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
|
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
MMM MMM '"(S,E)-3-HYDROXY-2-((3-HYDROXY-2-MET' non-polymer 37 23 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_MMM
#
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
MMM OXT O OC -0.500 0.000 0.000 0.000
MMM CA C C 0.000 -1.109 -0.313 0.487
MMM OA O OC -0.500 -1.211 -1.327 1.212
MMM CAA C CT 0.000 -2.323 0.533 0.200
MMM CAB C CH3 0.000 -2.125 1.280 -1.120
MMM HAB3 H H 0.000 -1.270 1.902 -1.049
MMM HAB2 H H 0.000 -1.988 0.582 -1.905
MMM HAB1 H H 0.000 -2.978 1.875 -1.322
MMM CBA C CH2 0.000 -2.521 1.543 1.333
MMM HBA1 H H 0.000 -3.400 2.156 1.124
MMM HBA2 H H 0.000 -1.640 2.185 1.406
MMM OGA O OH1 0.000 -2.707 0.845 2.566
MMM HGA H H 0.000 -2.831 1.483 3.281
MMM NA N N 0.000 -3.505 -0.327 0.101
MMM C4A C C1 0.000 -4.664 0.192 -0.142
MMM H4A H H 0.000 -4.761 1.257 -0.271
MMM C4 C CR6 0.000 -5.855 -0.675 -0.242
MMM C3 C CR6 0.000 -5.753 -2.065 -0.076
MMM O3 O OH1 0.000 -4.551 -2.643 0.180
MMM HO3 H H 0.000 -4.122 -2.876 -0.654
MMM C2 C CR6 0.000 -6.900 -2.839 -0.180
MMM C2A C CH3 0.000 -6.810 -4.332 -0.005
MMM H2A3 H H 0.000 -6.016 -4.563 0.657
MMM H2A2 H H 0.000 -7.720 -4.696 0.394
MMM H2A1 H H 0.000 -6.629 -4.787 -0.944
MMM C5 C CR6 0.000 -7.119 -0.134 -0.504
MMM C6 C CR16 0.000 -8.206 -0.980 -0.590
MMM H6 H H 0.000 -9.187 -0.569 -0.794
MMM N1 N NRD6 0.000 -8.068 -2.282 -0.428
MMM C5A C CH2 0.000 -7.292 1.351 -0.690
MMM H5A1 H H 0.000 -6.686 1.685 -1.535
MMM H5A2 H H 0.000 -6.970 1.871 0.215
MMM OP4 O O2 0.000 -8.667 1.644 -0.945
MMM P P P 0.000 -9.215 3.137 -1.192
MMM OP1 O OP -0.666 -8.816 4.020 -0.031
MMM OP2 O OP -0.666 -8.623 3.685 -2.472
MMM OP3 O OP -0.666 -10.724 3.108 -1.307
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
MMM OXT n/a CA START
MMM CA OXT CAA .
MMM OA CA . .
MMM CAA CA NA .
MMM CAB CAA HAB1 .
MMM HAB3 CAB . .
MMM HAB2 CAB . .
MMM HAB1 CAB . .
MMM CBA CAA OGA .
MMM HBA1 CBA . .
MMM HBA2 CBA . .
MMM OGA CBA HGA .
MMM HGA OGA . .
MMM NA CAA C4A .
MMM C4A NA C4 .
MMM H4A C4A . .
MMM C4 C4A C5 .
MMM C3 C4 C2 .
MMM O3 C3 HO3 .
MMM HO3 O3 . .
MMM C2 C3 C2A .
MMM C2A C2 H2A1 .
MMM H2A3 C2A . .
MMM H2A2 C2A . .
MMM H2A1 C2A . .
MMM C5 C4 C5A .
MMM C6 C5 N1 .
MMM H6 C6 . .
MMM N1 C6 . .
MMM C5A C5 OP4 .
MMM H5A1 C5A . .
MMM H5A2 C5A . .
MMM OP4 C5A P .
MMM P OP4 OP3 .
MMM OP1 P . .
MMM OP2 P . .
