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
|
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
2MG 2MG '2N-METHYLGUANOSINE-5'-MONOPHOSPHATE ' RNA 39 25 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_2MG
#
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
2MG OP3 O OP -0.666 0.000 0.000 0.000
2MG P P P 0.000 -1.148 0.288 -0.943
2MG OP1 O OP -0.666 -1.469 -0.957 -1.742
2MG OP2 O OP -0.666 -0.757 1.404 -1.886
2MG "O5'" O O2 0.000 -2.442 0.731 -0.095
2MG "C5'" C CH2 0.000 -2.760 -0.358 0.772
2MG "H5'" H H 0.000 -1.913 -0.558 1.431
2MG "H5''" H H 0.000 -2.972 -1.248 0.174
2MG "C4'" C CH1 0.000 -3.988 -0.001 1.611
2MG "H4'" H H 0.000 -3.784 0.885 2.229
2MG "C3'" C CH1 0.000 -4.400 -1.194 2.502
2MG "H3'" H H 0.000 -4.045 -2.139 2.068
2MG "C2'" C CH1 0.000 -5.945 -1.146 2.504
2MG "H2'" H H 0.000 -6.359 -2.067 2.072
2MG "O2'" O OH1 0.000 -6.438 -0.952 3.832
2MG "HO2'" H H 0.000 -6.165 -1.694 4.388
2MG "C1'" C CH1 0.000 -6.282 0.068 1.612
2MG "H1'" H H 0.000 -6.433 0.965 2.228
2MG "O4'" O O2 0.000 -5.130 0.233 0.759
2MG N9 N NR5 0.000 -7.477 -0.205 0.809
2MG C4 C CR56 0.000 -8.768 0.084 1.155
2MG C5 C CR56 0.000 -9.563 -0.353 0.090
2MG N7 N NRD5 0.000 -8.732 -0.881 -0.842
2MG C8 C CR15 0.000 -7.503 -0.795 -0.422
2MG H8 H H 0.000 -6.633 -1.139 -0.966
2MG N3 N NRD6 0.000 -9.343 0.652 2.221
2MG C2 C CR6 0.000 -10.647 0.808 2.287
2MG N2 N NH1 0.000 -11.192 1.395 3.401
2MG HN2 H H 0.000 -12.192 1.522 3.467
2MG CM2 C CH3 0.000 -10.323 1.839 4.494
2MG HM23 H H 0.000 -9.786 1.011 4.881
2MG HM22 H H 0.000 -9.638 2.563 4.133
2MG HM21 H H 0.000 -10.911 2.266 5.265
2MG N1 N NR16 0.000 -11.474 0.397 1.284
2MG HN1 H H 0.000 -12.501 0.529 1.374
2MG C6 C CR6 0.000 -10.964 -0.179 0.174
2MG O6 O O 0.000 -11.695 -0.544 -0.731
2MG "O3'" O OH1 0.000 -3.891 -1.028 3.827
2MG "HO3'" H H 0.000 -4.178 -1.799 4.335
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
2MG OP3 n/a P START
2MG P OP3 "O5'" .
2MG OP1 P . .
2MG OP2 P . .
2MG "O5'" P "C5'" .
2MG "C5'" "O5'" "C4'" .
2MG "H5'" "C5'" . .
2MG "H5''" "C5'" . .
2MG "C4'" "C5'" "C3'" .
2MG "H4'" "C4'" . .
2MG "C3'" "C4'" "O3'" .
2MG "H3'" "C3'" . .
2MG "C2'" "C3'" "C1'" .
2MG "H2'" "C2'" . .
2MG "O2'" "C2'" "HO2'" .
2MG "HO2'" "O2'" . .
2MG "C1'" "C2'" N9 .
2MG "H1'" "C1'" . .
2MG "O4'" "C1'" . .
2MG N9 "C1'" C4 .
2MG C4 N9 N3 .
2MG C5 C4 N7 .
2MG N7 C5 C8 .
2MG C8 N7 H8 .
2MG H8 C8 . .
2MG N3 C4 C2 .
2MG C2 N3 N1 .
2MG N2 C2 CM2 .
2MG HN2 N2 . .
2MG CM2 N2 HM21 .
2MG HM23 CM2 . .
2MG HM22 CM2 . .
2MG HM21 CM2 . .
2MG N1 C2 C6 .
2MG HN1 N1 . .
2MG C6 N1 O6 .
2MG O6 C6 . .
2MG "O3'" "C3'" . END
2MG "HO3'" "O3'" . .
