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
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
|
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
D09 D09 '5-[(2R)-2-(2-methoxyphenyl)propyl]fu' non-polymer 40 22 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_D09
#
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
D09 "N4'" N NH2 0.000 0.000 0.000 0.000
D09 "HN4'" H H 0.000 -0.351 -0.382 0.873
D09 HN4A H H 0.000 0.960 0.329 -0.043
D09 "C4'" C CR6 0.000 -0.817 0.071 -1.114
D09 "C5'" C CR56 0.000 -2.143 -0.381 -1.062
D09 "N3'" N NRD6 0.000 -0.363 0.572 -2.259
D09 "C2'" C CR6 0.000 -1.146 0.642 -3.329
D09 "N2'" N NH2 0.000 -0.629 1.171 -4.499
D09 HN2A H H 0.000 0.331 1.498 -4.537
D09 "HN2'" H H 0.000 -1.204 1.238 -5.333
D09 "N1'" N NRD6 0.000 -2.401 0.225 -3.319
D09 "C8'" C CR56 0.000 -2.938 -0.290 -2.217
D09 "O8'" O O2 0.000 -4.147 -0.787 -1.906
D09 "C7'" C CR15 0.000 -4.187 -1.195 -0.624
D09 "H7'" H H 0.000 -5.049 -1.634 -0.138
D09 "C6'" C CR5 0.000 -3.002 -0.978 -0.037
D09 "C9'" C CH2 0.000 -2.626 -1.291 1.390
D09 "H9'" H H 0.000 -1.582 -1.608 1.429
D09 "H9'A" H H 0.000 -3.264 -2.094 1.765
D09 C11 C CH1 0.000 -2.815 -0.042 2.252
D09 H11 H H 0.000 -2.242 0.791 1.821
D09 C10 C CH3 0.000 -4.298 0.328 2.296
D09 H10B H H 0.000 -4.644 0.522 1.314
D09 H10A H H 0.000 -4.851 -0.475 2.712
D09 H10 H H 0.000 -4.430 1.193 2.893
D09 "C'1" C CR6 0.000 -2.324 -0.319 3.650
D09 "C'2" C CR6 0.000 -1.295 0.442 4.188
D09 O13 O O2 0.000 -0.729 1.436 3.455
D09 C13 C CH3 0.000 0.320 2.182 4.076
D09 H13B H H 0.000 0.673 2.922 3.404
D09 H13A H H 0.000 -0.048 2.649 4.952
D09 H13 H H 0.000 1.115 1.530 4.331
D09 "C'6" C CR16 0.000 -2.894 -1.333 4.395
D09 "H'6" H H 0.000 -3.690 -1.934 3.972
D09 "C'5" C CR16 0.000 -2.448 -1.583 5.680
D09 "H'5" H H 0.000 -2.900 -2.375 6.264
D09 "C'4" C CR16 0.000 -1.428 -0.823 6.220
D09 "H'4" H H 0.000 -1.081 -1.021 7.227
D09 "C'3" C CR16 0.000 -0.851 0.189 5.478
D09 "H'3" H H 0.000 -0.052 0.785 5.902
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
D09 "N4'" n/a "C4'" START
D09 "HN4'" "N4'" . .
D09 HN4A "N4'" . .
D09 "C4'" "N4'" "N3'" .
D09 "C5'" "C4'" . .
D09 "N3'" "C4'" "C2'" .
D09 "C2'" "N3'" "N1'" .
D09 "N2'" "C2'" "HN2'" .
D09 HN2A "N2'" . .
D09 "HN2'" "N2'" . .
D09 "N1'" "C2'" "C8'" .
D09 "C8'" "N1'" "O8'" .
D09 "O8'" "C8'" "C7'" .
D09 "C7'" "O8'" "C6'" .
D09 "H7'" "C7'" . .
D09 "C6'" "C7'" "C9'" .
D09 "C9'" "C6'" C11 .
D09 "H9'" "C9'" . .
