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
|
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
CJO CJO '"[(2R,4R)-2-[(1R,2R)-1-amino-2-hydro' non-polymer 43 23 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_CJO
#
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
CJO O3 O OC -0.500 0.000 0.000 0.000
CJO C3 C C 0.000 0.308 0.676 -1.006
CJO OXT O OC -0.500 1.511 0.890 -1.273
CJO CA3 C CH2 0.000 -0.772 1.232 -1.899
CJO HA3 H H 0.000 -0.649 0.835 -2.909
CJO HA3A H H 0.000 -0.696 2.321 -1.927
CJO N3 N N 0.000 -2.084 0.845 -1.377
CJO C1 C CH1 0.000 -2.875 1.621 -0.413
CJO HC1 H H 0.000 -2.226 2.002 0.388
CJO CA1 C CH1 0.000 -3.574 2.783 -1.121
CJO HA1 H H 0.000 -2.825 3.407 -1.628
CJO CB1 C CH1 0.000 -4.328 3.628 -0.091
CJO HB1 H H 0.000 -3.609 4.096 0.596
CJO OG1 O OH1 0.000 -5.220 2.792 0.649
CJO HOG1 H H 0.000 -5.852 2.381 0.043
CJO CG1 C CH3 0.000 -5.128 4.715 -0.811
CJO HG1B H H 0.000 -5.651 5.300 -0.100
CJO HG1A H H 0.000 -4.468 5.336 -1.360
CJO HG1 H H 0.000 -5.821 4.264 -1.474
CJO N1 N NH2 0.000 -4.523 2.255 -2.110
CJO HN1A H H 0.000 -4.420 2.487 -3.091
CJO HN1 H H 0.000 -5.286 1.656 -1.818
CJO C2 C C 0.000 -2.752 -0.278 -1.708
CJO O2 O O 0.000 -2.371 -1.126 -2.487
CJO CA2 C CH1 0.000 -4.059 -0.304 -0.944
CJO HA2 H H 0.000 -4.891 -0.007 -1.598
CJO N2 N NH1 0.000 -3.878 0.686 0.145
CJO HN2 H H 0.000 -4.330 0.716 1.048
CJO CB2 C CH2 0.000 -4.308 -1.696 -0.362
CJO HB2 H H 0.000 -3.526 -1.932 0.363
CJO HB2A H H 0.000 -4.291 -2.435 -1.166
CJO CG2 C CR6 0.000 -5.651 -1.723 0.320
CJO CD2 C CR16 0.000 -5.751 -1.402 1.661
CJO HD2 H H 0.000 -4.864 -1.132 2.221
CJO CE2 C CR16 0.000 -6.982 -1.426 2.288
CJO HE2 H H 0.000 -7.060 -1.176 3.339
CJO CZ C CR6 0.000 -8.119 -1.772 1.571
CJO OH O OH1 0.000 -9.330 -1.796 2.186
CJO HOH H H 0.000 -9.745 -0.925 2.114
CJO CE1 C CR16 0.000 -8.014 -2.098 0.227
CJO HE1 H H 0.000 -8.899 -2.372 -0.334
CJO CD1 C CR16 0.000 -6.781 -2.073 -0.396
CJO HD1 H H 0.000 -6.699 -2.327 -1.445
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
CJO O3 n/a C3 START
CJO C3 O3 CA3 .
CJO OXT C3 . .
CJO CA3 C3 N3 .
CJO HA3 CA3 . .
CJO HA3A CA3 . .
CJO N3 CA3 C2 .
CJO C1 N3 CA1 .
CJO HC1 C1 . .
CJO CA1 C1 N1 .
CJO HA1 CA1 . .
CJO CB1 CA1 CG1 .
CJO HB1 CB1 . .
CJO OG1 CB1 HOG1 .
CJO HOG1 OG1 . .
CJO CG1 CB1 HG1 .
CJO HG1B CG1 . .
CJO HG1A CG1 . .
CJO HG1 CG1 . .
CJO N1 CA1 HN1 .
CJO HN1A N1 . .
CJO HN1 N1 . .
CJO C2 N3 CA2 .
CJO O2 C2 . .
CJO CA2 C2 CB2 .
CJO HA2 CA2 . .
CJO N2 CA2 HN2 .
CJO HN2 N2 . .
CJO CB2 CA2 CG2 .
CJO HB2 CB2 . .
CJO HB2A CB2 . .
CJO CG2 CB2 CD2 .
CJO CD2 CG2 CE2 .
CJO HD2 CD2 . .
CJO CE2 CD2 CZ .
CJO HE2 CE2 . .
CJO CZ CE2 CE1 .
CJO OH CZ HOH .
CJO HOH OH . .
CJO CE1 CZ CD1 .
CJO HE1 CE1 . .
CJO CD1 CE1 HD1 .
