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
|
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
2TP 2TP '"2-(3-{[4-(HYDROXYAMINO)-2-METHYLPYR' non-polymer 43 27 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_2TP
#
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
2TP O23 O OP -0.666 0.000 0.000 0.000
2TP P2 P P 0.000 -0.827 1.236 0.279
2TP O21 O OP -0.666 0.000 1.995 1.293
2TP O22 O OP -0.666 -2.262 0.976 0.681
2TP O11 O O2 0.000 -0.654 2.113 -1.067
2TP P1 P P 0.000 -1.142 3.611 -1.428
2TP O12 O OP -0.500 -0.780 3.763 -2.858
2TP O13 O OP -0.500 -0.598 4.669 -0.543
2TP O5G O O2 0.000 -2.756 3.476 -1.424
2TP C5B C CH2 0.000 -3.387 2.498 -2.232
2TP H5B1 H H 0.000 -3.034 1.506 -1.941
2TP H5B2 H H 0.000 -3.137 2.679 -3.279
2TP C5A C CH2 0.000 -4.900 2.576 -2.048
2TP H5A1 H H 0.000 -5.351 1.803 -2.674
2TP H5A2 H H 0.000 -5.227 3.559 -2.393
2TP C5 C CR5 0.000 -5.324 2.378 -0.621
2TP S1 S S2 0.000 -5.664 0.800 -0.060
2TP C2 C CR15 0.000 -6.031 1.409 1.496
2TP H2 H H 0.000 -6.337 0.798 2.336
2TP C4 C CR5 0.000 -5.493 3.302 0.360
2TP C4A C CH3 0.000 -5.316 4.761 0.330
2TP H4A3 H H 0.000 -6.050 5.185 -0.301
2TP H4A2 H H 0.000 -5.422 5.141 1.310
2TP H4A1 H H 0.000 -4.352 4.984 -0.040
2TP N3 N NR5 1.000 -5.893 2.716 1.540
2TP C35 C CH2 0.000 -6.148 3.459 2.752
2TP H351 H H 0.000 -6.913 2.945 3.337
2TP H352 H H 0.000 -6.500 4.460 2.494
2TP "C5'" C CR6 0.000 -4.882 3.563 3.558
2TP "C6'" C CR16 0.000 -3.725 2.992 3.097
2TP "H6'" H H 0.000 -3.748 2.471 2.148
2TP "N1'" N NRD6 0.000 -2.557 3.048 3.771
2TP "C4'" C CR6 0.000 -4.817 4.213 4.762
2TP "N4'" N NH1 0.000 -5.990 4.818 5.277
2TP "H4'" H H 0.000 -6.841 4.771 4.735
2TP "O4'" O OH1 0.000 -6.011 5.463 6.483
2TP H4 H H 0.000 -6.219 6.403 6.517
2TP "N3'" N NRD6 0.000 -3.685 4.308 5.489
2TP "C2'" C CR6 0.000 -2.608 3.712 4.942
2TP C2A C CH3 0.000 -1.336 3.794 5.716
2TP H2A3 H H 0.000 -1.469 3.326 6.656
2TP H2A2 H H 0.000 -0.568 3.303 5.179
2TP H2A1 H H 0.000 -1.078 4.810 5.858
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
2TP O23 n/a P2 START
2TP P2 O23 O11 .
2TP O21 P2 . .
2TP O22 P2 . .
2TP O11 P2 P1 .
2TP P1 O11 O5G .
2TP O12 P1 . .
2TP O13 P1 . .
2TP O5G P1 C5B .
2TP C5B O5G C5A .
2TP H5B1 C5B . .
2TP H5B2 C5B . .
2TP C5A C5B C5 .
2TP H5A1 C5A . .
2TP H5A2 C5A . .
2TP C5 C5A C4 .
2TP S1 C5 C2 .
2TP C2 S1 H2 .
2TP H2 C2 . .
2TP C4 C5 N3 .
2TP C4A C4 H4A1 .
2TP H4A3 C4A . .
2TP H4A2 C4A . .
2TP H4A1 C4A . .
2TP N3 C4 C35 .
2TP C35 N3 "C5'" .
2TP H351 C35 . .
2TP H352 C35 . .
2TP "C5'" C35 "C4'" .
2TP "C6'" "C5'" "N1'" .
2TP "H6'" "C6'" . .
2TP "N1'" "C6'" . .
2TP "C4'" "C5'" "N3'" .
2TP "N4'" "C4'" "O4'" .
2TP "H4'" "N4'" . .
2TP "O4'" "N4'" H4 .
2TP H4 "O4'" . .
2TP "N3'" "C4'" "C2'" .
2TP "C2'" "N3'" C2A .
2TP C2A "C2'" H2A1 .
2TP H2A3 C2A . .
2TP H2A2 C2A . .
