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
|
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
PPP PPP '3-PHENYL-1,2-PROPANDIOL ' non-polymer 23 11 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PPP
#
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
PPP O2 O OH1 0.000 0.000 0.000 0.000
PPP HO2 H H 0.000 -0.058 0.757 0.598
PPP C2 C CH1 0.000 -0.190 0.441 -1.345
PPP H2 H H 0.000 -0.124 -0.420 -2.025
PPP C1 C CH2 0.000 0.892 1.460 -1.706
PPP H11 H H 0.000 0.825 2.315 -1.030
PPP H12 H H 0.000 0.745 1.796 -2.734
PPP O1 O OH1 0.000 2.180 0.853 -1.581
PPP HO1 H H 0.000 2.863 1.499 -1.809
PPP C3 C CH2 0.000 -1.568 1.090 -1.478
PPP H31 H H 0.000 -1.713 1.427 -2.507
PPP H32 H H 0.000 -1.634 1.946 -0.803
PPP "C1'" C CR6 0.000 -2.633 0.086 -1.123
PPP "C6'" C CR16 0.000 -3.180 -0.718 -2.105
PPP "H6'" H H 0.000 -2.845 -0.624 -3.131
PPP "C5'" C CR16 0.000 -4.154 -1.643 -1.779
PPP "H5'" H H 0.000 -4.576 -2.278 -2.548
PPP "C4'" C CR16 0.000 -4.589 -1.756 -0.473
PPP "H4'" H H 0.000 -5.355 -2.477 -0.218
PPP "C3'" C CR16 0.000 -4.046 -0.949 0.509
PPP "H3'" H H 0.000 -4.387 -1.038 1.533
PPP "C2'" C CR16 0.000 -3.068 -0.027 0.183
PPP "H2'" H H 0.000 -2.644 0.606 0.952
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
PPP O2 n/a C2 START
PPP HO2 O2 . .
PPP C2 O2 C3 .
PPP H2 C2 . .
PPP C1 C2 O1 .
PPP H11 C1 . .
PPP H12 C1 . .
PPP O1 C1 HO1 .
PPP HO1 O1 . .
PPP C3 C2 "C1'" .
PPP H31 C3 . .
PPP H32 C3 . .
PPP "C1'" C3 "C6'" .
PPP "C6'" "C1'" "C5'" .
PPP "H6'" "C6'" . .
PPP "C5'" "C6'" "C4'" .
PPP "H5'" "C5'" . .
PPP "C4'" "C5'" "C3'" .
PPP "H4'" "C4'" . .
PPP "C3'" "C4'" "C2'" .
PPP "H3'" "C3'" . .
PPP "C2'" "C3'" "H2'" .
PPP "H2'" "C2'" . END
PPP "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
PPP C1 C2 single 1.524 0.020
PPP O1 C1 single 1.432 0.020
PPP H11 C1 single 1.092 0.020
PPP H12 C1 single 1.092 0.020
PPP C3 C2 single 1.524 0.020
PPP C2 O2 single 1.432 0.020
PPP H2 C2 single 1.099 0.020
PPP "C1'" C3 single 1.511 0.020
PPP H31 C3 single 1.092 0.020
PPP H32 C3 single 1.092 0.020
PPP "C1'" "C2'" double 1.390 0.020
PPP "C6'" "C1'" single 1.390 0.020
PPP "C2'" "C3'" single 1.390 0.020
PPP "H2'" "C2'" single 1.083 0.020
PPP "C3'" "C4'" double 1.390 0.020
PPP "H3'" "C3'" single 1.083 0.020
PPP "C4'" "C5'" single 1.390 0.020
PPP "H4'" "C4'" single 1.083 0.020
PPP "C5'" "C6'" double 1.390 0.020
PPP "H5'" "C5'" single 1.083 0.020