CJO HD1 CD1 . END
CJO C1 N2 . ADD
CJO CG2 CD1 . 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
CJO N1 CA1 single 1.450 0.020
CJO HN1 N1 single 1.010 0.020
CJO HN1A N1 single 1.010 0.020
CJO CA1 C1 single 1.524 0.020
CJO CB1 CA1 single 1.524 0.020
CJO HA1 CA1 single 1.099 0.020
CJO OG1 CB1 single 1.432 0.020
CJO CG1 CB1 single 1.524 0.020
CJO HB1 CB1 single 1.099 0.020
CJO HG1 CG1 single 1.059 0.020
CJO HG1A CG1 single 1.059 0.020
CJO HG1B CG1 single 1.059 0.020
CJO HOG1 OG1 single 0.967 0.020
CJO C1 N3 single 1.455 0.020
CJO C1 N2 single 1.450 0.020
CJO N2 CA2 single 1.450 0.020
CJO C2 N3 single 1.330 0.020
CJO N3 CA3 single 1.455 0.020
CJO O2 C2 double 1.220 0.020
CJO CA2 C2 single 1.500 0.020
CJO CB2 CA2 single 1.524 0.020
CJO HA2 CA2 single 1.099 0.020
CJO CA3 C3 single 1.510 0.020
CJO HA3 CA3 single 1.092 0.020
CJO HA3A CA3 single 1.092 0.020
CJO C3 O3 deloc 1.250 0.020
CJO OXT C3 deloc 1.250 0.020
CJO CG2 CB2 single 1.511 0.020
CJO HB2 CB2 single 1.092 0.020
CJO HB2A CB2 single 1.092 0.020
CJO CD2 CG2 double 1.390 0.020
CJO CG2 CD1 single 1.390 0.020
CJO CD1 CE1 double 1.390 0.020
CJO HD1 CD1 single 1.083 0.020
CJO CE2 CD2 single 1.390 0.020
CJO HD2 CD2 single 1.083 0.020
CJO CE1 CZ single 1.390 0.020
CJO HE1 CE1 single 1.083 0.020
CJO CZ CE2 double 1.390 0.020
CJO HE2 CE2 single 1.083 0.020
CJO OH CZ single 1.362 0.020
CJO HOH OH single 0.967 0.020
CJO HC1 C1 single 1.099 0.020
CJO HN2 N2 single 1.010 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
CJO O3 C3 OXT 123.000 3.000
CJO O3 C3 CA3 118.500 3.000
CJO OXT C3 CA3 118.500 3.000
CJO C3 CA3 HA3 109.470 3.000
CJO C3 CA3 HA3A 109.470 3.000
CJO C3 CA3 N3 109.500 3.000
CJO HA3 CA3 HA3A 107.900 3.000
CJO HA3 CA3 N3 109.470 3.000
CJO HA3A CA3 N3 109.470 3.000
CJO CA3 N3 C1 112.000 3.000
CJO CA3 N3 C2 127.000 3.000
CJO C1 N3 C2 121.000 3.000
CJO N3 C1 HC1 109.470 3.000
CJO N3 C1 CA1 105.000 3.000
CJO N3 C1 N2 109.500 3.000
CJO HC1 C1 CA1 108.340 3.000
CJO HC1 C1 N2 108.550 3.000
CJO CA1 C1 N2 110.000 3.000
CJO C1 CA1 HA1 108.340 3.000
CJO C1 CA1 CB1 111.000 3.000
CJO C1 CA1 N1 109.470 3.000
CJO HA1 CA1 CB1 108.340 3.000
CJO HA1 CA1 N1 109.470 3.000
CJO CB1 CA1 N1 109.470 3.000
CJO CA1 CB1 HB1 108.340 3.000
CJO CA1 CB1 OG1 109.470 3.000
CJO CA1 CB1 CG1 111.000 3.000
CJO HB1 CB1 OG1 109.470 3.000
CJO HB1 CB1 CG1 108.340 3.000
CJO OG1 CB1 CG1 109.470 3.000
CJO CB1 OG1 HOG1 109.470 3.000
CJO CB1 CG1 HG1B 109.470 3.000
CJO CB1 CG1 HG1A 109.470 3.000
CJO CB1 CG1 HG1 109.470 3.000
CJO HG1B CG1 HG1A 109.470 3.000
CJO HG1B CG1 HG1 109.470 3.000
CJO HG1A CG1 HG1 109.470 3.000
CJO CA1 N1 HN1A 120.000 3.000
CJO CA1 N1 HN1 120.000 3.000
CJO HN1A N1 HN1 120.000 3.000
CJO N3 C2 O2 123.000 3.000
CJO N3 C2 CA2 116.500 3.000
CJO O2 C2 CA2 120.500 3.000
CJO C2 CA2 HA2 108.810 3.000
CJO C2 CA2 N2 111.600 3.000
