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
|
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
MRD MRD '(4R)-2-METHYLPENTANE-2,4-DIOL ' non-polymer 22 8 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_MRD
#
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
MRD O4 O OH1 0.000 0.000 0.000 0.000
MRD HA H H 0.000 0.177 -0.950 0.019
MRD C4 C CH1 0.000 -1.217 0.271 0.697
MRD H4 H H 0.000 -1.419 1.351 0.675
MRD C5 C CH3 0.000 -1.087 -0.194 2.150
MRD H5C3 H H 0.000 -1.988 0.008 2.669
MRD H5C2 H H 0.000 -0.893 -1.235 2.172
MRD H5C1 H H 0.000 -0.288 0.323 2.617
MRD C3 C CH2 0.000 -2.369 -0.476 0.024
MRD H3C1 H H 0.000 -3.298 -0.270 0.558
MRD H3C2 H H 0.000 -2.168 -1.550 0.046
MRD C2 C CT 0.000 -2.499 -0.010 -1.428
MRD CM C CH3 0.000 -2.779 1.492 -1.457
MRD HMC3 H H 0.000 -1.982 2.010 -0.991
MRD HMC2 H H 0.000 -2.869 1.815 -2.462
MRD HMC1 H H 0.000 -3.681 1.694 -0.940
MRD O2 O OH1 0.000 -1.282 -0.282 -2.126
MRD H2 H H 0.000 -1.105 -1.232 -2.106
MRD C1 C CH3 0.000 -3.651 -0.758 -2.102
MRD H1C3 H H 0.000 -3.457 -1.800 -2.081
MRD H1C2 H H 0.000 -4.554 -0.558 -1.585
MRD H1C1 H H 0.000 -3.742 -0.437 -3.107
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
MRD O4 n/a C4 START
MRD HA O4 . .
MRD C4 O4 C3 .
MRD H4 C4 . .
MRD C5 C4 H5C1 .
MRD H5C3 C5 . .
MRD H5C2 C5 . .
MRD H5C1 C5 . .
MRD C3 C4 C2 .
MRD H3C1 C3 . .
MRD H3C2 C3 . .
MRD C2 C3 C1 .
MRD CM C2 HMC1 .
MRD HMC3 CM . .
MRD HMC2 CM . .
MRD HMC1 CM . .
MRD O2 C2 H2 .
MRD H2 O2 . .
MRD C1 C2 H1C1 .
MRD H1C3 C1 . .
MRD H1C2 C1 . .
MRD H1C1 C1 . END
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
MRD C1 C2 single 1.524 0.020
MRD H1C1 C1 single 1.059 0.020
MRD H1C2 C1 single 1.059 0.020
MRD H1C3 C1 single 1.059 0.020
MRD O2 C2 single 1.432 0.020
MRD CM C2 single 1.524 0.020
MRD C2 C3 single 1.524 0.020
MRD H2 O2 single 0.967 0.020
MRD HMC1 CM single 1.059 0.020
MRD HMC2 CM single 1.059 0.020
MRD HMC3 CM single 1.059 0.020
MRD C3 C4 single 1.524 0.020
MRD H3C1 C3 single 1.092 0.020
MRD H3C2 C3 single 1.092 0.020
MRD C4 O4 single 1.432 0.020
MRD C5 C4 single 1.524 0.020
MRD H4 C4 single 1.099 0.020
MRD HA O4 single 0.967 0.020
MRD H5C1 C5 single 1.059 0.020
MRD H5C2 C5 single 1.059 0.020
MRD H5C3 C5 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
MRD HA O4 C4 109.470 3.000
MRD O4 C4 H4 109.470 3.000
MRD O4 C4 C5 109.470 3.000
MRD O4 C4 C3 109.470 3.000
MRD H4 C4 C5 108.340 3.000
MRD H4 C4 C3 108.340 3.000
MRD C5 C4 C3 111.000 3.000
MRD C4 C5 H5C3 109.470 3.000
MRD C4 C5 H5C2 109.470 3.000
MRD C4 C5 H5C1 109.470 3.000
MRD H5C3 C5 H5C2 109.470 3.000
MRD H5C3 C5 H5C1 109.470 3.000
MRD H5C2 C5 H5C1 109.470 3.000
MRD C4 C3 H3C1 109.470 3.000
MRD C4 C3 H3C2 109.470 3.000
MRD C4 C3 C2 111.000 3.000
MRD H3C1 C3 H3C2 107.900 3.000
MRD H3C1 C3 C2 109.470 3.000
MRD H3C2 C3 C2 109.470 3.000
MRD C3 C2 CM 111.000 3.000
MRD C3 C2 O2 109.470 3.000
MRD C3 C2 C1 111.000 3.000
MRD CM C2 O2 109.470 3.000
MRD CM C2 C1 111.000 3.000
MRD O2 C2 C1 109.470 3.000
MRD C2 CM HMC3 109.470 3.000
MRD C2 CM HMC2 109.470 3.000
MRD C2 CM HMC1 109.470 3.000
MRD HMC3 CM HMC2 109.470 3.000
MRD HMC3 CM HMC1 109.470 3.000
MRD HMC2 CM HMC1 109.470 3.000
MRD C2 O2 H2 109.470 3.000
MRD C2 C1 H1C3 109.470 3.000
MRD C2 C1 H1C2 109.470 3.000
MRD C2 C1 H1C1 109.470 3.000
MRD H1C3 C1 H1C2 109.470 3.000
MRD H1C3 C1 H1C1 109.470 3.000
MRD H1C2 C1 H1C1 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
MRD var_1 HA O4 C4 C3 -59.952 20.000 1
MRD var_2 O4 C4 C5 H5C1 59.935 20.000 3
MRD var_3 O4 C4 C3 C2 -60.045 20.000 3
MRD var_4 C4 C3 C2 C1 -179.996 20.000 1
MRD var_5 C3 C2 CM HMC1 -60.003 20.000 1
MRD var_6 C3 C2 O2 H2 59.926 20.000 1
MRD var_7 C3 C2 C1 H1C1 -179.987 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
MRD chir_01 C2 C1 O2 CM negativ
MRD chir_02 C4 C3 O4 C5 positiv
# ------------------------------------------------------
|
