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
|
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
AAD AAD '(2-AMINOOXY-ETHYL)-[5-(6-AMINO-PURIN' non-polymer 46 24 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_AAD
#
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
AAD "O2'" O OH1 0.000 0.000 0.000 0.000
AAD HO2 H H 0.000 0.708 0.468 -0.460
AAD "C2'" C CH1 0.000 -1.223 0.676 -0.216
AAD HC2 H H 0.000 -1.958 -0.011 -0.658
AAD "C3'" C CH1 0.000 -1.076 1.908 -1.088
AAD HC3 H H 0.000 -1.058 1.649 -2.156
AAD "O3'" O OH1 0.000 0.089 2.630 -0.704
AAD HO3 H H 0.000 0.285 3.301 -1.371
AAD "C4'" C CH1 0.000 -2.344 2.668 -0.715
AAD HC4 H H 0.000 -3.190 2.230 -1.262
AAD "C5'" C CH2 0.000 -2.319 4.163 -0.975
AAD HC51 H H 0.000 -2.141 4.325 -2.041
AAD HC52 H H 0.000 -1.500 4.600 -0.400
AAD SD S ST 1.000 -3.885 4.949 -0.495
AAD HSD H H 0.000 -4.390 4.721 0.607
AAD CE C CH3 0.000 -3.414 6.630 -0.961
AAD HCE3 H H 0.000 -3.538 6.787 -2.012
AAD HCE2 H H 0.000 -4.013 7.353 -0.449
AAD HCE1 H H 0.000 -2.390 6.823 -0.719
AAD CG C CH2 0.000 -4.779 4.556 -2.016
AAD HCG1 H H 0.000 -5.164 3.537 -1.940
AAD HCG2 H H 0.000 -4.083 4.618 -2.855
AAD CB C CH2 0.000 -5.930 5.518 -2.238
AAD HCB1 H H 0.000 -6.465 5.238 -3.148
AAD HCB2 H H 0.000 -5.538 6.532 -2.346
AAD O2 O O2 0.000 -6.818 5.467 -1.128
AAD N2 N NH2 0.000 -7.898 6.404 -1.391
AAD HN22 H H 0.000 -8.460 6.367 -2.257
AAD HN21 H H 0.000 -8.153 7.151 -0.724
AAD "C1'" C CH1 0.000 -1.776 1.271 1.074
AAD HC1 H H 0.000 -0.937 1.583 1.712
AAD "O4'" O O2 0.000 -2.537 2.438 0.697
AAD N9 N NR5 0.000 -2.631 0.358 1.828
AAD C4 C CR56 0.000 -3.972 0.156 1.653
AAD C5 C CR56 0.000 -4.323 -0.796 2.597
AAD N7 N NRD5 0.000 -3.230 -1.173 3.336
AAD C8 C CR15 0.000 -2.232 -0.464 2.850
AAD HC8 H H 0.000 -1.215 -0.523 3.216
AAD N3 N NRD6 0.000 -4.778 0.750 0.760
AAD C2 C CR16 0.000 -6.043 0.293 0.889
AAD HC2A H H 0.000 -6.766 0.720 0.205
AAD N1 N NRD6 0.000 -6.530 -0.626 1.757
AAD C6 C CR6 0.000 -5.658 -1.185 2.631
AAD N6 N NH2 0.000 -6.102 -2.145 3.556
AAD HN62 H H 0.000 -6.950 -2.686 3.384
AAD HN61 H H 0.000 -5.586 -2.320 4.418
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
AAD "O2'" n/a "C2'" START
AAD HO2 "O2'" . .
AAD "C2'" "O2'" "C1'" .
AAD HC2 "C2'" . .
AAD "C3'" "C2'" "C4'" .
AAD HC3 "C3'" . .
AAD "O3'" "C3'" HO3 .
AAD HO3 "O3'" . .
AAD "C4'" "C3'" "C5'" .
AAD HC4 "C4'" . .
AAD "C5'" "C4'" SD .
