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
|
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
OPM OPM 'O1-PENTYL-MANNOSE ' pyranose 39 17 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_OPM
#
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
OPM C1 C CH1 0.000 0.000 0.000 0.000
OPM H1 H H 0.000 0.774 -0.646 0.438
OPM C2 C CH1 0.000 0.625 0.876 -1.088
OPM H2 H H 0.000 1.431 1.484 -0.654
OPM O2 O OH1 0.000 1.156 0.048 -2.124
OPM HO2 H H 0.000 1.836 -0.531 -1.755
OPM O1 O O2 0.000 -0.556 0.832 1.018
OPM "C1'" C CH2 0.000 -1.117 -0.037 2.002
OPM "H1'1" H H 0.000 -0.333 -0.679 2.409
OPM "H1'2" H H 0.000 -1.890 -0.656 1.541
OPM "C2'" C CH2 0.000 -1.734 0.795 3.128
OPM "H2'1" H H 0.000 -2.516 1.437 2.718
OPM "H2'2" H H 0.000 -0.960 1.414 3.587
OPM "C3'" C CH2 0.000 -2.336 -0.136 4.182
OPM "H3'1" H H 0.000 -1.552 -0.778 4.589
OPM "H3'2" H H 0.000 -3.108 -0.755 3.721
OPM "C4'" C CH2 0.000 -2.951 0.696 5.308
OPM "H4'1" H H 0.000 -3.734 1.338 4.900
OPM "H4'2" H H 0.000 -2.177 1.315 5.767
OPM "C5'" C CH3 0.000 -3.552 -0.236 6.362
OPM "H5'3" H H 0.000 -4.303 -0.840 5.919
OPM "H5'2" H H 0.000 -2.793 -0.860 6.762
OPM "H5'1" H H 0.000 -3.981 0.338 7.144
OPM O5 O O2 0.000 -1.028 -0.809 -0.564
OPM C5 C CH1 0.000 -2.091 0.056 -0.959
OPM H5 H H 0.000 -2.378 0.694 -0.110
OPM C4 C CH1 0.000 -1.637 0.936 -2.125
OPM H4 H H 0.000 -1.328 0.300 -2.967
OPM O4 O OH1 0.000 -2.714 1.781 -2.535
OPM HO4 H H 0.000 -2.425 2.336 -3.271
OPM C3 C CH1 0.000 -0.453 1.796 -1.669
OPM H3 H H 0.000 -0.787 2.505 -0.899
OPM O3 O OH1 0.000 0.075 2.513 -2.786
OPM HO3 H H 0.000 0.822 3.054 -2.497
OPM C6 C CH2 0.000 -3.295 -0.783 -1.394
OPM H61 H H 0.000 -3.009 -1.417 -2.237
OPM H62 H H 0.000 -4.108 -0.121 -1.698
OPM O6 O OH1 0.000 -3.725 -1.601 -0.306
OPM HO6 H H 0.000 -4.482 -2.111 -0.622
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
OPM C1 n/a O5 START
OPM H1 C1 . .
OPM C2 C1 O2 .
OPM H2 C2 . .
OPM O2 C2 HO2 .
OPM HO2 O2 . .
OPM O1 C1 "C1'" .
OPM "C1'" O1 "C2'" .
OPM "H1'1" "C1'" . .
OPM "H1'2" "C1'" . .
OPM "C2'" "C1'" "C3'" .
OPM "H2'1" "C2'" . .
OPM "H2'2" "C2'" . .
OPM "C3'" "C2'" "C4'" .
OPM "H3'1" "C3'" . .
OPM "H3'2" "C3'" . .
OPM "C4'" "C3'" "C5'" .
OPM "H4'1" "C4'" . .
OPM "H4'2" "C4'" . .
OPM "C5'" "C4'" "H5'1" .
OPM "H5'3" "C5'" . .
OPM "H5'2" "C5'" . .
OPM "H5'1" "C5'" . .
OPM O5 C1 . END
OPM C5 O5 C6 .
OPM H5 C5 . .
OPM C4 C5 C3 .
OPM H4 C4 . .
OPM O4 C4 HO4 .
