PDB Chemical Component VR0
The following tables include covalent bond distance, bond angle and torsion angle values for the experimental model and ideal geometries stored in the definition for this chemical component.
Bond Distances for VR0
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C1 |
NH3 |
1.470 |
1.466 |
| C1 |
H5 |
1.101 |
1.090 |
| C1 |
H4 |
1.100 |
1.090 |
| C1 |
H3 |
1.100 |
1.090 |
| NH2 |
CZ |
1.330 |
1.302 |
| NH2 |
HH22 |
1.000 |
0.970 |
| O1 |
C6 |
1.231 |
1.216 |
| O |
C |
1.230 |
1.208 |
| CG |
CD |
1.531 |
1.531 |
| CG |
CB |
1.529 |
1.529 |
| CG |
HG2 |
1.100 |
1.090 |
| CG |
HG3 |
1.100 |
1.090 |
| CD |
NE |
1.469 |
1.465 |
| CD |
HD2 |
1.100 |
1.089 |
| CD |
HD3 |
1.100 |
1.090 |
| CB |
CA |
1.530 |
1.531 |
| CB |
HB2 |
1.100 |
1.090 |
| CB |
HB3 |
1.100 |
1.090 |
| NH3 |
C6 |
1.331 |
1.348 |
| NH3 |
HH33 |
1.001 |
0.970 |
| NE |
CZ |
1.330 |
1.375 |
| NE |
HE |
1.000 |
0.970 |
| NH1 |
CZ |
1.332 |
1.381 |
| NH1 |
C6 |
1.341 |
1.347 |
| NH1 |
HH11 |
1.000 |
0.970 |
| N |
CA |
1.469 |
1.469 |
| N |
H2 |
1.000 |
1.009 |
| N |
H |
1.000 |
1.009 |
| C |
CA |
1.529 |
1.507 |
| C |
OXT |
1.430 |
1.343 |
| CA |
HA |
1.100 |
1.090 |
| OXT |
HXT |
0.950 |
0.968 |
Bond Angles for VR0
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| NH3 |
C1 |
H5 |
109.5 |
109.4 |
| NH3 |
C1 |
H4 |
109.5 |
109.4 |
| NH3 |
C1 |
H3 |
109.4 |
109.4 |
| C1 |
NH3 |
C6 |
117.9 |
120.0 |
| C1 |
NH3 |
HH33 |
121.1 |
120.0 |
| H5 |
C1 |
H4 |
109.4 |
109.5 |
| H5 |
C1 |
H3 |
109.5 |
109.5 |
| H4 |
C1 |
H3 |
109.5 |
109.5 |
| CZ |
NH2 |
HH22 |
112.0 |
120.0 |
| NH2 |
CZ |
NE |
119.5 |
120.0 |
| NH2 |
CZ |
NH1 |
122.1 |
120.0 |
| O1 |
C6 |
NH3 |
122.6 |
120.0 |
| O1 |
C6 |
NH1 |
120.2 |
120.0 |
| O |
C |
CA |
119.9 |
120.0 |
| O |
C |
OXT |
120.0 |
120.0 |
| CD |
CG |
CB |
111.1 |
109.5 |
| CD |
CG |
HG2 |
108.9 |
109.5 |
| CD |
CG |
HG3 |
109.0 |
109.5 |
| CG |
CD |
NE |
108.7 |
109.5 |
| CG |
CD |
HD2 |
109.7 |
109.4 |
| CG |
CD |
HD3 |
109.7 |
109.4 |
| CB |
