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
|
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
O2G O2G '2'-DEOXY-N,N-DIMETHYL-5'-O-[OXIDO(OX' RNA 41 25 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_O2G
#
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
O2G OP3 O OP -0.666 0.000 0.000 0.000
O2G P P P 0.000 -0.304 1.266 -0.771
O2G OP1 O OP -0.666 0.145 1.102 -2.206
O2G OP2 O OP -0.666 0.432 2.429 -0.141
O2G "O5'" O O2 0.000 -1.888 1.549 -0.733
O2G "C5'" C CH2 0.000 -2.596 1.851 0.471
O2G "H5'" H H 0.000 -2.185 2.759 0.917
O2G "H5'A" H H 0.000 -2.490 1.022 1.173
O2G "C4'" C CH1 0.000 -4.078 2.064 0.151
O2G "H4'" H H 0.000 -4.202 2.855 -0.603
O2G "C3'" C CH1 0.000 -4.870 2.408 1.439
O2G "H3'" H H 0.000 -4.491 1.835 2.296
O2G "C2'" C CH2 0.000 -6.304 1.959 1.067
O2G "H2'" H H 0.000 -6.918 2.794 0.724
O2G "H2'A" H H 0.000 -6.805 1.458 1.897
O2G "C1'" C CH1 0.000 -6.099 0.961 -0.090
O2G "H1'" H H 0.000 -6.579 1.341 -1.002
O2G "O4'" O O2 0.000 -4.683 0.833 -0.298
O2G N9 N NR5 0.000 -6.669 -0.340 0.268
O2G C4 C CR56 0.000 -7.974 -0.723 0.111
O2G C5 C CR56 0.000 -8.052 -2.037 0.585
O2G N7 N NRD5 0.000 -6.814 -2.386 1.009
O2G C8 C CR15 0.000 -5.998 -1.390 0.825
O2G H8 H H 0.000 -4.945 -1.393 1.075
O2G N3 N NRD6 0.000 -9.067 -0.128 -0.378
O2G C2 C CR6 0.000 -10.223 -0.754 -0.414
O2G N2 N N 0.000 -11.319 -0.101 -0.919
O2G CM2 C CH3 0.000 -12.588 -0.816 -1.081
O2G HM2B H H 0.000 -13.357 -0.295 -0.570
O2G HM2A H H 0.000 -12.831 -0.880 -2.110
O2G HM2 H H 0.000 -12.499 -1.793 -0.679
O2G CM1 C CH3 0.000 -11.221 1.311 -1.297
O2G HM1B H H 0.000 -12.162 1.780 -1.165
O2G HM1A H H 0.000 -10.500 1.792 -0.688
O2G HM1 H H 0.000 -10.930 1.387 -2.313
O2G N1 N NR16 0.000 -10.363 -2.032 0.038
O2G HN1 H H 0.000 -11.293 -2.497 -0.005
O2G C6 C CR6 0.000 -9.302 -2.699 0.540
O2G O6 O O 0.000 -9.418 -3.843 0.948
O2G "O3'" O OH1 0.000 -4.827 3.811 1.705
O2G "HO3'" H H 0.000 -5.309 4.075 2.501
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
O2G OP3 n/a P START
O2G P OP3 "O5'" .
O2G OP1 P . .
O2G OP2 P . .
O2G "O5'" P "C5'" .
O2G "C5'" "O5'" "C4'" .
O2G "H5'" "C5'" . .
O2G "H5'A" "C5'" . .
O2G "C4'" "C5'" "C3'" .
O2G "H4'" "C4'" . .
O2G "C3'" "C4'" "O3'" .
O2G "H3'" "C3'" . .
O2G "C2'" "C3'" "C1'" .
O2G "H2'" "C2'" . .
O2G "H2'A" "C2'" . .
O2G "C1'" "C2'" N9 .
O2G "H1'" "C1'" . .
O2G "O4'" "C1'" . .
O2G N9 "C1'" C4 .
O2G C4 N9 N3 .
O2G C5 C4 N7 .
O2G N7 C5 C8 .
O2G C8 N7 H8 .
O2G H8 C8 . .
O2G N3 C4 C2 .
O2G C2 N3 N1 .
O2G N2 C2 CM1 .
O2G CM2 N2 HM2 .
O2G HM2B CM2 . .
O2G HM2A CM2 . .
O2G HM2 CM2 . .
O2G CM1 N2 HM1 .
O2G HM1B CM1 . .
O2G HM1A CM1 . .
O2G HM1 CM1 . .
O2G N1 C2 C6 .
O2G HN1 N1 . .
O2G C6 N1 O6 .
O2G O6 C6 . .
O2G "O3'" "C3'" . END
O2G "HO3'" "O3'" . .
