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
|
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
LP8 LP8 '3-cyclopentyl-1,4-dihydroxy-1,8-naph' non-polymer 32 18 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_LP8
#
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
LP8 O3 O O 0.000 0.000 0.000 0.000
LP8 C C CR6 0.000 -1.216 -0.085 0.005
LP8 C2 C CR6 0.000 -1.809 -1.358 -0.013
LP8 C11 C CH1 0.000 -0.945 -2.591 -0.036
LP8 H11 H H 0.000 -1.575 -3.492 -0.022
LP8 C15 C CH2 0.000 0.008 -2.593 1.177
LP8 H15 H H 0.000 -0.365 -3.218 1.990
LP8 H15A H H 0.000 0.195 -1.584 1.551
LP8 C14 C CH2 0.000 1.324 -3.192 0.624
LP8 H14 H H 0.000 1.296 -4.282 0.558
LP8 H14A H H 0.000 2.201 -2.887 1.200
LP8 C13 C CH2 0.000 1.404 -2.589 -0.800
LP8 H13 H H 0.000 2.015 -3.198 -1.469
LP8 H13A H H 0.000 1.786 -1.566 -0.790
LP8 C12 C CH2 0.000 -0.058 -2.589 -1.293
LP8 H12A H H 0.000 -0.267 -3.480 -1.889
LP8 H12 H H 0.000 -0.268 -1.697 -1.887
LP8 C1 C CR6 0.000 -3.171 -1.476 -0.008
LP8 O10 O OH1 0.000 -3.761 -2.693 -0.023
LP8 H151 H H 0.000 -4.721 -2.584 -0.018
LP8 C5 C CR66 0.000 -3.976 -0.248 0.003
LP8 C6 C CR16 0.000 -5.374 -0.295 0.002
LP8 H6 H H 0.000 -5.901 -1.241 -0.011
LP8 C7 C CR16 0.000 -6.062 0.903 0.018
LP8 H7 H H 0.000 -7.145 0.911 0.019
LP8 C8 C CR16 0.000 -5.354 2.095 0.035
LP8 H8 H H 0.000 -5.898 3.032 0.048
LP8 N9 N NRD6 0.000 -4.038 2.116 0.034
LP8 C4 C CR66 0.000 -3.325 0.998 0.019
LP8 N N NR6 0.000 -1.949 1.040 0.020
LP8 O O OH1 0.000 -1.293 2.295 0.037
LP8 HO H H 0.000 -0.329 2.331 0.037
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
LP8 O3 n/a C START
LP8 C O3 C2 .
LP8 C2 C C1 .
LP8 C11 C2 C15 .
LP8 H11 C11 . .
LP8 C15 C11 C14 .
LP8 H15 C15 . .
LP8 H15A C15 . .
LP8 C14 C15 C13 .
LP8 H14 C14 . .
LP8 H14A C14 . .
LP8 C13 C14 C12 .
LP8 H13 C13 . .
LP8 H13A C13 . .
LP8 C12 C13 H12 .
LP8 H12A C12 . .
LP8 H12 C12 . .
LP8 C1 C2 C5 .
LP8 O10 C1 H151 .
LP8 H151 O10 . .
LP8 C5 C1 C6 .
LP8 C6 C5 C7 .
LP8 H6 C6 . .
LP8 C7 C6 C8 .
LP8 H7 C7 . .
LP8 C8 C7 N9 .
LP8 H8 C8 . .
LP8 N9 C8 C4 .
LP8 C4 N9 N .
LP8 N C4 O .
LP8 O N HO .
LP8 HO O . END
LP8 C N . ADD
LP8 C4 C5 . ADD
LP8 C11 C12 . 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
LP8 C2 C single 1.487 0.020
LP8 C O3 double 1.250 0.020
LP8 C N single 1.410 0.020
LP8 O N single 1.434 0.020
LP8 HO O single 0.967 0.020
LP8 C1 C2 double 1.487 0.020
LP8 C11 C2 single 1.480 0.020
LP8 N C4 single 1.410 0.020
LP8 C4 C5 double 1.490 0.020
LP8 C5 C1 single 1.490 0.020
LP8 C6 C5 single 1.390 0.020
LP8 H6 C6 single 1.083 0.020
LP8 C7 C6 double 1.390 0.020
LP8 H7 C7 single 1.083 0.020
LP8 C8 C7 single 1.390 0.020
LP8 N9 C8 double 1.337 0.020
LP8 H8 C8 single 1.083 0.020
LP8 C4 N9 single 1.350 0.020
LP8 O10 C1 single 1.362 0.020
LP8 H151 O10 single 0.967 0.020
LP8 C11 C12 single 1.524 0.020
LP8 H11 C11 single 1.099 0.020
LP8 C12 C13 single 1.524 0.020
LP8 H12 C12 single 1.092 0.020
LP8 H12A C12 single 1.092 0.020
LP8 H13 C13 single 1.092 0.020
LP8 H13A C13 single 1.092 0.020
LP8 C13 C14 single 1.524 0.020
LP8 H14 C14 single 1.092 0.020
LP8 H14A C14 single 1.092 0.020
LP8 C15 C11 single 1.524 0.020
LP8 C14 C15 single 1.524 0.020