CG |
HG2 |
108.9 |
109.5 |
| CB |
CG |
HG3 |
108.9 |
109.5 |
| CG |
CB |
CA |
111.1 |
109.5 |
| CG |
CB |
HB2 |
108.9 |
109.5 |
| CG |
CB |
HB3 |
108.9 |
109.5 |
| HG2 |
CG |
HG3 |
110.0 |
109.4 |
| NE |
CD |
HD2 |
109.7 |
109.5 |
| NE |
CD |
HD3 |
109.8 |
109.5 |
| CD |
NE |
CZ |
121.2 |
120.0 |
| CD |
NE |
HE |
119.4 |
120.0 |
| HD2 |
CD |
HD3 |
109.2 |
109.5 |
| CA |
CB |
HB2 |
108.9 |
109.5 |
| CA |
CB |
HB3 |
108.9 |
109.5 |
| CB |
CA |
N |
109.3 |
109.4 |
| CB |
CA |
C |
109.3 |
109.5 |
| CB |
CA |
HA |
109.6 |
109.4 |
| HB2 |
CB |
HB3 |
110.0 |
109.4 |
| C6 |
NH3 |
HH33 |
121.0 |
120.0 |
| NH3 |
C6 |
NH1 |
116.8 |
120.0 |
| CZ |
NE |
HE |
119.4 |
120.0 |
| NE |
CZ |
NH1 |
118.3 |
120.0 |
| CZ |
NH1 |
C6 |
125.1 |
120.0 |
| CZ |
NH1 |
HH11 |
117.4 |
120.0 |
| C6 |
NH1 |
HH11 |
117.5 |
120.0 |
| CA |
N |
H2 |
109.5 |
111.0 |
| CA |
N |
H |
109.5 |
111.0 |
| N |
CA |
C |
109.0 |
109.5 |
| N |
CA |
HA |
109.8 |
109.5 |
| H2 |
N |
H |
109.5 |
111.0 |
| CA |
C |
OXT |
120.1 |
120.0 |
| C |
CA |
HA |
109.9 |
109.5 |
| C |
OXT |
HXT |
109.5 |
117.0 |
Torsion Angles for VR0
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| H5 |
C1 |
NH3 |
H4 |
240.0 |
240.0 |
| H5 |
C1 |
NH3 |
H3 |
120.0 |
120.0 |
| H4 |
C1 |
NH3 |
H3 |
240.0 |
240.0 |
| O1 |
C6 |
NH3 |
C1 |
354.0 |
0.1 |
| C6 |
NH3 |
C1 |
HH33 |
180.0 |
179.9 |
| C1 |
NH3 |
C6 |
NH1 |
180.2 |
180.0 |
| NH3 |
C1 |
H5 |
H4 |
120.0 |
120.0 |
| NH3 |
C1 |
H5 |
H3 |
240.0 |
240.1 |
| H5 |
C1 |
NH3 |
C6 |
180.0 |
180.0 |
| H5 |
C1 |
NH3 |
HH33 |
0.0 |
0.1 |
| H4 |
C1 |
H5 |
H3 |
120.0 |
120.1 |
| NH3 |
C1 |
H4 |
H5 |
240.0 |
240.0 |
| NH3 |
C1 |
H4 |
H3 |
120.0 |
120.0 |
| H4 |
C1 |
NH3 |
C6 |
300.0 |
300.0 |
| H4 |
C1 |
NH3 |
HH33 |
120.0 |
120.1 |
| H5 |
C1 |
H4 |
H3 |
240.0 |
239.9 |
| NH3 |
C1 |
H3 |
H5 |
120.0 |
119.9 |
| NH3 |
C1 |
H3 |
H4 |
240.0 |
240.0 |
| H3 |
C1 |
NH3 |
C6 |
60.0 |
60.0 |
| H3 |
C1 |
NH3 |
HH33 |
240.0 |
240.1 |
| H5 |
C1 |
H3 |
H4 |
120.0 |
120.1 |
| CD |
NE |
CZ |
NH2 |
356.1 |
6.2 |
