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
|
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
XY2 XY2 'N,N'-DIMETHYL-N-(ACETYL)-N'-(7-NITRO' non-polymer 36 21 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_XY2
#
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
XY2 O9 O O 0.000 0.000 0.000 0.000
XY2 N8 N N 1.000 -0.814 -0.902 0.087
XY2 O10 O O -1.000 -0.449 -2.062 0.009
XY2 C1 C CR6 0.000 -2.247 -0.589 0.286
XY2 C21 C CR16 0.000 -3.153 -1.594 0.381
XY2 H21 H H 0.000 -2.803 -2.616 0.308
XY2 C20 C CR16 0.000 -4.518 -1.365 0.571
XY2 H20 H H 0.000 -5.189 -2.212 0.640
XY2 C4 C CR6 0.000 -5.028 -0.102 0.670
XY2 C3 C CR56 0.000 -4.114 1.030 0.571
XY2 N7 N NRD5 0.000 -4.155 2.335 0.614
XY2 O6 O O2 0.000 -3.030 2.774 0.475
XY2 N5 N NRD5 0.000 -2.145 1.952 0.336
XY2 C2 C CR56 0.000 -2.668 0.750 0.376
XY2 N11 N NT 0.000 -6.390 0.101 0.858
XY2 C12 C CH3 0.000 -6.777 -0.688 2.035
XY2 H123 H H 0.000 -7.828 -0.651 2.155
XY2 H122 H H 0.000 -6.472 -1.693 1.902
XY2 H121 H H 0.000 -6.309 -0.288 2.897
XY2 C13 C CH2 0.000 -7.070 -0.502 -0.296
XY2 H131 H H 0.000 -6.985 -1.590 -0.240
XY2 H132 H H 0.000 -6.603 -0.150 -1.218
XY2 C14 C CH2 0.000 -8.546 -0.103 -0.285
XY2 H141 H H 0.000 -8.629 0.985 -0.341
XY2 H142 H H 0.000 -9.011 -0.455 0.638
XY2 N15 N N 0.000 -9.225 -0.705 -1.436
XY2 C16 C CH3 0.000 -9.934 -1.978 -1.285
XY2 H163 H H 0.000 -9.242 -2.746 -1.052
XY2 H162 H H 0.000 -10.646 -1.898 -0.503
XY2 H161 H H 0.000 -10.432 -2.217 -2.189
XY2 C17 C C 0.000 -9.195 -0.089 -2.634
XY2 O18 O O 0.000 -9.837 -0.534 -3.561
XY2 C19 C CH3 0.000 -8.363 1.154 -2.821
XY2 H193 H H 0.000 -7.586 0.959 -3.515
XY2 H192 H H 0.000 -8.974 1.937 -3.189
XY2 H191 H H 0.000 -7.942 1.442 -1.893
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
XY2 O9 n/a N8 START
XY2 N8 O9 C1 .
XY2 O10 N8 . .
XY2 C1 N8 C21 .
XY2 C21 C1 C20 .
XY2 H21 C21 . .
XY2 C20 C21 C4 .
XY2 H20 C20 . .
XY2 C4 C20 N11 .
XY2 C3 C4 N7 .
XY2 N7 C3 O6 .
XY2 O6 N7 N5 .
XY2 N5 O6 C2 .
XY2 C2 N5 . .
XY2 N11 C4 C13 .
XY2 C12 N11 H121 .
XY2 H123 C12 . .
XY2 H122 C12 . .
XY2 H121 C12 . .
XY2 C13 N11 C14 .
XY2 H131 C13 . .
XY2 H132 C13 . .
XY2 C14 C13 N15 .
XY2 H141 C14 . .
XY2 H142 C14 . .
XY2 N15 C14 C17 .
XY2 C16 N15 H161 .
XY2 H163 C16 . .
XY2 H162 C16 . .
XY2 H161 C16 . .
XY2 C17 N15 C19 .
XY2 O18 C17 . .
XY2 C19 C17 H191 .
