atom [nX2r5,nX3r5,nX2r6,nX3r6] nb "sp2 N in aromatic r5, like imidazole and analogs"
atom [#7X3r6]([#6])([#6])[#1] n3 "sp3 N"
atom [nX2r6,nX3r6] nb "sp2 N in aromatic r6, like pyridine and analogs"
atom [#7X3](=[*])(-[*])-[*] na "sp2 N with 3 subst"
//atom [#7X3H2] nh "Amine Nitrogen"
atom [#7X3H2]-[R;a] nh "Amine Nitrogen"
atom [#7X3H2]-[r6;a] nh "Amine Nitrogen"
atom [#7X3]-[R;a] nh "amine N next to aromatic ring"
atom [#7X3]-[CX3]=[O,S] n "sp2 N in amides"
atom [#7X3]=[#6X3]-[#8X1] n "sp2 N+ in resonance structure of amide"
atom [#7D3]-[#6X3]=[#6,#7,#8,#16,#15] n "sp2 N in amides and other analogs"
atom [#7D3]=[#6X3]-[#6,#7,#8,#16,#15] n "sp2 N in amides and other analogs"
atom [#7X3r5]([#6X3]=[#8])([#6X3])[#1] n "sp2 N in amides"
atom [#7X3r5]([#6X3]=[#8])([#6X3])[#6X4] n "sp2 N in amides"
atom [#7X3r6]([#6X3]=[#8])([#6X3]=[#8])[#1] n "sp2 N in amides"
atom [#7X3r6]([#6X3]=[#8])([#6X3]=[#8])[#6X4] n "sp2 N in amides"
atom [#7X3r6]([#6X3]=[#8])([#6X3])[#1] n "sp2 N in amides"
atom [#7X3r6]([#6X3]=[#8])([#6X3])[#6X4] n "sp2 N in amides"
atom [#7D4] n4 "sp3 N"
#atom [ND3](=*)(-*)(-*) n4 "sp3 N"
//atom [ND3](=O)(=O)-* no "N in nitro group"
atom [NX3](-[OX1])(=[OX1])-* no "N in nitro group"
atom [NX3r5]1[CX3r5]=[CX3r5][CX3r5]=[CX3r5]1 nb "sp2 N pyrrole"
// SMARTS rules for oxygens
atom [OD1] o
//atom [$([#8D1]~[#6^2]~[#8D1])] o
atom [OD1]=[#6] o "O in C=O"
atom [OD1]=[#7] o "O in N=O"
atom [OD1]=[#16] o "O in S=O"
atom [#8X1]#[#6,#7,#8,#16,#15] o1 "sp oxygen"
atom [#8X1]=[#6,#7,#8,#16,#15] o "sp2 oxygen"
atom [#8X1]-[#1,#6,#7,#8,#16,#15] o3 "sp3 oxygen"
atom [#8X1]-[#6X3]=[#7X3] o "O- in amide resonance structure"
//atom [OD1]-[CD3] om "O in O=C-O like acetate"
//atom [OD1]=[CD3]-[OD1] om "O in O=C-O like acetate"
//atom [OD1]-[PD4] om "O in O=P-O like fosfate"
//atom [OD1]=[PD4]-[OD1] om "O in O=P-O like fosfate"
//atom [OD1]-[SD4] om "O in O=S-O like sulfate"
//atom [OD1]=[SD4]-[OD1] om "O in O=S-O like sulfate"
atom [#8D1]-[#6,#15,#16]=[#8D1] om "O in O=C-O (acetate), O=P-O (fosfate), O=S-O (sulfate)
atom [#8D1]=[#6,#15,#16]-[#8D1] om "O in O=C-O (acetate), O=P-O (fosfate), O=S-O (sulfate)
atom [OX2]([#6,#7])[#6,#7] os "O in esters and ethers"
atom [OX2&H0] os "O in esters and ethers"
atom [#8X2&H0] os "O in esters and ethers"
atom [OX2;R]([#6])[#6] os "O in esters and ethers"
atom [OX2&H0]([#6])[#6] os "O in esters and ethers"
atom [OX2]([#6])[#6] os "O in esters and ethers"
atom [OX2r5](-[#6X3]=[#6X3])[#15X3] os "O in esters and ethers"
atom [OX2&H0][#15X4]=[OX1] o "O"
atom [OX2&H0][#16X4]=[OX1] o "O"
atom [OX2&H0][#16X4]-[#6X4] o "O"
atom [OX2&H0]([#15X4])[#6] os "sp3 O in esters and ethers"
atom [OX2r5]([#15X3][Cl])[#6] os "sp3 O in esters and ethers"
atom [OX2&H0]([#16X4])[#6] os "sp3 O in esters and ethers"
atom [OX2]([#1])* oh "sp3 O in hydroxyl group"
atom [OX2]([#1])[#1] ow "O in water"
atom [OX2&H0;!R][CX3]=[OX1] o "O"
atom [OX2&H0;!R][NX2]=[OX1] o "O"
atom [OX2&H0;!R][NX3]=[OX1] o "O"
atom [OX2&H0;!R]([#6X4])([NX3]=[OX1]) os "O in esters and ethers"
atom [OX2&H0;!R]([#6X3])([CX3]=[OX1]) os "O in esters and ethers"
atom [OX2]([#6X3]=[OX1])[#6X4] os "O in esters and ethers"
atom [OX2]([#6X3]=[OX1])[#6X3]=[OX1] os "O in esters and ethers"
