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
|
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
PTS PTS '"(4S-TRANS)-4-(AMINO)-5,6-DIHYDRO-6-' non-polymer 29 17 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PTS
#
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
PTS O17 O OS 0.000 0.000 0.000 0.000
PTS S8 S ST 0.000 -0.858 1.123 0.155
PTS O16 O OS 0.000 -0.645 2.344 -0.537
PTS C7 C CH1 0.000 -1.311 1.397 1.900
PTS H7 H H 0.000 -0.404 1.459 2.518
PTS C15 C CH3 0.000 -2.120 2.688 2.031
PTS H153 H H 0.000 -2.992 2.622 1.433
PTS H152 H H 0.000 -2.398 2.832 3.043
PTS H151 H H 0.000 -1.533 3.509 1.707
PTS C6 C CH2 0.000 -2.164 0.200 2.341
PTS H61 H H 0.000 -2.251 0.213 3.430
PTS H62 H H 0.000 -1.665 -0.720 2.029
PTS C5 C CH1 0.000 -3.549 0.263 1.720
PTS H5 H H 0.000 -4.030 1.206 2.016
PTS N14 N NH2 0.000 -4.351 -0.861 2.219
PTS HN42 H H 0.000 -3.952 -1.523 2.874
PTS HN41 H H 0.000 -5.309 -0.981 1.913
PTS C9 C CR5 0.000 -2.385 0.552 -0.497
PTS S1 S S2 0.000 -2.831 0.306 -2.192
PTS C4 C CR5 0.000 -3.493 0.194 0.201
PTS C3 C CR15 0.000 -4.580 -0.243 -0.564
PTS H3 H H 0.000 -5.494 -0.552 -0.073
PTS C2 C CR5 0.000 -4.496 -0.281 -1.912
PTS S10 S ST 0.000 -5.709 -0.782 -3.088
PTS O11 O OS 0.000 -4.988 -1.141 -4.257
PTS O12 O OS 0.000 -6.604 -1.628 -2.381
PTS N13 N NH2 0.000 -6.587 0.560 -3.495
PTS HN32 H H 0.000 -6.378 1.467 -3.080
PTS HN31 H H 0.000 -7.349 0.502 -4.168
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
PTS O17 n/a S8 START
PTS S8 O17 C9 .
PTS O16 S8 . .
PTS C7 S8 C6 .
PTS H7 C7 . .
PTS C15 C7 H151 .
PTS H153 C15 . .
PTS H152 C15 . .
PTS H151 C15 . .
PTS C6 C7 C5 .
PTS H61 C6 . .
PTS H62 C6 . .
PTS C5 C6 N14 .
PTS H5 C5 . .
PTS N14 C5 HN41 .
PTS HN42 N14 . .
PTS HN41 N14 . .
PTS C9 S8 C4 .
PTS S1 C9 . .
PTS C4 C9 C3 .
PTS C3 C4 C2 .
PTS H3 C3 . .
PTS C2 C3 S10 .
PTS S10 C2 N13 .
PTS O11 S10 . .
PTS O12 S10 . .
PTS N13 S10 HN31 .
PTS HN32 N13 . .
PTS HN31 N13 . END
PTS S1 C2 . ADD
PTS C4 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
PTS S1 C2 single 1.745 0.020
PTS S1 C9 single 1.745 0.020
PTS C2 C3 double 1.387 0.020
PTS S10 C2 single 1.645 0.020
PTS C3 C4 single 1.387 0.020
PTS H3 C3 single 1.083 0.020
PTS C4 C5 single 1.480 0.020
PTS C4 C9 double 1.490 0.020
PTS C5 C6 single 1.524 0.020
PTS N14 C5 single 1.450 0.020
PTS H5 C5 single 1.099 0.020
PTS C6 C7 single 1.524 0.020
PTS H61 C6 single 1.092 0.020
PTS H62 C6 single 1.092 0.020
PTS C7 S8 single 1.665 0.020
PTS C15 C7 single 1.524 0.020
PTS H7 C7 single 1.099 0.020
PTS C9 S8 single 1.645 0.020
PTS O16 S8 double 1.436 0.020
PTS S8 O17 double 1.436 0.020
PTS O11 S10 double 1.436 0.020
PTS O12 S10 double 1.436 0.020
PTS N13 S10 single 1.600 0.020
PTS HN31 N13 single 1.010 0.020
PTS HN32 N13 single 1.010 0.020
PTS HN41 N14 single 1.010 0.020
PTS HN42 N14 single 1.010 0.020
PTS H151 C15 single 1.059 0.020
PTS H152 C15 single 1.059 0.020
