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
|
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
CDM CDM '4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYT' non-polymer 56 33 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_CDM
#
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
CDM O2B O OP -0.500 0.000 0.000 0.000
CDM PB P P 0.000 -1.218 -0.225 0.815
CDM O1B O OP -0.500 -1.763 1.081 1.259
CDM O3B O O2 0.000 -0.845 -1.116 2.102
CDM C1M C CH2 0.000 0.133 -0.385 2.843
CDM H1M1 H H 0.000 -0.285 0.578 3.143
CDM H1M2 H H 0.000 1.012 -0.218 2.217
CDM C2M C CH1 0.000 0.533 -1.180 4.087
CDM H2M1 H H 0.000 -0.353 -1.348 4.715
CDM C3M C CT 0.000 1.579 -0.396 4.880
CDM C5M C CH3 0.000 2.813 -0.163 4.007
CDM H5M3 H H 0.000 2.538 0.389 3.145
CDM H5M2 H H 0.000 3.538 0.380 4.556
CDM H5M1 H H 0.000 3.219 -1.096 3.712
CDM O3M O OH1 0.000 1.031 0.862 5.276
CDM H3M H H 0.000 0.253 0.714 5.829
CDM C4M C CH2 0.000 1.979 -1.192 6.124
CDM H4M1 H H 0.000 2.396 -2.154 5.821
CDM H4M2 H H 0.000 1.098 -1.358 6.747
CDM O4M O OH1 0.000 2.957 -0.460 6.864
CDM H4M H H 0.000 3.209 -0.963 7.650
CDM O2M O OH1 0.000 1.081 -2.438 3.690
CDM H2M2 H H 0.000 1.860 -2.290 3.138
CDM O3A O O2 0.000 -2.321 -0.993 -0.070
CDM PA P P 0.000 -2.645 -0.051 -1.333
CDM O1A O OP -0.500 -1.405 0.172 -2.115
CDM O2A O OP -0.500 -3.169 1.252 -0.856
CDM "O5'" O O2 0.000 -3.746 -0.762 -2.266
CDM "C5'" C CH2 0.000 -3.990 0.119 -3.364
CDM "H5'1" H H 0.000 -3.060 0.279 -3.913
CDM "H5'2" H H 0.000 -4.358 1.075 -2.987
CDM "C4'" C CH1 0.000 -5.034 -0.501 -4.294
CDM "H4'" H H 0.000 -4.674 -1.470 -4.667
CDM "C3'" C CH1 0.000 -5.310 0.445 -5.478
CDM "H3'" H H 0.000 -4.736 1.376 -5.366
CDM "O3'" O OH1 0.000 -4.996 -0.188 -6.719
CDM H3T H H 0.000 -5.232 0.400 -7.449
CDM "C2'" C CH1 0.000 -6.831 0.732 -5.384
CDM "H2'" H H 0.000 -7.020 1.683 -4.866
CDM "O2'" O OH1 0.000 -7.430 0.731 -6.682
CDM "HO'2" H H 0.000 -7.102 1.486 -7.189
CDM "O4'" O O2 0.000 -6.273 -0.680 -3.588
CDM "C1'" C CH1 0.000 -7.336 -0.467 -4.542
CDM "H1'" H H 0.000 -7.471 -1.355 -5.176
CDM N1 N NR6 0.000 -8.585 -0.129 -3.856
CDM C6 C CR16 0.000 -9.688 -0.908 -4.036
CDM H6 H H 0.000 -9.647 -1.775 -4.684
CDM C5 C CR16 0.000 -10.838 -0.587 -3.395
CDM H5 H H 0.000 -11.726 -1.192 -3.523
CDM C4 C CR6 0.000 -10.859 0.549 -2.560
CDM N4 N NH2 0.000 -12.013 0.898 -1.897
CDM H42 H H 0.000 -12.854 0.342 -2.005
CDM H41 H H 0.000 -12.032 1.714 -1.296
CDM N3 N NRD6 0.000 -9.760 1.277 -2.415
CDM C2 C CR6 0.000 -8.636 0.944 -3.048
CDM O2 O O 0.000 -7.639 1.631 -2.899
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
CDM O2B n/a PB START
CDM PB O2B O3A .
CDM O1B PB . .
CDM O3B PB C1M .
CDM C1M O3B C2M .
CDM H1M1 C1M . .
CDM H1M2 C1M . .
CDM C2M C1M O2M .
CDM H2M1 C2M . .
CDM C3M C2M C4M .
CDM C5M C3M H5M1 .
CDM H5M3 C5M . .
CDM H5M2 C5M . .
CDM H5M1 C5M . .
