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
|
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
PCP PCP '1-ALPHA-PYROPHOSPHORYL-2-ALPHA,3-ALP' non-polymer 32 22 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PCP
#
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
PCP O3B O OP -0.666 0.000 0.000 0.000
PCP PB P P 0.000 -0.127 0.840 -1.252
PCP O1B O OP -0.666 0.270 0.015 -2.456
PCP O2B O OP -0.666 0.782 2.045 -1.145
PCP O3A O O2 0.000 -1.651 1.332 -1.416
PCP PA P P 0.000 -2.559 0.007 -1.525
PCP O1A O OP -0.500 -2.132 -0.789 -2.701
PCP O2A O OP -0.500 -2.397 -0.804 -0.294
PCP O1 O O2 0.000 -4.104 0.425 -1.690
PCP C1 C CH1 0.000 -4.854 -0.786 -1.781
PCP H1 H H 0.000 -4.189 -1.657 -1.694
PCP C5 C CH2 0.000 -5.950 -0.832 -0.690
PCP H51 H H 0.000 -5.621 -0.392 0.254
PCP H52 H H 0.000 -6.322 -1.842 -0.510
PCP C4 C CH1 0.000 -7.079 0.036 -1.301
PCP H4 H H 0.000 -6.867 1.104 -1.152
PCP C3 C CH1 0.000 -7.052 -0.315 -2.803
PCP H3 H H 0.000 -7.796 -1.095 -3.020
PCP O3 O OH1 0.000 -7.323 0.850 -3.583
PCP HO3 H H 0.000 -7.293 0.622 -4.522
PCP C2 C CH1 0.000 -5.638 -0.838 -3.108
PCP H2 H H 0.000 -5.691 -1.873 -3.474
PCP O2 O OH1 0.000 -5.009 -0.006 -4.083
PCP HO2 H H 0.000 -5.520 -0.029 -4.903
PCP CP C CH2 0.000 -8.430 -0.332 -0.684
PCP HP1 H H 0.000 -8.632 -1.391 -0.859
PCP HP2 H H 0.000 -9.215 0.269 -1.146
PCP OP O O2 0.000 -8.397 -0.077 0.721
PCP P P P 0.000 -9.843 -0.483 1.302
PCP O1P O OP -0.666 -10.103 -1.948 1.027
PCP O2P O OP -0.666 -9.874 -0.236 2.794
PCP O3P O OP -0.666 -10.909 0.353 0.629
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
PCP O3B n/a PB START
PCP PB O3B O3A .
PCP O1B PB . .
PCP O2B PB . .
PCP O3A PB PA .
PCP PA O3A O1 .
PCP O1A PA . .
PCP O2A PA . .
PCP O1 PA C1 .
PCP C1 O1 C5 .
PCP H1 C1 . .
PCP C5 C1 C4 .
PCP H51 C5 . .
PCP H52 C5 . .
PCP C4 C5 CP .
PCP H4 C4 . .
PCP C3 C4 C2 .
PCP H3 C3 . .
PCP O3 C3 HO3 .
PCP HO3 O3 . .
PCP C2 C3 O2 .
PCP H2 C2 . .
PCP O2 C2 HO2 .
PCP HO2 O2 . .
PCP CP C4 OP .
PCP HP1 CP . .
PCP HP2 CP . .
PCP OP CP P .
PCP P OP O3P .
PCP O1P P . .
PCP O2P P . .
