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
|
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
PAT PAT 'ALPHA-PHOSPHONO-TRYPTOPHAN ' peptide 31 19 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PAT
#
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
PAT N N NH2 0.000 0.000 0.000 0.000
PAT HN1 H H 0.000 0.924 -0.368 -0.182
PAT HN2 H H 0.000 -0.289 0.867 -0.433
PAT CA C CT 0.000 -0.919 -0.722 0.890
PAT CB C CH2 0.000 -2.234 -0.969 0.122
PAT HB2 H H 0.000 -1.967 -1.496 -0.796
PAT HB3 H H 0.000 -2.642 0.013 -0.128
PAT CG C CR5 0.000 -3.266 -1.764 0.877
PAT CD2 C CR56 0.000 -4.260 -1.229 1.718
PAT CE3 C CR16 0.000 -4.629 0.067 2.126
PAT HE3 H H 0.000 -4.084 0.931 1.766
PAT CZ3 C CR16 0.000 -5.708 0.226 3.001
PAT HZ3 H H 0.000 -5.999 1.220 3.319
PAT CH2 C CR16 0.000 -6.415 -0.881 3.471
PAT HH2 H H 0.000 -7.247 -0.734 4.148
PAT CZ2 C CR16 0.000 -6.066 -2.177 3.079
PAT HZ2 H H 0.000 -6.613 -3.039 3.442
PAT CE2 C CR56 0.000 -4.985 -2.320 2.204
PAT NE1 N NR15 0.000 -4.426 -3.454 1.659
PAT HNE1 H H 0.000 -4.754 -4.425 1.838
PAT CD1 C CR15 0.000 -3.375 -3.120 0.847
PAT HD1 H H 0.000 -2.750 -3.804 0.288
PAT P P P 0.000 -1.051 0.474 2.233
PAT O2P O OH1 0.000 -1.761 -0.345 3.437
PAT HOP2 H H 0.000 -1.981 0.103 4.266
PAT O3P O OH1 0.000 0.463 0.646 2.775
PAT HOP3 H H 0.000 0.658 1.282 3.478
PAT O1P O O 0.000 -1.729 1.762 1.868
PAT C C C 0.000 -0.231 -2.026 1.263
PAT O O OC -0.500 0.018 -2.375 2.439
PAT OXT O OC -0.500 0.096 -2.722 0.277
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
PAT N n/a CA START
PAT HN1 N . .
PAT HN2 N . .
PAT CA N C .
PAT CB CA CG .
PAT HB2 CB . .
PAT HB3 CB . .
PAT CG CB CD2 .
PAT CD2 CG CE3 .
PAT CE3 CD2 CZ3 .
PAT HE3 CE3 . .
PAT CZ3 CE3 CH2 .
PAT HZ3 CZ3 . .
PAT CH2 CZ3 CZ2 .
PAT HH2 CH2 . .
PAT CZ2 CH2 CE2 .
PAT HZ2 CZ2 . .
PAT CE2 CZ2 NE1 .
PAT NE1 CE2 CD1 .
PAT HNE1 NE1 . .
PAT CD1 NE1 HD1 .
PAT HD1 CD1 . .
PAT P CA O1P .
PAT O2P P HOP2 .
PAT HOP2 O2P . .
PAT O3P P HOP3 .
PAT HOP3 O3P . .
PAT O1P P . .
PAT C CA . END
PAT O C . .
PAT OXT C . .
PAT CG CD1 . ADD
PAT CD2 CE2 . 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
PAT CA N single 1.462 0.020
PAT C CA single 1.507 0.020
PAT CB CA single 1.524 0.020
PAT P CA single 1.812 0.020
PAT O C deloc 1.250 0.020
PAT OXT C deloc 1.250 0.020
PAT CG CB single 1.510 0.020
PAT HB2 CB single 1.092 0.020
PAT HB3 CB single 1.092 0.020
PAT CG CD1 double 1.387 0.020
PAT CD2 CG single 1.490 0.020
PAT CD1 NE1 single 1.350 0.020
PAT HD1 CD1 single 1.083 0.020
PAT CD2 CE2 double 1.490 0.020
PAT CE3 CD2 single 1.390 0.020
PAT NE1 CE2 single 1.340 0.020
PAT CE2 CZ2 single 1.390 0.020
PAT CZ3 CE3 double 1.390 0.020
PAT HE3 CE3 single 1.083 0.020
PAT CZ2 CH2 double 1.390 0.020
PAT HZ2 CZ2 single 1.083 0.020
PAT CH2 CZ3 single 1.390 0.020
PAT HZ3 CZ3 single 1.083 0.020
PAT HH2 CH2 single 1.083 0.020
PAT O1P P double 1.480 0.020
PAT O2P P single 1.610 0.020
PAT O3P P single 1.610 0.020
PAT HOP2 O2P single 0.967 0.020
PAT HOP3 O3P single 0.967 0.020
PAT HN1 N single 1.010 0.020