2MG "C4'" "O4'" . ADD
2MG N9 C8 . ADD
2MG 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
2MG OP1 P deloc 1.510 0.020
2MG OP2 P deloc 1.510 0.020
2MG P OP3 deloc 1.510 0.020
2MG "O5'" P single 1.610 0.020
2MG "C5'" "O5'" single 1.426 0.020
2MG "C4'" "C5'" single 1.524 0.020
2MG "H5'" "C5'" single 1.092 0.020
2MG "H5''" "C5'" single 1.092 0.020
2MG "C4'" "O4'" single 1.426 0.020
2MG "C3'" "C4'" single 1.524 0.020
2MG "H4'" "C4'" single 1.099 0.020
2MG "O4'" "C1'" single 1.426 0.020
2MG "O3'" "C3'" single 1.432 0.020
2MG "C2'" "C3'" single 1.524 0.020
2MG "H3'" "C3'" single 1.099 0.020
2MG "HO3'" "O3'" single 0.967 0.020
2MG "O2'" "C2'" single 1.432 0.020
2MG "C1'" "C2'" single 1.524 0.020
2MG "H2'" "C2'" single 1.099 0.020
2MG "HO2'" "O2'" single 0.967 0.020
2MG N9 "C1'" single 1.485 0.020
2MG "H1'" "C1'" single 1.099 0.020
2MG N9 C8 single 1.337 0.020
2MG C4 N9 single 1.337 0.020
2MG C8 N7 double 1.350 0.020
2MG H8 C8 single 1.083 0.020
2MG N7 C5 single 1.350 0.020
2MG C5 C6 single 1.490 0.020
2MG C5 C4 double 1.490 0.020
2MG O6 C6 double 1.250 0.020
2MG C6 N1 single 1.337 0.020
2MG N1 C2 single 1.337 0.020
2MG HN1 N1 single 1.040 0.020
2MG N2 C2 single 1.350 0.020
2MG C2 N3 double 1.350 0.020
2MG CM2 N2 single 1.450 0.020
2MG HN2 N2 single 1.010 0.020
2MG HM21 CM2 single 1.059 0.020
2MG HM22 CM2 single 1.059 0.020
2MG HM23 CM2 single 1.059 0.020
2MG N3 C4 single 1.355 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
2MG OP3 P OP1 119.900 3.000
2MG OP3 P OP2 119.900 3.000
2MG OP3 P "O5'" 108.200 3.000
2MG OP1 P OP2 119.900 3.000
2MG OP1 P "O5'" 108.200 3.000
2MG OP2 P "O5'" 108.200 3.000
2MG P "O5'" "C5'" 120.500 3.000
2MG "O5'" "C5'" "H5'" 109.470 3.000
2MG "O5'" "C5'" "H5''" 109.470 3.000
2MG "O5'" "C5'" "C4'" 109.470 3.000
2MG "H5'" "C5'" "H5''" 107.900 3.000
2MG "H5'" "C5'" "C4'" 109.470 3.000
2MG "H5''" "C5'" "C4'" 109.470 3.000
2MG "C5'" "C4'" "H4'" 108.340 3.000
2MG "C5'" "C4'" "C3'" 111.000 3.000
2MG "C5'" "C4'" "O4'" 109.470 3.000
2MG "H4'" "C4'" "C3'" 108.340 3.000
2MG "H4'" "C4'" "O4'" 109.470 3.000
2MG "C3'" "C4'" "O4'" 109.470 3.000
2MG "C4'" "C3'" "H3'" 108.340 3.000
2MG "C4'" "C3'" "C2'" 111.000 3.000
2MG "C4'" "C3'" "O3'" 109.470 3.000
2MG "H3'" "C3'" "C2'" 108.340 3.000
2MG "H3'" "C3'" "O3'" 109.470 3.000
2MG "C2'" "C3'" "O3'" 109.470 3.000
2MG "C3'" "C2'" "H2'" 108.340 3.000
2MG "C3'" "C2'" "O2'" 109.470 3.000
2MG "C3'" "C2'" "C1'" 111.000 3.000
2MG "H2'" "C2'" "O2'" 109.470 3.000
2MG "H2'" "C2'" "C1'" 108.340 3.000
2MG "O2'" "C2'" "C1'" 109.470 3.000
2MG "C2'" "O2'" "HO2'" 109.470 3.000
2MG "C2'" "C1'" "H1'" 108.340 3.000
2MG "C2'" "C1'" "O4'" 109.470 3.000
2MG "C2'" "C1'" N9 109.470 3.000
2MG "H1'" "C1'" "O4'" 109.470 3.000
2MG "H1'" "C1'" N9 109.470 3.000
