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
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
|
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
MU2 MU2 'N-ACETYLMURAMYL-L-ALANYL-D-ISOGLUTAM' non-polymer 65 34 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_MU2
#
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
MU2 O23 O OC -0.500 0.000 0.000 0.000
MU2 C28 C C 0.000 0.540 0.798 0.798
MU2 O22 O OC -0.500 1.535 0.437 1.466
MU2 C24 C CH1 0.000 -0.006 2.193 0.955
MU2 H24 H H 0.000 -0.315 2.351 1.998
MU2 C25 C CH2 0.000 1.075 3.210 0.585
MU2 H251 H H 0.000 1.319 3.111 -0.474
MU2 H252 H H 0.000 1.970 3.021 1.183
MU2 C26 C CH2 0.000 0.562 4.624 0.864
MU2 H261 H H 0.000 0.318 4.720 1.924
MU2 H262 H H 0.000 -0.333 4.810 0.267
MU2 C27 C C 0.000 1.628 5.626 0.499
MU2 O21 O O 0.000 2.692 5.246 0.061
MU2 N20 N NH2 0.000 1.398 6.944 0.661
MU2 HB2 H H 0.000 2.111 7.621 0.418
MU2 HA1 H H 0.000 0.510 7.266 1.028
MU2 N5 N NH1 0.000 -1.162 2.367 0.072
MU2 HE H H 0.000 -1.041 2.778 -0.843
MU2 C22 C C 0.000 -2.387 1.980 0.480
MU2 O19 O O 0.000 -2.533 1.488 1.580
MU2 C21 C CH1 0.000 -3.576 2.159 -0.428
MU2 H21 H H 0.000 -3.416 1.594 -1.357
MU2 C23 C CH3 0.000 -3.749 3.643 -0.757
MU2 H233 H H 0.000 -4.584 3.770 -1.397
MU2 H232 H H 0.000 -3.905 4.188 0.138
MU2 H231 H H 0.000 -2.877 4.002 -1.241
MU2 N4 N NH1 0.000 -4.781 1.664 0.241
MU2 HD H H 0.000 -4.823 1.635 1.250
MU2 C19 C C 0.000 -5.835 1.247 -0.488
MU2 O18 O O 0.000 -5.786 1.282 -1.700
MU2 C18 C CH1 0.000 -7.075 0.738 0.200
MU2 H18 H H 0.000 -6.804 -0.076 0.887
MU2 C20 C CH3 0.000 -7.723 1.877 0.992
MU2 H203 H H 0.000 -7.071 2.185 1.768
MU2 H202 H H 0.000 -7.912 2.695 0.345
MU2 H201 H H 0.000 -8.636 1.542 1.411
MU2 O3 O O2 0.000 -7.997 0.251 -0.776
MU2 C3 C CH1 0.000 -8.758 -0.782 -0.148
MU2 H3 H H 0.000 -8.653 -0.705 0.944
MU2 C2 C CH1 0.000 -8.252 -2.152 -0.616
MU2 H2 H H 0.000 -8.255 -2.187 -1.715
MU2 N2 N NH1 0.000 -6.890 -2.374 -0.125
MU2 HB H H 0.000 -6.577 -1.915 0.719
MU2 C7 C C 0.000 -6.055 -3.190 -0.798
MU2 C8 C CH3 0.000 -4.654 -3.418 -0.292
MU2 H8C3 H H 0.000 -4.009 -3.613 -1.109
MU2 H8C2 H H 0.000 -4.317 -2.555 0.223
MU2 H8C1 H H 0.000 -4.645 -4.247 0.368
MU2 O7 O O 0.000 -6.430 -3.740 -1.811
MU2 C4 C CH1 0.000 -10.234 -0.643 -0.534
MU2 H4 H H 0.000 -10.326 -0.611 -1.629
MU2 O4 O OH1 0.000 -10.762 0.562 0.025
MU2 HC H H 0.000 -11.694 0.649 -0.219
MU2 C5 C CH1 0.000 -11.008 -1.845 0.010
MU2 H5 H H 0.000 -10.895 -1.888 1.103
MU2 C6 C CH2 0.000 -12.490 -1.699 -0.343
MU2 H6C1 H H 0.000 -12.611 -1.742 -1.427
MU2 H6C2 H H 0.000 -12.858 -0.739 0.025
MU2 O6 O OH1 0.000 -13.231 -2.759 0.264
MU2 H6 H H 0.000 -14.167 -2.666 0.040
MU2 O5 O O2 0.000 -10.501 -3.047 -0.566
MU2 C1 C CH1 0.000 -9.178 -3.240 -0.069
MU2 H1 H H 0.000 -8.810 -4.226 -0.384
MU2 O1 O OH1 0.000 -9.193 -3.171 1.358
MU2 HA H H 0.000 -9.773 -3.861 1.708
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
MU2 O23 n/a C28 START
MU2 C28 O23 C24 .
