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
|
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
AD9 AD9 'ADP METAVANADATE ' non-polymer 45 31 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_AD9
#
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
AD9 O2A O OP -0.500 65.048 42.747 -23.972
AD9 PA P P 0.000 65.172 41.519 -23.150
AD9 O1A O OP -0.500 66.543 41.173 -22.704
AD9 O3A O O2 0.000 64.413 40.400 -24.074
AD9 PB P P 0.000 64.930 39.588 -25.394
AD9 O1B O OP -0.500 66.278 40.175 -25.590
AD9 O2B O OP -0.500 64.952 38.129 -25.130
AD9 O3B O O2 0.000 64.287 40.076 -26.683
AD9 VG V V 0.000 63.474 40.173 -28.255
AD9 O2G O OH1 0.000 64.541 41.182 -29.056
AD9 H2G1 H H 0.000 64.284 41.414 -29.910
AD9 O3G O OH1 0.000 61.810 40.809 -28.151
AD9 H3G1 H H 0.000 61.480 40.955 -27.291
AD9 O1G O O 0.000 63.583 38.692 -28.857
AD9 "O5'" O O2 0.000 64.037 41.736 -22.026
AD9 "C5'" C CH2 0.000 62.828 42.559 -22.116
AD9 "H5'1" H H 0.000 61.964 41.920 -22.311
AD9 "H5'2" H H 0.000 62.936 43.281 -22.928
AD9 "C4'" C CH1 0.000 62.631 43.289 -20.818
AD9 "H4'" H H 0.000 61.686 43.850 -20.825
AD9 "C3'" C CH1 0.000 63.802 44.197 -20.405
AD9 "H3'" H H 0.000 64.759 43.688 -20.587
AD9 "O3'" O OH1 0.000 63.765 45.465 -21.120
AD9 HA H H 0.000 63.757 46.198 -20.487
AD9 "C2'" C CH1 0.000 63.556 44.342 -18.886
AD9 "H2'" H H 0.000 64.442 44.714 -18.352
AD9 "O2'" O OH1 0.000 62.364 45.129 -18.599
AD9 HB H H 0.000 62.309 45.306 -17.648
AD9 "C1'" C CH1 0.000 63.218 42.862 -18.519
AD9 "H1'" H H 0.000 62.460 42.853 -17.724
AD9 "O4'" O O2 0.000 62.638 42.293 -19.742
AD9 N9 N NR5 0.000 64.369 42.056 -18.094
AD9 C4 C CR56 0.000 65.129 42.278 -16.954
AD9 C5 C CR56 0.000 66.105 41.252 -16.946
AD9 N7 N NRD5 0.000 65.959 40.422 -18.058
AD9 C8 C CR15 0.000 64.930 40.916 -18.715
AD9 H8 H H 0.000 64.552 40.492 -19.637
AD9 N3 N NRD6 0.000 64.987 43.264 -16.010
AD9 C2 C CR16 0.000 65.903 43.184 -15.009
AD9 H2 H H 0.000 65.847 43.938 -14.233
AD9 N1 N NRD6 0.000 66.889 42.243 -14.887
AD9 C6 C CR6 0.000 67.016 41.259 -15.845
AD9 N6 N NH2 0.000 68.002 40.334 -15.695
AD9 H6N2 H H 0.000 68.238 39.989 -14.774
AD9 H6N1 H H 0.000 68.501 39.989 -16.504
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
AD9 O2A n/a PA START
AD9 PA O2A "O5'" .
AD9 O1A PA . .
AD9 O3A PA PB .
AD9 PB O3A O3B .
AD9 O1B PB . .
AD9 O2B PB . .
AD9 O3B PB VG .
AD9 VG O3B O1G .
AD9 O2G VG H2G1 .
AD9 H2G1 O2G . .
AD9 O3G VG H3G1 .
AD9 H3G1 O3G . .
AD9 O1G VG . .
AD9 "O5'" PA "C5'" .
AD9 "C5'" "O5'" "C4'" .
AD9 "H5'1" "C5'" . .
