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
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
|
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
DKY DKY '1-(3-deoxy-3-fluoro-beta-D-glucopyra' non-polymer 45 27 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DKY
#
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
DKY O11 O O 0.000 0.000 0.000 0.000
DKY C11 C C 0.000 0.259 0.283 1.153
DKY C12 C CR6 0.000 1.668 0.378 1.590
DKY C17 C CR16 0.000 1.970 0.707 2.914
DKY H17 H H 0.000 1.173 0.898 3.621
DKY C16 C CR16 0.000 3.287 0.789 3.317
DKY H16 H H 0.000 3.523 1.035 4.345
DKY C15 C CR16 0.000 4.307 0.558 2.411
DKY H15 H H 0.000 5.339 0.630 2.732
DKY C14 C CR16 0.000 4.015 0.237 1.097
DKY H14 H H 0.000 4.818 0.057 0.394
DKY C13 C CR16 0.000 2.702 0.145 0.682
DKY H13 H H 0.000 2.474 -0.106 -0.347
DKY N3 N NH1 0.000 -0.736 0.507 2.032
DKY HN3 H H 0.000 -0.520 0.742 2.991
DKY C9 C CR6 0.000 -2.052 0.418 1.624
DKY C8 C CR16 0.000 -3.097 0.651 2.540
DKY H8 H H 0.000 -2.878 0.903 3.570
DKY C7 C CR16 0.000 -4.378 0.557 2.112
DKY H7 H H 0.000 -5.198 0.733 2.798
DKY N2 N NRD6 0.000 -2.340 0.111 0.366
DKY C10 C CR6 0.000 -3.606 0.016 -0.038
DKY O10 O O 0.000 -3.845 -0.272 -1.199
DKY N1 N NR6 0.000 -4.626 0.240 0.812
DKY C1 C CH1 0.000 -6.007 0.133 0.336
DKY H1 H H 0.000 -6.697 0.260 1.183
DKY O5 O O2 0.000 -6.211 -1.151 -0.256
DKY C5 C CH1 0.000 -7.540 -1.370 -0.733
DKY H5 H H 0.000 -8.250 -1.264 0.099
DKY C6 C CH2 0.000 -7.646 -2.780 -1.317
DKY H6 H H 0.000 -6.881 -2.915 -2.084
DKY H6A H H 0.000 -8.634 -2.915 -1.762
DKY O6 O OH1 0.000 -7.455 -3.742 -0.278
DKY HO6 H H 0.000 -7.523 -4.632 -0.648
DKY C4 C CH1 0.000 -7.867 -0.341 -1.819
DKY H4 H H 0.000 -7.184 -0.474 -2.669
DKY O4 O OH1 0.000 -9.216 -0.521 -2.255
DKY HO4 H H 0.000 -9.423 0.132 -2.938
DKY C3 C CH1 0.000 -7.699 1.068 -1.242
DKY H3 H H 0.000 -8.418 1.219 -0.424
DKY F3 F F 0.000 -7.927 2.015 -2.247
DKY C2 C CH1 0.000 -6.273 1.223 -0.706
DKY H2 H H 0.000 -5.556 1.122 -1.534
DKY O2 O OH1 0.000 -6.125 2.509 -0.102
DKY HO2 H H 0.000 -6.293 3.195 -0.761
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
DKY O11 n/a C11 START
DKY C11 O11 N3 .
DKY C12 C11 C17 .
DKY C17 C12 C16 .
DKY H17 C17 . .
DKY C16 C17 C15 .
DKY H16 C16 . .
DKY C15 C16 C14 .
DKY H15 C15 . .
DKY C14 C15 C13 .
DKY H14 C14 . .
DKY C13 C14 H13 .
DKY H13 C13 . .
DKY N3 C11 C9 .
DKY HN3 N3 . .
DKY C9 N3 N2 .
DKY C8 C9 C7 .
DKY H8 C8 . .
DKY C7 C8 H7 .
DKY H7 C7 . .
DKY N2 C9 C10 .
DKY C10 N2 N1 .
DKY O10 C10 . .
DKY N1 C10 C1 .
DKY C1 N1 O5 .
DKY H1 C1 . .
DKY O5 C1 C5 .
DKY C5 O5 C4 .
DKY H5 C5 . .
DKY C6 C5 O6 .
DKY H6 C6 . .
DKY H6A C6 . .
DKY O6 C6 HO6 .
DKY HO6 O6 . .
DKY C4 C5 C3 .
DKY H4 C4 . .
DKY O4 C4 HO4 .
DKY HO4 O4 . .
DKY C3 C4 C2 .
DKY H3 C3 . .
DKY F3 C3 . .
DKY C2 C3 O2 .
DKY H2 C2 . .
DKY O2 C2 HO2 .