2TP H2A1 C2A . END
2TP "N1'" "C2'" . ADD
2TP 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
2TP "N1'" "C2'" double 1.350 0.020
2TP "N1'" "C6'" single 1.337 0.020
2TP C2A "C2'" single 1.506 0.020
2TP "C2'" "N3'" single 1.350 0.020
2TP H2A1 C2A single 1.059 0.020
2TP H2A2 C2A single 1.059 0.020
2TP H2A3 C2A single 1.059 0.020
2TP "N3'" "C4'" double 1.350 0.020
2TP "N4'" "C4'" single 1.350 0.020
2TP "C4'" "C5'" single 1.487 0.020
2TP "O4'" "N4'" single 1.392 0.020
2TP "H4'" "N4'" single 1.010 0.020
2TP "C6'" "C5'" double 1.390 0.020
2TP "C5'" C35 single 1.511 0.020
2TP "H6'" "C6'" single 1.083 0.020
2TP C35 N3 single 1.462 0.020
2TP H351 C35 single 1.092 0.020
2TP H352 C35 single 1.092 0.020
2TP N3 C2 double 1.337 0.020
2TP N3 C4 single 1.337 0.020
2TP C2 S1 single 1.745 0.020
2TP H2 C2 single 1.083 0.020
2TP S1 C5 single 1.745 0.020
2TP C4 C5 double 1.490 0.020
2TP C5 C5A single 1.510 0.020
2TP C4A C4 single 1.506 0.020
2TP H4A1 C4A single 1.059 0.020
2TP H4A2 C4A single 1.059 0.020
2TP H4A3 C4A single 1.059 0.020
2TP C5A C5B single 1.524 0.020
2TP H5A1 C5A single 1.092 0.020
2TP H5A2 C5A single 1.092 0.020
2TP C5B O5G single 1.426 0.020
2TP H5B1 C5B single 1.092 0.020
2TP H5B2 C5B single 1.092 0.020
2TP O5G P1 single 1.610 0.020
2TP P1 O11 single 1.610 0.020
2TP O12 P1 deloc 1.510 0.020
2TP O13 P1 deloc 1.510 0.020
2TP O11 P2 single 1.610 0.020
2TP O21 P2 deloc 1.510 0.020
2TP O22 P2 deloc 1.510 0.020
2TP P2 O23 deloc 1.510 0.020
2TP H4 "O4'" single 0.967 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
2TP O23 P2 O21 119.900 3.000
2TP O23 P2 O22 119.900 3.000
2TP O23 P2 O11 108.200 3.000
2TP O21 P2 O22 119.900 3.000
2TP O21 P2 O11 108.200 3.000
2TP O22 P2 O11 108.200 3.000
2TP P2 O11 P1 120.500 3.000
2TP O11 P1 O12 108.200 3.000
2TP O11 P1 O13 108.200 3.000
2TP O11 P1 O5G 102.600 3.000
2TP O12 P1 O13 119.900 3.000
2TP O12 P1 O5G 108.200 3.000
2TP O13 P1 O5G 108.200 3.000
2TP P1 O5G C5B 120.500 3.000
2TP O5G C5B H5B1 109.470 3.000
2TP O5G C5B H5B2 109.470 3.000
2TP O5G C5B C5A 109.470 3.000
2TP H5B1 C5B H5B2 107.900 3.000
2TP H5B1 C5B C5A 109.470 3.000
2TP H5B2 C5B C5A 109.470 3.000
2TP C5B C5A H5A1 109.470 3.000
2TP C5B C5A H5A2 109.470 3.000
2TP C5B C5A C5 109.470 3.000
2TP H5A1 C5A H5A2 107.900 3.000
2TP H5A1 C5A C5 109.470 3.000
2TP H5A2 C5A C5 109.470 3.000
2TP C5A C5 S1 108.000 3.000
2TP C5A C5 C4 126.000 3.000
2TP S1 C5 C4 108.000 3.000
2TP C5 S1 C2 90.725 3.000
2TP S1 C2 H2 108.000 3.000
2TP S1 C2 N3 108.000 3.000
2TP H2 C2 N3 126.000 3.000
2TP C5 C4 C4A 126.000 3.000
2TP C5 C4 N3 108.000 3.000
2TP C4A C4 N3 126.000 3.000
2TP C4 C4A H4A3 109.470 3.000
2TP C4 C4A H4A2 109.470 3.000
2TP C4 C4A H4A1 109.470 3.000
2TP H4A3 C4A H4A2 109.470 3.000
2TP H4A3 C4A H4A1 109.470 3.000
2TP H4A2 C4A H4A1 109.470 3.000
2TP C4 N3 C35 126.000 3.000