D09 "H9'A" "C9'" . .
D09 C11 "C9'" "C'1" .
D09 H11 C11 . .
D09 C10 C11 H10 .
D09 H10B C10 . .
D09 H10A C10 . .
D09 H10 C10 . .
D09 "C'1" C11 "C'6" .
D09 "C'2" "C'1" O13 .
D09 O13 "C'2" C13 .
D09 C13 O13 H13 .
D09 H13B C13 . .
D09 H13A C13 . .
D09 H13 C13 . .
D09 "C'6" "C'1" "C'5" .
D09 "H'6" "C'6" . .
D09 "C'5" "C'6" "C'4" .
D09 "H'5" "C'5" . .
D09 "C'4" "C'5" "C'3" .
D09 "H'4" "C'4" . .
D09 "C'3" "C'4" "H'3" .
D09 "H'3" "C'3" . END
D09 "C'2" "C'3" . ADD
D09 "C6'" "C5'" . ADD
D09 "C5'" "C8'" . 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
D09 C13 O13 single 1.426 0.020
D09 O13 "C'2" single 1.370 0.020
D09 "C'2" "C'3" double 1.390 0.020
D09 "C'2" "C'1" single 1.487 0.020
D09 "C'3" "C'4" single 1.390 0.020
D09 "C'4" "C'5" double 1.390 0.020
D09 "C'5" "C'6" single 1.390 0.020
D09 "C'6" "C'1" double 1.390 0.020
D09 "C'1" C11 single 1.480 0.020
D09 C10 C11 single 1.524 0.020
D09 C11 "C9'" single 1.524 0.020
D09 "C9'" "C6'" single 1.510 0.020
D09 "C6'" "C5'" single 1.490 0.020
D09 "C6'" "C7'" double 1.387 0.020
D09 "C5'" "C8'" double 1.490 0.020
D09 "C5'" "C4'" single 1.490 0.020
D09 "C7'" "O8'" single 1.380 0.020
D09 "O8'" "C8'" single 1.329 0.020
D09 "C8'" "N1'" single 1.355 0.020
D09 "N1'" "C2'" double 1.350 0.020
D09 "N2'" "C2'" single 1.355 0.020
D09 "C2'" "N3'" single 1.350 0.020
D09 "N3'" "C4'" double 1.350 0.020
D09 "C4'" "N4'" single 1.355 0.020
D09 H13 C13 single 1.059 0.020
D09 H13A C13 single 1.059 0.020
D09 H13B C13 single 1.059 0.020
D09 "H'3" "C'3" single 1.083 0.020
D09 "H'4" "C'4" single 1.083 0.020
D09 "H'5" "C'5" single 1.083 0.020
D09 "H'6" "C'6" single 1.083 0.020
D09 H11 C11 single 1.099 0.020
D09 H10 C10 single 1.059 0.020
D09 H10A C10 single 1.059 0.020
D09 H10B C10 single 1.059 0.020
D09 "H9'" "C9'" single 1.092 0.020
D09 "H9'A" "C9'" single 1.092 0.020
D09 "H7'" "C7'" single 1.083 0.020
D09 "HN2'" "N2'" single 1.010 0.020
D09 HN2A "N2'" single 1.010 0.020
D09 "HN4'" "N4'" single 1.010 0.020
D09 HN4A "N4'" single 1.010 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
D09 "HN4'" "N4'" HN4A 120.000 3.000
D09 "HN4'" "N4'" "C4'" 120.000 3.000
D09 HN4A "N4'" "C4'" 120.000 3.000
D09 "N4'" "C4'" "C5'" 120.000 3.000
D09 "N4'" "C4'" "N3'" 120.000 3.000
D09 "C5'" "C4'" "N3'" 120.000 3.000