atom [OX3&H0] os "O in esters and ethers"
atom [#8X2!H]-[#6X3]=[#6,#7,#8,#16,#15] o2 "sp2 oxygen, like in ester and other analogs"
atom [OX3H] oh "O in hydroxyl group"
atom [#8X1]-[#1] om "O in hydroxide ion"
atom [oX2r5] o2 "sp2 O, aromatic 5r"
atom [oX2r6] o2 "sp2 O, aromatic 6r"
//atom [OD1]=[ND3]=[OD1] on "N in nitro group"
atom [#8X1]=[#7X3]-[#8X1] on "N in nitro group"
atom [#8X1]-[#7X3]=[#8X1] on "N in nitro group"
// SMARTS rules for sulfur
atom [SX1] s "sp2 sulfur"
atom [#16X1] s "sp2 sulfur"
atom [#16X1](=[C,O]) s "sp2 sulfur"
atom [#16X1]#[#6,#7,#8,#16,#15] s1 "sp sulfur"
atom [#16X1]=[#6,#7,#8,#16,#15] st "sp2 sulfur, t=two"
atom [#16X1]-[#6,#7,#8,#16,#15] s3 "sp3 sulfur"
atom [SX2] ss "sp3 sulphur"
atom [#16X2] ss "sp3 sulphur"
atom [sX2r5] st "sp2 S, aromatic 5r"
atom [sX2r6] st "sp2 S, aromatic 6r"
atom [#16X2]-[#6X3]=[#6,#7,#8,#16,#15] st "sp2 sulfur, like in thiolester and other analogs"
atom [SX2]=* s2 "sp2 sulphur"
atom [SX2]#* s2 "sp2 sulphur"
atom [SX2H] sh "sp3 S in thiol"
atom [#16X2H1]-[#6X3]=[#6,#7,#8,#16,#15] st "sp2 sulfur, like in carbothioic S-acid and other analogs"
atom [SX3] s4 "hypervalent S"
atom [SX3](=*)-*=* sx "conjugated S"
atom [SX3](=*)-*#* sx "conjugated S"
atom [SX4] s6 "hypervalent S"
atom [SX4](=*)-*=* sy "conjugated S"
atom [SX4](=*)-*#* sy "conjugated S"
atom [SX5] s7 "sp3d S, hypervalent S"
atom [SX6] s8 "sp3d2 S, hypervalent S"
atom [He] He ""
atom [Li] Li ""
atom [Be] Be ""
atom [B] B ""
atom [Ne] Ne ""
atom [Na] Na ""
atom [Mg] Mg ""
atom [Al] Al ""
atom [Si] Si ""
atom [Ar] Ar ""
atom [K] K ""
atom [Ca] Ca ""
atom [Sc] Sc ""
atom [Ti] Ti ""
atom [V] V ""
atom [Cr] Cr ""
atom [Mn] Mn ""
atom [Fe] Fe ""
atom [Co] Co ""
atom [Ni] Ni ""
atom [Cu] Cu ""
atom [Zn] Zn ""
atom [Ga] Ga ""
atom [Ge] Ge ""
atom [As] As ""
atom [Se] Se ""
atom [Kr] Kr ""
atom [Rb] Rb ""
atom [Sr] Sr ""
atom [Y] Y ""
atom [Zr] Zr ""
atom [Nb] Nb ""
atom [Mo] Mo ""
atom [Tc] Tc ""
atom [Ru] Ru ""
atom [Rh] Rh ""
atom [Pd] Pd ""
atom [Ag] Ag ""
atom [Cd] Cd ""
atom [In] In ""
atom [Sn] Sn ""
atom [Sb] Sb ""
atom [Te] Te ""
atom [Xe] Xe ""
atom [Cs] Cs ""
atom [Ba] Ba ""
atom [La] La ""
atom [Ce] Ce ""
atom [Pr] Pr ""
atom [Nd] Nd ""
atom [Pm] Pm ""
atom [Sm] Sm ""
atom [Eu] Eu ""
atom [Gd] Gd ""
atom [Tb] Tb ""
atom [Dy] Dy ""
atom [Ho] Ho ""
atom [Er] Er ""
atom [Tm] Tm ""
atom [Yb] Yb ""
atom [Lu] Lu ""
atom [Hf] Hf ""
atom [Ta] Ta ""
atom [W] W ""
atom [Re] Re ""
atom [Os] Os ""
atom [Ir] Ir ""
atom [Pt] Pt ""
atom [Au] Au ""
atom [Hg] Hg ""
atom [Tl] Tl ""
atom [Pb] Pb ""
atom [Bi] Bi ""
atom [Po] Po ""
atom [At] At ""
atom [Rn] Rn ""
atom [Fr] Fr ""
atom [Ra] Ra ""
atom [Ac] Ac ""
atom [Th] Th ""
atom [Pa] Pa ""
atom [U] U ""
atom [Np] Np ""
atom [Pu] Pu ""
atom [Am] Am ""
atom [Cm] Cm ""
atom [Bk] Bk ""
atom [Cf] Cf ""
atom [Es] Es ""
atom [Fm] Fm ""
atom [Md] Md ""
atom [No] No ""
atom [Lr] Lr ""
// SMART rules for alkali halides
atom [#3D0] Li+ "lithium ion"
atom [#11D0] Na+ "sodium ion"
atom [#19D0] K+ "potassium ion"
atom [#37D0] Rb+ "rubidium ion"
atom [#55D0] Cs+ "caesium ion"
atom [#9D0] F- "fluoride"
atom [#17D0] Cl- "chloride"
atom [#35D0] Br- "bromide"
atom [#53D0] I- "iodide"