MMM OP3 P . END
MMM N1 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
MMM N1 C2 double 1.350 0.020
MMM N1 C6 single 1.337 0.020
MMM C2A C2 single 1.506 0.020
MMM C2 C3 single 1.487 0.020
MMM H2A1 C2A single 1.059 0.020
MMM H2A2 C2A single 1.059 0.020
MMM H2A3 C2A single 1.059 0.020
MMM C3 C4 double 1.487 0.020
MMM O3 C3 single 1.362 0.020
MMM HO3 O3 single 0.967 0.020
MMM C5 C4 single 1.487 0.020
MMM C4 C4A single 1.480 0.020
MMM C4A NA double 1.260 0.020
MMM H4A C4A single 1.077 0.020
MMM C6 C5 double 1.390 0.020
MMM C5A C5 single 1.511 0.020
MMM H6 C6 single 1.083 0.020
MMM OP4 C5A single 1.426 0.020
MMM H5A1 C5A single 1.092 0.020
MMM H5A2 C5A single 1.092 0.020
MMM P OP4 single 1.610 0.020
MMM OP1 P deloc 1.510 0.020
MMM OP2 P deloc 1.510 0.020
MMM OP3 P deloc 1.510 0.020
MMM NA CAA single 1.455 0.020
MMM CAB CAA single 1.524 0.020
MMM CBA CAA single 1.524 0.020
MMM CAA CA single 1.507 0.020
MMM OGA CBA single 1.432 0.020
MMM HBA1 CBA single 1.092 0.020
MMM HBA2 CBA single 1.092 0.020
MMM HGA OGA single 0.967 0.020
MMM HAB1 CAB single 1.059 0.020
MMM HAB2 CAB single 1.059 0.020
MMM HAB3 CAB single 1.059 0.020
MMM OA CA deloc 1.250 0.020
MMM CA OXT 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
MMM OXT CA OA 123.000 3.000
MMM OXT CA CAA 118.500 3.000
MMM OA CA CAA 118.500 3.000
MMM CA CAA CAB 109.470 3.000
MMM CA CAA CBA 109.470 3.000
MMM CA CAA NA 111.600 3.000
MMM CAB CAA CBA 111.000 3.000
MMM CAB CAA NA 111.600 3.000
MMM CBA CAA NA 111.600 3.000
MMM CAA CAB HAB3 109.470 3.000
MMM CAA CAB HAB2 109.470 3.000
MMM CAA CAB HAB1 109.470 3.000
MMM HAB3 CAB HAB2 109.470 3.000
MMM HAB3 CAB HAB1 109.470 3.000
MMM HAB2 CAB HAB1 109.470 3.000
MMM CAA CBA HBA1 109.470 3.000
MMM CAA CBA HBA2 109.470 3.000
MMM CAA CBA OGA 109.470 3.000
MMM HBA1 CBA HBA2 107.900 3.000
MMM HBA1 CBA OGA 109.470 3.000
MMM HBA2 CBA OGA 109.470 3.000
MMM CBA OGA HGA 109.470 3.000
MMM CAA NA C4A 121.000 3.000
MMM NA C4A H4A 120.000 3.000
MMM NA C4A C4 120.000 3.000
MMM H4A C4A C4 120.000 3.000
MMM C4A C4 C3 120.000 3.000
MMM C4A C4 C5 120.000 3.000
MMM C3 C4 C5 120.000 3.000
MMM C4 C3 O3 120.000 3.000
MMM C4 C3 C2 120.000 3.000
MMM O3 C3 C2 120.000 3.000
MMM C3 O3 HO3 109.470 3.000
MMM C3 C2 C2A 120.000 3.000
MMM C3 C2 N1 120.000 3.000
MMM C2A C2 N1 120.000 3.000
MMM C2 C2A H2A3 109.470 3.000
MMM C2 C2A H2A2 109.470 3.000
MMM C2 C2A H2A1 109.470 3.000
MMM H2A3 C2A H2A2 109.470 3.000
MMM H2A3 C2A H2A1 109.470 3.000
MMM H2A2 C2A H2A1 109.470 3.000
MMM C4 C5 C6 120.000 3.000
MMM C4 C5 C5A 120.000 3.000
MMM C6 C5 C5A 120.000 3.000
MMM C5 C6 H6 120.000 3.000
MMM C5 C6 N1 120.000 3.000
MMM H6 C6 N1 120.000 3.000
MMM C6 N1 C2 120.000 3.000
MMM C5 C5A H5A1 109.470 3.000
MMM C5 C5A H5A2 109.470 3.000
MMM C5 C5A OP4 109.470 3.000
MMM H5A1 C5A H5A2 107.900 3.000
MMM H5A1 C5A OP4 109.470 3.000
MMM H5A2 C5A OP4 109.470 3.000
MMM C5A OP4 P 120.500 3.000
MMM OP4 P OP1 108.200 3.000
MMM OP4 P OP2 108.200 3.000
MMM OP4 P OP3 108.200 3.000
MMM OP1 P OP2 119.900 3.000
MMM OP1 P OP3 119.900 3.000
MMM OP2 P OP3 119.900 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
MMM var_1 OXT CA CAA NA 145.046 20.000 1
MMM var_2 CA CAA CAB HAB1 -179.995 20.000 1
MMM var_3 CA CAA CBA OGA -60.012 20.000 1
MMM var_4 CAA CBA OGA HGA 179.964 20.000 1
MMM var_5 CA CAA NA C4A -179.980 20.000 1
MMM CONST_1 CAA NA C4A C4 179.976 0.000 0
MMM var_6 NA C4A C4 C5 179.989 20.000 1
MMM CONST_2 C4A C4 C3 C2 180.000 0.000 0
MMM var_7 C4 C3 O3 HO3 -89.993 20.000 1
MMM CONST_3 C4 C3 C2 C2A 180.000 0.000 0
MMM var_8 C3 C2 C2A H2A1 -89.983 20.000 1
MMM CONST_4 C4A C4 C5 C5A 0.000 0.000 0
MMM CONST_5 C4 C5 C6 N1 0.000 0.000 0
MMM CONST_6 C5 C6 N1 C2 0.000 0.000 0
MMM CONST_7 C6 N1 C2 C3 0.000 0.000 0
MMM var_9 C4 C5 C5A OP4 179.954 20.000 2
MMM var_10 C5 C5A OP4 P 179.989 20.000 1
MMM var_11 C5A OP4 P OP3 -174.965 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
MMM chir_01 CAA NA CBA CAB 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
MMM plan-1 N1 0.020
MMM plan-1 C2 0.020
MMM plan-1 C6 0.020
MMM plan-1 C3 0.020
MMM plan-1 C4 0.020
MMM plan-1 C5 0.020
MMM plan-1 C2A 0.020
MMM plan-1 O3 0.020
MMM plan-1 C4A 0.020
MMM plan-1 C5A 0.020
MMM plan-1 H6 0.020
MMM plan-1 H4A 0.020
MMM plan-2 C4A 0.020
MMM plan-2 C4 0.020
MMM plan-2 NA 0.020
MMM plan-2 H4A 0.020
MMM plan-2 CAA 0.020
MMM plan-3 CA 0.020
MMM plan-3 CAA 0.020
MMM plan-3 OA 0.020
MMM plan-3 OXT 0.020
# ------------------------------------------------------
|
