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
|
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
2MA 2MA '2-METHYLADENOSINE-5'-MONOPHOSPHATE ' RNA 38 24 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_2MA
#
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
2MA OP3 O OP -0.666 0.000 0.000 0.000
2MA P P P 0.000 -1.170 -0.168 0.944
2MA OP1 O OP -0.666 -1.502 1.165 1.578
2MA OP2 O OP -0.666 -0.808 -1.165 2.023
2MA "O5'" O O2 0.000 -2.448 -0.705 0.125
2MA "C5'" C CH2 0.000 -2.740 0.273 -0.873
2MA "H5'" H H 0.000 -1.876 0.388 -1.532
2MA "H5''" H H 0.000 -2.959 1.228 -0.392
2MA "C4'" C CH1 0.000 -3.952 -0.178 -1.692
2MA "H4'" H H 0.000 -3.740 -1.133 -2.194
2MA "C3'" C CH1 0.000 -4.335 0.899 -2.730
2MA "H3'" H H 0.000 -3.983 1.889 -2.405
2MA "C2'" C CH1 0.000 -5.880 0.858 -2.761
2MA "H2'" H H 0.000 -6.297 1.827 -2.453
2MA "O2'" O OH1 0.000 -6.344 0.507 -4.067
2MA "HO2'" H H 0.000 -6.053 1.175 -4.702
2MA "C1'" C CH1 0.000 -6.245 -0.238 -1.737
2MA "H1'" H H 0.000 -6.388 -1.203 -2.244
2MA "O4'" O O2 0.000 -5.113 -0.303 -0.844
2MA N9 N NR5 0.000 -7.455 0.134 -1.001
2MA C4 C CR56 0.000 -8.728 -0.186 -1.336
2MA C5 C CR56 0.000 -9.543 0.372 -0.333
2MA N7 N NRD5 0.000 -8.750 1.003 0.534
2MA C8 C CR15 0.000 -7.506 0.869 0.150
2MA H8 H H 0.000 -6.647 1.278 0.667
2MA N3 N NRD6 0.000 -9.270 -0.884 -2.349
2MA C2 C CR6 0.000 -10.573 -0.910 -2.486
2MA CM2 C CH3 0.000 -11.158 -1.767 -3.578
2MA HM23 H H 0.000 -11.799 -2.494 -3.151
2MA HM22 H H 0.000 -11.710 -1.159 -4.246
2MA HM21 H H 0.000 -10.377 -2.251 -4.104
2MA N1 N NR16 0.000 -11.424 -0.199 -1.696
2MA HN1 H H 0.000 -12.371 0.062 -2.038
2MA C6 C CR6 0.000 -11.002 0.174 -0.415
2MA N6 N N 0.000 -11.816 0.336 0.602
2MA HN6 H H 0.000 -12.743 0.191 0.479
2MA "O3'" O OH1 0.000 -3.797 0.573 -4.013
2MA "HO3'" H H 0.000 -4.068 1.279 -4.616
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
2MA OP3 n/a P START
2MA P OP3 "O5'" .
2MA OP1 P . .
2MA OP2 P . .
2MA "O5'" P "C5'" .
2MA "C5'" "O5'" "C4'" .
2MA "H5'" "C5'" . .
2MA "H5''" "C5'" . .
2MA "C4'" "C5'" "C3'" .
2MA "H4'" "C4'" . .
2MA "C3'" "C4'" "O3'" .
2MA "H3'" "C3'" . .
2MA "C2'" "C3'" "C1'" .
2MA "H2'" "C2'" . .
2MA "O2'" "C2'" "HO2'" .
2MA "HO2'" "O2'" . .
2MA "C1'" "C2'" N9 .
2MA "H1'" "C1'" . .
2MA "O4'" "C1'" . .
2MA N9 "C1'" C4 .
2MA C4 N9 N3 .
2MA C5 C4 N7 .
2MA N7 C5 C8 .
2MA C8 N7 H8 .
2MA H8 C8 . .
2MA N3 C4 C2 .
2MA C2 N3 N1 .
2MA CM2 C2 HM21 .
2MA HM23 CM2 . .
2MA HM22 CM2 . .
2MA HM21 CM2 . .
2MA N1 C2 C6 .
2MA HN1 N1 . .
2MA C6 N1 N6 .
2MA N6 C6 HN6 .
2MA HN6 N6 . .
2MA "O3'" "C3'" . END
2MA "HO3'" "O3'" . .
