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
|
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
D3T D3T '2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPH' non-polymer 41 28 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_D3T
#
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
D3T O3G O OP -0.666 0.000 0.000 0.000
D3T PG P P 0.000 -0.953 1.162 0.174
D3T O1G O OP -0.666 -2.349 0.658 -0.119
D3T O2G O OP -0.666 -0.929 1.625 1.615
D3T O3B O O2 0.000 -0.630 2.357 -0.833
D3T PB P P 0.000 -1.355 3.781 -1.066
D3T O1B O OP -0.500 -1.397 4.680 0.112
D3T O2B O OP -0.500 -0.664 4.340 -2.253
D3T O3A O O2 0.000 -2.799 3.328 -1.631
D3T PA P P 0.000 -4.044 4.176 -2.213
D3T O1A O OP -0.500 -3.742 4.995 -3.412
D3T O2A O OP -0.500 -4.506 4.959 -1.041
D3T "O5'" O O2 0.000 -5.215 3.080 -2.439
D3T "C5'" C CH2 0.000 -5.605 2.230 -1.374
D3T "H5'1" H H 0.000 -5.969 2.831 -0.538
D3T "H5'2" H H 0.000 -4.750 1.635 -1.047
D3T "C4'" C CH1 0.000 -6.714 1.305 -1.857
D3T "H4'" H H 0.000 -7.560 1.904 -2.222
D3T "C3'" C CH2 0.000 -7.196 0.341 -0.784
D3T "H3'1" H H 0.000 -8.235 0.037 -0.926
D3T "H3'2" H H 0.000 -7.068 0.736 0.226
D3T "C2'" C CH2 0.000 -6.290 -0.849 -0.978
D3T "H2'1" H H 0.000 -6.744 -1.789 -0.656
D3T "H2'2" H H 0.000 -5.318 -0.731 -0.495
D3T "C1'" C CH1 0.000 -6.110 -0.864 -2.484
D3T "H1'" H H 0.000 -6.924 -1.445 -2.940
D3T "O4'" O O2 0.000 -6.197 0.497 -2.929
D3T N1 N NR6 0.000 -4.852 -1.418 -2.890
D3T C2 C CR6 0.000 -4.729 -2.785 -3.219
D3T O2 O O 0.000 -5.664 -3.587 -3.186
D3T N3 N NR16 0.000 -3.443 -3.189 -3.596
D3T HN3 H H 0.000 -3.326 -4.192 -3.844
D3T C4 C CR6 0.000 -2.309 -2.395 -3.677
D3T O4 O O 0.000 -1.208 -2.817 -4.018
D3T C5 C CR6 0.000 -2.520 -0.968 -3.314
D3T C5M C CH3 0.000 -1.343 -0.047 -3.374
D3T H5M3 H H 0.000 -0.967 -0.022 -4.363
D3T H5M2 H H 0.000 -1.643 0.925 -3.084
D3T H5M1 H H 0.000 -0.590 -0.397 -2.718
D3T C6 C CR16 0.000 -3.748 -0.578 -2.952
D3T H6 H H 0.000 -3.890 0.463 -2.690
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
D3T O3G n/a PG START
D3T PG O3G O3B .
D3T O1G PG . .
D3T O2G PG . .
D3T O3B PG PB .
D3T PB O3B O3A .
D3T O1B PB . .
D3T O2B PB . .
D3T O3A PB PA .
D3T PA O3A "O5'" .
D3T O1A PA . .
D3T O2A PA . .
D3T "O5'" PA "C5'" .
D3T "C5'" "O5'" "C4'" .
D3T "H5'1" "C5'" . .
D3T "H5'2" "C5'" . .
D3T "C4'" "C5'" "C3'" .
D3T "H4'" "C4'" . .
D3T "C3'" "C4'" "C2'" .
D3T "H3'1" "C3'" . .
D3T "H3'2" "C3'" . .
D3T "C2'" "C3'" "C1'" .
D3T "H2'1" "C2'" . .
D3T "H2'2" "C2'" . .
D3T "C1'" "C2'" N1 .
D3T "H1'" "C1'" . .
D3T "O4'" "C1'" . .
D3T N1 "C1'" C2 .
D3T C2 N1 N3 .
D3T O2 C2 . .
D3T N3 C2 C4 .
D3T HN3 N3 . .
D3T C4 N3 C5 .
D3T O4 C4 . .
D3T C5 C4 C6 .
D3T C5M C5 H5M1 .
D3T H5M3 C5M . .
D3T H5M2 C5M . .
D3T H5M1 C5M . .