O2G "C4'" "O4'" . ADD
O2G N9 C8 . ADD
O2G 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
O2G P OP3 deloc 1.510 0.020
O2G OP1 P deloc 1.510 0.020
O2G OP2 P deloc 1.510 0.020
O2G "O5'" P single 1.610 0.020
O2G "C5'" "O5'" single 1.426 0.020
O2G "C4'" "C5'" single 1.524 0.020
O2G "C4'" "O4'" single 1.426 0.020
O2G "C3'" "C4'" single 1.524 0.020
O2G "O3'" "C3'" single 1.432 0.020
O2G "C2'" "C3'" single 1.524 0.020
O2G "O4'" "C1'" single 1.426 0.020
O2G "C1'" "C2'" single 1.524 0.020
O2G N9 "C1'" single 1.485 0.020
O2G N9 C8 single 1.337 0.020
O2G C8 N7 double 1.350 0.020
O2G N7 C5 single 1.350 0.020
O2G C5 C6 single 1.490 0.020
O2G O6 C6 double 1.250 0.020
O2G C6 N1 single 1.337 0.020
O2G N1 C2 single 1.337 0.020
O2G N2 C2 single 1.400 0.020
O2G C2 N3 double 1.350 0.020
O2G C4 N9 single 1.337 0.020
O2G C5 C4 double 1.490 0.020
O2G N3 C4 single 1.355 0.020
O2G CM1 N2 single 1.455 0.020
O2G CM2 N2 single 1.455 0.020
O2G "H5'" "C5'" single 1.092 0.020
O2G "H5'A" "C5'" single 1.092 0.020
O2G "H4'" "C4'" single 1.099 0.020
O2G "H3'" "C3'" single 1.099 0.020
O2G "HO3'" "O3'" single 0.967 0.020
O2G "H2'" "C2'" single 1.092 0.020
O2G "H2'A" "C2'" single 1.092 0.020
O2G "H1'" "C1'" single 1.099 0.020
O2G H8 C8 single 1.083 0.020
O2G HN1 N1 single 1.040 0.020
O2G HM1 CM1 single 1.059 0.020
O2G HM1A CM1 single 1.059 0.020
O2G HM1B CM1 single 1.059 0.020
O2G HM2 CM2 single 1.059 0.020
O2G HM2A CM2 single 1.059 0.020
O2G HM2B CM2 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
O2G OP3 P OP1 119.900 3.000
O2G OP3 P OP2 119.900 3.000
O2G OP3 P "O5'" 108.200 3.000
O2G OP1 P OP2 119.900 3.000
O2G OP1 P "O5'" 108.200 3.000
O2G OP2 P "O5'" 108.200 3.000
O2G P "O5'" "C5'" 120.500 3.000
O2G "O5'" "C5'" "H5'" 109.470 3.000
O2G "O5'" "C5'" "H5'A" 109.470 3.000
O2G "O5'" "C5'" "C4'" 109.470 3.000
O2G "H5'" "C5'" "H5'A" 107.900 3.000
O2G "H5'" "C5'" "C4'" 109.470 3.000
O2G "H5'A" "C5'" "C4'" 109.470 3.000
O2G "C5'" "C4'" "H4'" 108.340 3.000
O2G "C5'" "C4'" "C3'" 111.000 3.000
O2G "C5'" "C4'" "O4'" 109.470 3.000
O2G "H4'" "C4'" "C3'" 108.340 3.000
O2G "H4'" "C4'" "O4'" 109.470 3.000
O2G "C3'" "C4'" "O4'" 109.470 3.000
O2G "C4'" "C3'" "H3'" 108.340 3.000
O2G "C4'" "C3'" "C2'" 111.000 3.000
O2G "C4'" "C3'" "O3'" 109.470 3.000
O2G "H3'" "C3'" "C2'" 108.340 3.000
O2G "H3'" "C3'" "O3'" 109.470 3.000
O2G "C2'" "C3'" "O3'" 109.470 3.000
O2G "C3'" "C2'" "H2'" 109.470 3.000
O2G "C3'" "C2'" "H2'A" 109.470 3.000
O2G "C3'" "C2'" "C1'" 111.000 3.000
O2G "H2'" "C2'" "H2'A" 107.900 3.000
O2G "H2'" "C2'" "C1'" 109.470 3.000
O2G "H2'A" "C2'" "C1'" 109.470 3.000
O2G "C2'" "C1'" "H1'" 108.340 3.000
O2G "C2'" "C1'" "O4'" 109.470 3.000
O2G "C2'" "C1'" N9 109.470 3.000
O2G "H1'" "C1'" "O4'" 109.470 3.000
O2G "H1'" "C1'" N9 109.470 3.000
O2G "O4'" "C1'" N9 109.470 3.000
O2G "C1'" "O4'" "C4'" 111.800 3.000