MU2 O22 C28 . .
MU2 C24 C28 N5 .
MU2 H24 C24 . .
MU2 C25 C24 C26 .
MU2 H251 C25 . .
MU2 H252 C25 . .
MU2 C26 C25 C27 .
MU2 H261 C26 . .
MU2 H262 C26 . .
MU2 C27 C26 N20 .
MU2 O21 C27 . .
MU2 N20 C27 HA1 .
MU2 HB2 N20 . .
MU2 HA1 N20 . .
MU2 N5 C24 C22 .
MU2 HE N5 . .
MU2 C22 N5 C21 .
MU2 O19 C22 . .
MU2 C21 C22 N4 .
MU2 H21 C21 . .
MU2 C23 C21 H231 .
MU2 H233 C23 . .
MU2 H232 C23 . .
MU2 H231 C23 . .
MU2 N4 C21 C19 .
MU2 HD N4 . .
MU2 C19 N4 C18 .
MU2 O18 C19 . .
MU2 C18 C19 O3 .
MU2 H18 C18 . .
MU2 C20 C18 H201 .
MU2 H203 C20 . .
MU2 H202 C20 . .
MU2 H201 C20 . .
MU2 O3 C18 C3 .
MU2 C3 O3 C4 .
MU2 H3 C3 . .
MU2 C2 C3 N2 .
MU2 H2 C2 . .
MU2 N2 C2 C7 .
MU2 HB N2 . .
MU2 C7 N2 O7 .
MU2 C8 C7 H8C1 .
MU2 H8C3 C8 . .
MU2 H8C2 C8 . .
MU2 H8C1 C8 . .
MU2 O7 C7 . .
MU2 C4 C3 C5 .
MU2 H4 C4 . .
MU2 O4 C4 HC .
MU2 HC O4 . .
MU2 C5 C4 O5 .
MU2 H5 C5 . .
MU2 C6 C5 O6 .
MU2 H6C1 C6 . .
MU2 H6C2 C6 . .
MU2 O6 C6 H6 .
MU2 H6 O6 . .
MU2 O5 C5 C1 .
MU2 C1 O5 O1 .
MU2 H1 C1 . .
MU2 O1 C1 HA .
MU2 HA O1 . END
MU2 C1 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
MU2 O1 C1 single 1.432 0.020
MU2 C1 C2 single 1.524 0.020
MU2 C1 O5 single 1.426 0.020
MU2 H1 C1 single 1.099 0.020
MU2 HA O1 single 0.967 0.020
MU2 N2 C2 single 1.450 0.020
MU2 C2 C3 single 1.524 0.020
MU2 H2 C2 single 1.099 0.020
MU2 C7 N2 single 1.330 0.020
MU2 HB N2 single 1.010 0.020
MU2 O7 C7 double 1.220 0.020
MU2 C8 C7 single 1.500 0.020
MU2 H8C1 C8 single 1.059 0.020
MU2 H8C2 C8 single 1.059 0.020
MU2 H8C3 C8 single 1.059 0.020
MU2 C3 O3 single 1.426 0.020
MU2 C4 C3 single 1.524 0.020
MU2 H3 C3 single 1.099 0.020
MU2 O3 C18 single 1.426 0.020
MU2 O4 C4 single 1.432 0.020
MU2 C5 C4 single 1.524 0.020
MU2 H4 C4 single 1.099 0.020
MU2 HC O4 single 0.967 0.020
MU2 O5 C5 single 1.426 0.020
MU2 C6 C5 single 1.524 0.020
MU2 H5 C5 single 1.099 0.020
MU2 O6 C6 single 1.432 0.020
MU2 H6C1 C6 single 1.092 0.020
MU2 H6C2 C6 single 1.092 0.020
MU2 H6 O6 single 0.967 0.020
MU2 C20 C18 single 1.524 0.020
MU2 C18 C19 single 1.500 0.020
MU2 H18 C18 single 1.099 0.020
MU2 H201 C20 single 1.059 0.020
MU2 H202 C20 single 1.059 0.020
MU2 H203 C20 single 1.059 0.020
MU2 O18 C19 double 1.220 0.020
MU2 C19 N4 single 1.330 0.020
MU2 N4 C21 single 1.450 0.020
