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
|
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
UMP UMP '. ' non-polymer 31 20 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_UMP
#
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
UMP OP3 O OP -0.666 0.000 0.000 0.000
UMP P P P 0.000 -1.087 -1.028 -0.224
UMP OP1 O OP -0.666 -1.451 -1.672 1.096
UMP OP2 O OP -0.666 -0.590 -2.087 -1.182
UMP "O5'" O O2 0.000 -2.386 -0.308 -0.846
UMP "C5'" C CH2 0.000 -2.875 0.593 0.149
UMP "H5'" H H 0.000 -2.101 1.325 0.388
UMP "H5''" H H 0.000 -3.135 0.033 1.050
UMP "C4'" C CH1 0.000 -4.117 1.314 -0.381
UMP "H4'" H H 0.000 -3.888 1.820 -1.329
UMP "O4'" O O2 0.000 -5.204 0.377 -0.562
UMP "C1'" C CH1 0.000 -6.404 1.181 -0.573
UMP "H1'" H H 0.000 -6.530 1.667 -1.550
UMP N1 N NR6 0.000 -7.575 0.359 -0.259
UMP C2 C CR6 0.000 -7.557 -0.440 0.823
UMP O2 O O 0.000 -6.570 -0.468 1.532
UMP C6 C CR16 0.000 -8.674 0.407 -1.072
UMP H6 H H 0.000 -8.679 1.050 -1.943
UMP C5 C CR16 0.000 -9.754 -0.352 -0.783
UMP H5 H H 0.000 -10.630 -0.324 -1.419
UMP C4 C CR6 0.000 -9.724 -1.184 0.362
UMP O4 O O 0.000 -10.685 -1.878 0.643
UMP N3 N NR16 0.000 -8.621 -1.202 1.138
UMP HN3 H H 0.000 -8.592 -1.807 1.983
UMP "C3'" C CH1 0.000 -4.643 2.330 0.656
UMP "H3'" H H 0.000 -4.324 2.046 1.668
UMP "C2'" C CH2 0.000 -6.179 2.241 0.529
UMP "H2''" H H 0.000 -6.621 3.190 0.218
UMP "H2'" H H 0.000 -6.649 1.908 1.457
UMP "O3'" O OH1 0.000 -4.189 3.648 0.341
UMP "HO3'" H H 0.000 -4.571 4.241 1.001
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
UMP OP3 n/a P START
UMP P OP3 "O5'" .
UMP OP1 P . .
UMP OP2 P . .
UMP "O5'" P "C5'" .
UMP "C5'" "O5'" "C4'" .
UMP "H5'" "C5'" . .
UMP "H5''" "C5'" . .
UMP "C4'" "C5'" "C3'" .
UMP "H4'" "C4'" . .
UMP "O4'" "C4'" "C1'" .
UMP "C1'" "O4'" N1 .
UMP "H1'" "C1'" . .
UMP N1 "C1'" C6 .
UMP C2 N1 O2 .
UMP O2 C2 . .
UMP C6 N1 C5 .
UMP H6 C6 . .
UMP C5 C6 C4 .
UMP H5 C5 . .
UMP C4 C5 N3 .
UMP O4 C4 . .
UMP N3 C4 HN3 .
UMP HN3 N3 . .
UMP "C3'" "C4'" "O3'" .
UMP "H3'" "C3'" . .
UMP "C2'" "C3'" "H2'" .
UMP "H2''" "C2'" . .
UMP "H2'" "C2'" . .
UMP "O3'" "C3'" . END
UMP "HO3'" "O3'" . .
UMP C2 N3 . ADD
UMP "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
UMP C2 N1 single 1.410 0.020
UMP C6 N1 single 1.337 0.020
UMP N1 "C1'" single 1.465 0.020
UMP C2 N3 single 1.337 0.020
UMP O2 C2 double 1.250 0.020
UMP N3 C4 single 1.337 0.020
UMP HN3 N3 single 1.040 0.020
UMP C4 C5 single 1.390 0.020
UMP O4 C4 double 1.250 0.020
UMP C5 C6 double 1.390 0.020
UMP H5 C5 single 1.083 0.020
UMP H6 C6 single 1.083 0.020
UMP "C1'" "C2'" single 1.524 0.020
UMP "C1'" "O4'" single 1.426 0.020
UMP "H1'" "C1'" single 1.099 0.020
UMP "C2'" "C3'" single 1.524 0.020
UMP "H2'" "C2'" single 1.092 0.020
UMP "H2''" "C2'" single 1.092 0.020
UMP "C3'" "C4'" single 1.524 0.020
UMP "O3'" "C3'" single 1.432 0.020
UMP "H3'" "C3'" single 1.099 0.020
UMP "O4'" "C4'" single 1.426 0.020
UMP "C4'" "C5'" single 1.524 0.020
UMP "H4'" "C4'" single 1.099 0.020
UMP "HO3'" "O3'" single 0.967 0.020
UMP "C5'" "O5'" single 1.426 0.020
UMP "H5'" "C5'" single 1.092 0.020
UMP "H5''" "C5'" single 1.092 0.020
UMP "O5'" P single 1.610 0.020
UMP OP1 P deloc 1.510 0.020
