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
|
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
DIH DIH '3-HYDROXY-4-HYDROXYMETHYL-1-(4-OXO-4' non-polymer 38 19 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DIH
#
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
DIH O6 O O 0.000 0.000 0.000 0.000
DIH C6 C C 0.000 -1.110 0.486 -0.023
DIH N1 N NH1 0.000 -1.339 1.853 -0.163
DIH H1 H H 0.000 -0.560 2.476 -0.319
DIH C2 C C1 0.000 -2.620 2.365 -0.090
DIH H2 H H 0.000 -2.772 3.359 0.293
DIH N3 N N 0.000 -3.653 1.659 -0.481
DIH C4 C CH1 0.000 -3.348 0.335 -0.958
DIH H4 H H 0.000 -2.840 0.401 -1.931
DIH C5 C CH1 0.000 -2.377 -0.297 0.099
DIH H5 H H 0.000 -2.793 -0.225 1.114
DIH N7 N NH1 0.000 -2.423 -1.672 -0.393
DIH H7 H H 0.000 -1.660 -2.325 -0.496
DIH C8 C C1 0.000 -3.789 -1.871 -0.690
DIH H8 H H 0.000 -4.281 -2.828 -0.660
DIH C9 C C 0.000 -4.397 -0.723 -1.013
DIH C10 C CH2 0.000 -5.850 -0.538 -1.369
DIH H101 H H 0.000 -6.252 -1.476 -1.758
DIH H102 H H 0.000 -5.942 0.240 -2.130
DIH "N1'" N NT1 1.000 -6.601 -0.142 -0.169
DIH "H1'" H H 0.000 -6.160 0.681 0.272
DIH "C6'" C CH2 0.000 -8.004 0.160 -0.523
DIH "H6'2" H H 0.000 -8.296 -0.373 -1.430
DIH "H6'1" H H 0.000 -8.141 1.234 -0.673
DIH "C2'" C CH2 0.000 -6.660 -1.270 0.796
DIH "H2'1" H H 0.000 -5.768 -1.328 1.424
DIH "H2'2" H H 0.000 -6.821 -2.231 0.305
DIH "C3'" C CH1 0.000 -7.891 -0.923 1.674
DIH "H3'" H H 0.000 -7.623 -0.187 2.445
DIH "O3'" O OH1 0.000 -8.435 -2.102 2.269
DIH "HO3'" H H 0.000 -7.771 -2.509 2.842
DIH "C4'" C CH1 0.000 -8.878 -0.310 0.655
DIH "H4'" H H 0.000 -9.597 -1.070 0.317
DIH "C5'" C CH2 0.000 -9.615 0.878 1.277
DIH "H5'1" H H 0.000 -10.203 1.384 0.508
DIH "H5'2" H H 0.000 -8.889 1.576 1.697
DIH "O5'" O OH1 0.000 -10.484 0.411 2.312
DIH "HO5'" H H 0.000 -10.950 1.161 2.704
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
DIH O6 n/a C6 START
DIH C6 O6 N1 .
DIH N1 C6 C2 .
DIH H1 N1 . .
DIH C2 N1 N3 .
DIH H2 C2 . .
DIH N3 C2 C4 .
DIH C4 N3 C9 .
DIH H4 C4 . .
DIH C5 C4 N7 .
DIH H5 C5 . .
DIH N7 C5 C8 .
DIH H7 N7 . .
DIH C8 N7 H8 .
DIH H8 C8 . .
DIH C9 C4 C10 .
DIH C10 C9 "N1'" .
DIH H101 C10 . .
DIH H102 C10 . .
DIH "N1'" C10 "C2'" .
DIH "H1'" "N1'" . .
DIH "C6'" "N1'" "H6'1" .
DIH "H6'2" "C6'" . .
DIH "H6'1" "C6'" . .
DIH "C2'" "N1'" "C3'" .
DIH "H2'1" "C2'" . .
DIH "H2'2" "C2'" . .
DIH "C3'" "C2'" "C4'" .
DIH "H3'" "C3'" . .
DIH "O3'" "C3'" "HO3'" .
DIH "HO3'" "O3'" . .
DIH "C4'" "C3'" "C5'" .
DIH "H4'" "C4'" . .
DIH "C5'" "C4'" "O5'" .
DIH "H5'1" "C5'" . .
DIH "H5'2" "C5'" . .
DIH "O5'" "C5'" "HO5'" .