D09 "C4'" "C5'" "C6'" 132.000 3.000
D09 "C4'" "C5'" "C8'" 120.000 3.000
D09 "C6'" "C5'" "C8'" 108.000 3.000
D09 "C4'" "N3'" "C2'" 120.000 3.000
D09 "N3'" "C2'" "N2'" 120.000 3.000
D09 "N3'" "C2'" "N1'" 120.000 3.000
D09 "N2'" "C2'" "N1'" 120.000 3.000
D09 "C2'" "N2'" HN2A 120.000 3.000
D09 "C2'" "N2'" "HN2'" 120.000 3.000
D09 HN2A "N2'" "HN2'" 120.000 3.000
D09 "C2'" "N1'" "C8'" 120.000 3.000
D09 "N1'" "C8'" "O8'" 120.000 3.000
D09 "N1'" "C8'" "C5'" 120.000 3.000
D09 "O8'" "C8'" "C5'" 120.000 3.000
D09 "C8'" "O8'" "C7'" 120.000 3.000
D09 "O8'" "C7'" "H7'" 126.000 3.000
D09 "O8'" "C7'" "C6'" 108.000 3.000
D09 "H7'" "C7'" "C6'" 126.000 3.000
D09 "C7'" "C6'" "C9'" 126.000 3.000
D09 "C7'" "C6'" "C5'" 108.000 3.000
D09 "C9'" "C6'" "C5'" 126.000 3.000
D09 "C6'" "C9'" "H9'" 109.470 3.000
D09 "C6'" "C9'" "H9'A" 109.470 3.000
D09 "C6'" "C9'" C11 109.470 3.000
D09 "H9'" "C9'" "H9'A" 107.900 3.000
D09 "H9'" "C9'" C11 109.470 3.000
D09 "H9'A" "C9'" C11 109.470 3.000
D09 "C9'" C11 H11 108.340 3.000
D09 "C9'" C11 C10 111.000 3.000
D09 "C9'" C11 "C'1" 109.470 3.000
D09 H11 C11 C10 108.340 3.000
D09 H11 C11 "C'1" 109.470 3.000
D09 C10 C11 "C'1" 109.470 3.000
D09 C11 C10 H10B 109.470 3.000
D09 C11 C10 H10A 109.470 3.000
D09 C11 C10 H10 109.470 3.000
D09 H10B C10 H10A 109.470 3.000
D09 H10B C10 H10 109.470 3.000
D09 H10A C10 H10 109.470 3.000
D09 C11 "C'1" "C'2" 120.000 3.000
D09 C11 "C'1" "C'6" 120.000 3.000
D09 "C'2" "C'1" "C'6" 120.000 3.000
D09 "C'1" "C'2" O13 120.000 3.000
D09 "C'1" "C'2" "C'3" 120.000 3.000
D09 O13 "C'2" "C'3" 120.000 3.000
D09 "C'2" O13 C13 120.000 3.000
D09 O13 C13 H13B 109.470 3.000
D09 O13 C13 H13A 109.470 3.000
D09 O13 C13 H13 109.470 3.000
D09 H13B C13 H13A 109.470 3.000
D09 H13B C13 H13 109.470 3.000
D09 H13A C13 H13 109.470 3.000
D09 "C'1" "C'6" "H'6" 120.000 3.000
D09 "C'1" "C'6" "C'5" 120.000 3.000
D09 "H'6" "C'6" "C'5" 120.000 3.000
D09 "C'6" "C'5" "H'5" 120.000 3.000
D09 "C'6" "C'5" "C'4" 120.000 3.000
D09 "H'5" "C'5" "C'4" 120.000 3.000
D09 "C'5" "C'4" "H'4" 120.000 3.000
D09 "C'5" "C'4" "C'3" 120.000 3.000
D09 "H'4" "C'4" "C'3" 120.000 3.000
D09 "C'4" "C'3" "H'3" 120.000 3.000
D09 "C'4" "C'3" "C'2" 120.000 3.000
D09 "H'3" "C'3" "C'2" 120.000 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