PTS H153 C15 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
PTS O17 S8 O16 109.500 3.000
PTS O17 S8 C7 109.500 3.000
PTS O17 S8 C9 109.500 3.000
PTS O16 S8 C7 109.500 3.000
PTS O16 S8 C9 109.500 3.000
PTS C7 S8 C9 109.500 3.000
PTS S8 C7 H7 109.500 3.000
PTS S8 C7 C15 109.500 3.000
PTS S8 C7 C6 109.500 3.000
PTS H7 C7 C15 108.340 3.000
PTS H7 C7 C6 108.340 3.000
PTS C15 C7 C6 111.000 3.000
PTS C7 C15 H153 109.470 3.000
PTS C7 C15 H152 109.470 3.000
PTS C7 C15 H151 109.470 3.000
PTS H153 C15 H152 109.470 3.000
PTS H153 C15 H151 109.470 3.000
PTS H152 C15 H151 109.470 3.000
PTS C7 C6 H61 109.470 3.000
PTS C7 C6 H62 109.470 3.000
PTS C7 C6 C5 111.000 3.000
PTS H61 C6 H62 107.900 3.000
PTS H61 C6 C5 109.470 3.000
PTS H62 C6 C5 109.470 3.000
PTS C6 C5 H5 108.340 3.000
PTS C6 C5 N14 109.470 3.000
PTS C6 C5 C4 109.470 3.000
PTS H5 C5 N14 109.470 3.000
PTS H5 C5 C4 109.470 3.000
PTS N14 C5 C4 109.470 3.000
PTS C5 N14 HN42 120.000 3.000
PTS C5 N14 HN41 120.000 3.000
PTS HN42 N14 HN41 120.000 3.000
PTS S8 C9 S1 108.000 3.000
PTS S8 C9 C4 108.000 3.000
PTS S1 C9 C4 108.000 3.000
PTS C9 S1 C2 97.519 3.000
PTS C9 C4 C3 108.000 3.000
PTS C9 C4 C5 126.000 3.000
PTS C3 C4 C5 108.000 3.000
PTS C4 C3 H3 126.000 3.000
PTS C4 C3 C2 108.000 3.000
PTS H3 C3 C2 126.000 3.000
PTS C3 C2 S10 108.000 3.000
PTS C3 C2 S1 108.000 3.000
PTS S10 C2 S1 108.000 3.000
PTS C2 S10 O11 109.500 3.000
PTS C2 S10 O12 109.500 3.000
PTS C2 S10 N13 109.500 3.000
PTS O11 S10 O12 109.500 3.000
PTS O11 S10 N13 109.500 3.000
PTS O12 S10 N13 109.500 3.000
PTS S10 N13 HN32 120.000 3.000
PTS S10 N13 HN31 120.000 3.000
PTS HN32 N13 HN31 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
PTS var_1 O17 S8 C7 C6 -60.000 20.000 1
PTS var_2 S8 C7 C15 H151 -61.188 20.000 3
PTS var_3 S8 C7 C6 C5 -60.000 20.000 3
PTS var_4 C7 C6 C5 N14 180.000 20.000 3
PTS var_5 C6 C5 N14 HN41 179.939 20.000 1
PTS var_6 O17 S8 C9 C4 120.000 20.000 1
PTS CONST_1 S8 C9 S1 C2 180.000 0.000 0
PTS CONST_2 C9 S1 C2 C3 0.000 0.000 0
PTS CONST_3 S8 C9 C4 C3 180.000 0.000 0
PTS var_7 C9 C4 C5 C6 -30.000 20.000 1
PTS CONST_4 C9 C4 C3 C2 0.000 0.000 0
PTS CONST_5 C4 C3 C2 S10 180.000 0.000 0
PTS var_8 C3 C2 S10 N13 90.117 20.000 1
PTS var_9 C2 S10 N13 HN31 179.989 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
PTS chir_01 C5 C4 C6 N14 positiv
PTS chir_02 C7 C6 S8 C15 negativ
PTS chir_03 S8 C7 C9 O16 negativ
PTS chir_04 S10 C2 O11 O12 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
PTS plan-1 C2 0.020
PTS plan-1 S1 0.020
PTS plan-1 C3 0.020
PTS plan-1 S10 0.020
PTS plan-1 C4 0.020
PTS plan-1 C9 0.020
PTS plan-1 H3 0.020
PTS plan-1 C5 0.020
PTS plan-1 S8 0.020
PTS plan-2 N13 0.020
PTS plan-2 S10 0.020
PTS plan-2 HN31 0.020
PTS plan-2 HN32 0.020
PTS plan-3 N14 0.020
PTS plan-3 C5 0.020
PTS plan-3 HN41 0.020
PTS plan-3 HN42 0.020
# ------------------------------------------------------
|