D3T C6 C5 H6 .
D3T H6 C6 . END
D3T "C4'" "O4'" . ADD
D3T N1 C6 . 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
D3T O1A PA deloc 1.510 0.020
D3T O2A PA deloc 1.510 0.020
D3T "O5'" PA single 1.610 0.020
D3T PA O3A single 1.610 0.020
D3T "C5'" "O5'" single 1.426 0.020
D3T "C4'" "C5'" single 1.524 0.020
D3T "H5'1" "C5'" single 1.092 0.020
D3T "H5'2" "C5'" single 1.092 0.020
D3T "C4'" "O4'" single 1.426 0.020
D3T "C3'" "C4'" single 1.524 0.020
D3T "H4'" "C4'" single 1.099 0.020
D3T "O4'" "C1'" single 1.426 0.020
D3T N1 "C1'" single 1.465 0.020
D3T "C1'" "C2'" single 1.524 0.020
D3T "H1'" "C1'" single 1.099 0.020
D3T N1 C6 single 1.337 0.020
D3T C2 N1 single 1.410 0.020
D3T C6 C5 double 1.390 0.020
D3T H6 C6 single 1.083 0.020
D3T O2 C2 double 1.250 0.020
D3T N3 C2 single 1.337 0.020
D3T C4 N3 single 1.337 0.020
D3T HN3 N3 single 1.040 0.020
D3T O4 C4 double 1.250 0.020
D3T C5 C4 single 1.487 0.020
D3T C5M C5 single 1.506 0.020
D3T H5M1 C5M single 1.059 0.020
D3T H5M2 C5M single 1.059 0.020
D3T H5M3 C5M single 1.059 0.020
D3T "C2'" "C3'" single 1.524 0.020
D3T "H2'1" "C2'" single 1.092 0.020
D3T "H2'2" "C2'" single 1.092 0.020
D3T "H3'1" "C3'" single 1.092 0.020
D3T "H3'2" "C3'" single 1.092 0.020
D3T O3A PB single 1.610 0.020
D3T O1B PB deloc 1.510 0.020
D3T O2B PB deloc 1.510 0.020
D3T PB O3B single 1.610 0.020
D3T O3B PG single 1.610 0.020
D3T O1G PG deloc 1.510 0.020
D3T O2G PG deloc 1.510 0.020
D3T PG O3G 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
D3T O3G PG O1G 119.900 3.000
D3T O3G PG O2G 119.900 3.000
D3T O3G PG O3B 108.200 3.000
D3T O1G PG O2G 119.900 3.000
D3T O1G PG O3B 108.200 3.000
D3T O2G PG O3B 108.200 3.000
D3T PG O3B PB 120.500 3.000
D3T O3B PB O1B 108.200 3.000
D3T O3B PB O2B 108.200 3.000
D3T O3B PB O3A 102.600 3.000
D3T O1B PB O2B 119.900 3.000
D3T O1B PB O3A 108.200 3.000
D3T O2B PB O3A 108.200 3.000
D3T PB O3A PA 120.500 3.000
D3T O3A PA O1A 108.200 3.000
D3T O3A PA O2A 108.200 3.000
D3T O3A PA "O5'" 102.600 3.000
D3T O1A PA O2A 119.900 3.000
D3T O1A PA "O5'" 108.200 3.000
D3T O2A PA "O5'" 108.200 3.000
D3T PA "O5'" "C5'" 120.500 3.000
D3T "O5'" "C5'" "H5'1" 109.470 3.000
D3T "O5'" "C5'" "H5'2" 109.470 3.000
D3T "O5'" "C5'" "C4'" 109.470 3.000
D3T "H5'1" "C5'" "H5'2" 107.900 3.000
D3T "H5'1" "C5'" "C4'" 109.470 3.000
D3T "H5'2" "C5'" "C4'" 109.470 3.000
D3T "C5'" "C4'" "H4'" 108.340 3.000
D3T "C5'" "C4'" "C3'" 109.470 3.000
D3T "C5'" "C4'" "O4'" 109.470 3.000
D3T "H4'" "C4'" "C3'" 108.340 3.000
D3T "H4'" "C4'" "O4'" 109.470 3.000
D3T "C3'" "C4'" "O4'" 109.470 3.000
D3T "C4'" "C3'" "H3'1" 109.470 3.000
D3T "C4'" "C3'" "H3'2" 109.470 3.000
D3T "C4'" "C3'" "C2'" 111.000 3.000