2MA "C4'" "O4'" . ADD
2MA N9 C8 . ADD
2MA 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
2MA OP1 P deloc 1.510 0.020
2MA OP2 P deloc 1.510 0.020
2MA P OP3 deloc 1.510 0.020
2MA "O5'" P single 1.610 0.020
2MA "C5'" "O5'" single 1.426 0.020
2MA "C4'" "C5'" single 1.524 0.020
2MA "H5'" "C5'" single 1.092 0.020
2MA "H5''" "C5'" single 1.092 0.020
2MA "C4'" "O4'" single 1.426 0.020
2MA "C3'" "C4'" single 1.524 0.020
2MA "H4'" "C4'" single 1.099 0.020
2MA "O4'" "C1'" single 1.426 0.020
2MA "O3'" "C3'" single 1.432 0.020
2MA "C2'" "C3'" single 1.524 0.020
2MA "H3'" "C3'" single 1.099 0.020
2MA "HO3'" "O3'" single 0.967 0.020
2MA "O2'" "C2'" single 1.432 0.020
2MA "C1'" "C2'" single 1.524 0.020
2MA "H2'" "C2'" single 1.099 0.020
2MA "HO2'" "O2'" single 0.967 0.020
2MA N9 "C1'" single 1.485 0.020
2MA "H1'" "C1'" single 1.099 0.020
2MA N9 C8 single 1.337 0.020
2MA C4 N9 single 1.337 0.020
2MA C8 N7 double 1.350 0.020
2MA H8 C8 single 1.083 0.020
2MA N7 C5 single 1.350 0.020
2MA C5 C6 single 1.490 0.020
2MA C5 C4 double 1.490 0.020
2MA N6 C6 double 1.355 0.020
2MA C6 N1 single 1.337 0.020
2MA HN6 N6 single 0.954 0.020
2MA N1 C2 single 1.337 0.020
2MA HN1 N1 single 1.040 0.020
2MA CM2 C2 single 1.506 0.020
2MA C2 N3 double 1.350 0.020
2MA HM21 CM2 single 1.059 0.020
2MA HM22 CM2 single 1.059 0.020
2MA HM23 CM2 single 1.059 0.020
2MA 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
2MA OP3 P OP1 119.900 3.000
2MA OP3 P OP2 119.900 3.000
2MA OP3 P "O5'" 108.200 3.000
2MA OP1 P OP2 119.900 3.000
2MA OP1 P "O5'" 108.200 3.000
2MA OP2 P "O5'" 108.200 3.000
2MA P "O5'" "C5'" 120.500 3.000
2MA "O5'" "C5'" "H5'" 109.470 3.000
2MA "O5'" "C5'" "H5''" 109.470 3.000
2MA "O5'" "C5'" "C4'" 109.470 3.000
2MA "H5'" "C5'" "H5''" 107.900 3.000
2MA "H5'" "C5'" "C4'" 109.470 3.000
2MA "H5''" "C5'" "C4'" 109.470 3.000
2MA "C5'" "C4'" "H4'" 108.340 3.000
2MA "C5'" "C4'" "C3'" 111.000 3.000
2MA "C5'" "C4'" "O4'" 109.470 3.000
2MA "H4'" "C4'" "C3'" 108.340 3.000
2MA "H4'" "C4'" "O4'" 109.470 3.000
2MA "C3'" "C4'" "O4'" 109.470 3.000
2MA "C4'" "C3'" "H3'" 108.340 3.000
2MA "C4'" "C3'" "C2'" 111.000 3.000
2MA "C4'" "C3'" "O3'" 109.470 3.000
2MA "H3'" "C3'" "C2'" 108.340 3.000
2MA "H3'" "C3'" "O3'" 109.470 3.000
2MA "C2'" "C3'" "O3'" 109.470 3.000
2MA "C3'" "C2'" "H2'" 108.340 3.000
2MA "C3'" "C2'" "O2'" 109.470 3.000
2MA "C3'" "C2'" "C1'" 111.000 3.000
2MA "H2'" "C2'" "O2'" 109.470 3.000
2MA "H2'" "C2'" "C1'" 108.340 3.000
2MA "O2'" "C2'" "C1'" 109.470 3.000
2MA "C2'" "O2'" "HO2'" 109.470 3.000
2MA "C2'" "C1'" "H1'" 108.340 3.000
2MA "C2'" "C1'" "O4'" 109.470 3.000
2MA "C2'" "C1'" N9 109.470 3.000
2MA "H1'" "C1'" "O4'" 109.470 3.000