2MG "O4'" "C1'" N9 109.470 3.000
2MG "C1'" "O4'" "C4'" 111.800 3.000
2MG "C1'" N9 C4 126.000 3.000
2MG "C1'" N9 C8 126.000 3.000
2MG C4 N9 C8 108.000 3.000
2MG N9 C4 C5 108.000 3.000
2MG N9 C4 N3 132.000 3.000
2MG C5 C4 N3 120.000 3.000
2MG C4 C5 N7 108.000 3.000
2MG C4 C5 C6 120.000 3.000
2MG N7 C5 C6 132.000 3.000
2MG C5 N7 C8 108.000 3.000
2MG N7 C8 H8 126.000 3.000
2MG N7 C8 N9 108.000 3.000
2MG H8 C8 N9 126.000 3.000
2MG C4 N3 C2 120.000 3.000
2MG N3 C2 N2 120.000 3.000
2MG N3 C2 N1 120.000 3.000
2MG N2 C2 N1 120.000 3.000
2MG C2 N2 HN2 120.000 3.000
2MG C2 N2 CM2 120.000 3.000
2MG HN2 N2 CM2 118.500 3.000
2MG N2 CM2 HM23 109.470 3.000
2MG N2 CM2 HM22 109.470 3.000
2MG N2 CM2 HM21 109.470 3.000
2MG HM23 CM2 HM22 109.470 3.000
2MG HM23 CM2 HM21 109.470 3.000
2MG HM22 CM2 HM21 109.470 3.000
2MG C2 N1 HN1 120.000 3.000
2MG C2 N1 C6 120.000 3.000
2MG HN1 N1 C6 120.000 3.000
2MG N1 C6 O6 120.000 3.000
2MG N1 C6 C5 120.000 3.000
2MG O6 C6 C5 120.000 3.000
2MG "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
2MG var_1 OP3 P "O5'" "C5'" -60.025 20.000 1
2MG var_2 P "O5'" "C5'" "C4'" 179.987 20.000 1
2MG var_3 "O5'" "C5'" "C4'" "C3'" 176.872 20.000 3
2MG var_4 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
2MG var_5 "C5'" "C4'" "C3'" "O3'" 90.000 20.000 3
2MG var_6 "C4'" "C3'" "C2'" "C1'" 0.000 20.000 3
2MG var_7 "C3'" "C2'" "O2'" "HO2'" -61.447 20.000 1
2MG var_8 "C3'" "C2'" "C1'" N9 150.000 20.000 3
2MG var_9 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
2MG var_10 "C2'" "C1'" N9 C4 91.494 20.000 1
2MG CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
2MG CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
2MG CONST_3 N9 C4 C5 N7 0.000 0.000 0
2MG CONST_4 C4 C5 C6 N1 0.000 0.000 0
2MG CONST_5 C4 C5 N7 C8 0.000 0.000 0
2MG CONST_6 C5 N7 C8 N9 0.000 0.000 0
2MG CONST_7 N9 C4 N3 C2 180.000 0.000 0
2MG CONST_8 C4 N3 C2 N1 0.000 0.000 0
2MG var_11 N3 C2 N2 CM2 0.010 20.000 1
2MG var_12 C2 N2 CM2 HM21 179.969 20.000 1
2MG CONST_9 N3 C2 N1 C6 0.000 0.000 0
2MG 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
2MG chir_01 "C4'" "C5'" "O4'" "C3'" negativ
2MG chir_02 "C3'" "C4'" "O3'" "C2'" negativ
2MG chir_03 "C2'" "C3'" "O2'" "C1'" negativ
2MG 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
2MG plan-1 N9 0.020
2MG plan-1 "C1'" 0.020
2MG plan-1 C8 0.020
2MG plan-1 C4 0.020
2MG plan-1 N7 0.020
2MG plan-1 H8 0.020
2MG plan-1 C5 0.020
2MG plan-1 C6 0.020
2MG plan-1 N1 0.020
2MG plan-1 C2 0.020
2MG plan-1 N3 0.020
2MG plan-1 O6 0.020
2MG plan-1 HN1 0.020
2MG plan-1 N2 0.020
2MG plan-1 HN2 0.020
2MG plan-2 N2 0.020
2MG plan-2 C2 0.020
2MG plan-2 CM2 0.020
2MG plan-2 HN2 0.020
# ------------------------------------------------------
|