LP8 H15 C15 single 1.092 0.020
LP8 H15A C15 single 1.092 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
LP8 O3 C C2 120.000 3.000
LP8 O3 C N 120.000 3.000
LP8 C2 C N 120.000 3.000
LP8 C C2 C11 120.000 3.000
LP8 C C2 C1 120.000 3.000
LP8 C11 C2 C1 120.000 3.000
LP8 C2 C11 H11 109.470 3.000
LP8 C2 C11 C15 109.470 3.000
LP8 C2 C11 C12 109.470 3.000
LP8 H11 C11 C15 108.340 3.000
LP8 H11 C11 C12 108.340 3.000
LP8 C15 C11 C12 109.470 3.000
LP8 C11 C15 H15 109.470 3.000
LP8 C11 C15 H15A 109.470 3.000
LP8 C11 C15 C14 111.000 3.000
LP8 H15 C15 H15A 107.900 3.000
LP8 H15 C15 C14 109.470 3.000
LP8 H15A C15 C14 109.470 3.000
LP8 C15 C14 H14 109.470 3.000
LP8 C15 C14 H14A 109.470 3.000
LP8 C15 C14 C13 111.000 3.000
LP8 H14 C14 H14A 107.900 3.000
LP8 H14 C14 C13 109.470 3.000
LP8 H14A C14 C13 109.470 3.000
LP8 C14 C13 H13 109.470 3.000
LP8 C14 C13 H13A 109.470 3.000
LP8 C14 C13 C12 111.000 3.000
LP8 H13 C13 H13A 107.900 3.000
LP8 H13 C13 C12 109.470 3.000
LP8 H13A C13 C12 109.470 3.000
LP8 C13 C12 H12A 109.470 3.000
LP8 C13 C12 H12 109.470 3.000
LP8 C13 C12 C11 111.000 3.000
LP8 H12A C12 H12 107.900 3.000
LP8 H12A C12 C11 109.470 3.000
LP8 H12 C12 C11 109.470 3.000
LP8 C2 C1 O10 120.000 3.000
LP8 C2 C1 C5 120.000 3.000
LP8 O10 C1 C5 120.000 3.000
LP8 C1 O10 H151 109.470 3.000
LP8 C1 C5 C6 120.000 3.000
LP8 C1 C5 C4 120.000 3.000
LP8 C6 C5 C4 120.000 3.000
LP8 C5 C6 H6 120.000 3.000
LP8 C5 C6 C7 120.000 3.000
LP8 H6 C6 C7 120.000 3.000
LP8 C6 C7 H7 120.000 3.000
LP8 C6 C7 C8 120.000 3.000
LP8 H7 C7 C8 120.000 3.000
LP8 C7 C8 H8 120.000 3.000
LP8 C7 C8 N9 120.000 3.000
LP8 H8 C8 N9 120.000 3.000
LP8 C8 N9 C4 120.000 3.000
LP8 N9 C4 N 120.000 3.000
LP8 N9 C4 C5 120.000 3.000
LP8 N C4 C5 120.000 3.000
LP8 C4 N O 120.000 3.000
LP8 C4 N C 120.000 3.000
LP8 O N C 120.000 3.000
LP8 N O HO 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
LP8 CONST_1 O3 C N C4 180.000 0.000 0
LP8 CONST_2 O3 C C2 C1 180.000 0.000 0
LP8 var_1 C C2 C11 C15 57.104 20.000 1
LP8 var_2 C2 C11 C12 C13 120.000 20.000 3
LP8 var_3 C2 C11 C15 C14 -150.000 20.000 3
LP8 var_4 C11 C15 C14 C13 30.000 20.000 3
LP8 var_5 C15 C14 C13 C12 -30.000 20.000 3
LP8 var_6 C14 C13 C12 C11 30.000 20.000 3
LP8 CONST_3 C C2 C1 C5 0.000 0.000 0
LP8 var_7 C2 C1 O10 H151 -179.934 20.000 1
LP8 CONST_4 C2 C1 C5 C6 180.000 0.000 0
LP8 CONST_5 C1 C5 C6 C7 180.000 0.000 0
LP8 CONST_6 C5 C6 C7 C8 0.000 0.000 0
LP8 CONST_7 C6 C7 C8 N9 0.000 0.000 0
LP8 CONST_8 C7 C8 N9 C4 0.000 0.000 0
LP8 CONST_9 C8 N9 C4 N 180.000 0.000 0
LP8 CONST_10 N9 C4 C5 C1 180.000 0.000 0
LP8 CONST_11 N9 C4 N O 0.000 0.000 0
LP8 var_8 C4 N O HO -179.982 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
LP8 chir_01 C11 C2 C12 C15 negativ
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
LP8 plan-1 C 0.020
LP8 plan-1 N 0.020
LP8 plan-1 C2 0.020
LP8 plan-1 O3 0.020
LP8 plan-1 C1 0.020
LP8 plan-1 O 0.020
LP8 plan-1 C4 0.020
LP8 plan-1 C5 0.020
LP8 plan-1 O10 0.020
LP8 plan-1 C11 0.020
LP8 plan-1 N9 0.020
LP8 plan-1 C6 0.020
LP8 plan-1 C7 0.020
LP8 plan-1 C8 0.020
LP8 plan-1 H6 0.020
LP8 plan-1 H7 0.020
LP8 plan-1 H8 0.020
# ------------------------------------------------------
|