UMP OP2 P deloc 1.510 0.020
UMP 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
UMP OP3 P OP1 119.900 3.000
UMP OP3 P OP2 119.900 3.000
UMP OP3 P "O5'" 108.200 3.000
UMP OP1 P OP2 119.900 3.000
UMP OP1 P "O5'" 108.200 3.000
UMP OP2 P "O5'" 108.200 3.000
UMP P "O5'" "C5'" 120.500 3.000
UMP "O5'" "C5'" "H5'" 109.470 3.000
UMP "O5'" "C5'" "H5''" 109.470 3.000
UMP "O5'" "C5'" "C4'" 109.470 3.000
UMP "H5'" "C5'" "H5''" 107.900 3.000
UMP "H5'" "C5'" "C4'" 109.470 3.000
UMP "H5''" "C5'" "C4'" 109.470 3.000
UMP "C5'" "C4'" "H4'" 108.340 3.000
UMP "C5'" "C4'" "O4'" 109.470 3.000
UMP "C5'" "C4'" "C3'" 111.000 3.000
UMP "H4'" "C4'" "O4'" 109.470 3.000
UMP "H4'" "C4'" "C3'" 108.340 3.000
UMP "O4'" "C4'" "C3'" 109.470 3.000
UMP "C4'" "O4'" "C1'" 111.800 3.000
UMP "O4'" "C1'" "H1'" 109.470 3.000
UMP "O4'" "C1'" N1 109.470 3.000
UMP "O4'" "C1'" "C2'" 109.470 3.000
UMP "H1'" "C1'" N1 109.470 3.000
UMP "H1'" "C1'" "C2'" 108.340 3.000
UMP N1 "C1'" "C2'" 109.470 3.000
UMP "C1'" N1 C2 120.000 3.000
UMP "C1'" N1 C6 120.000 3.000
UMP C2 N1 C6 120.000 3.000
UMP N1 C2 O2 120.000 3.000
UMP N1 C2 N3 120.000 3.000
UMP O2 C2 N3 120.000 3.000
UMP N1 C6 H6 120.000 3.000
UMP N1 C6 C5 120.000 3.000
UMP H6 C6 C5 120.000 3.000
UMP C6 C5 H5 120.000 3.000
UMP C6 C5 C4 120.000 3.000
UMP H5 C5 C4 120.000 3.000
UMP C5 C4 O4 120.000 3.000
UMP C5 C4 N3 120.000 3.000
UMP O4 C4 N3 120.000 3.000
UMP C4 N3 HN3 120.000 3.000
UMP C4 N3 C2 120.000 3.000
UMP HN3 N3 C2 120.000 3.000
UMP "C4'" "C3'" "H3'" 108.340 3.000
UMP "C4'" "C3'" "C2'" 111.000 3.000
UMP "C4'" "C3'" "O3'" 109.470 3.000
UMP "H3'" "C3'" "C2'" 108.340 3.000
UMP "H3'" "C3'" "O3'" 109.470 3.000
UMP "C2'" "C3'" "O3'" 109.470 3.000
UMP "C3'" "C2'" "H2''" 109.470 3.000
UMP "C3'" "C2'" "H2'" 109.470 3.000
UMP "C3'" "C2'" "C1'" 111.000 3.000
UMP "H2''" "C2'" "H2'" 107.900 3.000
UMP "H2''" "C2'" "C1'" 109.470 3.000
UMP "H2'" "C2'" "C1'" 109.470 3.000
UMP "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
UMP var_1 OP3 P "O5'" "C5'" -65.026 20.000 1
UMP var_2 P "O5'" "C5'" "C4'" -179.970 20.000 1
UMP var_3 "O5'" "C5'" "C4'" "C3'" -178.123 20.000 3
UMP var_4 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
UMP var_5 "C4'" "O4'" "C1'" N1 -150.000 20.000 1
UMP var_6 "O4'" "C1'" "C2'" "C3'" 30.000 20.000 3
UMP var_7 "O4'" "C1'" N1 C6 -129.549 20.000 1
UMP CONST_1 "C1'" N1 C2 O2 0.000 0.000 0
UMP CONST_2 N1 C2 N3 C4 0.000 0.000 0
UMP CONST_3 "C1'" N1 C6 C5 180.000 0.000 0
UMP CONST_4 N1 C6 C5 C4 0.000 0.000 0
UMP CONST_5 C6 C5 C4 N3 0.000 0.000 0
UMP CONST_6 C5 C4 N3 C2 0.000 0.000 0
UMP var_8 "C5'" "C4'" "C3'" "O3'" 90.000 20.000 3
UMP var_9 "C4'" "C3'" "C2'" "C1'" 0.000 20.000 3
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
UMP chir_01 "C1'" "C2'" "O4'" N1 negativ
UMP chir_02 "C3'" "C2'" "C4'" "O3'" negativ
UMP chir_03 "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
UMP plan-1 C2 0.020
UMP plan-1 N3 0.020
UMP plan-1 O2 0.020
UMP plan-1 N1 0.020
UMP plan-1 C4 0.020
UMP plan-1 C5 0.020
UMP plan-1 C6 0.020
UMP plan-1 HN3 0.020
UMP plan-1 O4 0.020
UMP plan-1 H5 0.020
UMP plan-1 H6 0.020
UMP plan-1 "C1'" 0.020
# ------------------------------------------------------
|