OPM HO4 O4 . .
OPM C3 C4 O3 .
OPM H3 C3 . .
OPM O3 C3 HO3 .
OPM HO3 O3 . .
OPM C6 C5 O6 .
OPM H61 C6 . .
OPM H62 C6 . .
OPM O6 C6 . .
OPM HO6 O6 . .
OPM C2 C3 . 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
OPM "C4'" "C3'" single 1.524 0.020
OPM "C3'" "C2'" single 1.524 0.020
OPM "H3'1" "C3'" single 1.092 0.020
OPM "H3'2" "C3'" single 1.092 0.020
OPM "C5'" "C4'" single 1.513 0.020
OPM "H4'1" "C4'" single 1.092 0.020
OPM "H4'2" "C4'" single 1.092 0.020
OPM "H5'1" "C5'" single 1.059 0.020
OPM "H5'2" "C5'" single 1.059 0.020
OPM "H5'3" "C5'" single 1.059 0.020
OPM "C2'" "C1'" single 1.524 0.020
OPM "C1'" O1 single 1.426 0.020
OPM "H1'1" "C1'" single 1.092 0.020
OPM "H1'2" "C1'" single 1.092 0.020
OPM "H2'1" "C2'" single 1.092 0.020
OPM "H2'2" "C2'" single 1.092 0.020
OPM O2 C2 single 1.432 0.020
OPM C2 C3 single 1.524 0.020
OPM C2 C1 single 1.524 0.020
OPM H2 C2 single 1.099 0.020
OPM HO2 O2 single 0.967 0.020
OPM O3 C3 single 1.432 0.020
OPM C3 C4 single 1.524 0.020
OPM H3 C3 single 1.099 0.020
OPM HO3 O3 single 0.967 0.020
OPM O4 C4 single 1.432 0.020
OPM C4 C5 single 1.524 0.020
OPM H4 C4 single 1.099 0.020
OPM HO4 O4 single 0.967 0.020
OPM C5 O5 single 1.426 0.020
OPM C6 C5 single 1.524 0.020
OPM H5 C5 single 1.099 0.020
OPM O5 C1 single 1.426 0.020
OPM O6 C6 single 1.432 0.020
OPM H61 C6 single 1.092 0.020
OPM H62 C6 single 1.092 0.020
OPM HO6 O6 single 0.967 0.020
OPM O1 C1 single 1.426 0.020
OPM H1 C1 single 1.099 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
OPM H1 C1 C2 108.340 3.000
OPM H1 C1 O1 109.470 3.000
OPM C2 C1 O1 109.470 3.000
OPM H1 C1 O5 109.470 3.000
OPM C2 C1 O5 109.470 3.000
OPM O1 C1 O5 109.470 3.000
OPM C1 C2 H2 108.340 3.000
OPM C1 C2 O2 109.470 3.000
OPM C1 C2 C3 111.000 3.000
OPM H2 C2 O2 109.470 3.000
OPM H2 C2 C3 108.340 3.000
OPM O2 C2 C3 109.470 3.000
OPM C2 O2 HO2 109.470 3.000
OPM C1 O1 "C1'" 111.800 3.000
OPM O1 "C1'" "H1'1" 109.470 3.000
OPM O1 "C1'" "H1'2" 109.470 3.000
OPM O1 "C1'" "C2'" 109.470 3.000
OPM "H1'1" "C1'" "H1'2" 107.900 3.000
OPM "H1'1" "C1'" "C2'" 109.470 3.000
OPM "H1'2" "C1'" "C2'" 109.470 3.000
OPM "C1'" "C2'" "H2'1" 109.470 3.000
OPM "C1'" "C2'" "H2'2" 109.470 3.000
OPM "C1'" "C2'" "C3'" 111.000 3.000
OPM "H2'1" "C2'" "H2'2" 107.900 3.000
OPM "H2'1" "C2'" "C3'" 109.470 3.000
OPM "H2'2" "C2'" "C3'" 109.470 3.000
OPM "C2'" "C3'" "H3'1" 109.470 3.000
