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
|
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
N1T N1T '. ' non-polymer 43 26 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_N1T
#
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
N1T O3B O OP -0.666 0.000 0.000 0.000
N1T PB P P 0.000 0.000 0.000 0.000
N1T O1B O OP -0.666 0.000 0.000 0.000
N1T O2B O OP -0.666 0.000 0.000 0.000
N1T O3A O O2 0.000 0.000 0.000 0.000
N1T PA P P 0.000 0.000 0.000 0.000
N1T O1A O OP -0.500 0.000 0.000 0.000
N1T O2A O OP -0.500 0.000 0.000 0.000
N1T O7 O O2 0.000 0.000 0.000 0.000
N1T C7 C CH2 0.000 0.000 0.000 0.000
N1T H71 H H 0.000 0.000 0.000 0.000
N1T H72 H H 0.000 0.000 0.000 0.000
N1T C6 C CH2 0.000 0.000 0.000 0.000
N1T H61 H H 0.000 0.000 0.000 0.000
N1T H62 H H 0.000 0.000 0.000 0.000
N1T C5 C CR5 0.000 0.000 0.000 0.000
N1T S1 S S2 0.000 0.000 0.000 0.000
N1T C2 C CR15 0.000 0.000 0.000 0.000
N1T H2 H H 0.000 0.000 0.000 0.000
N1T C4 C CR5 0.000 0.000 0.000 0.000
N1T CM4 C CH3 0.000 0.000 0.000 0.000
N1T HM43 H H 0.000 0.000 0.000 0.000
N1T HM42 H H 0.000 0.000 0.000 0.000
N1T HM41 H H 0.000 0.000 0.000 0.000
N1T N3 N NR5 1.000 0.000 0.000 0.000
N1T "C7'" C CH2 0.000 0.000 0.000 0.000
N1T "H7'1" H H 0.000 0.000 0.000 0.000
N1T "H7'2" H H 0.000 0.000 0.000 0.000
N1T "C5'" C CR6 0.000 0.000 0.000 0.000
N1T "C6'" C CR16 0.000 0.000 0.000 0.000
N1T "H6'" H H 0.000 0.000 0.000 0.000
N1T "C1'" C CR16 0.000 0.000 0.000 0.000
N1T "H1'" H H 0.000 0.000 0.000 0.000
N1T "C4'" C CR6 0.000 0.000 0.000 0.000
N1T "N4'" N NH2 0.000 0.000 0.000 0.000
N1T HN42 H H 0.000 0.000 0.000 0.000
N1T HN41 H H 0.000 0.000 0.000 0.000
N1T "N3'" N NRD6 0.000 0.000 0.000 0.000
N1T "C2'" C CR6 0.000 0.000 0.000 0.000
N1T CM2 C CH3 0.000 0.000 0.000 0.000
N1T HM23 H H 0.000 0.000 0.000 0.000
N1T HM22 H H 0.000 0.000 0.000 0.000
N1T HM21 H H 0.000 0.000 0.000 0.000
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
N1T O3B n/a PB START
N1T PB O3B O3A .
N1T O1B PB . .
N1T O2B PB . .
N1T O3A PB PA .
N1T PA O3A O7 .
N1T O1A PA . .
N1T O2A PA . .
N1T O7 PA C7 .
N1T C7 O7 C6 .
N1T H71 C7 . .
N1T H72 C7 . .
N1T C6 C7 C5 .
N1T H61 C6 . .
N1T H62 C6 . .
N1T C5 C6 C4 .
N1T S1 C5 C2 .
N1T C2 S1 H2 .
N1T H2 C2 . .
N1T C4 C5 N3 .
N1T CM4 C4 HM41 .
N1T HM43 CM4 . .
N1T HM42 CM4 . .
N1T HM41 CM4 . .
N1T N3 C4 "C7'" .
N1T "C7'" N3 "C5'" .
N1T "H7'1" "C7'" . .
N1T "H7'2" "C7'" . .
N1T "C5'" "C7'" "C4'" .
N1T "C6'" "C5'" "C1'" .
N1T "H6'" "C6'" . .
N1T "C1'" "C6'" "H1'" .
N1T "H1'" "C1'" . .
N1T "C4'" "C5'" "N3'" .
N1T "N4'" "C4'" HN41 .
N1T HN42 "N4'" . .
N1T HN41 "N4'" . .
N1T "N3'" "C4'" "C2'" .
N1T "C2'" "N3'" CM2 .
N1T CM2 "C2'" HM21 .
N1T HM23 CM2 . .
N1T HM22 CM2 . .
