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
|
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
2MU 2MU '2',5-DIMETHYLURIDINE-5'-MONOPHOSPHAT' RNA 38 23 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_2MU
#
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
2MU OP3 O OP -0.666 0.000 0.000 0.000
2MU P P P 0.000 -1.218 -0.120 0.889
2MU OP1 O OP -0.666 -1.699 1.261 1.276
2MU OP2 O OP -0.666 -0.856 -0.895 2.138
2MU "O5'" O O2 0.000 -2.387 -0.892 0.097
2MU "C5'" C CH2 0.000 -2.683 -0.116 -1.064
2MU "H5'" H H 0.000 -1.786 -0.029 -1.681
2MU "H5''" H H 0.000 -3.012 0.880 -0.760
2MU "C4'" C CH1 0.000 -3.792 -0.799 -1.867
2MU "H4'" H H 0.000 -3.473 -1.809 -2.160
2MU "O4'" O O2 0.000 -4.993 -0.874 -1.080
2MU "C1'" C CH1 0.000 -6.103 -0.732 -1.990
2MU "H1'" H H 0.000 -6.290 -1.676 -2.521
2MU N1 N NR6 0.000 -7.304 -0.296 -1.276
2MU C2 C CR6 0.000 -7.285 0.855 -0.580
2MU O2 O O 0.000 -6.270 1.525 -0.558
2MU C6 C CR16 0.000 -8.434 -1.066 -1.316
2MU H6 H H 0.000 -8.441 -1.993 -1.876
2MU C5 C CR6 0.000 -9.542 -0.664 -0.656
2MU C5M C CH3 0.000 -10.795 -1.500 -0.689
2MU HM53 H H 0.000 -11.124 -1.605 -1.690
2MU HM52 H H 0.000 -10.593 -2.457 -0.282
2MU HM51 H H 0.000 -11.551 -1.027 -0.118
2MU C4 C CR6 0.000 -9.509 0.551 0.067
2MU O4 O O 0.000 -10.496 0.934 0.671
2MU N3 N NR16 0.000 -8.375 1.281 0.082
2MU HN3 H H 0.000 -8.344 2.178 0.609
2MU "C3'" C CH1 0.000 -4.118 0.032 -3.122
2MU "H3'" H H 0.000 -3.522 0.956 -3.137
2MU "C2'" C CH1 0.000 -5.623 0.361 -2.978
2MU "H2'" H H 0.000 -5.765 1.364 -2.551
2MU "O2'" O O2 0.000 -6.293 0.245 -4.235
2MU "C6'" C CH3 0.000 -6.313 1.550 -4.815
2MU "H6'3" H H 0.000 -6.831 2.215 -4.173
2MU "H6'2" H H 0.000 -5.320 1.893 -4.950
2MU "H6'1" H H 0.000 -6.804 1.513 -5.753
2MU "O3'" O OH1 0.000 -3.885 -0.732 -4.306
2MU "HO3'" H H 0.000 -2.935 -0.907 -4.343
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
2MU OP3 n/a P START
2MU P OP3 "O5'" .
2MU OP1 P . .
2MU OP2 P . .
2MU "O5'" P "C5'" .
2MU "C5'" "O5'" "C4'" .
2MU "H5'" "C5'" . .
2MU "H5''" "C5'" . .
2MU "C4'" "C5'" "C3'" .
2MU "H4'" "C4'" . .
2MU "O4'" "C4'" "C1'" .
2MU "C1'" "O4'" N1 .
2MU "H1'" "C1'" . .
2MU N1 "C1'" C6 .
2MU C2 N1 O2 .
2MU O2 C2 . .
2MU C6 N1 C5 .
2MU H6 C6 . .
2MU C5 C6 C4 .
2MU C5M C5 HM51 .
2MU HM53 C5M . .
2MU HM52 C5M . .
2MU HM51 C5M . .
2MU C4 C5 N3 .
2MU O4 C4 . .
2MU N3 C4 HN3 .
2MU HN3 N3 . .
2MU "C3'" "C4'" "O3'" .
2MU "H3'" "C3'" . .
2MU "C2'" "C3'" "O2'" .
2MU "H2'" "C2'" . .
2MU "O2'" "C2'" "C6'" .
2MU "C6'" "O2'" "H6'1" .
2MU "H6'3" "C6'" . .
2MU "H6'2" "C6'" . .
2MU "H6'1" "C6'" . .
