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
|
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
M2S M2S '3-{[(R)-methylsulfinyl]methyl}-L-val' peptide 26 12 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_M2S
#
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
M2S N N NH2 0.000 0.000 0.000 0.000
M2S HN1 H H 0.000 0.820 -0.090 -0.588
M2S HN2 H H 0.000 -0.248 0.910 0.372
M2S CA C CH1 0.000 -0.822 -1.177 0.311
M2S HA H H 0.000 -0.768 -1.387 1.388
M2S CB C CT 0.000 -2.274 -0.903 -0.083
M2S CG1 C CH3 0.000 -2.350 -0.609 -1.582
M2S HG13 H H 0.000 -3.356 -0.419 -1.856
M2S HG12 H H 0.000 -1.758 0.240 -1.807
M2S HG11 H H 0.000 -1.990 -1.444 -2.126
M2S CG2 C CH3 0.000 -3.130 -2.129 0.240
M2S HG23 H H 0.000 -4.137 -1.941 -0.032
M2S HG22 H H 0.000 -2.770 -2.966 -0.301
M2S HG21 H H 0.000 -3.079 -2.334 1.279
M2S CG C CH2 0.000 -2.796 0.303 0.700
M2S HG2 H H 0.000 -2.184 1.178 0.470
M2S HG3 H H 0.000 -2.741 0.093 1.770
M2S SD S S3 0.000 -4.519 0.629 0.234
M2S OE O O 0.000 -4.578 0.984 -1.141
M2S CE C CH3 0.000 -4.951 2.069 1.249
M2S HE3 H H 0.000 -5.959 2.367 1.068
M2S HE2 H H 0.000 -4.851 1.841 2.286
M2S HE1 H H 0.000 -4.312 2.892 1.024
M2S C C C 0.000 -0.308 -2.366 -0.460
M2S O O OC -0.500 0.406 -2.193 -1.473
M2S OXT O OC -0.500 -0.595 -3.524 -0.087
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
M2S N n/a CA START
M2S HN1 N . .
M2S HN2 N . .
M2S CA N C .
M2S HA CA . .
M2S CB CA CG .
M2S CG1 CB HG11 .
M2S HG13 CG1 . .
M2S HG12 CG1 . .
M2S HG11 CG1 . .
M2S CG2 CB HG21 .
M2S HG23 CG2 . .
M2S HG22 CG2 . .
M2S HG21 CG2 . .
M2S CG CB SD .
M2S HG2 CG . .
M2S HG3 CG . .
M2S SD CG CE .
M2S OE SD . .
M2S CE SD HE1 .
M2S HE3 CE . .
M2S HE2 CE . .
M2S HE1 CE . .
M2S C CA . END
M2S O C . .
M2S OXT C . .
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
M2S CA N single 1.450 0.020
M2S CB CA single 1.524 0.020
M2S C CA single 1.500 0.020
M2S CG1 CB single 1.524 0.020
M2S CG2 CB single 1.524 0.020
M2S CG CB single 1.524 0.020
M2S SD CG single 1.707 0.020
M2S OE SD double 1.480 0.020
M2S CE SD single 1.707 0.020
M2S O C deloc 1.250 0.020
M2S OXT C deloc 1.250 0.020
M2S HA CA single 1.099 0.020
M2S HG11 CG1 single 1.059 0.020
M2S HG12 CG1 single 1.059 0.020
M2S HG13 CG1 single 1.059 0.020
M2S HG21 CG2 single 1.059 0.020
M2S HG22 CG2 single 1.059 0.020
M2S HG23 CG2 single 1.059 0.020
M2S HG2 CG single 1.092 0.020
M2S HG3 CG single 1.092 0.020
M2S HE1 CE single 1.059 0.020
M2S HE2 CE single 1.059 0.020
M2S HE3 CE single 1.059 0.020
M2S HN1 N single 1.010 0.020
M2S HN2 N 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
M2S HN1 N HN2 120.000 3.000
M2S HN1 N CA 120.000 3.000
M2S HN2 N CA 120.000 3.000
M2S N CA HA 109.470 3.000
M2S N CA CB 109.500 3.000
M2S N CA C 109.470 3.000
M2S HA CA CB 108.340 3.000
M2S HA CA C 108.810 3.000
M2S CB CA C 109.470 3.000
M2S CA CB CG1 111.000 3.000
M2S CA CB CG2 111.000 3.000
M2S CA CB CG 111.000 3.000
M2S CG1 CB CG2 111.000 3.000
M2S CG1 CB CG 111.000 3.000
M2S CG2 CB CG 111.000 3.000
M2S CB CG1 HG13 109.470 3.000
M2S CB CG1 HG12 109.470 3.000
M2S CB CG1 HG11 109.470 3.000
M2S HG13 CG1 HG12 109.470 3.000
M2S HG13 CG1 HG11 109.470 3.000
M2S HG12 CG1 HG11 109.470 3.000
M2S CB CG2 HG23 109.470 3.000
M2S CB CG2 HG22 109.470 3.000
M2S CB CG2 HG21 109.470 3.000
M2S HG23 CG2 HG22 109.470 3.000
M2S HG23 CG2 HG21 109.470 3.000
M2S HG22 CG2 HG21 109.470 3.000
M2S CB CG HG2 109.470 3.000
M2S CB CG HG3 109.470 3.000
M2S CB CG SD 109.500 3.000
M2S HG2 CG HG3 107.900 3.000
M2S HG2 CG SD 109.500 3.000
M2S HG3 CG SD 109.500 3.000
M2S CG SD OE 109.440 3.000
M2S CG SD CE 102.989 3.000
M2S OE SD CE 109.472 3.000
M2S SD CE HE3 109.500 3.000
M2S SD CE HE2 109.500 3.000
M2S SD CE HE1 109.500 3.000
M2S HE3 CE HE2 109.470 3.000
M2S HE3 CE HE1 109.470 3.000
M2S HE2 CE HE1 109.470 3.000
M2S CA C O 118.500 3.000
M2S CA C OXT 118.500 3.000
M2S O C OXT 123.000 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
M2S var_1 HN2 N CA C 175.000 20.000 1
M2S var_2 N CA CB CG -60.045 20.000 1
M2S var_3 CA CB CG1 HG11 60.003 20.000 1
M2S var_4 CA CB CG2 HG21 59.984 20.000 1
M2S var_5 CA CB CG SD -179.984 20.000 1
M2S var_6 CB CG SD CE -179.990 20.000 1
M2S var_7 CG SD CE HE1 60.048 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
M2S chir_01 CA N CB C negativ
M2S chir_02 CB CA CG1 CG2 negativ
M2S chir_03 SD CG OE CE 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
M2S plan-1 N 0.020
M2S plan-1 CA 0.020
M2S plan-1 HN1 0.020
M2S plan-1 HN2 0.020
M2S plan-2 C 0.020
M2S plan-2 CA 0.020
M2S plan-2 O 0.020
M2S plan-2 OXT 0.020
# ------------------------------------------------------
|