N1T HM21 CM2 . END
N1T "C1'" "C2'" . ADD
N1T N3 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
N1T "C1'" "C2'" single 1.390 0.020
N1T "C1'" "C6'" double 1.390 0.020
N1T "H1'" "C1'" single 1.083 0.020
N1T CM2 "C2'" single 1.506 0.020
N1T "C2'" "N3'" double 1.350 0.020
N1T HM21 CM2 single 1.059 0.020
N1T HM22 CM2 single 1.059 0.020
N1T HM23 CM2 single 1.059 0.020
N1T "N3'" "C4'" single 1.350 0.020
N1T "N4'" "C4'" single 1.355 0.020
N1T "C4'" "C5'" double 1.487 0.020
N1T HN41 "N4'" single 1.010 0.020
N1T HN42 "N4'" single 1.010 0.020
N1T "C6'" "C5'" single 1.390 0.020
N1T "C5'" "C7'" single 1.511 0.020
N1T "H6'" "C6'" single 1.083 0.020
N1T "C7'" N3 single 1.462 0.020
N1T "H7'1" "C7'" single 1.092 0.020
N1T "H7'2" "C7'" single 1.092 0.020
N1T N3 C2 double 1.337 0.020
N1T N3 C4 single 1.337 0.020
N1T C2 S1 single 1.745 0.020
N1T H2 C2 single 1.083 0.020
N1T S1 C5 single 1.745 0.020
N1T C4 C5 double 1.490 0.020
N1T C5 C6 single 1.510 0.020
N1T CM4 C4 single 1.506 0.020
N1T HM41 CM4 single 1.059 0.020
N1T HM42 CM4 single 1.059 0.020
N1T HM43 CM4 single 1.059 0.020
N1T C6 C7 single 1.524 0.020
N1T H61 C6 single 1.092 0.020
N1T H62 C6 single 1.092 0.020
N1T C7 O7 single 1.426 0.020
N1T H71 C7 single 1.092 0.020
N1T H72 C7 single 1.092 0.020
N1T O7 PA single 1.610 0.020
N1T O1A PA deloc 1.510 0.020
N1T O2A PA deloc 1.510 0.020
N1T PA O3A single 1.610 0.020
N1T O3A PB single 1.610 0.020
N1T O1B PB deloc 1.510 0.020
N1T O2B PB deloc 1.510 0.020
N1T PB O3B 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
N1T O3B PB O1B 119.900 3.000
N1T O3B PB O2B 119.900 3.000
N1T O3B PB O3A 108.200 3.000
N1T O1B PB O2B 119.900 3.000
N1T O1B PB O3A 108.200 3.000
N1T O2B PB O3A 108.200 3.000
N1T PB O3A PA 120.500 3.000
N1T O3A PA O1A 108.200 3.000
N1T O3A PA O2A 108.200 3.000
N1T O3A PA O7 102.600 3.000
N1T O1A PA O2A 119.900 3.000
N1T O1A PA O7 108.200 3.000
N1T O2A PA O7 108.200 3.000
N1T PA O7 C7 120.500 3.000
N1T O7 C7 H71 109.470 3.000
N1T O7 C7 H72 109.470 3.000
N1T O7 C7 C6 109.470 3.000
N1T H71 C7 H72 107.900 3.000
N1T H71 C7 C6 109.470 3.000
N1T H72 C7 C6 109.470 3.000
N1T C7 C6 H61 109.470 3.000
N1T C7 C6 H62 109.470 3.000
N1T C7 C6 C5 109.470 3.000
N1T H61 C6 H62 107.900 3.000
N1T H61 C6 C5 109.470 3.000
N1T H62 C6 C5 109.470 3.000
N1T C6 C5 S1 108.000 3.000
N1T C6 C5 C4 126.000 3.000
N1T S1 C5 C4 108.000 3.000
N1T C5 S1 C2 90.000 3.000
N1T S1 C2 H2 108.000 3.000
N1T S1 C2 N3 108.000 3.000
N1T H2 C2 N3 126.000 3.000
N1T C5 C4 CM4 126.000 3.000
N1T C5 C4 N3 108.000 3.000
N1T CM4 C4 N3 126.000 3.000
N1T C4 CM4 HM43 109.470 3.000
N1T C4 CM4 HM42 109.470 3.000
N1T C4 CM4 HM41 109.470 3.000
N1T HM43 CM4 HM42 109.470 3.000
N1T HM43 CM4 HM41 109.470 3.000
N1T HM42 CM4 HM41 109.470 3.000
N1T C4 N3 "C7'" 126.000 3.000
N1T C4 N3 C2 108.000 3.000