AAD HC51 "C5'" . .
AAD HC52 "C5'" . .
AAD SD "C5'" CG .
AAD HSD SD . .
AAD CE SD HCE1 .
AAD HCE3 CE . .
AAD HCE2 CE . .
AAD HCE1 CE . .
AAD CG SD CB .
AAD HCG1 CG . .
AAD HCG2 CG . .
AAD CB CG O2 .
AAD HCB1 CB . .
AAD HCB2 CB . .
AAD O2 CB N2 .
AAD N2 O2 HN21 .
AAD HN22 N2 . .
AAD HN21 N2 . .
AAD "C1'" "C2'" N9 .
AAD HC1 "C1'" . .
AAD "O4'" "C1'" . .
AAD N9 "C1'" C4 .
AAD C4 N9 N3 .
AAD C5 C4 N7 .
AAD N7 C5 C8 .
AAD C8 N7 HC8 .
AAD HC8 C8 . .
AAD N3 C4 C2 .
AAD C2 N3 N1 .
AAD HC2A C2 . .
AAD N1 C2 C6 .
AAD C6 N1 N6 .
AAD N6 C6 HN61 .
AAD HN62 N6 . .
AAD HN61 N6 . END
AAD "C4'" "O4'" . ADD
AAD N9 C8 . ADD
AAD C5 C6 . 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
AAD "C4'" "O4'" single 1.426 0.020
AAD "C4'" "C3'" single 1.524 0.020
AAD "C5'" "C4'" single 1.524 0.020
AAD HC4 "C4'" single 1.099 0.020
AAD "O4'" "C1'" single 1.426 0.020
AAD "O3'" "C3'" single 1.432 0.020
AAD "C3'" "C2'" single 1.524 0.020
AAD HC3 "C3'" single 1.099 0.020
AAD HO3 "O3'" single 0.967 0.020
AAD "C2'" "O2'" single 1.432 0.020
AAD "C1'" "C2'" single 1.524 0.020
AAD HC2 "C2'" single 1.099 0.020
AAD HO2 "O2'" single 0.967 0.020
AAD N9 "C1'" single 1.485 0.020
AAD HC1 "C1'" single 1.099 0.020
AAD N9 C8 single 1.337 0.020
AAD C4 N9 single 1.337 0.020
AAD C8 N7 double 1.350 0.020
AAD HC8 C8 single 1.083 0.020
AAD N7 C5 single 1.350 0.020
AAD C5 C6 double 1.490 0.020
AAD C5 C4 single 1.490 0.020
AAD N6 C6 single 1.355 0.020
AAD C6 N1 single 1.350 0.020
AAD HN61 N6 single 1.010 0.020
AAD HN62 N6 single 1.010 0.020
AAD N1 C2 double 1.337 0.020
AAD C2 N3 single 1.337 0.020
AAD HC2A C2 single 1.083 0.020
AAD N3 C4 double 1.355 0.020
AAD N2 O2 single 1.335 0.020
AAD HN21 N2 single 1.010 0.020
AAD HN22 N2 single 1.010 0.020
AAD O2 CB single 1.426 0.020
AAD CB CG single 1.524 0.020
AAD HCB1 CB single 1.092 0.020
AAD HCB2 CB single 1.092 0.020
AAD CG SD single 1.662 0.020
AAD HCG1 CG single 1.092 0.020
AAD HCG2 CG single 1.092 0.020
AAD CE SD single 1.662 0.020
AAD SD "C5'" single 1.662 0.020
AAD HCE1 CE single 1.059 0.020
AAD HCE2 CE single 1.059 0.020
AAD HCE3 CE single 1.059 0.020
AAD HC51 "C5'" single 1.092 0.020
AAD HC52 "C5'" single 1.092 0.020
AAD HSD SD single 1.234 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
AAD HO2 "O2'" "C2'" 109.470 3.000
AAD "O2'" "C2'" HC2 109.470 3.000
