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
|
global_
_lib_name ?
_lib_version ?
_lib_update ?
# ------------------------------------------------
#
# --- LIST OF MONOMERS ---
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
CDK CDK '4-[4-(3,4-DIMETHYL-2-OXO-2,3-DIHYDRO' non-polymer 50 29 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_CDK
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
CDK O2 O OS 0.000 0.000 0.000 0.000
CDK S S ST 0.000 -0.942 -0.053 -1.062
CDK O1 O OS 0.000 -0.978 0.899 -2.117
CDK N2 N NH1 0.000 -0.759 -1.536 -1.776
CDK H2 H H 0.000 -0.056 -2.177 -1.437
CDK C6 C CH2 0.000 -1.618 -1.918 -2.900
CDK H61C H H 0.000 -1.688 -1.086 -3.603
CDK H62C H H 0.000 -2.615 -2.163 -2.528
CDK C7 C CH2 0.000 -1.021 -3.137 -3.606
CDK H71C H H 0.000 0.007 -2.918 -3.901
CDK H72C H H 0.000 -1.612 -3.367 -4.495
CDK O O O2 0.000 -1.036 -4.257 -2.720
CDK C8 C CH3 0.000 -0.497 -5.454 -3.285
CDK H83C H H 0.000 0.512 -5.291 -3.564
CDK H82C H H 0.000 -0.544 -6.235 -2.571
CDK H81C H H 0.000 -1.059 -5.725 -4.141
CDK C5 C CR6 0.000 -2.537 -0.027 -0.314
CDK C10 C CR16 0.000 -2.693 -0.448 0.994
CDK H10 H H 0.000 -1.834 -0.793 1.556
CDK C9 C CR16 0.000 -3.941 -0.428 1.584
CDK H9 H H 0.000 -4.062 -0.759 2.608
CDK C4 C CR16 0.000 -3.632 0.410 -1.038
CDK H4 H H 0.000 -3.507 0.736 -2.063
CDK C3 C CR16 0.000 -4.883 0.431 -0.454
CDK H3 H H 0.000 -5.740 0.772 -1.022
CDK C2 C CR6 0.000 -5.042 0.015 0.861
CDK N1 N NH1 0.000 -6.308 0.036 1.454
CDK H1 H H 0.000 -6.560 -0.670 2.131
CDK C1 C CR6 0.000 -7.216 1.024 1.113
CDK N N NRD6 0.000 -8.445 0.965 1.601
CDK N3 N NRD6 0.000 -6.832 2.004 0.308
CDK C11 C CR16 0.000 -7.671 2.965 -0.046
CDK H11 H H 0.000 -7.347 3.758 -0.709
CDK C12 C CR16 0.000 -8.965 2.946 0.438
CDK H12 H H 0.000 -9.671 3.721 0.163
CDK C C CR6 0.000 -9.343 1.902 1.292
CDK C15 C CR5 0.000 -10.713 1.836 1.835
CDK C16 C CR5 0.000 -11.222 0.901 2.655
CDK C17 C CH3 0.000 -10.397 -0.261 3.144
CDK H173 H H 0.000 -10.064 -0.831 2.316
CDK H172 H H 0.000 -9.560 0.102 3.682
CDK H171 H H 0.000 -10.987 -0.871 3.778
CDK S1 S S2 0.000 -12.044 2.970 1.545
CDK C14 C CR5 0.000 -13.171 2.129 2.538
CDK O3 O O 0.000 -14.329 2.437 2.754
CDK N4 N NR5 0.000 -12.516 1.063 3.022
CDK C13 C CH3 0.000 -13.175 0.110 3.918
CDK H133 H H 0.000 -14.207 0.075 3.692
CDK H132 H H 0.000 -12.748 -0.848 3.782
CDK H131 H H 0.000 -13.040 0.422 4.919
loop_
_chem_comp_tree.comp_id
_chem_comp_tree.atom_id
_chem_comp_tree.atom_back
_chem_comp_tree.atom_forward
_chem_comp_tree.connect_type
CDK O2 n/a S START
CDK S O2 C5 .