OPM "C2'" "C3'" "H3'2" 109.470 3.000
OPM "C2'" "C3'" "C4'" 111.000 3.000
OPM "H3'1" "C3'" "H3'2" 107.900 3.000
OPM "H3'1" "C3'" "C4'" 109.470 3.000
OPM "H3'2" "C3'" "C4'" 109.470 3.000
OPM "C3'" "C4'" "H4'1" 109.470 3.000
OPM "C3'" "C4'" "H4'2" 109.470 3.000
OPM "C3'" "C4'" "C5'" 111.000 3.000
OPM "H4'1" "C4'" "H4'2" 107.900 3.000
OPM "H4'1" "C4'" "C5'" 109.470 3.000
OPM "H4'2" "C4'" "C5'" 109.470 3.000
OPM "C4'" "C5'" "H5'3" 109.470 3.000
OPM "C4'" "C5'" "H5'2" 109.470 3.000
OPM "C4'" "C5'" "H5'1" 109.470 3.000
OPM "H5'3" "C5'" "H5'2" 109.470 3.000
OPM "H5'3" "C5'" "H5'1" 109.470 3.000
OPM "H5'2" "C5'" "H5'1" 109.470 3.000
OPM C1 O5 C5 111.800 3.000
OPM O5 C5 H5 109.470 3.000
OPM O5 C5 C4 109.470 3.000
OPM O5 C5 C6 109.470 3.000
OPM H5 C5 C4 108.340 3.000
OPM H5 C5 C6 108.340 3.000
OPM C4 C5 C6 111.000 3.000
OPM C5 C4 H4 108.340 3.000
OPM C5 C4 O4 109.470 3.000
OPM C5 C4 C3 111.000 3.000
OPM H4 C4 O4 109.470 3.000
OPM H4 C4 C3 108.340 3.000
OPM O4 C4 C3 109.470 3.000
OPM C4 O4 HO4 109.470 3.000
OPM C4 C3 H3 108.340 3.000
OPM C4 C3 O3 109.470 3.000
OPM C4 C3 C2 111.000 3.000
OPM H3 C3 O3 109.470 3.000
OPM H3 C3 C2 108.340 3.000
OPM O3 C3 C2 109.470 3.000
OPM C3 O3 HO3 109.470 3.000
OPM C5 C6 H61 109.470 3.000
OPM C5 C6 H62 109.470 3.000
OPM C5 C6 O6 109.470 3.000
OPM H61 C6 H62 107.900 3.000
OPM H61 C6 O6 109.470 3.000
OPM H62 C6 O6 109.470 3.000
OPM C6 O6 HO6 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
OPM var_1 O5 C1 C2 O2 -60.000 20.000 3
OPM var_2 C1 C2 C3 C4 -60.000 20.000 3
OPM var_3 C1 C2 O2 HO2 -60.382 20.000 1
OPM var_4 O5 C1 O1 "C1'" 59.865 20.000 1
OPM var_5 C1 O1 "C1'" "C2'" -179.988 20.000 1
OPM var_6 O1 "C1'" "C2'" "C3'" 179.986 20.000 3
OPM var_7 "C1'" "C2'" "C3'" "C4'" 179.964 20.000 3
OPM var_8 "C2'" "C3'" "C4'" "C5'" -179.970 20.000 3
OPM var_9 "C3'" "C4'" "C5'" "H5'1" -179.899 20.000 3
OPM var_10 C1 O5 C5 C6 180.000 20.000 1
OPM var_11 O5 C5 C4 C3 -60.000 20.000 3
OPM var_12 C5 C4 O4 HO4 179.930 20.000 1
OPM var_13 C5 C4 C3 O3 180.000 20.000 3
OPM var_14 C4 C3 O3 HO3 -179.955 20.000 1
OPM var_15 O5 C5 C6 O6 59.996 20.000 3
OPM var_1 C5 O5 C1 C2 -60.000 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
OPM chir_01 C2 O2 C3 C1 negativ
OPM chir_02 C3 C2 O3 C4 negativ
OPM chir_03 C4 C3 O4 C5 positiv
OPM chir_04 C5 C4 O5 C6 positiv
OPM chir_05 C1 C2 O5 O1 positiv
# ------------------------------------------------------
|