D3T "H3'1" "C3'" "H3'2" 107.900 3.000
D3T "H3'1" "C3'" "C2'" 109.470 3.000
D3T "H3'2" "C3'" "C2'" 109.470 3.000
D3T "C3'" "C2'" "H2'1" 109.470 3.000
D3T "C3'" "C2'" "H2'2" 109.470 3.000
D3T "C3'" "C2'" "C1'" 111.000 3.000
D3T "H2'1" "C2'" "H2'2" 107.900 3.000
D3T "H2'1" "C2'" "C1'" 109.470 3.000
D3T "H2'2" "C2'" "C1'" 109.470 3.000
D3T "C2'" "C1'" "H1'" 108.340 3.000
D3T "C2'" "C1'" "O4'" 109.470 3.000
D3T "C2'" "C1'" N1 109.470 3.000
D3T "H1'" "C1'" "O4'" 109.470 3.000
D3T "H1'" "C1'" N1 109.470 3.000
D3T "O4'" "C1'" N1 109.470 3.000
D3T "C1'" "O4'" "C4'" 111.800 3.000
D3T "C1'" N1 C2 120.000 3.000
D3T "C1'" N1 C6 120.000 3.000
D3T C2 N1 C6 120.000 3.000
D3T N1 C2 O2 120.000 3.000
D3T N1 C2 N3 120.000 3.000
D3T O2 C2 N3 120.000 3.000
D3T C2 N3 HN3 120.000 3.000
D3T C2 N3 C4 120.000 3.000
D3T HN3 N3 C4 120.000 3.000
D3T N3 C4 O4 120.000 3.000
D3T N3 C4 C5 120.000 3.000
D3T O4 C4 C5 120.000 3.000
D3T C4 C5 C5M 120.000 3.000
D3T C4 C5 C6 120.000 3.000
D3T C5M C5 C6 120.000 3.000
D3T C5 C5M H5M3 109.470 3.000
D3T C5 C5M H5M2 109.470 3.000
D3T C5 C5M H5M1 109.470 3.000
D3T H5M3 C5M H5M2 109.470 3.000
D3T H5M3 C5M H5M1 109.470 3.000
D3T H5M2 C5M H5M1 109.470 3.000
D3T C5 C6 H6 120.000 3.000
D3T C5 C6 N1 120.000 3.000
D3T H6 C6 N1 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
D3T var_1 O3G PG O3B PB 178.583 20.000 1
D3T var_2 PG O3B PB O3A -65.424 20.000 1
D3T var_3 O3B PB O3A PA -174.123 20.000 1
D3T var_4 PB O3A PA "O5'" -174.035 20.000 1
D3T var_5 O3A PA "O5'" "C5'" 53.410 20.000 1
D3T var_6 PA "O5'" "C5'" "C4'" -179.971 20.000 1
D3T var_7 "O5'" "C5'" "C4'" "C3'" 179.554 20.000 3
D3T var_8 "C5'" "C4'" "O4'" "C1'" 120.000 20.000 1
D3T var_9 "C5'" "C4'" "C3'" "C2'" -90.000 20.000 3
D3T var_10 "C4'" "C3'" "C2'" "C1'" -30.000 20.000 3
D3T var_11 "C3'" "C2'" "C1'" N1 150.000 20.000 3
D3T var_12 "C2'" "C1'" "O4'" "C4'" 0.000 20.000 1
D3T var_13 "C2'" "C1'" N1 C2 93.606 20.000 1
D3T CONST_1 "C1'" N1 C6 C5 180.000 0.000 0
D3T CONST_2 "C1'" N1 C2 N3 180.000 0.000 0
D3T CONST_3 N1 C2 N3 C4 0.000 0.000 0
D3T CONST_4 C2 N3 C4 C5 0.000 0.000 0
D3T CONST_5 N3 C4 C5 C6 0.000 0.000 0
D3T var_14 C4 C5 C5M H5M1 -59.571 20.000 1
D3T CONST_6 C4 C5 C6 N1 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
D3T chir_01 "C4'" "C5'" "O4'" "C3'" negativ
D3T chir_02 "C1'" "O4'" N1 "C2'" 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
D3T plan-1 N1 0.020
D3T plan-1 "C1'" 0.020
D3T plan-1 C6 0.020
D3T plan-1 C2 0.020
D3T plan-1 N3 0.020
D3T plan-1 C4 0.020
D3T plan-1 C5 0.020
D3T plan-1 H6 0.020
D3T plan-1 O2 0.020
D3T plan-1 HN3 0.020
D3T plan-1 O4 0.020
D3T plan-1 C5M 0.020
# ------------------------------------------------------
|