CDK O1 S . .
CDK N2 S C6 .
CDK H2 N2 . .
CDK C6 N2 C7 .
CDK H61C C6 . .
CDK H62C C6 . .
CDK C7 C6 O .
CDK H71C C7 . .
CDK H72C C7 . .
CDK O C7 C8 .
CDK C8 O H81C .
CDK H83C C8 . .
CDK H82C C8 . .
CDK H81C C8 . .
CDK C5 S C4 .
CDK C10 C5 C9 .
CDK H10 C10 . .
CDK C9 C10 H9 .
CDK H9 C9 . .
CDK C4 C5 C3 .
CDK H4 C4 . .
CDK C3 C4 C2 .
CDK H3 C3 . .
CDK C2 C3 N1 .
CDK N1 C2 C1 .
CDK H1 N1 . .
CDK C1 N1 N3 .
CDK N C1 . .
CDK N3 C1 C11 .
CDK C11 N3 C12 .
CDK H11 C11 . .
CDK C12 C11 C .
CDK H12 C12 . .
CDK C C12 C15 .
CDK C15 C S1 .
CDK C16 C15 C17 .
CDK C17 C16 H171 .
CDK H173 C17 . .
CDK H172 C17 . .
CDK H171 C17 . .
CDK S1 C15 C14 .
CDK C14 S1 N4 .
CDK O3 C14 . .
CDK N4 C14 C13 .
CDK C13 N4 H131 .
CDK H133 C13 . .
CDK H132 C13 . .
CDK H131 C13 . END
CDK C16 N4 . ADD
CDK C N . ADD
CDK C2 C9 . ADD
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
CDK C17 C16 single 1.506 0.020
CDK C16 N4 single 1.337 0.020
CDK C16 C15 double 1.490 0.020
CDK C13 N4 single 1.485 0.020
CDK N4 C14 single 1.337 0.020
CDK O3 C14 double 1.285 0.020
CDK C14 S1 single 1.745 0.020
CDK S1 C15 single 1.745 0.020
CDK C15 C single 1.490 0.020
CDK C N double 1.350 0.020
CDK C C12 single 1.390 0.020
CDK N C1 single 1.350 0.020
CDK C12 C11 double 1.390 0.020
CDK C11 N3 single 1.337 0.020
CDK N3 C1 double 1.350 0.020
CDK C1 N1 single 1.350 0.020
CDK N1 C2 single 1.350 0.020
CDK C2 C9 single 1.390 0.020
CDK C2 C3 double 1.390 0.020
CDK C9 C10 double 1.390 0.020
CDK C10 C5 single 1.390 0.020
CDK C3 C4 single 1.390 0.020
CDK C4 C5 double 1.390 0.020
CDK C5 S single 1.595 0.020
CDK O1 S double 1.436 0.020
CDK S O2 double 1.436 0.020
CDK N2 S single 1.600 0.020
CDK C6 N2 single 1.450 0.020
CDK C7 C6 single 1.524 0.020
CDK O C7 single 1.426 0.020
CDK C8 O single 1.426 0.020
CDK H171 C17 single 1.059 0.020
CDK H172 C17 single 1.059 0.020
CDK H173 C17 single 1.059 0.020
CDK H131 C13 single 1.059 0.020
CDK H132 C13 single 1.059 0.020
CDK H133 C13 single 1.059 0.020
CDK H12 C12 single 1.083 0.020
CDK H11 C11 single 1.083 0.020
CDK H1 N1 single 1.010 0.020
CDK H9 C9 single 1.083 0.020
CDK H3 C3 single 1.083 0.020
CDK H10 C10 single 1.083 0.020
CDK H4 C4 single 1.083 0.020
CDK H2 N2 single 1.010 0.020
CDK H61C C6 single 1.092 0.020
CDK H62C C6 single 1.092 0.020
CDK H71C C7 single 1.092 0.020
CDK H72C C7 single 1.092 0.020
CDK H81C C8 single 1.059 0.020
CDK H82C C8 single 1.059 0.020