D09 CONST_1 HN4A "N4'" "C4'" "N3'" -0.104 0.000 0
D09 CONST_2 "N4'" "C4'" "C5'" "C6'" 0.000 0.000 0
D09 CONST_3 "C4'" "C5'" "C8'" "N1'" 0.000 0.000 0
D09 CONST_4 "N4'" "C4'" "N3'" "C2'" 180.000 0.000 0
D09 CONST_5 "C4'" "N3'" "C2'" "N1'" 0.000 0.000 0
D09 CONST_6 "N3'" "C2'" "N2'" "HN2'" -179.936 0.000 0
D09 CONST_7 "N3'" "C2'" "N1'" "C8'" 0.000 0.000 0
D09 CONST_8 "C2'" "N1'" "C8'" "O8'" 180.000 0.000 0
D09 CONST_9 "N1'" "C8'" "O8'" "C7'" 180.000 0.000 0
D09 CONST_10 "C8'" "O8'" "C7'" "C6'" 0.000 0.000 0
D09 CONST_11 "O8'" "C7'" "C6'" "C9'" 180.000 0.000 0
D09 CONST_12 "C7'" "C6'" "C5'" "C4'" 180.000 0.000 0
D09 var_1 "C7'" "C6'" "C9'" C11 -95.296 20.000 2
D09 var_2 "C6'" "C9'" C11 "C'1" -174.980 20.000 3
D09 var_3 "C9'" C11 C10 H10 -179.982 20.000 3
D09 var_4 "C9'" C11 "C'1" "C'6" -59.749 20.000 1
D09 CONST_13 C11 "C'1" "C'2" O13 0.000 0.000 0
D09 CONST_14 "C'1" "C'2" "C'3" "C'4" 0.000 0.000 0
D09 var_5 "C'1" "C'2" O13 C13 179.717 20.000 1
D09 var_6 "C'2" O13 C13 H13 60.001 20.000 1
D09 CONST_15 C11 "C'1" "C'6" "C'5" 180.000 0.000 0
D09 CONST_16 "C'1" "C'6" "C'5" "C'4" 0.000 0.000 0
D09 CONST_17 "C'6" "C'5" "C'4" "C'3" 0.000 0.000 0
D09 CONST_18 "C'5" "C'4" "C'3" "C'2" 0.000 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
D09 chir_01 C11 "C'1" C10 "C9'" 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
D09 plan-1 "C'2" 0.020
D09 plan-1 O13 0.020
D09 plan-1 "C'3" 0.020
D09 plan-1 "C'1" 0.020
D09 plan-1 "C'4" 0.020
D09 plan-1 "C'5" 0.020
D09 plan-1 "C'6" 0.020
D09 plan-1 "H'3" 0.020
D09 plan-1 "H'4" 0.020
D09 plan-1 "H'5" 0.020
D09 plan-1 "H'6" 0.020
D09 plan-1 C11 0.020
D09 plan-2 "C6'" 0.020
D09 plan-2 "C9'" 0.020
D09 plan-2 "C5'" 0.020
D09 plan-2 "C7'" 0.020
D09 plan-2 "O8'" 0.020
D09 plan-2 "C8'" 0.020
D09 plan-2 "C4'" 0.020
D09 plan-2 "N1'" 0.020
D09 plan-2 "C2'" 0.020
D09 plan-2 "N3'" 0.020
D09 plan-2 "H7'" 0.020
D09 plan-2 "N2'" 0.020
D09 plan-2 "N4'" 0.020
D09 plan-2 HN2A 0.020
D09 plan-2 "HN2'" 0.020
D09 plan-2 "HN4'" 0.020
D09 plan-2 HN4A 0.020
D09 plan-3 "N2'" 0.020
D09 plan-3 "C2'" 0.020
D09 plan-3 "HN2'" 0.020
D09 plan-3 HN2A 0.020
D09 plan-4 "N4'" 0.020
D09 plan-4 "C4'" 0.020
D09 plan-4 "HN4'" 0.020
D09 plan-4 HN4A 0.020
# ------------------------------------------------------
|