2MU "O3'" "C3'" . END
2MU "HO3'" "O3'" . .
2MU C2 N3 . ADD
2MU "C1'" "C2'" . 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
2MU C2 N1 single 1.410 0.020
2MU C6 N1 single 1.337 0.020
2MU N1 "C1'" single 1.465 0.020
2MU C2 N3 single 1.337 0.020
2MU O2 C2 double 1.250 0.020
2MU N3 C4 single 1.337 0.020
2MU HN3 N3 single 1.040 0.020
2MU C4 C5 single 1.487 0.020
2MU O4 C4 double 1.250 0.020
2MU C5M C5 single 1.506 0.020
2MU C5 C6 double 1.390 0.020
2MU HM51 C5M single 1.059 0.020
2MU HM52 C5M single 1.059 0.020
2MU HM53 C5M single 1.059 0.020
2MU H6 C6 single 1.083 0.020
2MU "C1'" "C2'" single 1.524 0.020
2MU "C1'" "O4'" single 1.426 0.020
2MU "H1'" "C1'" single 1.099 0.020
2MU "O2'" "C2'" single 1.426 0.020
2MU "C2'" "C3'" single 1.524 0.020
2MU "H2'" "C2'" single 1.099 0.020
2MU "C6'" "O2'" single 1.426 0.020
2MU "C3'" "C4'" single 1.524 0.020
2MU "O3'" "C3'" single 1.432 0.020
2MU "H3'" "C3'" single 1.099 0.020
2MU "O4'" "C4'" single 1.426 0.020
2MU "C4'" "C5'" single 1.524 0.020
2MU "H4'" "C4'" single 1.099 0.020
2MU "HO3'" "O3'" single 0.967 0.020
2MU "C5'" "O5'" single 1.426 0.020
2MU "H5'" "C5'" single 1.092 0.020
2MU "H5''" "C5'" single 1.092 0.020
2MU "O5'" P single 1.610 0.020
2MU "H6'1" "C6'" single 1.059 0.020
2MU "H6'2" "C6'" single 1.059 0.020
2MU "H6'3" "C6'" single 1.059 0.020
2MU OP1 P deloc 1.510 0.020
2MU OP2 P deloc 1.510 0.020
2MU P OP3 deloc 1.510 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
2MU OP3 P OP1 119.900 3.000
2MU OP3 P OP2 119.900 3.000
2MU OP3 P "O5'" 108.200 3.000
2MU OP1 P OP2 119.900 3.000
2MU OP1 P "O5'" 108.200 3.000
2MU OP2 P "O5'" 108.200 3.000
2MU P "O5'" "C5'" 120.500 3.000
2MU "O5'" "C5'" "H5'" 109.470 3.000
2MU "O5'" "C5'" "H5''" 109.470 3.000
2MU "O5'" "C5'" "C4'" 109.470 3.000
2MU "H5'" "C5'" "H5''" 107.900 3.000
2MU "H5'" "C5'" "C4'" 109.470 3.000
2MU "H5''" "C5'" "C4'" 109.470 3.000
2MU "C5'" "C4'" "H4'" 108.340 3.000
2MU "C5'" "C4'" "O4'" 109.470 3.000
2MU "C5'" "C4'" "C3'" 111.000 3.000
2MU "H4'" "C4'" "O4'" 109.470 3.000
2MU "H4'" "C4'" "C3'" 108.340 3.000
2MU "O4'" "C4'" "C3'" 109.470 3.000
2MU "C4'" "O4'" "C1'" 111.800 3.000
2MU "O4'" "C1'" "H1'" 109.470 3.000
2MU "O4'" "C1'" N1 109.470 3.000
2MU "O4'" "C1'" "C2'" 109.470 3.000
2MU "H1'" "C1'" N1 109.470 3.000
2MU "H1'" "C1'" "C2'" 108.340 3.000
2MU N1 "C1'" "C2'" 109.470 3.000
2MU "C1'" N1 C2 120.000 3.000
2MU "C1'" N1 C6 120.000 3.000
2MU C2 N1 C6 120.000 3.000
2MU N1 C2 O2 120.000 3.000
2MU N1 C2 N3 120.000 3.000
2MU O2 C2 N3 120.000 3.000
2MU N1 C6 H6 120.000 3.000
2MU N1 C6 C5 120.000 3.000
2MU H6 C6 C5 120.000 3.000