AD9 "H5'2" "C5'" . .
AD9 "C4'" "C5'" "C3'" .
AD9 "H4'" "C4'" . .
AD9 "C3'" "C4'" "C2'" .
AD9 "H3'" "C3'" . .
AD9 "O3'" "C3'" HA .
AD9 HA "O3'" . .
AD9 "C2'" "C3'" "C1'" .
AD9 "H2'" "C2'" . .
AD9 "O2'" "C2'" HB .
AD9 HB "O2'" . .
AD9 "C1'" "C2'" N9 .
AD9 "H1'" "C1'" . .
AD9 "O4'" "C1'" . .
AD9 N9 "C1'" C4 .
AD9 C4 N9 N3 .
AD9 C5 C4 N7 .
AD9 N7 C5 C8 .
AD9 C8 N7 H8 .
AD9 H8 C8 . .
AD9 N3 C4 C2 .
AD9 C2 N3 N1 .
AD9 H2 C2 . .
AD9 N1 C2 C6 .
AD9 C6 N1 N6 .
AD9 N6 C6 H6N1 .
AD9 H6N2 N6 . .
AD9 H6N1 N6 . END
AD9 "C4'" "O4'" . ADD
AD9 N9 C8 . ADD
AD9 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
AD9 O1G VG double 1.910 0.020
AD9 O2G VG single 2.105 0.020
AD9 O3G VG single 2.105 0.020
AD9 VG O3B single 2.004 0.020
AD9 O1B PB deloc 1.510 0.020
AD9 O2B PB deloc 1.510 0.020
AD9 O3B PB single 1.610 0.020
AD9 PB O3A single 1.610 0.020
AD9 O1A PA deloc 1.510 0.020
AD9 PA O2A deloc 1.510 0.020
AD9 O3A PA single 1.610 0.020
AD9 "O5'" PA single 1.610 0.020
AD9 "C5'" "O5'" single 1.426 0.020
AD9 "C4'" "C5'" single 1.524 0.020
AD9 "C4'" "O4'" single 1.426 0.020
AD9 "C3'" "C4'" single 1.524 0.020
AD9 "O4'" "C1'" single 1.426 0.020
AD9 "O3'" "C3'" single 1.432 0.020
AD9 "C2'" "C3'" single 1.524 0.020
AD9 "O2'" "C2'" single 1.432 0.020
AD9 "C1'" "C2'" single 1.524 0.020
AD9 N9 "C1'" single 1.485 0.020
AD9 N9 C8 single 1.337 0.020
AD9 C4 N9 single 1.337 0.020
AD9 C8 N7 double 1.350 0.020
AD9 N7 C5 single 1.350 0.020
AD9 C5 C6 single 1.490 0.020
AD9 C5 C4 double 1.490 0.020
AD9 N6 C6 single 1.355 0.020
AD9 C6 N1 double 1.350 0.020
AD9 N1 C2 single 1.337 0.020
AD9 C2 N3 double 1.337 0.020
AD9 N3 C4 single 1.355 0.020
AD9 H2G1 O2G single 0.967 0.020
AD9 H3G1 O3G single 0.967 0.020
AD9 "H5'1" "C5'" single 1.092 0.020
AD9 "H5'2" "C5'" single 1.092 0.020
AD9 "H4'" "C4'" single 1.099 0.020
AD9 "H3'" "C3'" single 1.099 0.020
AD9 "H1'" "C1'" single 1.099 0.020
AD9 HA "O3'" single 0.967 0.020
AD9 "H2'" "C2'" single 1.099 0.020
AD9 HB "O2'" single 0.967 0.020
AD9 H8 C8 single 1.083 0.020
AD9 H6N1 N6 single 1.010 0.020
AD9 H6N2 N6 single 1.010 0.020
AD9 H2 C2 single 1.083 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
AD9 O2A PA O1A 119.900 3.000
AD9 O2A PA O3A 108.200 3.000
AD9 O2A PA "O5'" 108.200 3.000