PPP "H6'" "C6'" single 1.083 0.020
PPP HO1 O1 single 0.967 0.020
PPP HO2 O2 single 0.967 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
PPP HO2 O2 C2 109.470 3.000
PPP O2 C2 H2 109.470 3.000
PPP O2 C2 C1 109.470 3.000
PPP O2 C2 C3 109.470 3.000
PPP H2 C2 C1 108.340 3.000
PPP H2 C2 C3 108.340 3.000
PPP C1 C2 C3 109.470 3.000
PPP C2 C1 H11 109.470 3.000
PPP C2 C1 H12 109.470 3.000
PPP C2 C1 O1 109.470 3.000
PPP H11 C1 H12 107.900 3.000
PPP H11 C1 O1 109.470 3.000
PPP H12 C1 O1 109.470 3.000
PPP C1 O1 HO1 109.470 3.000
PPP C2 C3 H31 109.470 3.000
PPP C2 C3 H32 109.470 3.000
PPP C2 C3 "C1'" 109.470 3.000
PPP H31 C3 H32 107.900 3.000
PPP H31 C3 "C1'" 109.470 3.000
PPP H32 C3 "C1'" 109.470 3.000
PPP C3 "C1'" "C6'" 120.000 3.000
PPP C3 "C1'" "C2'" 120.000 3.000
PPP "C6'" "C1'" "C2'" 120.000 3.000
PPP "C1'" "C6'" "H6'" 120.000 3.000
PPP "C1'" "C6'" "C5'" 120.000 3.000
PPP "H6'" "C6'" "C5'" 120.000 3.000
PPP "C6'" "C5'" "H5'" 120.000 3.000
PPP "C6'" "C5'" "C4'" 120.000 3.000
PPP "H5'" "C5'" "C4'" 120.000 3.000
PPP "C5'" "C4'" "H4'" 120.000 3.000
PPP "C5'" "C4'" "C3'" 120.000 3.000
PPP "H4'" "C4'" "C3'" 120.000 3.000
PPP "C4'" "C3'" "H3'" 120.000 3.000
PPP "C4'" "C3'" "C2'" 120.000 3.000
PPP "H3'" "C3'" "C2'" 120.000 3.000
PPP "C3'" "C2'" "H2'" 120.000 3.000
PPP "C3'" "C2'" "C1'" 120.000 3.000
PPP "H2'" "C2'" "C1'" 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
PPP var_1 HO2 O2 C2 C3 -60.068 20.000 1
PPP var_2 O2 C2 C1 O1 59.973 20.000 3
PPP var_3 C2 C1 O1 HO1 -179.940 20.000 1
PPP var_4 O2 C2 C3 "C1'" -59.960 20.000 3
PPP var_5 C2 C3 "C1'" "C6'" -90.317 20.000 2
PPP CONST_1 C3 "C1'" "C2'" "C3'" 180.000 0.000 0
PPP CONST_2 C3 "C1'" "C6'" "C5'" 180.000 0.000 0
PPP CONST_3 "C1'" "C6'" "C5'" "C4'" 0.000 0.000 0
PPP CONST_4 "C6'" "C5'" "C4'" "C3'" 0.000 0.000 0
PPP CONST_5 "C5'" "C4'" "C3'" "C2'" 0.000 0.000 0
PPP CONST_6 "C4'" "C3'" "C2'" "C1'" 0.000 0.000 0
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
PPP chir_01 C2 C1 C3 O2 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
PPP plan-1 "C1'" 0.020
PPP plan-1 C3 0.020
PPP plan-1 "C2'" 0.020
PPP plan-1 "C6'" 0.020
PPP plan-1 "C3'" 0.020
PPP plan-1 "C4'" 0.020
PPP plan-1 "C5'" 0.020
PPP plan-1 "H2'" 0.020
PPP plan-1 "H3'" 0.020
PPP plan-1 "H4'" 0.020
PPP plan-1 "H5'" 0.020
PPP plan-1 "H6'" 0.020
# ------------------------------------------------------
|