DKY HO2 O2 . END
DKY C1 C2 . ADD
DKY N1 C7 . ADD
DKY C12 C13 . 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
DKY C1 C2 single 1.524 0.020
DKY O5 C1 single 1.426 0.020
DKY C1 N1 single 1.465 0.020
DKY H1 C1 single 1.099 0.020
DKY N1 C7 single 1.337 0.020
DKY N1 C10 single 1.410 0.020
DKY C2 C3 single 1.524 0.020
DKY O2 C2 single 1.432 0.020
DKY H2 C2 single 1.099 0.020
DKY C10 N2 single 1.350 0.020
DKY N2 C9 double 1.350 0.020
DKY HO2 O2 single 0.967 0.020
DKY F3 C3 single 1.370 0.020
DKY C3 C4 single 1.524 0.020
DKY H3 C3 single 1.099 0.020
DKY C9 N3 single 1.350 0.020
DKY N3 C11 single 1.330 0.020
DKY HN3 N3 single 1.010 0.020
DKY O4 C4 single 1.432 0.020
DKY C4 C5 single 1.524 0.020
DKY H4 C4 single 1.099 0.020
DKY HO4 O4 single 0.967 0.020
DKY C6 C5 single 1.524 0.020
DKY C5 O5 single 1.426 0.020
DKY H5 C5 single 1.099 0.020
DKY O6 C6 single 1.432 0.020
DKY H6 C6 single 1.092 0.020
DKY H6A C6 single 1.092 0.020
DKY HO6 O6 single 0.967 0.020
DKY C7 C8 double 1.390 0.020
DKY H7 C7 single 1.083 0.020
DKY C8 C9 single 1.390 0.020
DKY H8 C8 single 1.083 0.020
DKY O10 C10 double 1.250 0.020
DKY C11 O11 double 1.220 0.020
DKY C12 C11 single 1.500 0.020
DKY C12 C13 double 1.390 0.020
DKY C17 C12 single 1.390 0.020
DKY C13 C14 single 1.390 0.020
DKY H13 C13 single 1.083 0.020
DKY C14 C15 double 1.390 0.020
DKY H14 C14 single 1.083 0.020
DKY C15 C16 single 1.390 0.020
DKY H15 C15 single 1.083 0.020
DKY C16 C17 double 1.390 0.020
DKY H16 C16 single 1.083 0.020
DKY H17 C17 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
DKY O11 C11 C12 120.500 3.000
DKY O11 C11 N3 123.000 3.000
DKY C12 C11 N3 120.000 3.000
DKY C11 C12 C17 120.000 3.000
DKY C11 C12 C13 120.000 3.000
DKY C17 C12 C13 120.000 3.000
DKY C12 C17 H17 120.000 3.000
DKY C12 C17 C16 120.000 3.000
DKY H17 C17 C16 120.000 3.000
DKY C17 C16 H16 120.000 3.000
DKY C17 C16 C15 120.000 3.000
DKY H16 C16 C15 120.000 3.000
DKY C16 C15 H15 120.000 3.000
DKY C16 C15 C14 120.000 3.000
DKY H15 C15 C14 120.000 3.000
DKY C15 C14 H14 120.000 3.000
DKY C15 C14 C13 120.000 3.000
DKY H14 C14 C13 120.000 3.000
DKY C14 C13 H13 120.000 3.000
DKY C14 C13 C12 120.000 3.000
DKY H13 C13 C12 120.000 3.000
DKY C11 N3 HN3 120.000 3.000
DKY C11 N3 C9 120.000 3.000
DKY HN3 N3 C9 120.000 3.000
DKY N3 C9 C8 120.000 3.000
DKY N3 C9 N2 120.000 3.000
DKY C8 C9 N2 120.000 3.000
DKY C9 C8 H8 120.000 3.000
DKY C9 C8 C7 120.000 3.000
DKY H8 C8 C7 120.000 3.000
DKY C8 C7 H7 120.000 3.000
DKY C8 C7 N1 120.000 3.000
DKY H7 C7 N1 120.000 3.000
DKY C9 N2 C10 120.000 3.000
DKY N2 C10 O10 120.000 3.000
DKY N2 C10 N1 120.000 3.000
DKY O10 C10 N1 120.000 3.000
DKY C10 N1 C1 120.000 3.000
DKY C10 N1 C7 120.000 3.000
DKY C1 N1 C7 120.000 3.000
DKY N1 C1 H1 109.470 3.000
DKY N1 C1 O5 109.470 3.000
DKY N1 C1 C2 109.470 3.000
DKY H1 C1 O5 109.470 3.000
DKY H1 C1 C2 108.340 3.000
DKY O5 C1 C2 109.470 3.000
DKY C1 O5 C5 111.800 3.000
DKY O5 C5 H5 109.470 3.000
DKY O5 C5 C6 109.470 3.000