MU2 HD N4 single 1.010 0.020
MU2 C23 C21 single 1.524 0.020
MU2 C21 C22 single 1.500 0.020
MU2 H21 C21 single 1.099 0.020
MU2 H231 C23 single 1.059 0.020
MU2 H232 C23 single 1.059 0.020
MU2 H233 C23 single 1.059 0.020
MU2 O19 C22 double 1.220 0.020
MU2 C22 N5 single 1.330 0.020
MU2 N5 C24 single 1.450 0.020
MU2 HE N5 single 1.010 0.020
MU2 C25 C24 single 1.524 0.020
MU2 C24 C28 single 1.500 0.020
MU2 H24 C24 single 1.099 0.020
MU2 C26 C25 single 1.524 0.020
MU2 H251 C25 single 1.092 0.020
MU2 H252 C25 single 1.092 0.020
MU2 C27 C26 single 1.510 0.020
MU2 H261 C26 single 1.092 0.020
MU2 H262 C26 single 1.092 0.020
MU2 N20 C27 single 1.332 0.020
MU2 O21 C27 double 1.220 0.020
MU2 HA1 N20 single 1.010 0.020
MU2 HB2 N20 single 1.010 0.020
MU2 O22 C28 deloc 1.250 0.020
MU2 C28 O23 deloc 1.250 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
MU2 O23 C28 O22 123.000 3.000
MU2 O23 C28 C24 118.500 3.000
MU2 O22 C28 C24 118.500 3.000
MU2 C28 C24 H24 108.810 3.000
MU2 C28 C24 C25 109.470 3.000
MU2 C28 C24 N5 111.600 3.000
MU2 H24 C24 C25 108.340 3.000
MU2 H24 C24 N5 108.550 3.000
MU2 C25 C24 N5 110.000 3.000
MU2 C24 C25 H251 109.470 3.000
MU2 C24 C25 H252 109.470 3.000
MU2 C24 C25 C26 111.000 3.000
MU2 H251 C25 H252 107.900 3.000
MU2 H251 C25 C26 109.470 3.000
MU2 H252 C25 C26 109.470 3.000
MU2 C25 C26 H261 109.470 3.000
MU2 C25 C26 H262 109.470 3.000
MU2 C25 C26 C27 109.470 3.000
MU2 H261 C26 H262 107.900 3.000
MU2 H261 C26 C27 109.470 3.000
MU2 H262 C26 C27 109.470 3.000
MU2 C26 C27 O21 120.500 3.000
MU2 C26 C27 N20 116.500 3.000
MU2 O21 C27 N20 123.000 3.000
MU2 C27 N20 HB2 120.000 3.000
MU2 C27 N20 HA1 120.000 3.000
MU2 HB2 N20 HA1 120.000 3.000
MU2 C24 N5 HE 118.500 3.000
MU2 C24 N5 C22 121.500 3.000
MU2 HE N5 C22 120.000 3.000
MU2 N5 C22 O19 123.000 3.000
MU2 N5 C22 C21 116.500 3.000
MU2 O19 C22 C21 120.500 3.000
MU2 C22 C21 H21 108.810 3.000
MU2 C22 C21 C23 109.470 3.000
MU2 C22 C21 N4 111.600 3.000
MU2 H21 C21 C23 108.340 3.000
MU2 H21 C21 N4 108.550 3.000
MU2 C23 C21 N4 110.000 3.000
MU2 C21 C23 H233 109.470 3.000
MU2 C21 C23 H232 109.470 3.000
MU2 C21 C23 H231 109.470 3.000
MU2 H233 C23 H232 109.470 3.000
MU2 H233 C23 H231 109.470 3.000
MU2 H232 C23 H231 109.470 3.000