AD9 O1A PA O3A 108.200 3.000
AD9 O1A PA "O5'" 108.200 3.000
AD9 O3A PA "O5'" 102.600 3.000
AD9 PA O3A PB 120.500 3.000
AD9 O3A PB O1B 108.200 3.000
AD9 O3A PB O2B 108.200 3.000
AD9 O3A PB O3B 102.600 3.000
AD9 O1B PB O2B 119.900 3.000
AD9 O1B PB O3B 108.200 3.000
AD9 O2B PB O3B 108.200 3.000
AD9 PB O3B VG 120.000 3.000
AD9 O3B VG O3G 113.300 3.000
AD9 O3B VG O2G 99.504 3.000
AD9 O3B VG O1G 104.562 3.000
AD9 O3G VG O2G 114.063 3.000
AD9 O3G VG O1G 114.503 3.000
AD9 O2G VG O1G 109.524 3.000
AD9 VG O3G H3G1 120.000 3.000
AD9 VG O2G H2G1 120.000 3.000
AD9 PA "O5'" "C5'" 120.500 3.000
AD9 "O5'" "C5'" "H5'1" 109.470 3.000
AD9 "O5'" "C5'" "H5'2" 109.470 3.000
AD9 "O5'" "C5'" "C4'" 109.470 3.000
AD9 "H5'1" "C5'" "H5'2" 107.900 3.000
AD9 "H5'1" "C5'" "C4'" 109.470 3.000
AD9 "H5'2" "C5'" "C4'" 109.470 3.000
AD9 "C5'" "C4'" "H4'" 108.340 3.000
AD9 "C5'" "C4'" "C3'" 111.000 3.000
AD9 "C5'" "C4'" "O4'" 109.470 3.000
AD9 "H4'" "C4'" "C3'" 108.340 3.000
AD9 "H4'" "C4'" "O4'" 109.470 3.000
AD9 "C3'" "C4'" "O4'" 109.470 3.000
AD9 "C4'" "C3'" "H3'" 108.340 3.000
AD9 "C4'" "C3'" "O3'" 109.470 3.000
AD9 "C4'" "C3'" "C2'" 111.000 3.000
AD9 "H3'" "C3'" "O3'" 109.470 3.000
AD9 "H3'" "C3'" "C2'" 108.340 3.000
AD9 "O3'" "C3'" "C2'" 109.470 3.000
AD9 "C3'" "O3'" HA 109.470 3.000
AD9 "C3'" "C2'" "H2'" 108.340 3.000
AD9 "C3'" "C2'" "O2'" 109.470 3.000
AD9 "C3'" "C2'" "C1'" 111.000 3.000
AD9 "H2'" "C2'" "O2'" 109.470 3.000
AD9 "H2'" "C2'" "C1'" 108.340 3.000
AD9 "O2'" "C2'" "C1'" 109.470 3.000
AD9 "C2'" "O2'" HB 109.470 3.000
AD9 "C2'" "C1'" "H1'" 108.340 3.000
AD9 "C2'" "C1'" "O4'" 109.470 3.000
AD9 "C2'" "C1'" N9 109.470 3.000
AD9 "H1'" "C1'" "O4'" 109.470 3.000
AD9 "H1'" "C1'" N9 109.470 3.000
AD9 "O4'" "C1'" N9 109.470 3.000
AD9 "C1'" "O4'" "C4'" 111.800 3.000
AD9 "C1'" N9 C4 126.000 3.000
AD9 "C1'" N9 C8 126.000 3.000
AD9 C4 N9 C8 108.000 3.000
AD9 N9 C4 C5 108.000 3.000
AD9 N9 C4 N3 132.000 3.000
AD9 C5 C4 N3 120.000 3.000
AD9 C4 C5 N7 108.000 3.000
AD9 C4 C5 C6 120.000 3.000
AD9 N7 C5 C6 132.000 3.000
AD9 C5 N7 C8 108.000 3.000
AD9 N7 C8 H8 126.000 3.000
AD9 N7 C8 N9 108.000 3.000
AD9 H8 C8 N9 126.000 3.000
AD9 C4 N3 C2 120.000 3.000
AD9 N3 C2 H2 120.000 3.000
AD9 N3 C2 N1 120.000 3.000
AD9 H2 C2 N1 120.000 3.000