CDM O3M C3M H3M .
CDM H3M O3M . .
CDM C4M C3M O4M .
CDM H4M1 C4M . .
CDM H4M2 C4M . .
CDM O4M C4M H4M .
CDM H4M O4M . .
CDM O2M C2M H2M2 .
CDM H2M2 O2M . .
CDM O3A PB PA .
CDM PA O3A "O5'" .
CDM O1A PA . .
CDM O2A PA . .
CDM "O5'" PA "C5'" .
CDM "C5'" "O5'" "C4'" .
CDM "H5'1" "C5'" . .
CDM "H5'2" "C5'" . .
CDM "C4'" "C5'" "O4'" .
CDM "H4'" "C4'" . .
CDM "C3'" "C4'" "C2'" .
CDM "H3'" "C3'" . .
CDM "O3'" "C3'" H3T .
CDM H3T "O3'" . .
CDM "C2'" "C3'" "O2'" .
CDM "H2'" "C2'" . .
CDM "O2'" "C2'" "HO'2" .
CDM "HO'2" "O2'" . .
CDM "O4'" "C4'" "C1'" .
CDM "C1'" "O4'" N1 .
CDM "H1'" "C1'" . .
CDM N1 "C1'" C6 .
CDM C6 N1 C5 .
CDM H6 C6 . .
CDM C5 C6 C4 .
CDM H5 C5 . .
CDM C4 C5 N3 .
CDM N4 C4 H41 .
CDM H42 N4 . .
CDM H41 N4 . .
CDM N3 C4 C2 .
CDM C2 N3 O2 .
CDM O2 C2 . END
CDM N1 C2 . ADD
CDM "C1'" "C2'" . 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
CDM N1 C2 single 1.410 0.020
CDM C6 N1 single 1.337 0.020
CDM N1 "C1'" single 1.465 0.020
CDM C2 N3 single 1.350 0.020
CDM O2 C2 double 1.250 0.020
CDM N3 C4 double 1.350 0.020
CDM C4 C5 single 1.390 0.020
CDM N4 C4 single 1.355 0.020
CDM C5 C6 double 1.390 0.020
CDM H5 C5 single 1.083 0.020
CDM H6 C6 single 1.083 0.020
CDM H41 N4 single 1.010 0.020
CDM H42 N4 single 1.010 0.020
CDM "C1'" "C2'" single 1.524 0.020
CDM "C1'" "O4'" single 1.426 0.020
CDM "H1'" "C1'" single 1.099 0.020
CDM "O2'" "C2'" single 1.432 0.020
CDM "C2'" "C3'" single 1.524 0.020
CDM "H2'" "C2'" single 1.099 0.020
CDM "HO'2" "O2'" single 0.967 0.020
CDM "C3'" "C4'" single 1.524 0.020
CDM "O3'" "C3'" single 1.432 0.020
CDM "H3'" "C3'" single 1.099 0.020
CDM "O4'" "C4'" single 1.426 0.020
CDM "C4'" "C5'" single 1.524 0.020
CDM "H4'" "C4'" single 1.099 0.020
CDM H3T "O3'" single 0.967 0.020
CDM "C5'" "O5'" single 1.426 0.020
CDM "H5'1" "C5'" single 1.092 0.020
CDM "H5'2" "C5'" single 1.092 0.020
CDM "O5'" PA single 1.610 0.020
CDM O1A PA deloc 1.510 0.020
CDM O2A PA deloc 1.510 0.020
CDM PA O3A single 1.610 0.020
CDM O3A PB single 1.610 0.020
CDM O1B PB deloc 1.510 0.020
CDM PB O2B deloc 1.510 0.020
CDM O3B PB single 1.610 0.020
CDM C1M O3B single 1.426 0.020
CDM C2M C1M single 1.524 0.020
CDM H1M1 C1M single 1.092 0.020
CDM H1M2 C1M single 1.092 0.020
CDM O2M C2M single 1.432 0.020
CDM C3M C2M single 1.524 0.020
CDM H2M1 C2M single 1.099 0.020
CDM H2M2 O2M single 0.967 0.020
CDM C4M C3M single 1.524 0.020
CDM C5M C3M single 1.524 0.020
CDM O3M C3M single 1.432 0.020
CDM O4M C4M single 1.432 0.020
CDM H4M1 C4M single 1.092 0.020
CDM H4M2 C4M single 1.092 0.020
CDM H5M1 C5M single 1.059 0.020
CDM H5M2 C5M single 1.059 0.020
CDM H5M3 C5M single 1.059 0.020
CDM H3M O3M single 0.967 0.020