O2G "C1'" N9 C4 126.000 3.000
O2G "C1'" N9 C8 126.000 3.000
O2G C4 N9 C8 108.000 3.000
O2G N9 C4 C5 108.000 3.000
O2G N9 C4 N3 132.000 3.000
O2G C5 C4 N3 120.000 3.000
O2G C4 C5 N7 108.000 3.000
O2G C4 C5 C6 120.000 3.000
O2G N7 C5 C6 132.000 3.000
O2G C5 N7 C8 108.000 3.000
O2G N7 C8 H8 126.000 3.000
O2G N7 C8 N9 108.000 3.000
O2G H8 C8 N9 126.000 3.000
O2G C4 N3 C2 120.000 3.000
O2G N3 C2 N2 120.000 3.000
O2G N3 C2 N1 120.000 3.000
O2G N2 C2 N1 120.000 3.000
O2G C2 N2 CM2 120.000 3.000
O2G C2 N2 CM1 120.000 3.000
O2G CM2 N2 CM1 120.000 3.000
O2G N2 CM2 HM2B 109.470 3.000
O2G N2 CM2 HM2A 109.470 3.000
O2G N2 CM2 HM2 109.470 3.000
O2G HM2B CM2 HM2A 109.470 3.000
O2G HM2B CM2 HM2 109.470 3.000
O2G HM2A CM2 HM2 109.470 3.000
O2G N2 CM1 HM1B 109.470 3.000
O2G N2 CM1 HM1A 109.470 3.000
O2G N2 CM1 HM1 109.470 3.000
O2G HM1B CM1 HM1A 109.470 3.000
O2G HM1B CM1 HM1 109.470 3.000
O2G HM1A CM1 HM1 109.470 3.000
O2G C2 N1 HN1 120.000 3.000
O2G C2 N1 C6 120.000 3.000
O2G HN1 N1 C6 120.000 3.000
O2G N1 C6 O6 120.000 3.000
O2G N1 C6 C5 120.000 3.000
O2G O6 C6 C5 120.000 3.000
O2G "C3'" "O3'" "HO3'" 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
O2G var_1 OP3 P "O5'" "C5'" 65.029 20.000 1
O2G var_2 P "O5'" "C5'" "C4'" 179.973 20.000 1
O2G var_3 "O5'" "C5'" "C4'" "C3'" -179.461 20.000 3
O2G var_4 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
O2G var_5 "C5'" "C4'" "C3'" "O3'" 90.000 20.000 3
O2G var_6 "C4'" "C3'" "C2'" "C1'" 30.000 20.000 3
O2G var_7 "C3'" "C2'" "C1'" N9 120.000 20.000 3
O2G var_8 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
O2G var_9 "C2'" "C1'" N9 C4 85.413 20.000 1
O2G CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
O2G CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
O2G CONST_3 N9 C4 C5 N7 0.000 0.000 0
O2G CONST_4 C4 C5 C6 N1 0.000 0.000 0
O2G CONST_5 C4 C5 N7 C8 0.000 0.000 0
O2G CONST_6 C5 N7 C8 N9 0.000 0.000 0
O2G CONST_7 N9 C4 N3 C2 180.000 0.000 0
O2G CONST_8 C4 N3 C2 N1 0.000 0.000 0
O2G var_10 N3 C2 N2 CM1 -5.519 20.000 1
O2G var_11 C2 N2 CM2 HM2 5.027 20.000 1
O2G var_12 C2 N2 CM1 HM1 90.027 20.000 1
O2G CONST_9 N3 C2 N1 C6 0.000 0.000 0
O2G CONST_10 C2 N1 C6 O6 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
O2G chir_01 "C4'" "C5'" "O4'" "C3'" negativ
O2G chir_02 "C3'" "C4'" "O3'" "C2'" negativ
O2G chir_03 "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
O2G plan-1 N9 0.020
O2G plan-1 "C1'" 0.020
O2G plan-1 C8 0.020
O2G plan-1 C4 0.020
O2G plan-1 N7 0.020
O2G plan-1 H8 0.020
O2G plan-1 C5 0.020
O2G plan-1 C6 0.020
O2G plan-1 N1 0.020
O2G plan-1 C2 0.020
O2G plan-1 N3 0.020
O2G plan-1 O6 0.020
O2G plan-1 HN1 0.020
O2G plan-1 N2 0.020
O2G plan-2 N2 0.020
O2G plan-2 C2 0.020
O2G plan-2 CM1 0.020
O2G plan-2 CM2 0.020
# ------------------------------------------------------
|