AAD "O2'" "C2'" "C3'" 109.470 3.000
AAD "O2'" "C2'" "C1'" 109.470 3.000
AAD HC2 "C2'" "C3'" 108.340 3.000
AAD HC2 "C2'" "C1'" 108.340 3.000
AAD "C3'" "C2'" "C1'" 111.000 3.000
AAD "C2'" "C3'" HC3 108.340 3.000
AAD "C2'" "C3'" "O3'" 109.470 3.000
AAD "C2'" "C3'" "C4'" 111.000 3.000
AAD HC3 "C3'" "O3'" 109.470 3.000
AAD HC3 "C3'" "C4'" 108.340 3.000
AAD "O3'" "C3'" "C4'" 109.470 3.000
AAD "C3'" "O3'" HO3 109.470 3.000
AAD "C3'" "C4'" HC4 108.340 3.000
AAD "C3'" "C4'" "C5'" 111.000 3.000
AAD "C3'" "C4'" "O4'" 109.470 3.000
AAD HC4 "C4'" "C5'" 108.340 3.000
AAD HC4 "C4'" "O4'" 109.470 3.000
AAD "C5'" "C4'" "O4'" 109.470 3.000
AAD "C4'" "C5'" HC51 109.470 3.000
AAD "C4'" "C5'" HC52 109.470 3.000
AAD "C4'" "C5'" SD 109.500 3.000
AAD HC51 "C5'" HC52 107.900 3.000
AAD HC51 "C5'" SD 109.500 3.000
AAD HC52 "C5'" SD 109.500 3.000
AAD "C5'" SD HSD 109.500 3.000
AAD "C5'" SD CE 109.500 3.000
AAD "C5'" SD CG 109.500 3.000
AAD HSD SD CE 109.500 3.000
AAD HSD SD CG 109.500 3.000
AAD CE SD CG 109.500 3.000
AAD SD CE HCE3 109.500 3.000
AAD SD CE HCE2 109.500 3.000
AAD SD CE HCE1 109.500 3.000
AAD HCE3 CE HCE2 109.470 3.000
AAD HCE3 CE HCE1 109.470 3.000
AAD HCE2 CE HCE1 109.470 3.000
AAD SD CG HCG1 109.500 3.000
AAD SD CG HCG2 109.500 3.000
AAD SD CG CB 109.500 3.000
AAD HCG1 CG HCG2 107.900 3.000
AAD HCG1 CG CB 109.470 3.000
AAD HCG2 CG CB 109.470 3.000
AAD CG CB HCB1 109.470 3.000
AAD CG CB HCB2 109.470 3.000
AAD CG CB O2 109.470 3.000
AAD HCB1 CB HCB2 107.900 3.000
AAD HCB1 CB O2 109.470 3.000
AAD HCB2 CB O2 109.470 3.000
AAD CB O2 N2 120.000 3.000
AAD O2 N2 HN22 120.000 3.000
AAD O2 N2 HN21 120.000 3.000
AAD HN22 N2 HN21 120.000 3.000
AAD "C2'" "C1'" HC1 108.340 3.000
AAD "C2'" "C1'" "O4'" 109.470 3.000
AAD "C2'" "C1'" N9 109.470 3.000
AAD HC1 "C1'" "O4'" 109.470 3.000
AAD HC1 "C1'" N9 109.470 3.000
AAD "O4'" "C1'" N9 109.470 3.000
AAD "C1'" "O4'" "C4'" 111.800 3.000
AAD "C1'" N9 C4 126.000 3.000
AAD "C1'" N9 C8 126.000 3.000
AAD C4 N9 C8 108.000 3.000
AAD N9 C4 C5 108.000 3.000
AAD N9 C4 N3 132.000 3.000
AAD C5 C4 N3 120.000 3.000
AAD C4 C5 N7 108.000 3.000
AAD C4 C5 C6 120.000 3.000
AAD N7 C5 C6 132.000 3.000
AAD C5 N7 C8 108.000 3.000
AAD N7 C8 HC8 126.000 3.000
AAD N7 C8 N9 108.000 3.000
AAD HC8 C8 N9 126.000 3.000
AAD C4 N3 C2 120.000 3.000
AAD N3 C2 HC2A 120.000 3.000