DIH "HO5'" "O5'" . END
DIH "C4'" "C6'" . ADD
DIH C9 C8 . ADD
DIH C5 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
DIH "O5'" "C5'" single 1.432 0.020
DIH "HO5'" "O5'" single 0.967 0.020
DIH "C5'" "C4'" single 1.524 0.020
DIH "H5'1" "C5'" single 1.092 0.020
DIH "H5'2" "C5'" single 1.092 0.020
DIH "C4'" "C6'" single 1.524 0.020
DIH "C4'" "C3'" single 1.524 0.020
DIH "H4'" "C4'" single 1.099 0.020
DIH "C6'" "N1'" single 1.472 0.020
DIH "H6'1" "C6'" single 1.092 0.020
DIH "H6'2" "C6'" single 1.092 0.020
DIH "O3'" "C3'" single 1.432 0.020
DIH "C3'" "C2'" single 1.524 0.020
DIH "H3'" "C3'" single 1.099 0.020
DIH "HO3'" "O3'" single 0.967 0.020
DIH "C2'" "N1'" single 1.472 0.020
DIH "H2'1" "C2'" single 1.092 0.020
DIH "H2'2" "C2'" single 1.092 0.020
DIH "N1'" C10 single 1.472 0.020
DIH "H1'" "N1'" single 1.033 0.020
DIH C10 C9 single 1.510 0.020
DIH H101 C10 single 1.092 0.020
DIH H102 C10 single 1.092 0.020
DIH C9 C8 double 1.340 0.020
DIH C9 C4 single 1.500 0.020
DIH C8 N7 single 1.330 0.020
DIH H8 C8 single 1.077 0.020
DIH N7 C5 single 1.450 0.020
DIH H7 N7 single 1.010 0.020
DIH C5 C6 single 1.500 0.020
DIH C5 C4 single 1.524 0.020
DIH H5 C5 single 1.099 0.020
DIH C6 O6 double 1.220 0.020
DIH N1 C6 single 1.330 0.020
DIH C2 N1 single 1.330 0.020
DIH H1 N1 single 1.010 0.020
DIH N3 C2 double 1.260 0.020
DIH H2 C2 single 1.077 0.020
DIH C4 N3 single 1.455 0.020
DIH H4 C4 single 1.099 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
DIH O6 C6 N1 123.000 3.000
DIH O6 C6 C5 120.500 3.000
DIH N1 C6 C5 116.500 3.000
DIH C6 N1 H1 120.000 3.000
DIH C6 N1 C2 120.000 3.000
DIH H1 N1 C2 120.000 3.000
DIH N1 C2 H2 120.000 3.000
DIH N1 C2 N3 120.000 3.000
DIH H2 C2 N3 120.000 3.000
DIH C2 N3 C4 120.000 3.000
DIH N3 C4 H4 109.470 3.000
DIH N3 C4 C5 105.000 3.000
DIH N3 C4 C9 111.600 3.000
DIH H4 C4 C5 108.340 3.000
DIH H4 C4 C9 108.810 3.000
DIH C5 C4 C9 109.470 3.000
DIH C4 C5 H5 108.340 3.000
DIH C4 C5 N7 110.000 3.000
DIH C4 C5 C6 109.470 3.000
DIH H5 C5 N7 108.550 3.000
DIH H5 C5 C6 108.810 3.000
DIH N7 C5 C6 111.600 3.000
DIH C5 N7 H7 118.500 3.000
DIH C5 N7 C8 120.000 3.000
DIH H7 N7 C8 120.000 3.000
DIH N7 C8 H8 120.000 3.000
DIH N7 C8 C9 120.000 3.000
DIH H8 C8 C9 120.000 3.000
DIH C4 C9 C10 120.000 3.000
DIH C4 C9 C8 120.000 3.000
DIH C10 C9 C8 120.000 3.000
DIH C9 C10 H101 109.470 3.000
DIH C9 C10 H102 109.470 3.000
DIH C9 C10 "N1'" 109.500 3.000
DIH H101 C10 H102 107.900 3.000
DIH H101 C10 "N1'" 109.500 3.000
DIH H102 C10 "N1'" 109.500 3.000
DIH C10 "N1'" "H1'" 109.500 3.000
DIH C10 "N1'" "C6'" 109.500 3.000
DIH C10 "N1'" "C2'" 109.500 3.000
DIH "H1'" "N1'" "C6'" 109.500 3.000
DIH "H1'" "N1'" "C2'" 109.500 3.000
DIH "C6'" "N1'" "C2'" 109.500 3.000
DIH "N1'" "C6'" "H6'2" 109.500 3.000
DIH "N1'" "C6'" "H6'1" 109.500 3.000
DIH "N1'" "C6'" "C4'" 109.500 3.000
DIH "H6'2" "C6'" "H6'1" 107.900 3.000
DIH "H6'2" "C6'" "C4'" 109.470 3.000
DIH "H6'1" "C6'" "C4'" 109.470 3.000