CDK H83C C8 single 1.059 0.020
loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
CDK O2 S O1 109.500 3.000
CDK O2 S N2 109.500 3.000
CDK O2 S C5 109.500 3.000
CDK O1 S N2 109.500 3.000
CDK O1 S C5 109.500 3.000
CDK N2 S C5 109.500 3.000
CDK S N2 H2 120.000 3.000
CDK S N2 C6 120.000 3.000
CDK H2 N2 C6 118.500 3.000
CDK N2 C6 H61C 109.470 3.000
CDK N2 C6 H62C 109.470 3.000
CDK N2 C6 C7 112.000 3.000
CDK H61C C6 H62C 107.900 3.000
CDK H61C C6 C7 109.470 3.000
CDK H62C C6 C7 109.470 3.000
CDK C6 C7 H71C 109.470 3.000
CDK C6 C7 H72C 109.470 3.000
CDK C6 C7 O 109.470 3.000
CDK H71C C7 H72C 107.900 3.000
CDK H71C C7 O 109.470 3.000
CDK H72C C7 O 109.470 3.000
CDK C7 O C8 111.800 3.000
CDK O C8 H83C 109.470 3.000
CDK O C8 H82C 109.470 3.000
CDK O C8 H81C 109.470 3.000
CDK H83C C8 H82C 109.470 3.000
CDK H83C C8 H81C 109.470 3.000
CDK H82C C8 H81C 109.470 3.000
CDK S C5 C10 120.000 3.000
CDK S C5 C4 120.000 3.000
CDK C10 C5 C4 120.000 3.000
CDK C5 C10 H10 120.000 3.000
CDK C5 C10 C9 120.000 3.000
CDK H10 C10 C9 120.000 3.000
CDK C10 C9 H9 120.000 3.000
CDK C10 C9 C2 120.000 3.000
CDK H9 C9 C2 120.000 3.000
CDK C5 C4 H4 120.000 3.000
CDK C5 C4 C3 120.000 3.000
CDK H4 C4 C3 120.000 3.000
CDK C4 C3 H3 120.000 3.000
CDK C4 C3 C2 120.000 3.000
CDK H3 C3 C2 120.000 3.000
CDK C3 C2 N1 120.000 3.000
CDK C3 C2 C9 120.000 3.000
CDK N1 C2 C9 120.000 3.000
CDK C2 N1 H1 120.000 3.000
CDK C2 N1 C1 120.000 3.000
CDK H1 N1 C1 120.000 3.000
CDK N1 C1 N 120.000 3.000
CDK N1 C1 N3 120.000 3.000
CDK N C1 N3 120.000 3.000
CDK C1 N C 120.000 3.000
CDK C1 N3 C11 120.000 3.000
CDK N3 C11 H11 120.000 3.000
CDK N3 C11 C12 120.000 3.000
CDK H11 C11 C12 120.000 3.000
CDK C11 C12 H12 120.000 3.000
CDK C11 C12 C 120.000 3.000
CDK H12 C12 C 120.000 3.000
CDK C12 C C15 120.000 3.000
CDK C12 C N 120.000 3.000
CDK C15 C N 120.000 3.000
CDK C C15 C16 126.000 3.000
CDK C C15 S1 108.000 3.000
CDK C16 C15 S1 108.000 3.000
CDK C15 C16 C17 126.000 3.000
CDK C15 C16 N4 108.000 3.000
CDK C17 C16 N4 126.000 3.000
CDK C16 C17 H173 109.470 3.000
CDK C16 C17 H172 109.470 3.000
CDK C16 C17 H171 109.470 3.000
CDK H173 C17 H172 109.470 3.000
CDK H173 C17 H171 109.470 3.000
CDK H172 C17 H171 109.470 3.000
CDK C15 S1 C14 94.836 3.000
CDK S1 C14 O3 108.000 3.000
CDK S1 C14 N4 108.000 3.000
CDK O3 C14 N4 108.000 3.000
CDK C14 N4 C13 126.000 3.000
CDK C14 N4 C16 108.000 3.000
CDK C13 N4 C16 126.000 3.000