CDM H4M O4M single 0.967 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
CDM O2B PB O1B 119.900 3.000
CDM O2B PB O3B 108.200 3.000
CDM O2B PB O3A 108.200 3.000
CDM O1B PB O3B 108.200 3.000
CDM O1B PB O3A 108.200 3.000
CDM O3B PB O3A 102.600 3.000
CDM PB O3B C1M 120.500 3.000
CDM O3B C1M H1M1 109.470 3.000
CDM O3B C1M H1M2 109.470 3.000
CDM O3B C1M C2M 109.470 3.000
CDM H1M1 C1M H1M2 107.900 3.000
CDM H1M1 C1M C2M 109.470 3.000
CDM H1M2 C1M C2M 109.470 3.000
CDM C1M C2M H2M1 108.340 3.000
CDM C1M C2M C3M 111.000 3.000
CDM C1M C2M O2M 109.470 3.000
CDM H2M1 C2M C3M 108.340 3.000
CDM H2M1 C2M O2M 109.470 3.000
CDM C3M C2M O2M 109.470 3.000
CDM C2M C3M C5M 111.000 3.000
CDM C2M C3M O3M 109.470 3.000
CDM C2M C3M C4M 111.000 3.000
CDM C5M C3M O3M 109.470 3.000
CDM C5M C3M C4M 111.000 3.000
CDM O3M C3M C4M 109.470 3.000
CDM C3M C5M H5M3 109.470 3.000
CDM C3M C5M H5M2 109.470 3.000
CDM C3M C5M H5M1 109.470 3.000
CDM H5M3 C5M H5M2 109.470 3.000
CDM H5M3 C5M H5M1 109.470 3.000
CDM H5M2 C5M H5M1 109.470 3.000
CDM C3M O3M H3M 109.470 3.000
CDM C3M C4M H4M1 109.470 3.000
CDM C3M C4M H4M2 109.470 3.000
CDM C3M C4M O4M 109.470 3.000
CDM H4M1 C4M H4M2 107.900 3.000
CDM H4M1 C4M O4M 109.470 3.000
CDM H4M2 C4M O4M 109.470 3.000
CDM C4M O4M H4M 109.470 3.000
CDM C2M O2M H2M2 109.470 3.000
CDM PB O3A PA 120.500 3.000
CDM O3A PA O1A 108.200 3.000
CDM O3A PA O2A 108.200 3.000
CDM O3A PA "O5'" 102.600 3.000
CDM O1A PA O2A 119.900 3.000
CDM O1A PA "O5'" 108.200 3.000
CDM O2A PA "O5'" 108.200 3.000
CDM PA "O5'" "C5'" 120.500 3.000
CDM "O5'" "C5'" "H5'1" 109.470 3.000
CDM "O5'" "C5'" "H5'2" 109.470 3.000
CDM "O5'" "C5'" "C4'" 109.470 3.000
CDM "H5'1" "C5'" "H5'2" 107.900 3.000
CDM "H5'1" "C5'" "C4'" 109.470 3.000
CDM "H5'2" "C5'" "C4'" 109.470 3.000
CDM "C5'" "C4'" "H4'" 108.340 3.000
CDM "C5'" "C4'" "C3'" 111.000 3.000
CDM "C5'" "C4'" "O4'" 109.470 3.000
CDM "H4'" "C4'" "C3'" 108.340 3.000
CDM "H4'" "C4'" "O4'" 109.470 3.000
CDM "C3'" "C4'" "O4'" 109.470 3.000
CDM "C4'" "C3'" "H3'" 108.340 3.000
CDM "C4'" "C3'" "O3'" 109.470 3.000
CDM "C4'" "C3'" "C2'" 111.000 3.000
CDM "H3'" "C3'" "O3'" 109.470 3.000
CDM "H3'" "C3'" "C2'" 108.340 3.000
CDM "O3'" "C3'" "C2'" 109.470 3.000
CDM "C3'" "O3'" H3T 109.470 3.000
CDM "C3'" "C2'" "H2'" 108.340 3.000
CDM "C3'" "C2'" "O2'" 109.470 3.000
CDM "C3'" "C2'" "C1'" 111.000 3.000
CDM "H2'" "C2'" "O2'" 109.470 3.000
CDM "H2'" "C2'" "C1'" 108.340 3.000
CDM "O2'" "C2'" "C1'" 109.470 3.000
CDM "C2'" "O2'" "HO'2" 109.470 3.000
CDM "C4'" "O4'" "C1'" 111.800 3.000
CDM "O4'" "C1'" "H1'" 109.470 3.000
CDM "O4'" "C1'" N1 109.470 3.000
CDM "O4'" "C1'" "C2'" 109.470 3.000
CDM "H1'" "C1'" N1 109.470 3.000
CDM "H1'" "C1'" "C2'" 108.340 3.000