XY2 H193 C19 . .
XY2 H192 C19 . .
XY2 H191 C19 . END
XY2 C1 C2 . ADD
XY2 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
XY2 C1 C2 single 1.490 0.020
XY2 C1 N8 single 1.400 0.020
XY2 C21 C1 double 1.390 0.020
XY2 C2 C3 single 1.490 0.020
XY2 C2 N5 double 1.350 0.020
XY2 N7 C3 double 1.350 0.020
XY2 C3 C4 single 1.490 0.020
XY2 C19 C17 single 1.500 0.020
XY2 H191 C19 single 1.059 0.020
XY2 H192 C19 single 1.059 0.020
XY2 H193 C19 single 1.059 0.020
XY2 O18 C17 double 1.220 0.020
XY2 C17 N15 single 1.330 0.020
XY2 C16 N15 single 1.455 0.020
XY2 N15 C14 single 1.455 0.020
XY2 H161 C16 single 1.059 0.020
XY2 H162 C16 single 1.059 0.020
XY2 H163 C16 single 1.059 0.020
XY2 C14 C13 single 1.524 0.020
XY2 H141 C14 single 1.092 0.020
XY2 H142 C14 single 1.092 0.020
XY2 C13 N11 single 1.469 0.020
XY2 H131 C13 single 1.092 0.020
XY2 H132 C13 single 1.092 0.020
XY2 C12 N11 single 1.469 0.020
XY2 N11 C4 single 1.405 0.020
XY2 H121 C12 single 1.059 0.020
XY2 H122 C12 single 1.059 0.020
XY2 H123 C12 single 1.059 0.020
XY2 N5 O6 single 1.337 0.020
XY2 O6 N7 single 1.337 0.020
XY2 O10 N8 single 1.400 0.020
XY2 N8 O9 double 1.220 0.020
XY2 C20 C21 single 1.390 0.020
XY2 H21 C21 single 1.083 0.020
XY2 C4 C20 double 1.390 0.020
XY2 H20 C20 single 1.083 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
XY2 O9 N8 O10 120.000 3.000
XY2 O9 N8 C1 120.000 3.000
XY2 O10 N8 C1 120.000 3.000
XY2 N8 C1 C21 120.000 3.000
XY2 N8 C1 C2 120.000 3.000
XY2 C21 C1 C2 120.000 3.000
XY2 C1 C21 H21 120.000 3.000
XY2 C1 C21 C20 120.000 3.000
XY2 H21 C21 C20 120.000 3.000
XY2 C21 C20 H20 120.000 3.000
XY2 C21 C20 C4 120.000 3.000
XY2 H20 C20 C4 120.000 3.000
XY2 C20 C4 C3 120.000 3.000
XY2 C20 C4 N11 120.000 3.000
XY2 C3 C4 N11 120.000 3.000
XY2 C4 C3 N7 132.000 3.000
XY2 C4 C3 C2 120.000 3.000
XY2 N7 C3 C2 108.000 3.000
XY2 C3 N7 O6 108.000 3.000
XY2 N7 O6 N5 120.000 3.000
XY2 O6 N5 C2 108.000 3.000
XY2 N5 C2 C1 132.000 3.000
XY2 N5 C2 C3 108.000 3.000
XY2 C1 C2 C3 120.000 3.000
XY2 C4 N11 C12 109.500 3.000
XY2 C4 N11 C13 109.500 3.000
XY2 C12 N11 C13 109.470 3.000
XY2 N11 C12 H123 109.470 3.000
XY2 N11 C12 H122 109.470 3.000
XY2 N11 C12 H121 109.470 3.000
XY2 H123 C12 H122 109.470 3.000
XY2 H123 C12 H121 109.470 3.000
XY2 H122 C12 H121 109.470 3.000
XY2 N11 C13 H131 109.470 3.000
XY2 N11 C13 H132 109.470 3.000
XY2 N11 C13 C14 109.470 3.000