AD9 C2 N1 C6 120.000 3.000
AD9 N1 C6 N6 120.000 3.000
AD9 N1 C6 C5 120.000 3.000
AD9 N6 C6 C5 120.000 3.000
AD9 C6 N6 H6N2 120.000 3.000
AD9 C6 N6 H6N1 120.000 3.000
AD9 H6N2 N6 H6N1 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
AD9 var_1 O2A PA O3A PB 78.460 20.000 1
AD9 var_2 PA O3A PB O3B -106.670 20.000 1
AD9 var_3 O3A PB O3B VG -132.494 20.000 1
AD9 var_4 PB O3B VG O1G -16.874 20.000 1
AD9 var_5 O3B VG O3G H3G1 -5.773 20.000 1
AD9 var_6 O3B VG O2G H2G1 -176.755 20.000 1
AD9 var_7 O2A PA "O5'" "C5'" 24.626 20.000 1
AD9 var_8 PA "O5'" "C5'" "C4'" -138.534 20.000 1
AD9 var_9 "O5'" "C5'" "C4'" "C3'" 58.315 20.000 3
AD9 var_10 "C5'" "C4'" "O4'" "C1'" 147.174 20.000 1
AD9 var_11 "C5'" "C4'" "C3'" "C2'" -159.325 20.000 3
AD9 var_12 "C4'" "C3'" "O3'" HA 124.205 20.000 1
AD9 var_13 "C4'" "C3'" "C2'" "C1'" 43.834 20.000 3
AD9 var_14 "C3'" "C2'" "O2'" HB -172.030 20.000 1
AD9 var_15 "C3'" "C2'" "C1'" N9 92.202 20.000 3
AD9 var_16 "C2'" "C1'" "O4'" "C4'" 1.484 20.000 1
AD9 var_17 "C2'" "C1'" N9 C4 64.425 20.000 1
AD9 CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
AD9 CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
AD9 CONST_3 N9 C4 C5 N7 0.000 0.000 0
AD9 CONST_4 C4 C5 C6 N1 0.000 0.000 0
AD9 CONST_5 C4 C5 N7 C8 0.000 0.000 0
AD9 CONST_6 C5 N7 C8 N9 0.000 0.000 0
AD9 CONST_7 N9 C4 N3 C2 180.000 0.000 0
AD9 CONST_8 C4 N3 C2 N1 0.000 0.000 0
AD9 CONST_9 N3 C2 N1 C6 0.000 0.000 0
AD9 CONST_10 C2 N1 C6 N6 180.000 0.000 0
AD9 CONST_11 N1 C6 N6 H6N1 -142.763 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
AD9 chir_01 "C4'" "C5'" "O4'" "C3'" negativ
AD9 chir_02 "C3'" "C4'" "O3'" "C2'" negativ
AD9 chir_03 "C2'" "C3'" "O2'" "C1'" negativ
AD9 chir_04 "C1'" "O4'" "C2'" N9 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
AD9 plan-1 N9 0.020
AD9 plan-1 "C1'" 0.020
AD9 plan-1 C8 0.020
AD9 plan-1 C4 0.020
AD9 plan-1 N7 0.020
AD9 plan-1 H8 0.020
AD9 plan-1 C5 0.020
AD9 plan-1 C6 0.020
AD9 plan-1 N1 0.020
AD9 plan-1 C2 0.020
AD9 plan-1 N3 0.020
AD9 plan-1 N6 0.020
AD9 plan-1 H2 0.020
AD9 plan-1 H6N2 0.020
AD9 plan-1 H6N1 0.020
AD9 plan-2 N6 0.020
AD9 plan-2 C6 0.020
AD9 plan-2 H6N1 0.020
AD9 plan-2 H6N2 0.020
# ------------------------------------------------------
|