AAD N3 C2 N1 120.000 3.000
AAD HC2A C2 N1 120.000 3.000
AAD C2 N1 C6 120.000 3.000
AAD N1 C6 N6 120.000 3.000
AAD N1 C6 C5 120.000 3.000
AAD N6 C6 C5 120.000 3.000
AAD C6 N6 HN62 120.000 3.000
AAD C6 N6 HN61 120.000 3.000
AAD HN62 N6 HN61 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
AAD var_1 HO2 "O2'" "C2'" "C1'" -114.125 20.000 1
AAD var_2 "O2'" "C2'" "C3'" "C4'" -150.000 20.000 3
AAD var_3 "C2'" "C3'" "O3'" HO3 168.056 20.000 1
AAD var_4 "C2'" "C3'" "C4'" "C5'" 150.000 20.000 3
AAD var_5 "C3'" "C4'" "O4'" "C1'" -30.000 20.000 1
AAD var_6 "C3'" "C4'" "C5'" SD 179.792 20.000 3
AAD var_7 "C4'" "C5'" SD CG -82.643 20.000 1
AAD var_8 "C5'" SD CE HCE1 -38.420 20.000 1
AAD var_9 "C5'" SD CG CB -156.502 20.000 1
AAD var_10 SD CG CB O2 -58.339 20.000 3
AAD var_11 CG CB O2 N2 179.990 20.000 1
AAD var_12 CB O2 N2 HN21 -125.766 20.000 1
AAD var_13 "O2'" "C2'" "C1'" N9 -90.000 20.000 3
AAD var_14 "C2'" "C1'" "O4'" "C4'" 0.000 20.000 1
AAD var_15 "C2'" "C1'" N9 C4 -85.826 20.000 1
AAD CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
AAD CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
AAD CONST_3 N9 C4 C5 N7 0.000 0.000 0
AAD CONST_4 C4 C5 C6 N1 0.000 0.000 0
AAD CONST_5 C4 C5 N7 C8 0.000 0.000 0
AAD CONST_6 C5 N7 C8 N9 0.000 0.000 0
AAD CONST_7 N9 C4 N3 C2 180.000 0.000 0
AAD CONST_8 C4 N3 C2 N1 0.000 0.000 0
AAD CONST_9 N3 C2 N1 C6 0.000 0.000 0
AAD CONST_10 C2 N1 C6 N6 180.000 0.000 0
AAD CONST_11 N1 C6 N6 HN61 -157.105 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
AAD chir_01 "C4'" "O4'" "C3'" "C5'" positiv
AAD chir_02 "C3'" "C4'" "O3'" "C2'" negativ
AAD chir_03 "C2'" "C3'" "O2'" "C1'" negativ
AAD chir_04 "C1'" "O4'" "C2'" N9 positiv
AAD chir_05 SD CG CE "C5'" positiv
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
AAD plan-1 N9 0.020
AAD plan-1 "C1'" 0.020
AAD plan-1 C8 0.020
AAD plan-1 C4 0.020
AAD plan-1 N7 0.020
AAD plan-1 HC8 0.020
AAD plan-1 C5 0.020
AAD plan-1 C6 0.020
AAD plan-1 N1 0.020
AAD plan-1 C2 0.020
AAD plan-1 N3 0.020
AAD plan-1 N6 0.020
AAD plan-1 HC2A 0.020
AAD plan-1 HN62 0.020
AAD plan-1 HN61 0.020
AAD plan-2 N6 0.020
AAD plan-2 C6 0.020
AAD plan-2 HN61 0.020
AAD plan-2 HN62 0.020
AAD plan-3 N2 0.020
AAD plan-3 O2 0.020
AAD plan-3 HN21 0.020
AAD plan-3 HN22 0.020
# ------------------------------------------------------
|