MU2 C21 N4 HD 118.500 3.000
MU2 C21 N4 C19 121.500 3.000
MU2 HD N4 C19 120.000 3.000
MU2 N4 C19 O18 123.000 3.000
MU2 N4 C19 C18 116.500 3.000
MU2 O18 C19 C18 120.500 3.000
MU2 C19 C18 H18 108.810 3.000
MU2 C19 C18 C20 109.470 3.000
MU2 C19 C18 O3 109.470 3.000
MU2 H18 C18 C20 108.340 3.000
MU2 H18 C18 O3 109.470 3.000
MU2 C20 C18 O3 109.470 3.000
MU2 C18 C20 H203 109.470 3.000
MU2 C18 C20 H202 109.470 3.000
MU2 C18 C20 H201 109.470 3.000
MU2 H203 C20 H202 109.470 3.000
MU2 H203 C20 H201 109.470 3.000
MU2 H202 C20 H201 109.470 3.000
MU2 C18 O3 C3 111.800 3.000
MU2 O3 C3 H3 109.470 3.000
MU2 O3 C3 C2 109.470 3.000
MU2 O3 C3 C4 109.470 3.000
MU2 H3 C3 C2 108.340 3.000
MU2 H3 C3 C4 108.340 3.000
MU2 C2 C3 C4 111.000 3.000
MU2 C3 C2 H2 108.340 3.000
MU2 C3 C2 N2 110.000 3.000
MU2 C3 C2 C1 111.000 3.000
MU2 H2 C2 N2 108.550 3.000
MU2 H2 C2 C1 108.340 3.000
MU2 N2 C2 C1 110.000 3.000
MU2 C2 N2 HB 118.500 3.000
MU2 C2 N2 C7 121.500 3.000
MU2 HB N2 C7 120.000 3.000
MU2 N2 C7 C8 116.500 3.000
MU2 N2 C7 O7 123.000 3.000
MU2 C8 C7 O7 123.000 3.000
MU2 C7 C8 H8C3 109.470 3.000
MU2 C7 C8 H8C2 109.470 3.000
MU2 C7 C8 H8C1 109.470 3.000
MU2 H8C3 C8 H8C2 109.470 3.000
MU2 H8C3 C8 H8C1 109.470 3.000
MU2 H8C2 C8 H8C1 109.470 3.000
MU2 C3 C4 H4 108.340 3.000
MU2 C3 C4 O4 109.470 3.000
MU2 C3 C4 C5 111.000 3.000
MU2 H4 C4 O4 109.470 3.000
MU2 H4 C4 C5 108.340 3.000
MU2 O4 C4 C5 109.470 3.000
MU2 C4 O4 HC 109.470 3.000
MU2 C4 C5 H5 108.340 3.000
MU2 C4 C5 C6 111.000 3.000
MU2 C4 C5 O5 109.470 3.000
MU2 H5 C5 C6 108.340 3.000
MU2 H5 C5 O5 109.470 3.000
MU2 C6 C5 O5 109.470 3.000
MU2 C5 C6 H6C1 109.470 3.000
MU2 C5 C6 H6C2 109.470 3.000
MU2 C5 C6 O6 109.470 3.000
MU2 H6C1 C6 H6C2 107.900 3.000
MU2 H6C1 C6 O6 109.470 3.000
MU2 H6C2 C6 O6 109.470 3.000
MU2 C6 O6 H6 109.470 3.000
MU2 C5 O5 C1 111.800 3.000
MU2 O5 C1 H1 109.470 3.000
MU2 O5 C1 O1 109.470 3.000
MU2 O5 C1 C2 109.470 3.000
MU2 H1 C1 O1 109.470 3.000
MU2 H1 C1 C2 108.340 3.000
MU2 O1 C1 C2 109.470 3.000
MU2 C1 O1 HA 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
MU2 var_1 O23 C28 C24 N5 0.062 20.000 3
MU2 var_2 C28 C24 C25 C26 -174.974 20.000 3
MU2 var_3 C24 C25 C26 C27 -179.984 20.000 3
MU2 var_4 C25 C26 C27 N20 -179.984 20.000 3