DKY O5 C5 C4 109.470 3.000
DKY H5 C5 C6 108.340 3.000
DKY H5 C5 C4 108.340 3.000
DKY C6 C5 C4 111.000 3.000
DKY C5 C6 H6 109.470 3.000
DKY C5 C6 H6A 109.470 3.000
DKY C5 C6 O6 109.470 3.000
DKY H6 C6 H6A 107.900 3.000
DKY H6 C6 O6 109.470 3.000
DKY H6A C6 O6 109.470 3.000
DKY C6 O6 HO6 109.470 3.000
DKY C5 C4 H4 108.340 3.000
DKY C5 C4 O4 109.470 3.000
DKY C5 C4 C3 111.000 3.000
DKY H4 C4 O4 109.470 3.000
DKY H4 C4 C3 108.340 3.000
DKY O4 C4 C3 109.470 3.000
DKY C4 O4 HO4 109.470 3.000
DKY C4 C3 H3 108.340 3.000
DKY C4 C3 F3 109.500 3.000
DKY C4 C3 C2 111.000 3.000
DKY H3 C3 F3 109.500 3.000
DKY H3 C3 C2 108.340 3.000
DKY F3 C3 C2 109.500 3.000
DKY C3 C2 H2 108.340 3.000
DKY C3 C2 O2 109.470 3.000
DKY C3 C2 C1 111.000 3.000
DKY H2 C2 O2 109.470 3.000
DKY H2 C2 C1 108.340 3.000
DKY O2 C2 C1 109.470 3.000
DKY C2 O2 HO2 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
DKY var_1 O11 C11 C12 C17 179.771 20.000 1
DKY CONST_1 C11 C12 C13 C14 180.000 0.000 0
DKY CONST_2 C11 C12 C17 C16 180.000 0.000 0
DKY CONST_3 C12 C17 C16 C15 0.000 0.000 0
DKY CONST_4 C17 C16 C15 C14 0.000 0.000 0
DKY CONST_5 C16 C15 C14 C13 0.000 0.000 0
DKY CONST_6 C15 C14 C13 C12 0.000 0.000 0
DKY CONST_7 O11 C11 N3 C9 0.000 0.000 0
DKY var_2 C11 N3 C9 N2 -0.028 20.000 1
DKY CONST_8 N3 C9 C8 C7 180.000 0.000 0
DKY CONST_9 C9 C8 C7 N1 0.000 0.000 0
DKY CONST_10 N3 C9 N2 C10 180.000 0.000 0
DKY CONST_11 C9 N2 C10 N1 0.000 0.000 0
DKY CONST_12 N2 C10 N1 C1 180.000 0.000 0
DKY CONST_13 C10 N1 C7 C8 0.000 0.000 0
DKY var_3 C10 N1 C1 O5 54.937 20.000 1
DKY var_4 N1 C1 C2 C3 180.000 20.000 3
DKY var_5 N1 C1 O5 C5 180.000 20.000 1
DKY var_6 C1 O5 C5 C4 60.000 20.000 1
DKY var_7 O5 C5 C6 O6 65.051 20.000 3
DKY var_8 C5 C6 O6 HO6 -179.975 20.000 1
DKY var_9 O5 C5 C4 C3 -60.000 20.000 3
DKY var_10 C5 C4 O4 HO4 179.739 20.000 1
DKY var_11 C5 C4 C3 C2 60.000 20.000 3
DKY var_12 C4 C3 C2 O2 180.000 20.000 3
DKY var_13 C3 C2 O2 HO2 -60.326 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
DKY chir_01 C1 N1 C2 O5 negativ
DKY chir_02 C2 C1 O2 C3 positiv
DKY chir_03 C3 C2 F3 C4 negativ
DKY chir_04 C4 C3 O4 C5 positiv
DKY chir_05 C5 C4 O5 C6 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
DKY plan-1 N1 0.020
DKY plan-1 C1 0.020
DKY plan-1 C7 0.020
DKY plan-1 C10 0.020
DKY plan-1 N2 0.020
DKY plan-1 C8 0.020
DKY plan-1 C9 0.020
DKY plan-1 H7 0.020
DKY plan-1 H8 0.020
DKY plan-1 N3 0.020
DKY plan-1 O10 0.020
DKY plan-1 HN3 0.020
DKY plan-2 N3 0.020
DKY plan-2 C9 0.020
DKY plan-2 C11 0.020
DKY plan-2 HN3 0.020
DKY plan-3 C11 0.020
DKY plan-3 N3 0.020
DKY plan-3 O11 0.020
DKY plan-3 C12 0.020
DKY plan-3 HN3 0.020
DKY plan-4 C12 0.020
DKY plan-4 C11 0.020
DKY plan-4 C13 0.020
DKY plan-4 C17 0.020
DKY plan-4 C14 0.020
DKY plan-4 C15 0.020
DKY plan-4 C16 0.020
DKY plan-4 H13 0.020
DKY plan-4 H14 0.020
DKY plan-4 H15 0.020
DKY plan-4 H16 0.020
DKY plan-4 H17 0.020
# ------------------------------------------------------
|