2TP C4 N3 C2 108.000 3.000
2TP C35 N3 C2 126.000 3.000
2TP N3 C35 H351 109.500 3.000
2TP N3 C35 H352 109.500 3.000
2TP N3 C35 "C5'" 109.500 3.000
2TP H351 C35 H352 107.900 3.000
2TP H351 C35 "C5'" 109.470 3.000
2TP H352 C35 "C5'" 109.470 3.000
2TP C35 "C5'" "C6'" 120.000 3.000
2TP C35 "C5'" "C4'" 120.000 3.000
2TP "C6'" "C5'" "C4'" 120.000 3.000
2TP "C5'" "C6'" "H6'" 120.000 3.000
2TP "C5'" "C6'" "N1'" 120.000 3.000
2TP "H6'" "C6'" "N1'" 120.000 3.000
2TP "C6'" "N1'" "C2'" 120.000 3.000
2TP "C5'" "C4'" "N4'" 120.000 3.000
2TP "C5'" "C4'" "N3'" 120.000 3.000
2TP "N4'" "C4'" "N3'" 120.000 3.000
2TP "C4'" "N4'" "H4'" 120.000 3.000
2TP "C4'" "N4'" "O4'" 120.000 3.000
2TP "H4'" "N4'" "O4'" 120.200 3.000
2TP "N4'" "O4'" H4 120.000 3.000
2TP "C4'" "N3'" "C2'" 120.000 3.000
2TP "N3'" "C2'" C2A 120.000 3.000
2TP "N3'" "C2'" "N1'" 120.000 3.000
2TP C2A "C2'" "N1'" 120.000 3.000
2TP "C2'" C2A H2A3 109.470 3.000
2TP "C2'" C2A H2A2 109.470 3.000
2TP "C2'" C2A H2A1 109.470 3.000
2TP H2A3 C2A H2A2 109.470 3.000
2TP H2A3 C2A H2A1 109.470 3.000
2TP H2A2 C2A H2A1 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
2TP var_1 O23 P2 O11 P1 -173.595 20.000 1
2TP var_2 P2 O11 P1 O5G -65.828 20.000 1
2TP var_3 O11 P1 O5G C5B -54.555 20.000 1
2TP var_4 P1 O5G C5B C5A 179.945 20.000 1
2TP var_5 O5G C5B C5A C5 -58.293 20.000 3
2TP var_6 C5B C5A C5 C4 89.981 20.000 2
2TP CONST_1 C5A C5 S1 C2 180.000 0.000 0
2TP CONST_2 C5 S1 C2 N3 0.000 0.000 0
2TP CONST_3 C5A C5 C4 N3 180.000 0.000 0
2TP var_7 C5 C4 C4A H4A1 -53.075 20.000 1
2TP CONST_4 C5 C4 N3 C35 180.000 0.000 0
2TP CONST_5 C4 N3 C2 S1 0.000 0.000 0
2TP var_8 C4 N3 C35 "C5'" -89.997 20.000 1
2TP var_9 N3 C35 "C5'" "C4'" -179.959 20.000 2
2TP CONST_6 C35 "C5'" "C6'" "N1'" 180.000 0.000 0
2TP CONST_7 "C5'" "C6'" "N1'" "C2'" 0.000 0.000 0
2TP CONST_8 "C6'" "N1'" "C2'" "N3'" 0.000 0.000 0
2TP CONST_9 C35 "C5'" "C4'" "N3'" 180.000 0.000 0
2TP var_10 "C5'" "C4'" "N4'" "O4'" 178.741 20.000 1
2TP var_11 "C4'" "N4'" "O4'" H4 117.922 20.000 1
2TP CONST_10 "C5'" "C4'" "N3'" "C2'" 0.000 0.000 0
2TP CONST_11 "C4'" "N3'" "C2'" C2A 180.000 0.000 0
2TP var_12 "N3'" "C2'" C2A H2A1 -59.251 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
2TP plan-1 "N1'" 0.020
2TP plan-1 "C2'" 0.020
2TP plan-1 "C6'" 0.020
2TP plan-1 "N3'" 0.020
2TP plan-1 "C4'" 0.020
2TP plan-1 "C5'" 0.020
2TP plan-1 C2A 0.020
2TP plan-1 "N4'" 0.020
2TP plan-1 C35 0.020
2TP plan-1 "H6'" 0.020
2TP plan-1 "H4'" 0.020
2TP plan-2 "N4'" 0.020
2TP plan-2 "C4'" 0.020
2TP plan-2 "O4'" 0.020
2TP plan-2 "H4'" 0.020
2TP plan-3 N3 0.020
2TP plan-3 C35 0.020
2TP plan-3 C2 0.020
2TP plan-3 C4 0.020
2TP plan-3 S1 0.020
2TP plan-3 C5 0.020
2TP plan-3 H2 0.020
2TP plan-3 C5A 0.020
2TP plan-3 C4A 0.020
# ------------------------------------------------------
|