PCP O3P P . END
PCP 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
PCP C1 C2 single 1.524 0.020
PCP C5 C1 single 1.524 0.020
PCP C1 O1 single 1.426 0.020
PCP H1 C1 single 1.099 0.020
PCP C2 C3 single 1.524 0.020
PCP O2 C2 single 1.432 0.020
PCP H2 C2 single 1.099 0.020
PCP C3 C4 single 1.524 0.020
PCP O3 C3 single 1.432 0.020
PCP H3 C3 single 1.099 0.020
PCP C4 C5 single 1.524 0.020
PCP CP C4 single 1.524 0.020
PCP H4 C4 single 1.099 0.020
PCP H51 C5 single 1.092 0.020
PCP H52 C5 single 1.092 0.020
PCP OP CP single 1.426 0.020
PCP HP1 CP single 1.092 0.020
PCP HP2 CP single 1.092 0.020
PCP O1 PA single 1.610 0.020
PCP HO2 O2 single 0.967 0.020
PCP HO3 O3 single 0.967 0.020
PCP P OP single 1.610 0.020
PCP O1P P deloc 1.510 0.020
PCP O2P P deloc 1.510 0.020
PCP O3P P deloc 1.510 0.020
PCP O1A PA deloc 1.510 0.020
PCP O2A PA deloc 1.510 0.020
PCP PA O3A single 1.610 0.020
PCP O3A PB single 1.610 0.020
PCP O1B PB deloc 1.510 0.020
PCP O2B PB deloc 1.510 0.020
PCP PB O3B deloc 1.510 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
PCP O3B PB O1B 119.900 3.000
PCP O3B PB O2B 119.900 3.000
PCP O3B PB O3A 108.200 3.000
PCP O1B PB O2B 119.900 3.000
PCP O1B PB O3A 108.200 3.000
PCP O2B PB O3A 108.200 3.000
PCP PB O3A PA 120.500 3.000
PCP O3A PA O1A 108.200 3.000
PCP O3A PA O2A 108.200 3.000
PCP O3A PA O1 102.600 3.000
PCP O1A PA O2A 119.900 3.000
PCP O1A PA O1 108.200 3.000
PCP O2A PA O1 108.200 3.000
PCP PA O1 C1 120.500 3.000
PCP O1 C1 H1 109.470 3.000
PCP O1 C1 C5 109.470 3.000
PCP O1 C1 C2 109.470 3.000
PCP H1 C1 C5 108.340 3.000
PCP H1 C1 C2 108.340 3.000
PCP C5 C1 C2 111.000 3.000
PCP C1 C5 H51 109.470 3.000
PCP C1 C5 H52 109.470 3.000
PCP C1 C5 C4 111.000 3.000
PCP H51 C5 H52 107.900 3.000
PCP H51 C5 C4 109.470 3.000
PCP H52 C5 C4 109.470 3.000
PCP C5 C4 H4 108.340 3.000
PCP C5 C4 C3 111.000 3.000
PCP C5 C4 CP 109.470 3.000
PCP H4 C4 C3 108.340 3.000
PCP H4 C4 CP 108.340 3.000
PCP C3 C4 CP 111.000 3.000
PCP C4 C3 H3 108.340 3.000
PCP C4 C3 O3 109.470 3.000
PCP C4 C3 C2 111.000 3.000
PCP H3 C3 O3 109.470 3.000
PCP H3 C3 C2 108.340 3.000
PCP O3 C3 C2 109.470 3.000
PCP C3 O3 HO3 109.470 3.000
PCP C3 C2 H2 108.340 3.000
PCP C3 C2 O2 109.470 3.000
PCP C3 C2 C1 111.000 3.000
PCP H2 C2 O2 109.470 3.000
PCP H2 C2 C1 108.340 3.000
PCP O2 C2 C1 109.470 3.000
PCP C2 O2 HO2 109.470 3.000
PCP C4 CP HP1 109.470 3.000
PCP C4 CP HP2 109.470 3.000
PCP C4 CP OP 109.470 3.000
PCP HP1 CP HP2 107.900 3.000
PCP HP1 CP OP 109.470 3.000
PCP HP2 CP OP 109.470 3.000
PCP CP OP P 120.500 3.000
PCP OP P O1P 108.200 3.000
PCP OP P O2P 108.200 3.000
PCP OP P O3P 108.200 3.000
PCP O1P P O2P 119.900 3.000
PCP O1P P O3P 119.900 3.000
PCP O2P P O3P 119.900 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
PCP var_1 O3B PB O3A PA -60.031 20.000 1
PCP var_2 PB O3A PA O1 179.943 20.000 1
PCP var_3 O3A PA O1 C1 179.986 20.000 1
PCP var_4 PA O1 C1 C5 123.739 20.000 1
PCP var_5 O1 C1 C2 C3 -90.000 20.000 3
PCP var_6 O1 C1 C5 C4 90.000 20.000 3
PCP var_7 C1 C5 C4 CP 150.000 20.000 3
PCP var_8 C5 C4 C3 C2 -30.000 20.000 3
PCP var_9 C4 C3 O3 HO3 179.316 20.000 1
PCP var_10 C4 C3 C2 O2 -120.000 20.000 3
PCP var_11 C3 C2 O2 HO2 -61.435 20.000 1
PCP var_12 C5 C4 CP OP 61.498 20.000 3
PCP var_13 C4 CP OP P 179.950 20.000 1
PCP var_14 CP OP P O3P -59.987 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
PCP chir_01 C1 C2 C5 O1 positiv
PCP chir_02 C2 C1 C3 O2 negativ
PCP chir_03 C3 C2 C4 O3 negativ
PCP chir_04 C4 C3 C5 CP positiv
# ------------------------------------------------------
|