XY2 H131 C13 H132 107.900 3.000
XY2 H131 C13 C14 109.470 3.000
XY2 H132 C13 C14 109.470 3.000
XY2 C13 C14 H141 109.470 3.000
XY2 C13 C14 H142 109.470 3.000
XY2 C13 C14 N15 105.000 3.000
XY2 H141 C14 H142 107.900 3.000
XY2 H141 C14 N15 109.470 3.000
XY2 H142 C14 N15 109.470 3.000
XY2 C14 N15 C16 120.000 3.000
XY2 C14 N15 C17 127.000 3.000
XY2 C16 N15 C17 127.000 3.000
XY2 N15 C16 H163 109.470 3.000
XY2 N15 C16 H162 109.470 3.000
XY2 N15 C16 H161 109.470 3.000
XY2 H163 C16 H162 109.470 3.000
XY2 H163 C16 H161 109.470 3.000
XY2 H162 C16 H161 109.470 3.000
XY2 N15 C17 O18 123.000 3.000
XY2 N15 C17 C19 116.500 3.000
XY2 O18 C17 C19 123.000 3.000
XY2 C17 C19 H193 109.470 3.000
XY2 C17 C19 H192 109.470 3.000
XY2 C17 C19 H191 109.470 3.000
XY2 H193 C19 H192 109.470 3.000
XY2 H193 C19 H191 109.470 3.000
XY2 H192 C19 H191 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
XY2 var_1 O9 N8 C1 C21 179.986 20.000 1
XY2 CONST_1 N8 C1 C2 N5 0.000 0.000 0
XY2 CONST_2 N8 C1 C21 C20 180.000 0.000 0
XY2 CONST_3 C1 C21 C20 C4 0.000 0.000 0
XY2 CONST_4 C21 C20 C4 N11 180.000 0.000 0
XY2 CONST_5 C20 C4 C3 N7 180.000 0.000 0
XY2 CONST_6 C4 C3 N7 O6 180.000 0.000 0
XY2 CONST_7 C3 N7 O6 N5 0.000 0.000 0
XY2 CONST_8 N7 O6 N5 C2 0.000 0.000 0
XY2 CONST_9 O6 N5 C2 C1 180.000 0.000 0
XY2 CONST_10 N5 C2 C3 C4 180.000 0.000 0
XY2 var_2 C20 C4 N11 C13 -60.023 20.000 1
XY2 var_3 C4 N11 C12 H121 66.203 20.000 1
XY2 var_4 C4 N11 C13 C14 -169.998 20.000 1
XY2 var_5 N11 C13 C14 N15 -179.968 20.000 3
XY2 var_6 C13 C14 N15 C17 -84.722 20.000 1
XY2 var_7 C14 N15 C16 H161 175.027 20.000 1
XY2 CONST_11 C14 N15 C17 C19 0.000 0.000 0
XY2 var_8 N15 C17 C19 H191 -4.889 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
XY2 chir_01 N11 C13 C12 C4 negativ
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
XY2 plan-1 C1 0.020
XY2 plan-1 C2 0.020
XY2 plan-1 N8 0.020
XY2 plan-1 C21 0.020
XY2 plan-1 C20 0.020
XY2 plan-1 C4 0.020
XY2 plan-1 C3 0.020
XY2 plan-1 N5 0.020
XY2 plan-1 O6 0.020
XY2 plan-1 N7 0.020
XY2 plan-1 H21 0.020
XY2 plan-1 H20 0.020
XY2 plan-1 N11 0.020
XY2 plan-2 C17 0.020
XY2 plan-2 C19 0.020
XY2 plan-2 O18 0.020
XY2 plan-2 N15 0.020
XY2 plan-3 N15 0.020
XY2 plan-3 C17 0.020
XY2 plan-3 C16 0.020
XY2 plan-3 C14 0.020
XY2 plan-4 N8 0.020
XY2 plan-4 C1 0.020
XY2 plan-4 O10 0.020
XY2 plan-4 O9 0.020
# ------------------------------------------------------
|