MU2 CONST_1 C26 C27 N20 HA1 0.000 0.000 0
MU2 var_5 C28 C24 N5 C22 84.945 20.000 3
MU2 CONST_2 C24 N5 C22 C21 180.000 0.000 0
MU2 var_6 N5 C22 C21 N4 179.988 20.000 3
MU2 var_7 C22 C21 C23 H231 59.949 20.000 3
MU2 var_8 C22 C21 N4 C19 -155.001 20.000 3
MU2 CONST_3 C21 N4 C19 C18 180.000 0.000 0
MU2 var_9 N4 C19 C18 O3 -175.003 20.000 3
MU2 var_10 C19 C18 C20 H201 175.401 20.000 3
MU2 var_11 C19 C18 O3 C3 150.681 20.000 1
MU2 var_12 C18 O3 C3 C4 137.595 20.000 1
MU2 var_13 O3 C3 C2 N2 60.000 20.000 3
MU2 var_14 C3 C2 N2 C7 -153.370 20.000 3
MU2 CONST_4 C2 N2 C7 O7 0.000 0.000 0
MU2 var_15 N2 C7 C8 H8C1 90.003 20.000 1
MU2 var_16 O3 C3 C4 C5 180.000 20.000 3
MU2 var_17 C3 C4 O4 HC 179.985 20.000 1
MU2 var_18 C3 C4 C5 O5 -60.000 20.000 3
MU2 var_19 C4 C5 C6 O6 -174.967 20.000 3
MU2 var_20 C5 C6 O6 H6 -179.973 20.000 1
MU2 var_21 C4 C5 O5 C1 60.000 20.000 1
MU2 var_22 C5 O5 C1 O1 60.000 20.000 1
MU2 var_23 O5 C1 C2 C3 60.000 20.000 3
MU2 var_24 O5 C1 O1 HA 60.040 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
MU2 chir_01 C1 O1 C2 O5 positiv
MU2 chir_02 C2 C1 N2 C3 positiv
MU2 chir_03 C3 C2 O3 C4 negativ
MU2 chir_04 C4 C3 O4 C5 positiv
MU2 chir_05 C5 C4 O5 C6 positiv
MU2 chir_06 C18 O3 C20 C19 positiv
MU2 chir_07 C21 N4 C23 C22 negativ
MU2 chir_08 C24 N5 C25 C28 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
MU2 plan-1 N2 0.020
MU2 plan-1 C2 0.020
MU2 plan-1 C7 0.020
MU2 plan-1 HB 0.020
MU2 plan-2 C7 0.020
MU2 plan-2 N2 0.020
MU2 plan-2 O7 0.020
MU2 plan-2 C8 0.020
MU2 plan-2 HB 0.020
MU2 plan-3 C19 0.020
MU2 plan-3 C18 0.020
MU2 plan-3 O18 0.020
MU2 plan-3 N4 0.020
MU2 plan-3 HD 0.020
MU2 plan-4 N4 0.020
MU2 plan-4 C19 0.020
MU2 plan-4 C21 0.020
MU2 plan-4 HD 0.020
MU2 plan-5 C22 0.020
MU2 plan-5 C21 0.020
MU2 plan-5 O19 0.020
MU2 plan-5 N5 0.020
MU2 plan-5 HE 0.020
MU2 plan-6 N5 0.020
MU2 plan-6 C22 0.020
MU2 plan-6 C24 0.020
MU2 plan-6 HE 0.020
MU2 plan-7 C27 0.020
MU2 plan-7 C26 0.020
MU2 plan-7 N20 0.020
MU2 plan-7 O21 0.020
MU2 plan-7 HB2 0.020
MU2 plan-7 HA1 0.020
MU2 plan-8 N20 0.020
MU2 plan-8 C27 0.020
MU2 plan-8 HA1 0.020
MU2 plan-8 HB2 0.020
MU2 plan-9 C28 0.020
MU2 plan-9 C24 0.020
MU2 plan-9 O22 0.020
MU2 plan-9 O23 0.020
# ------------------------------------------------------
|