CDK N4 C13 H133 109.470 3.000
CDK N4 C13 H132 109.470 3.000
CDK N4 C13 H131 109.470 3.000
CDK H133 C13 H132 109.470 3.000
CDK H133 C13 H131 109.470 3.000
CDK H132 C13 H131 109.470 3.000
loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
CDK var_1 O2 S N2 C6 178.592 20.000 1
CDK var_2 S N2 C6 C7 165.024 20.000 3
CDK var_3 N2 C6 C7 O 64.910 20.000 3
CDK var_4 C6 C7 O C8 179.984 20.000 1
CDK var_5 C7 O C8 H81C -59.930 20.000 1
CDK var_6 O2 S C5 C4 156.666 20.000 1
CDK CONST_1 S C5 C10 C9 180.000 0.000 0
CDK CONST_2 C5 C10 C9 C2 0.000 0.000 0
CDK CONST_3 S C5 C4 C3 180.000 0.000 0
CDK CONST_4 C5 C4 C3 C2 0.000 0.000 0
CDK CONST_5 C4 C3 C2 N1 180.000 0.000 0
CDK CONST_6 C3 C2 C9 C10 0.000 0.000 0
CDK var_7 C3 C2 N1 C1 -33.862 20.000 1
CDK var_8 C2 N1 C1 N3 -5.480 20.000 1
CDK CONST_7 N1 C1 N C 180.000 0.000 0
CDK CONST_8 N1 C1 N3 C11 180.000 0.000 0
CDK CONST_9 C1 N3 C11 C12 0.000 0.000 0
CDK CONST_10 N3 C11 C12 C 0.000 0.000 0
CDK CONST_11 C11 C12 C C15 180.000 0.000 0
CDK CONST_12 C12 C N C1 0.000 0.000 0
CDK var_9 C12 C C15 S1 -0.214 20.000 1
CDK CONST_13 C C15 C16 C17 0.000 0.000 0
CDK CONST_14 C15 C16 N4 C14 0.000 0.000 0
CDK var_10 C15 C16 C17 H171 179.755 20.000 1
CDK CONST_15 C C15 S1 C14 180.000 0.000 0
CDK CONST_16 C15 S1 C14 N4 0.000 0.000 0
CDK CONST_17 S1 C14 N4 C13 180.000 0.000 0
CDK var_11 C14 N4 C13 H131 -89.960 20.000 1
loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
CDK chir_01 S C5 O1 O2 negativ
loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
CDK plan-1 C16 0.020
CDK plan-1 C17 0.020
CDK plan-1 N4 0.020
CDK plan-1 C15 0.020
CDK plan-1 C14 0.020
CDK plan-1 S1 0.020
CDK plan-1 C13 0.020
CDK plan-1 O3 0.020
CDK plan-1 C 0.020
CDK plan-2 C 0.020
CDK plan-2 C15 0.020
CDK plan-2 N 0.020
CDK plan-2 C12 0.020
CDK plan-2 C11 0.020
CDK plan-2 N3 0.020
CDK plan-2 C1 0.020
CDK plan-2 H12 0.020
CDK plan-2 H11 0.020
CDK plan-2 N1 0.020
CDK plan-2 H1 0.020
CDK plan-3 N1 0.020
CDK plan-3 C1 0.020
CDK plan-3 C2 0.020
CDK plan-3 H1 0.020
CDK plan-4 C2 0.020
CDK plan-4 N1 0.020
CDK plan-4 C9 0.020
CDK plan-4 C3 0.020
CDK plan-4 C10 0.020
CDK plan-4 C4 0.020
CDK plan-4 C5 0.020
CDK plan-4 H9 0.020
CDK plan-4 H10 0.020
CDK plan-4 H3 0.020
CDK plan-4 H4 0.020
CDK plan-4 S 0.020
CDK plan-4 H1 0.020
CDK plan-5 N2 0.020
CDK plan-5 S 0.020
CDK plan-5 C6 0.020
CDK plan-5 H2 0.020
# ------------------------------------------------------
|
