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
|
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
MSN MSN '(1R,2R,3R,4S,5R)-4-AMINO-5-(METHYLTH' non-polymer 24 11 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_MSN
#
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
MSN O2 O OH1 0.000 0.000 0.000 0.000
MSN HO2 H H 0.000 0.417 0.818 0.303
MSN C2 C CH1 0.000 -1.073 0.315 -0.889
MSN H2 H H 0.000 -0.692 0.870 -1.757
MSN C3 C CH1 0.000 -2.142 1.152 -0.154
MSN H3 H H 0.000 -2.599 1.879 -0.839
MSN O3 O OH1 0.000 -1.570 1.818 0.973
MSN HO3 H H 0.000 -2.263 2.289 1.455
MSN C4 C CH1 0.000 -3.190 0.109 0.308
MSN H4 H H 0.000 -4.170 0.583 0.460
MSN O4 O OH1 0.000 -2.761 -0.555 1.498
MSN HO4 H H 0.000 -2.738 0.078 2.229
MSN C1 C CH1 0.000 -1.772 -0.976 -1.354
MSN H1 H H 0.000 -1.288 -1.851 -0.898
MSN S6 S S2 0.000 -1.706 -1.101 -3.163
MSN C7 C CH3 0.000 0.078 -1.331 -3.397
MSN H73 H H 0.000 0.607 -0.497 -3.006
MSN H72 H H 0.000 0.401 -2.210 -2.895
MSN H71 H H 0.000 0.300 -1.425 -4.432
MSN C5 C CH1 0.000 -3.238 -0.879 -0.884
MSN H5 H H 0.000 -3.874 -0.481 -1.687
MSN N5 N NH2 0.000 -3.726 -2.194 -0.447
MSN HN52 H H 0.000 -3.117 -3.003 -0.482
MSN HN51 H H 0.000 -4.675 -2.301 -0.108
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
MSN O2 n/a C2 START
MSN HO2 O2 . .
MSN C2 O2 C1 .
MSN H2 C2 . .
MSN C3 C2 C4 .
MSN H3 C3 . .
MSN O3 C3 HO3 .
MSN HO3 O3 . .
MSN C4 C3 O4 .
MSN H4 C4 . .
MSN O4 C4 HO4 .
MSN HO4 O4 . .
MSN C1 C2 C5 .
MSN H1 C1 . .
MSN S6 C1 C7 .
MSN C7 S6 H71 .
MSN H73 C7 . .
MSN H72 C7 . .
MSN H71 C7 . .
MSN C5 C1 N5 .
MSN H5 C5 . .
MSN N5 C5 HN51 .
MSN HN52 N5 . .
MSN HN51 N5 . END
MSN C5 C4 . 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
MSN N5 C5 single 1.450 0.020
MSN C5 C4 single 1.524 0.020
MSN C5 C1 single 1.524 0.020
MSN H5 C5 single 1.099 0.020
MSN HN51 N5 single 1.010 0.020
MSN HN52 N5 single 1.010 0.020
MSN O4 C4 single 1.432 0.020
MSN C4 C3 single 1.524 0.020
MSN H4 C4 single 1.099 0.020
MSN HO4 O4 single 0.967 0.020
MSN O3 C3 single 1.432 0.020
MSN C3 C2 single 1.524 0.020
MSN H3 C3 single 1.099 0.020
MSN HO3 O3 single 0.967 0.020
MSN C2 O2 single 1.432 0.020
MSN C1 C2 single 1.524 0.020
MSN H2 C2 single 1.099 0.020
MSN HO2 O2 single 0.967 0.020
MSN S6 C1 single 1.765 0.020
MSN H1 C1 single 1.099 0.020
MSN C7 S6 single 1.762 0.020
MSN H71 C7 single 1.059 0.020
MSN H72 C7 single 1.059 0.020
MSN H73 C7 single 1.059 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
MSN HO2 O2 C2 109.470 3.000
MSN O2 C2 H2 109.470 3.000
MSN O2 C2 C3 109.470 3.000
MSN O2 C2 C1 109.470 3.000
MSN H2 C2 C3 108.340 3.000
MSN H2 C2 C1 108.340 3.000
MSN C3 C2 C1 111.000 3.000
MSN C2 C3 H3 108.340 3.000
MSN C2 C3 O3 109.470 3.000
MSN C2 C3 C4 111.000 3.000
MSN H3 C3 O3 109.470 3.000
MSN H3 C3 C4 108.340 3.000
MSN O3 C3 C4 109.470 3.000
MSN C3 O3 HO3 109.470 3.000
MSN C3 C4 H4 108.340 3.000
MSN C3 C4 O4 109.470 3.000
MSN C3 C4 C5 111.000 3.000
MSN H4 C4 O4 109.470 3.000
MSN H4 C4 C5 108.340 3.000
MSN O4 C4 C5 109.470 3.000
MSN C4 O4 HO4 109.470 3.000
MSN C2 C1 H1 108.340 3.000
MSN C2 C1 S6 109.500 3.000
MSN C2 C1 C5 111.000 3.000
MSN H1 C1 S6 109.500 3.000
MSN H1 C1 C5 108.340 3.000
MSN S6 C1 C5 109.500 3.000
MSN C1 S6 C7 100.002 3.000
MSN S6 C7 H73 109.500 3.000
MSN S6 C7 H72 109.500 3.000
MSN S6 C7 H71 109.500 3.000
MSN H73 C7 H72 109.470 3.000
MSN H73 C7 H71 109.470 3.000
MSN H72 C7 H71 109.470 3.000
MSN C1 C5 H5 108.340 3.000
MSN C1 C5 N5 109.470 3.000
MSN C1 C5 C4 111.000 3.000
MSN H5 C5 N5 109.470 3.000
MSN H5 C5 C4 108.340 3.000
MSN N5 C5 C4 109.470 3.000
MSN C5 N5 HN52 120.000 3.000
MSN C5 N5 HN51 120.000 3.000
MSN HN52 N5 HN51 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
MSN var_1 HO2 O2 C2 C1 -178.605 20.000 1
MSN var_2 O2 C2 C3 C4 -90.000 20.000 3
MSN var_3 C2 C3 O3 HO3 -176.232 20.000 1
MSN var_4 C2 C3 C4 O4 90.000 20.000 3
MSN var_5 C3 C4 O4 HO4 66.555 20.000 1
MSN var_6 O2 C2 C1 C5 120.000 20.000 3
MSN var_7 C2 C1 S6 C7 67.086 20.000 1
MSN var_8 C1 S6 C7 H71 179.993 20.000 1
MSN var_9 C2 C1 C5 N5 -150.000 20.000 3
MSN var_10 C1 C5 C4 C3 30.000 20.000 3
MSN var_11 C1 C5 N5 HN51 -179.954 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
MSN chir_01 C5 N5 C4 C1 negativ
MSN chir_02 C4 C5 O4 C3 negativ
MSN chir_03 C3 C4 O3 C2 negativ
MSN chir_04 C2 C3 O2 C1 negativ
MSN chir_05 C1 C5 C2 S6 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
MSN plan-1 N5 0.020
MSN plan-1 C5 0.000
MSN plan-1 HN51 0.000
MSN plan-1 HN52 0.000
# ------------------------------------------------------
|