2MA "H1'" "C1'" N9 109.470 3.000
2MA "O4'" "C1'" N9 109.470 3.000
2MA "C1'" "O4'" "C4'" 111.800 3.000
2MA "C1'" N9 C4 126.000 3.000
2MA "C1'" N9 C8 126.000 3.000
2MA C4 N9 C8 108.000 3.000
2MA N9 C4 C5 108.000 3.000
2MA N9 C4 N3 132.000 3.000
2MA C5 C4 N3 120.000 3.000
2MA C4 C5 N7 108.000 3.000
2MA C4 C5 C6 120.000 3.000
2MA N7 C5 C6 132.000 3.000
2MA C5 N7 C8 108.000 3.000
2MA N7 C8 H8 126.000 3.000
2MA N7 C8 N9 108.000 3.000
2MA H8 C8 N9 126.000 3.000
2MA C4 N3 C2 120.000 3.000
2MA N3 C2 CM2 120.000 3.000
2MA N3 C2 N1 120.000 3.000
2MA CM2 C2 N1 120.000 3.000
2MA C2 CM2 HM23 109.470 3.000
2MA C2 CM2 HM22 109.470 3.000
2MA C2 CM2 HM21 109.470 3.000
2MA HM23 CM2 HM22 109.470 3.000
2MA HM23 CM2 HM21 109.470 3.000
2MA HM22 CM2 HM21 109.470 3.000
2MA C2 N1 HN1 120.000 3.000
2MA C2 N1 C6 120.000 3.000
2MA HN1 N1 C6 120.000 3.000
2MA N1 C6 N6 120.000 3.000
2MA N1 C6 C5 120.000 3.000
2MA N6 C6 C5 120.000 3.000
2MA C6 N6 HN6 120.000 3.000
2MA "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
2MA var_1 OP3 P "O5'" "C5'" -60.005 20.000 1
2MA var_2 P "O5'" "C5'" "C4'" -179.977 20.000 1
2MA var_3 "O5'" "C5'" "C4'" "C3'" 176.936 20.000 3
2MA var_4 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
2MA var_5 "C5'" "C4'" "C3'" "O3'" 90.000 20.000 3
2MA var_6 "C4'" "C3'" "C2'" "C1'" 0.000 20.000 3
2MA var_7 "C3'" "C2'" "O2'" "HO2'" -61.426 20.000 1
2MA var_8 "C3'" "C2'" "C1'" N9 150.000 20.000 3
2MA var_9 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
2MA var_10 "C2'" "C1'" N9 C4 91.519 20.000 1
2MA CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
2MA CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
2MA CONST_3 N9 C4 C5 N7 0.000 0.000 0
2MA CONST_4 C4 C5 C6 N1 -30.000 0.000 0
2MA CONST_5 C4 C5 N7 C8 0.000 0.000 0
2MA CONST_6 C5 N7 C8 N9 0.000 0.000 0
2MA CONST_7 N9 C4 N3 C2 180.000 0.000 0
2MA CONST_8 C4 N3 C2 N1 0.000 0.000 0
2MA var_11 N3 C2 CM2 HM21 0.018 20.000 1
2MA CONST_9 N3 C2 N1 C6 -30.000 0.000 0
2MA CONST_10 C2 N1 C6 N6 -150.000 0.000 0
2MA CONST_11 N1 C6 N6 HN6 0.384 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
2MA chir_01 "C4'" "C5'" "O4'" "C3'" negativ
2MA chir_02 "C3'" "C4'" "O3'" "C2'" negativ
2MA chir_03 "C2'" "C3'" "O2'" "C1'" negativ
2MA 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
2MA plan-1 N9 0.020
2MA plan-1 "C1'" 0.020
2MA plan-1 C8 0.020
2MA plan-1 C4 0.020
2MA plan-1 N7 0.020
2MA plan-1 H8 0.020
2MA plan-1 C5 0.020
2MA plan-1 C6 0.020
2MA plan-1 N1 0.020
2MA plan-1 C2 0.020
2MA plan-1 N3 0.020
2MA plan-1 N6 0.020
2MA plan-1 HN6 0.020
2MA plan-1 HN1 0.020
2MA plan-1 CM2 0.020
# ------------------------------------------------------
|