N1T "C7'" N3 C2 126.000 3.000
N1T N3 "C7'" "H7'1" 109.500 3.000
N1T N3 "C7'" "H7'2" 109.500 3.000
N1T N3 "C7'" "C5'" 109.500 3.000
N1T "H7'1" "C7'" "H7'2" 107.900 3.000
N1T "H7'1" "C7'" "C5'" 109.470 3.000
N1T "H7'2" "C7'" "C5'" 109.470 3.000
N1T "C7'" "C5'" "C6'" 120.000 3.000
N1T "C7'" "C5'" "C4'" 120.000 3.000
N1T "C6'" "C5'" "C4'" 120.000 3.000
N1T "C5'" "C6'" "H6'" 120.000 3.000
N1T "C5'" "C6'" "C1'" 120.000 3.000
N1T "H6'" "C6'" "C1'" 120.000 3.000
N1T "C6'" "C1'" "H1'" 120.000 3.000
N1T "C6'" "C1'" "C2'" 120.000 3.000
N1T "H1'" "C1'" "C2'" 120.000 3.000
N1T "C5'" "C4'" "N4'" 120.000 3.000
N1T "C5'" "C4'" "N3'" 120.000 3.000
N1T "N4'" "C4'" "N3'" 120.000 3.000
N1T "C4'" "N4'" HN42 120.000 3.000
N1T "C4'" "N4'" HN41 120.000 3.000
N1T HN42 "N4'" HN41 120.000 3.000
N1T "C4'" "N3'" "C2'" 120.000 3.000
N1T "N3'" "C2'" CM2 120.000 3.000
N1T "N3'" "C2'" "C1'" 120.000 3.000
N1T CM2 "C2'" "C1'" 120.000 3.000
N1T "C2'" CM2 HM23 109.470 3.000
N1T "C2'" CM2 HM22 109.470 3.000
N1T "C2'" CM2 HM21 109.470 3.000
N1T HM23 CM2 HM22 109.470 3.000
N1T HM23 CM2 HM21 109.470 3.000
N1T HM22 CM2 HM21 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
N1T var_1 O3B PB O3A PA 0.000 20.000 1
N1T var_2 PB O3A PA O7 0.000 20.000 1
N1T var_3 O3A PA O7 C7 0.000 20.000 1
N1T var_4 PA O7 C7 C6 0.000 20.000 1
N1T var_5 O7 C7 C6 C5 0.000 20.000 3
N1T var_6 C7 C6 C5 C4 0.000 20.000 2
N1T CONST_1 C6 C5 S1 C2 0.000 0.000 0
N1T CONST_2 C5 S1 C2 N3 0.000 0.000 0
N1T CONST_3 C6 C5 C4 N3 0.000 0.000 0
N1T var_7 C5 C4 CM4 HM41 0.000 20.000 1
N1T CONST_4 C5 C4 N3 "C7'" 0.000 0.000 0
N1T CONST_5 C4 N3 C2 S1 0.000 0.000 0
N1T var_8 C4 N3 "C7'" "C5'" 0.000 20.000 1
N1T var_9 N3 "C7'" "C5'" "C4'" 0.000 20.000 2
N1T CONST_6 "C7'" "C5'" "C6'" "C1'" 0.000 0.000 0
N1T CONST_7 "C5'" "C6'" "C1'" "C2'" 0.000 0.000 0
N1T CONST_8 "C6'" "C1'" "C2'" "N3'" 0.000 0.000 0
N1T CONST_9 "C7'" "C5'" "C4'" "N3'" 0.000 0.000 0
N1T CONST_10 "C5'" "C4'" "N4'" HN41 0.000 0.000 0
N1T CONST_11 "C5'" "C4'" "N3'" "C2'" 0.000 0.000 0
N1T CONST_12 "C4'" "N3'" "C2'" CM2 0.000 0.000 0
N1T var_10 "N3'" "C2'" CM2 HM21 0.000 20.000 1
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
N1T plan-1 "C1'" 0.020
N1T plan-1 "C2'" 0.020
N1T plan-1 "C6'" 0.020
N1T plan-1 "H1'" 0.020
N1T plan-1 "N3'" 0.020
N1T plan-1 "C4'" 0.020
N1T plan-1 "C5'" 0.020
N1T plan-1 CM2 0.020
N1T plan-1 "N4'" 0.020
N1T plan-1 "C7'" 0.020
N1T plan-1 "H6'" 0.020
N1T plan-1 HN42 0.020
N1T plan-1 HN41 0.020
N1T plan-2 "N4'" 0.020
N1T plan-2 "C4'" 0.020
N1T plan-2 HN41 0.020
N1T plan-2 HN42 0.020
N1T plan-3 N3 0.020
N1T plan-3 "C7'" 0.020
N1T plan-3 C2 0.020
N1T plan-3 C4 0.020
N1T plan-3 S1 0.020
N1T plan-3 C5 0.020
N1T plan-3 H2 0.020
N1T plan-3 C6 0.020
N1T plan-3 CM4 0.020
# ------------------------------------------------------
|