CDM N1 "C1'" "C2'" 109.470 3.000
CDM "C1'" N1 C6 120.000 3.000
CDM "C1'" N1 C2 120.000 3.000
CDM C6 N1 C2 120.000 3.000
CDM N1 C6 H6 120.000 3.000
CDM N1 C6 C5 120.000 3.000
CDM H6 C6 C5 120.000 3.000
CDM C6 C5 H5 120.000 3.000
CDM C6 C5 C4 120.000 3.000
CDM H5 C5 C4 120.000 3.000
CDM C5 C4 N4 120.000 3.000
CDM C5 C4 N3 120.000 3.000
CDM N4 C4 N3 120.000 3.000
CDM C4 N4 H42 120.000 3.000
CDM C4 N4 H41 120.000 3.000
CDM H42 N4 H41 120.000 3.000
CDM C4 N3 C2 120.000 3.000
CDM N3 C2 O2 120.000 3.000
CDM N3 C2 N1 120.000 3.000
CDM O2 C2 N1 120.000 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
CDM var_1 O2B PB O3B C1M 59.969 20.000 1
CDM var_2 PB O3B C1M C2M 179.954 20.000 1
CDM var_3 O3B C1M C2M O2M 60.059 20.000 3
CDM var_4 C1M C2M C3M C4M 180.000 20.000 1
CDM var_5 C2M C3M C5M H5M1 -59.967 20.000 1
CDM var_6 C2M C3M O3M H3M 60.029 20.000 1
CDM var_7 C2M C3M C4M O4M 179.992 20.000 1
CDM var_8 C3M C4M O4M H4M -179.990 20.000 1
CDM var_9 C1M C2M O2M H2M2 60.038 20.000 1
CDM var_10 O2B PB O3A PA -59.972 20.000 1
CDM var_11 PB O3A PA "O5'" 179.979 20.000 1
CDM var_12 O3A PA "O5'" "C5'" -179.985 20.000 1
CDM var_13 PA "O5'" "C5'" "C4'" -179.975 20.000 1
CDM var_14 "O5'" "C5'" "C4'" "O4'" 61.656 20.000 3
CDM var_15 "C5'" "C4'" "C3'" "C2'" -120.000 20.000 3
CDM var_16 "C4'" "C3'" "O3'" H3T 176.190 20.000 1
CDM var_17 "C4'" "C3'" "C2'" "O2'" -150.000 20.000 3
CDM var_18 "C3'" "C2'" "O2'" "HO'2" -67.382 20.000 1
CDM var_19 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
CDM var_20 "C4'" "O4'" "C1'" N1 -150.000 20.000 1
CDM var_21 "O4'" "C1'" "C2'" "C3'" 30.000 20.000 3
CDM var_22 "O4'" "C1'" N1 C6 -121.450 20.000 1
CDM CONST_1 "C1'" N1 C2 N3 180.000 0.000 0
CDM CONST_2 "C1'" N1 C6 C5 180.000 0.000 0
CDM CONST_3 N1 C6 C5 C4 0.000 0.000 0
CDM CONST_4 C6 C5 C4 N3 0.000 0.000 0
CDM CONST_5 C5 C4 N4 H41 -179.991 0.000 0
CDM CONST_6 C5 C4 N3 C2 0.000 0.000 0
CDM CONST_7 C4 N3 C2 O2 180.000 0.000 0
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
CDM chir_01 "C1'" N1 "C2'" "O4'" negativ
CDM chir_02 "C2'" "C1'" "O2'" "C3'" positiv
CDM chir_03 "C3'" "C2'" "C4'" "O3'" negativ
CDM chir_04 "C4'" "C3'" "O4'" "C5'" positiv
CDM chir_05 C2M C1M O2M C3M negativ
CDM chir_06 C3M C2M C4M C5M 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
CDM plan-1 N1 0.020
CDM plan-1 C2 0.020
CDM plan-1 C6 0.020
CDM plan-1 "C1'" 0.020
CDM plan-1 N3 0.020
CDM plan-1 C4 0.020
CDM plan-1 C5 0.020
CDM plan-1 O2 0.020
CDM plan-1 N4 0.020
CDM plan-1 H5 0.020
CDM plan-1 H6 0.020
CDM plan-1 H42 0.020
CDM plan-1 H41 0.020
CDM plan-2 N4 0.020
CDM plan-2 C4 0.020
CDM plan-2 H41 0.020
CDM plan-2 H42 0.020
# ------------------------------------------------------
|