2MU C6 C5 C5M 120.000 3.000
2MU C6 C5 C4 120.000 3.000
2MU C5M C5 C4 120.000 3.000
2MU C5 C5M HM53 109.470 3.000
2MU C5 C5M HM52 109.470 3.000
2MU C5 C5M HM51 109.470 3.000
2MU HM53 C5M HM52 109.470 3.000
2MU HM53 C5M HM51 109.470 3.000
2MU HM52 C5M HM51 109.470 3.000
2MU C5 C4 O4 120.000 3.000
2MU C5 C4 N3 120.000 3.000
2MU O4 C4 N3 120.000 3.000
2MU C4 N3 HN3 120.000 3.000
2MU C4 N3 C2 120.000 3.000
2MU HN3 N3 C2 120.000 3.000
2MU "C4'" "C3'" "H3'" 108.340 3.000
2MU "C4'" "C3'" "C2'" 111.000 3.000
2MU "C4'" "C3'" "O3'" 109.470 3.000
2MU "H3'" "C3'" "C2'" 108.340 3.000
2MU "H3'" "C3'" "O3'" 109.470 3.000
2MU "C2'" "C3'" "O3'" 109.470 3.000
2MU "C3'" "C2'" "H2'" 108.340 3.000
2MU "C3'" "C2'" "O2'" 109.470 3.000
2MU "C3'" "C2'" "C1'" 111.000 3.000
2MU "H2'" "C2'" "O2'" 109.470 3.000
2MU "H2'" "C2'" "C1'" 108.340 3.000
2MU "O2'" "C2'" "C1'" 109.470 3.000
2MU "C2'" "O2'" "C6'" 111.800 3.000
2MU "O2'" "C6'" "H6'3" 109.470 3.000
2MU "O2'" "C6'" "H6'2" 109.470 3.000
2MU "O2'" "C6'" "H6'1" 109.470 3.000
2MU "H6'3" "C6'" "H6'2" 109.470 3.000
2MU "H6'3" "C6'" "H6'1" 109.470 3.000
2MU "H6'2" "C6'" "H6'1" 109.470 3.000
2MU "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
2MU var_1 OP3 P "O5'" "C5'" -60.014 20.000 1
2MU var_2 P "O5'" "C5'" "C4'" 179.965 20.000 1
2MU var_3 "O5'" "C5'" "C4'" "C3'" -179.973 20.000 3
2MU var_4 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
2MU var_5 "C4'" "O4'" "C1'" N1 -150.000 20.000 1
2MU var_6 "O4'" "C1'" "C2'" "C3'" 30.000 20.000 3
2MU var_7 "O4'" "C1'" N1 C6 -121.418 20.000 1
2MU CONST_1 "C1'" N1 C2 O2 0.000 0.000 0
2MU CONST_2 N1 C2 N3 C4 0.000 0.000 0
2MU CONST_3 "C1'" N1 C6 C5 180.000 0.000 0
2MU CONST_4 N1 C6 C5 C4 0.000 0.000 0
2MU var_8 C6 C5 C5M HM51 -179.979 20.000 1
2MU CONST_5 C6 C5 C4 N3 0.000 0.000 0
2MU CONST_6 C5 C4 N3 C2 0.000 0.000 0
2MU var_9 "C5'" "C4'" "C3'" "O3'" 120.000 20.000 3
2MU var_10 "C4'" "C3'" "C2'" "O2'" -150.000 20.000 3
2MU var_11 "C3'" "C2'" "O2'" "C6'" -94.314 20.000 1
2MU var_12 "C2'" "O2'" "C6'" "H6'1" -179.959 20.000 1
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
2MU chir_01 "C1'" "C2'" "O4'" N1 negativ
2MU chir_02 "C2'" "C1'" "O2'" "C3'" positiv
2MU chir_03 "C3'" "C2'" "C4'" "O3'" negativ
2MU chir_04 "C4'" "C3'" "O4'" "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
2MU plan-1 C2 0.020
2MU plan-1 N3 0.020
2MU plan-1 O2 0.020
2MU plan-1 N1 0.020
2MU plan-1 C4 0.020
2MU plan-1 C5 0.020
2MU plan-1 C6 0.020
2MU plan-1 HN3 0.020
2MU plan-1 O4 0.020
2MU plan-1 C5M 0.020
2MU plan-1 H6 0.020
2MU plan-1 "C1'" 0.020
# ------------------------------------------------------
|