CJO C2 CA2 CB2 109.470 3.000
CJO HA2 CA2 N2 108.550 3.000
CJO HA2 CA2 CB2 108.340 3.000
CJO N2 CA2 CB2 110.000 3.000
CJO CA2 N2 HN2 118.500 3.000
CJO CA2 N2 C1 120.000 3.000
CJO HN2 N2 C1 118.500 3.000
CJO CA2 CB2 HB2 109.470 3.000
CJO CA2 CB2 HB2A 109.470 3.000
CJO CA2 CB2 CG2 109.470 3.000
CJO HB2 CB2 HB2A 107.900 3.000
CJO HB2 CB2 CG2 109.470 3.000
CJO HB2A CB2 CG2 109.470 3.000
CJO CB2 CG2 CD2 120.000 3.000
CJO CB2 CG2 CD1 120.000 3.000
CJO CD2 CG2 CD1 120.000 3.000
CJO CG2 CD2 HD2 120.000 3.000
CJO CG2 CD2 CE2 120.000 3.000
CJO HD2 CD2 CE2 120.000 3.000
CJO CD2 CE2 HE2 120.000 3.000
CJO CD2 CE2 CZ 120.000 3.000
CJO HE2 CE2 CZ 120.000 3.000
CJO CE2 CZ OH 120.000 3.000
CJO CE2 CZ CE1 120.000 3.000
CJO OH CZ CE1 120.000 3.000
CJO CZ OH HOH 109.470 3.000
CJO CZ CE1 HE1 120.000 3.000
CJO CZ CE1 CD1 120.000 3.000
CJO HE1 CE1 CD1 120.000 3.000
CJO CE1 CD1 HD1 120.000 3.000
CJO CE1 CD1 CG2 120.000 3.000
CJO HD1 CD1 CG2 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
CJO var_1 O3 C3 CA3 N3 0.056 20.000 3
CJO var_2 C3 CA3 N3 C2 -90.091 20.000 1
CJO var_3 CA3 N3 C1 CA1 90.000 20.000 3
CJO var_4 N3 C1 N2 CA2 -30.000 20.000 3
CJO var_5 N3 C1 CA1 N1 63.171 20.000 3
CJO var_6 C1 CA1 CB1 CG1 -174.972 20.000 3
CJO var_7 CA1 CB1 OG1 HOG1 -59.959 20.000 1
CJO var_8 CA1 CB1 CG1 HG1 59.949 20.000 3
CJO var_9 C1 CA1 N1 HN1 59.995 20.000 1
CJO CONST_1 CA3 N3 C2 CA2 180.000 0.000 0
CJO var_10 N3 C2 CA2 CB2 -150.000 20.000 3
CJO var_11 C2 CA2 N2 C1 30.000 20.000 3
CJO var_12 C2 CA2 CB2 CG2 -176.497 20.000 3
CJO var_13 CA2 CB2 CG2 CD2 -90.249 20.000 2
CJO CONST_2 CB2 CG2 CD1 CE1 180.000 0.000 0
CJO CONST_3 CB2 CG2 CD2 CE2 180.000 0.000 0
CJO CONST_4 CG2 CD2 CE2 CZ 0.000 0.000 0
CJO CONST_5 CD2 CE2 CZ CE1 0.000 0.000 0
CJO var_14 CE2 CZ OH HOH 89.936 20.000 1
CJO CONST_6 CE2 CZ CE1 CD1 0.000 0.000 0
CJO CONST_7 CZ CE1 CD1 CG2 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
CJO chir_01 CA1 N1 CB1 C1 negativ
CJO chir_02 CB1 CA1 CG1 OG1 negativ
CJO chir_03 C1 CA1 N2 N3 negativ
CJO chir_04 CA2 N2 C2 CB2 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
CJO plan-1 N1 0.020
CJO plan-1 CA1 0.020
CJO plan-1 HN1 0.020
CJO plan-1 HN1A 0.020
CJO plan-2 N2 0.020
CJO plan-2 C1 0.020
CJO plan-2 CA2 0.020
CJO plan-2 HN2 0.020
CJO plan-3 N3 0.020
CJO plan-3 C1 0.020
CJO plan-3 C2 0.020
CJO plan-3 CA3 0.020
CJO plan-4 C2 0.020
CJO plan-4 N3 0.020
CJO plan-4 O2 0.020
CJO plan-4 CA2 0.020
CJO plan-5 C3 0.020
CJO plan-5 CA3 0.020
CJO plan-5 OXT 0.020
CJO plan-5 O3 0.020
CJO plan-6 CG2 0.020
CJO plan-6 CB2 0.020
CJO plan-6 CD1 0.020
CJO plan-6 CD2 0.020
CJO plan-6 CE1 0.020
CJO plan-6 CE2 0.020
CJO plan-6 CZ 0.020
CJO plan-6 HD1 0.020
CJO plan-6 HD2 0.020
CJO plan-6 HE1 0.020
CJO plan-6 HE2 0.020
CJO plan-6 OH 0.020
# ------------------------------------------------------
|
