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
|
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
NA8 NA8 '(1S)-1-CARBOXY-2-NAPHTHALEN-2-YLETHA' non-polymer 29 16 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_NA8
#
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
NA8 OXT O OC -0.500 0.000 0.000 0.000
NA8 C11 C C 0.000 -0.910 -0.856 -0.067
NA8 O2 O OC -0.500 -0.652 -2.061 0.148
NA8 C10 C CH1 0.000 -2.318 -0.434 -0.399
NA8 H10 H H 0.000 -2.295 0.335 -1.183
NA8 N N NT3 1.000 -3.079 -1.597 -0.876
NA8 HN3 H H 0.000 -4.041 -1.304 -1.102
NA8 HN2 H H 0.000 -2.623 -1.978 -1.720
NA8 HN1 H H 0.000 -3.099 -2.317 -0.137
NA8 C9 C CH2 0.000 -2.989 0.135 0.853
NA8 H91C H H 0.000 -2.375 0.942 1.259
NA8 H92C H H 0.000 -3.091 -0.655 1.601
NA8 C2 C CR6 0.000 -4.351 0.669 0.495
NA8 C3 C CR16 0.000 -4.485 1.998 0.098
NA8 H3 H H 0.000 -3.608 2.632 0.052
NA8 C4 C CR16 0.000 -5.702 2.512 -0.232
NA8 H4 H H 0.000 -5.791 3.548 -0.537
NA8 C4A C CR66 0.000 -6.841 1.692 -0.175
NA8 C8A C CR66 0.000 -6.706 0.340 0.228
NA8 C1 C CR16 0.000 -5.434 -0.154 0.562
NA8 H1 H H 0.000 -5.315 -1.186 0.871
NA8 C8 C CR16 0.000 -7.846 -0.479 0.287
NA8 H8 H H 0.000 -7.757 -1.514 0.594
NA8 C7 C CR16 0.000 -9.062 0.034 -0.044
NA8 H7 H H 0.000 -9.939 -0.600 0.001
NA8 C6 C CR16 0.000 -9.196 1.364 -0.440
NA8 H6 H H 0.000 -10.175 1.747 -0.699
NA8 C5 C CR16 0.000 -8.114 2.187 -0.507
NA8 H5 H H 0.000 -8.234 3.219 -0.816
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
NA8 OXT n/a C11 START
NA8 C11 OXT C10 .
NA8 O2 C11 . .
NA8 C10 C11 C9 .
NA8 H10 C10 . .
NA8 N C10 HN1 .
NA8 HN3 N . .
NA8 HN2 N . .
NA8 HN1 N . .
NA8 C9 C10 C2 .
NA8 H91C C9 . .
NA8 H92C C9 . .
NA8 C2 C9 C3 .
NA8 C3 C2 C4 .
NA8 H3 C3 . .
NA8 C4 C3 C4A .
NA8 H4 C4 . .
NA8 C4A C4 C8A .
NA8 C8A C4A C8 .
NA8 C1 C8A H1 .
NA8 H1 C1 . .
NA8 C8 C8A C7 .
NA8 H8 C8 . .
NA8 C7 C8 C6 .
NA8 H7 C7 . .
NA8 C6 C7 C5 .
NA8 H6 C6 . .
NA8 C5 C6 H5 .
NA8 H5 C5 . END
NA8 C1 C2 . ADD
NA8 C4A C5 . 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
NA8 O2 C11 deloc 1.250 0.020
NA8 C10 C11 single 1.500 0.020
NA8 C11 OXT deloc 1.250 0.020
NA8 N C10 single 1.488 0.020
NA8 C1 C2 single 1.390 0.020
NA8 C1 C8A double 1.390 0.020
NA8 C3 C2 double 1.390 0.020
NA8 C2 C9 single 1.511 0.020
NA8 C4 C3 single 1.390 0.020
NA8 C4A C4 double 1.390 0.020
NA8 C4A C5 single 1.390 0.020
NA8 C8A C4A single 1.490 0.020
NA8 C5 C6 double 1.390 0.020
NA8 C6 C7 single 1.390 0.020
NA8 C7 C8 double 1.390 0.020
NA8 C8 C8A single 1.390 0.020
NA8 C9 C10 single 1.524 0.020
NA8 H10 C10 single 1.099 0.020
NA8 HN1 N single 1.033 0.020
NA8 HN2 N single 1.033 0.020
NA8 HN3 N single 1.033 0.020
NA8 H1 C1 single 1.083 0.020
NA8 H3 C3 single 1.083 0.020
NA8 H91C C9 single 1.092 0.020
NA8 H92C C9 single 1.092 0.020
NA8 H4 C4 single 1.083 0.020
NA8 H5 C5 single 1.083 0.020
NA8 H6 C6 single 1.083 0.020