DIH "N1'" "C2'" "H2'1" 109.500 3.000
DIH "N1'" "C2'" "H2'2" 109.500 3.000
DIH "N1'" "C2'" "C3'" 109.500 3.000
DIH "H2'1" "C2'" "H2'2" 107.900 3.000
DIH "H2'1" "C2'" "C3'" 109.470 3.000
DIH "H2'2" "C2'" "C3'" 109.470 3.000
DIH "C2'" "C3'" "H3'" 108.340 3.000
DIH "C2'" "C3'" "O3'" 109.470 3.000
DIH "C2'" "C3'" "C4'" 111.000 3.000
DIH "H3'" "C3'" "O3'" 109.470 3.000
DIH "H3'" "C3'" "C4'" 108.340 3.000
DIH "O3'" "C3'" "C4'" 109.470 3.000
DIH "C3'" "O3'" "HO3'" 109.470 3.000
DIH "C3'" "C4'" "H4'" 108.340 3.000
DIH "C3'" "C4'" "C5'" 111.000 3.000
DIH "C3'" "C4'" "C6'" 111.000 3.000
DIH "H4'" "C4'" "C5'" 108.340 3.000
DIH "H4'" "C4'" "C6'" 108.340 3.000
DIH "C5'" "C4'" "C6'" 109.470 3.000
DIH "C4'" "C5'" "H5'1" 109.470 3.000
DIH "C4'" "C5'" "H5'2" 109.470 3.000
DIH "C4'" "C5'" "O5'" 109.470 3.000
DIH "H5'1" "C5'" "H5'2" 107.900 3.000
DIH "H5'1" "C5'" "O5'" 109.470 3.000
DIH "H5'2" "C5'" "O5'" 109.470 3.000
DIH "C5'" "O5'" "HO5'" 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
DIH CONST_1 O6 C6 N1 C2 180.000 0.000 0
DIH var_1 C6 N1 C2 N3 -30.000 20.000 1
DIH var_2 N1 C2 N3 C4 0.000 20.000 1
DIH var_3 C2 N3 C4 C9 150.000 20.000 3
DIH var_4 N3 C4 C5 N7 180.000 20.000 3
DIH var_5 C4 C5 C6 O6 -150.000 20.000 3
DIH var_6 C4 C5 N7 C8 -30.000 20.000 3
DIH var_7 C5 N7 C8 C9 30.000 20.000 1
DIH var_8 N3 C4 C9 C10 30.000 20.000 3
DIH var_9 C4 C9 C8 N7 0.000 20.000 1
DIH var_10 C4 C9 C10 "N1'" -85.325 20.000 3
DIH var_11 C9 C10 "N1'" "C2'" -68.514 20.000 1
DIH var_12 C10 "N1'" "C6'" "C4'" 150.000 20.000 1
DIH var_13 C10 "N1'" "C2'" "C3'" -150.000 20.000 1
DIH var_14 "N1'" "C2'" "C3'" "C4'" 30.000 20.000 3
DIH var_15 "C2'" "C3'" "O3'" "HO3'" 61.457 20.000 1
DIH var_16 "C2'" "C3'" "C4'" "C5'" -150.000 20.000 3
DIH var_17 "C3'" "C4'" "C6'" "N1'" 0.000 20.000 3
DIH var_18 "C3'" "C4'" "C5'" "O5'" -67.773 20.000 3
DIH var_19 "C4'" "C5'" "O5'" "HO5'" -180.000 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
DIH chir_01 "C4'" "C5'" "C6'" "C3'" negativ
DIH chir_02 "C3'" "C4'" "O3'" "C2'" negativ
DIH chir_03 "N1'" "C6'" "C2'" C10 negativ
DIH chir_04 C5 N7 C6 C4 negativ
DIH chir_05 C4 C9 C5 N3 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
DIH plan-1 C9 0.020
DIH plan-1 C10 0.020
DIH plan-1 C8 0.020
DIH plan-1 C4 0.020
DIH plan-1 H8 0.020
DIH plan-2 C8 0.020
DIH plan-2 C9 0.020
DIH plan-2 N7 0.020
DIH plan-2 H8 0.020
DIH plan-2 H7 0.020
DIH plan-3 N7 0.020
DIH plan-3 C8 0.020
DIH plan-3 C5 0.020
DIH plan-3 H7 0.020
DIH plan-3 H8 0.020
DIH plan-4 C6 0.020
DIH plan-4 C5 0.020
DIH plan-4 O6 0.020
DIH plan-4 N1 0.020
DIH plan-4 H1 0.020
DIH plan-5 N1 0.020
DIH plan-5 C6 0.020
DIH plan-5 C2 0.020
DIH plan-5 H1 0.020
DIH plan-5 H2 0.020
DIH plan-6 C2 0.020
DIH plan-6 N1 0.020
DIH plan-6 N3 0.020
DIH plan-6 H2 0.020
DIH plan-6 H1 0.020
DIH plan-7 N3 0.020
DIH plan-7 C2 0.020
DIH plan-7 C4 0.020
DIH plan-7 H2 0.020
# ------------------------------------------------------
|