PAT HN2 N single 1.010 0.020
PAT HNE1 NE1 single 1.040 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
PAT HN1 N HN2 120.000 3.000
PAT HN1 N CA 120.000 3.000
PAT HN2 N CA 120.000 3.000
PAT N CA CB 109.500 3.000
PAT N CA P 109.500 3.000
PAT N CA C 109.500 3.000
PAT CB CA P 109.500 3.000
PAT CB CA C 109.470 3.000
PAT P CA C 109.500 3.000
PAT CA CB HB2 109.470 3.000
PAT CA CB HB3 109.470 3.000
PAT CA CB CG 109.470 3.000
PAT HB2 CB HB3 107.900 3.000
PAT HB2 CB CG 109.470 3.000
PAT HB3 CB CG 109.470 3.000
PAT CB CG CD2 126.000 3.000
PAT CB CG CD1 126.000 3.000
PAT CD2 CG CD1 108.000 3.000
PAT CG CD2 CE3 126.000 3.000
PAT CG CD2 CE2 108.000 3.000
PAT CE3 CD2 CE2 120.000 3.000
PAT CD2 CE3 HE3 120.000 3.000
PAT CD2 CE3 CZ3 120.000 3.000
PAT HE3 CE3 CZ3 120.000 3.000
PAT CE3 CZ3 HZ3 120.000 3.000
PAT CE3 CZ3 CH2 120.000 3.000
PAT HZ3 CZ3 CH2 120.000 3.000
PAT CZ3 CH2 HH2 120.000 3.000
PAT CZ3 CH2 CZ2 120.000 3.000
PAT HH2 CH2 CZ2 120.000 3.000
PAT CH2 CZ2 HZ2 120.000 3.000
PAT CH2 CZ2 CE2 120.000 3.000
PAT HZ2 CZ2 CE2 120.000 3.000
PAT CZ2 CE2 NE1 132.000 3.000
PAT CZ2 CE2 CD2 120.000 3.000
PAT NE1 CE2 CD2 108.000 3.000
PAT CE2 NE1 HNE1 126.000 3.000
PAT CE2 NE1 CD1 108.000 3.000
PAT HNE1 NE1 CD1 126.000 3.000
PAT NE1 CD1 HD1 126.000 3.000
PAT NE1 CD1 CG 108.000 3.000
PAT HD1 CD1 CG 126.000 3.000
PAT CA P O3P 109.500 3.000
PAT CA P O2P 109.500 3.000
PAT CA P O1P 109.500 3.000
PAT O3P P O2P 109.500 3.000
PAT O3P P O1P 109.500 3.000
PAT O2P P O1P 109.500 3.000
PAT P O3P HOP3 120.000 3.000
PAT P O2P HOP2 120.000 3.000
PAT CA C O 118.500 3.000
PAT CA C OXT 118.500 3.000
PAT O C OXT 123.000 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
PAT var_1 HN2 N CA C 175.000 20.000 1
PAT var_2 N CA CB CG 177.108 20.000 1
PAT var_3 CA CB CG CD2 89.948 20.000 2
PAT CONST_1 CB CG CD1 NE1 180.000 0.000 0
PAT CONST_2 CB CG CD2 CE3 0.000 0.000 0
PAT CONST_3 CG CD2 CE2 CZ2 180.000 0.000 0
PAT CONST_4 CG CD2 CE3 CZ3 180.000 0.000 0
PAT CONST_5 CD2 CE3 CZ3 CH2 0.000 0.000 0
PAT CONST_6 CE3 CZ3 CH2 CZ2 0.000 0.000 0
PAT CONST_7 CZ3 CH2 CZ2 CE2 0.000 0.000 0
PAT CONST_8 CH2 CZ2 CE2 NE1 180.000 0.000 0
PAT CONST_9 CZ2 CE2 NE1 CD1 180.000 0.000 0
PAT CONST_10 CE2 NE1 CD1 CG 0.000 0.000 0
PAT var_4 N CA P O1P 66.382 20.000 1
PAT var_5 CA P O3P HOP3 176.858 20.000 1
PAT var_6 CA P O2P HOP2 -177.030 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
PAT chir_01 CA N C CB 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
PAT plan-1 N 0.020
PAT plan-1 CA 0.020
PAT plan-1 HN1 0.020
PAT plan-1 HN2 0.020
PAT plan-2 C 0.020
PAT plan-2 CA 0.020
PAT plan-2 O 0.020
PAT plan-2 OXT 0.020
PAT plan-3 CG 0.020
PAT plan-3 CB 0.020
PAT plan-3 CD1 0.020
PAT plan-3 CD2 0.020
PAT plan-3 NE1 0.020
PAT plan-3 HD1 0.020
PAT plan-3 CE2 0.020
PAT plan-3 CE3 0.020
PAT plan-3 CZ2 0.020
PAT plan-3 CZ3 0.020
PAT plan-3 CH2 0.020
PAT plan-3 HNE1 0.020
PAT plan-3 HE3 0.020
PAT plan-3 HZ2 0.020
PAT plan-3 HZ3 0.020
PAT plan-3 HH2 0.020
# ------------------------------------------------------
|
