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
|
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
SCY SCY 'S-ACETYL-CYSTEINE ' peptide 18 10 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_SCY
#
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
SCY N N NH2 0.000 0.000 0.000 0.000
SCY HN1 H H 0.000 0.926 -0.368 0.185
SCY HN2 H H 0.000 -0.366 -0.029 -0.944
SCY CA C CH1 0.000 -0.803 0.570 1.090
SCY HA H H 0.000 -0.956 1.643 0.909
SCY CB C CH2 0.000 -2.159 -0.135 1.147
SCY HB2 H H 0.000 -2.755 0.289 1.957
SCY HB3 H H 0.000 -2.007 -1.201 1.328
SCY SG S S2 0.000 -3.026 0.094 -0.425
SCY CD C C 0.000 -4.468 -0.768 -0.099
SCY OCD O O 0.000 -4.624 -1.302 0.980
SCY CE C CH3 0.000 -5.544 -0.864 -1.149
SCY HE3 H H 0.000 -5.880 0.108 -1.402
SCY HE2 H H 0.000 -5.154 -1.338 -2.013
SCY HE1 H H 0.000 -6.356 -1.430 -0.773
SCY C C C 0.000 -0.081 0.379 2.399
SCY O O OC -0.500 0.674 -0.606 2.559
SCY OXT O OC -0.500 -0.236 1.205 3.325
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
SCY N n/a CA START
SCY HN1 N . .
SCY HN2 N . .
SCY CA N C .
SCY HA CA . .
SCY CB CA SG .
SCY HB2 CB . .
SCY HB3 CB . .
SCY SG CB CD .
SCY CD SG CE .
SCY OCD CD . .
SCY CE CD HE1 .
SCY HE3 CE . .
SCY HE2 CE . .
SCY HE1 CE . .
SCY C CA . END
SCY O C . .
SCY OXT C . .
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
SCY CA N single 1.450 0.020
SCY CB CA single 1.524 0.020
SCY C CA single 1.500 0.020
SCY HA CA single 1.099 0.020
SCY SG CB single 1.762 0.020
SCY HB2 CB single 1.092 0.020
SCY HB3 CB single 1.092 0.020
SCY CD SG single 1.665 0.020
SCY OCD CD double 1.220 0.020
SCY CE CD single 1.500 0.020
SCY HE1 CE single 1.059 0.020
SCY HE2 CE single 1.059 0.020
SCY HE3 CE single 1.059 0.020
SCY O C deloc 1.250 0.020
SCY OXT C deloc 1.250 0.020
SCY HN1 N single 1.010 0.020
SCY HN2 N single 1.010 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
SCY HN1 N HN2 120.000 3.000
SCY HN1 N CA 120.000 3.000
SCY HN2 N CA 120.000 3.000
SCY N CA HA 109.470 3.000
SCY N CA CB 109.470 3.000
SCY N CA C 109.470 3.000
SCY HA CA CB 108.340 3.000
SCY HA CA C 108.810 3.000
SCY CB CA C 109.470 3.000
SCY CA CB HB2 109.470 3.000
SCY CA CB HB3 109.470 3.000
SCY CA CB SG 109.500 3.000
SCY HB2 CB HB3 107.900 3.000
SCY HB2 CB SG 109.500 3.000
SCY HB3 CB SG 109.500 3.000
SCY CB SG CD 100.029 3.000
SCY SG CD OCD 120.000 3.000
SCY SG CD CE 120.000 3.000
SCY OCD CD CE 123.000 3.000
SCY CD CE HE3 109.470 3.000
SCY CD CE HE2 109.470 3.000
SCY CD CE HE1 109.470 3.000
SCY HE3 CE HE2 109.470 3.000
SCY HE3 CE HE1 109.470 3.000
SCY HE2 CE HE1 109.470 3.000
SCY CA C O 118.500 3.000
SCY CA C OXT 118.500 3.000
SCY 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
SCY var_1 HN2 N CA C 175.000 20.000 1
SCY var_2 N CA CB SG -59.960 20.000 3
SCY var_3 CA CB SG CD 179.991 20.000 1
SCY var_4 CB SG CD CE 179.996 20.000 1
SCY var_5 SG CD CE HE1 -179.950 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
SCY chir_01 CA N CB C 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
SCY plan-1 N 0.020
SCY plan-1 CA 0.020
SCY plan-1 HN1 0.020
SCY plan-1 HN2 0.020
SCY plan-2 CD 0.020
SCY plan-2 SG 0.020
SCY plan-2 OCD 0.020
SCY plan-2 CE 0.020
SCY plan-3 C 0.020
SCY plan-3 CA 0.020
SCY plan-3 O 0.020
SCY plan-3 OXT 0.020
# ------------------------------------------------------
|