NA8 H7 C7 single 1.083 0.020
NA8 H8 C8 single 1.083 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
NA8 OXT C11 O2 123.000 3.000
NA8 OXT C11 C10 118.500 3.000
NA8 O2 C11 C10 118.500 3.000
NA8 C11 C10 H10 108.810 3.000
NA8 C11 C10 N 111.600 3.000
NA8 C11 C10 C9 109.470 3.000
NA8 H10 C10 N 108.550 3.000
NA8 H10 C10 C9 108.340 3.000
NA8 N C10 C9 110.000 3.000
NA8 C10 N HN3 109.470 3.000
NA8 C10 N HN2 109.470 3.000
NA8 C10 N HN1 109.470 3.000
NA8 HN3 N HN2 109.470 3.000
NA8 HN3 N HN1 109.470 3.000
NA8 HN2 N HN1 109.470 3.000
NA8 C10 C9 H91C 109.470 3.000
NA8 C10 C9 H92C 109.470 3.000
NA8 C10 C9 C2 109.470 3.000
NA8 H91C C9 H92C 107.900 3.000
NA8 H91C C9 C2 109.470 3.000
NA8 H92C C9 C2 109.470 3.000
NA8 C9 C2 C3 120.000 3.000
NA8 C9 C2 C1 120.000 3.000
NA8 C3 C2 C1 120.000 3.000
NA8 C2 C3 H3 120.000 3.000
NA8 C2 C3 C4 120.000 3.000
NA8 H3 C3 C4 120.000 3.000
NA8 C3 C4 H4 120.000 3.000
NA8 C3 C4 C4A 120.000 3.000
NA8 H4 C4 C4A 120.000 3.000
NA8 C4 C4A C8A 120.000 3.000
NA8 C4 C4A C5 120.000 3.000
NA8 C8A C4A C5 120.000 3.000
NA8 C4A C8A C1 120.000 3.000
NA8 C4A C8A C8 120.000 3.000
NA8 C1 C8A C8 120.000 3.000
NA8 C8A C1 H1 120.000 3.000
NA8 C8A C1 C2 120.000 3.000
NA8 H1 C1 C2 120.000 3.000
NA8 C8A C8 H8 120.000 3.000
NA8 C8A C8 C7 120.000 3.000
NA8 H8 C8 C7 120.000 3.000
NA8 C8 C7 H7 120.000 3.000
NA8 C8 C7 C6 120.000 3.000
NA8 H7 C7 C6 120.000 3.000
NA8 C7 C6 H6 120.000 3.000
NA8 C7 C6 C5 120.000 3.000
NA8 H6 C6 C5 120.000 3.000
NA8 C6 C5 H5 120.000 3.000
NA8 C6 C5 C4A 120.000 3.000
NA8 H5 C5 C4A 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
NA8 var_1 OXT C11 C10 C9 -79.712 20.000 3
NA8 var_2 C11 C10 N HN1 60.025 20.000 1
NA8 var_3 C11 C10 C9 C2 175.005 20.000 3
NA8 var_4 C10 C9 C2 C3 -89.982 20.000 2
NA8 CONST_1 C9 C2 C3 C4 180.000 0.000 0
NA8 CONST_2 C2 C3 C4 C4A 0.000 0.000 0
NA8 CONST_3 C3 C4 C4A C8A 0.000 0.000 0
NA8 CONST_4 C4 C4A C5 C6 180.000 0.000 0
NA8 CONST_5 C4 C4A C8A C8 180.000 0.000 0
NA8 CONST_6 C4A C8A C1 C2 0.000 0.000 0
NA8 CONST_7 C8A C1 C2 C9 180.000 0.000 0
NA8 CONST_8 C4A C8A C8 C7 0.000 0.000 0
NA8 CONST_9 C8A C8 C7 C6 0.000 0.000 0
NA8 CONST_10 C8 C7 C6 C5 0.000 0.000 0
NA8 CONST_11 C7 C6 C5 C4A 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
NA8 chir_01 C10 C11 N C9 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
NA8 plan-1 C11 0.020
NA8 plan-1 O2 0.020
NA8 plan-1 C10 0.020
NA8 plan-1 OXT 0.020
NA8 plan-2 C1 0.020
NA8 plan-2 C2 0.020
NA8 plan-2 C8A 0.020
NA8 plan-2 H1 0.020
NA8 plan-2 C3 0.020
NA8 plan-2 C4 0.020
NA8 plan-2 C9 0.020
NA8 plan-2 H3 0.020
NA8 plan-2 C4A 0.020
NA8 plan-2 H4 0.020
NA8 plan-2 C5 0.020
NA8 plan-2 C6 0.020
NA8 plan-2 C7 0.020
NA8 plan-2 C8 0.020
NA8 plan-2 H5 0.020
NA8 plan-2 H6 0.020
NA8 plan-2 H7 0.020
NA8 plan-2 H8 0.020
# ------------------------------------------------------
|