| NH2 |
CZ |
NE |
HE |
176.2 |
186.1 |
| NE |
CZ |
NH2 |
NH1 |
184.5 |
180.0 |
| NH2 |
CZ |
NH1 |
C6 |
6.8 |
186.3 |
| NH2 |
CZ |
NH1 |
HH11 |
186.8 |
6.3 |
| HH22 |
NH2 |
CZ |
NE |
184.5 |
174.9 |
| HH22 |
NH2 |
CZ |
NH1 |
0.0 |
354.9 |
| C1 |
NH3 |
C6 |
O1 |
354.0 |
0.1 |
| O1 |
C6 |
NH3 |
HH33 |
174.0 |
180.0 |
| NH3 |
C6 |
O1 |
NH1 |
186.5 |
180.0 |
| CZ |
NH1 |
C6 |
O1 |
7.7 |
355.2 |
| O1 |
C6 |
NH1 |
HH11 |
187.7 |
175.2 |
| CB |
CA |
C |
O |
73.4 |
100.0 |
| N |
CA |
C |
O |
314.1 |
340.0 |
| CA |
C |
O |
OXT |
180.0 |
180.0 |
| O |
C |
CA |
HA |
193.7 |
219.9 |
| O |
C |
OXT |
HXT |
0.0 |
0.0 |
| CB |
CG |
CD |
HG2 |
240.0 |
239.9 |
| CB |
CG |
CD |
HG3 |
120.0 |
120.0 |
| CD |
CG |
CB |
CA |
185.9 |
180.0 |
| CD |
CG |
CB |
HB2 |
305.9 |
300.1 |
| CD |
CG |
CB |
HB3 |
65.9 |
60.0 |
| HG2 |
CG |
CD |
HG3 |
240.0 |
240.1 |
| NE |
CD |
CG |
HD2 |
240.0 |
240.0 |
| NE |
CD |
CG |
HD3 |
120.0 |
120.0 |
| CG |
CD |
NE |
CZ |
116.0 |
180.0 |
| CG |
CD |
NE |
HE |
296.0 |
0.1 |
| HD2 |
CD |
CG |
HD3 |
240.0 |
240.0 |
| CD |
CG |
CB |
HG2 |
120.0 |
120.0 |
| CD |
CG |
CB |
HG3 |
240.0 |
240.0 |
| CB |
CG |
CD |
NE |
183.0 |
180.0 |
| CB |
CG |
CD |
HD2 |
303.0 |
300.0 |
| CB |
CG |
CD |
HD3 |
63.0 |
60.0 |
| HG2 |
CG |
CB |
HG3 |
120.0 |
120.0 |
| CA |
CB |
CG |
HB2 |
240.0 |
239.9 |
| CA |
CB |
CG |
HB3 |
120.0 |
120.0 |
| CG |
CB |
CA |
N |
304.4 |
295.0 |
| CG |
CB |
CA |
C |
185.2 |
175.0 |
| CG |
CB |
CA |
HA |
64.8 |
55.1 |
| HB2 |
CB |
CG |
HB3 |
240.0 |
240.0 |
| CD |
CG |
HG2 |
CB |
238.7 |
239.9 |
| CD |
CG |
HG2 |
HG3 |
119.4 |
120.0 |
| HG2 |
CG |
CD |
NE |
303.0 |
300.0 |
| HG2 |
CG |
CD |
HD2 |
63.0 |
60.1 |
| HG2 |
CG |
CD |
HD3 |
183.0 |
180.0 |
| CB |
CG |
HG2 |
HG3 |
240.7 |
240.0 |
| HG2 |
CG |
CB |
CA |
65.9 |
60.0 |
| HG2 |
CG |
CB |
HB2 |
186.0 |
180.0 |
| HG2 |
CG |
CB |
HB3 |
305.9 |
300.0 |
| CD |
CG |
HG3 |
CB |
121.3 |
120.0 |
| CD |
CG |
HG3 |
HG2 |
240.7 |
240.0 |
| HG3 |
CG |
CD |
NE |
63.0 |
60.0 |
| HG3 |
CG |
CD |
HD2 |
183.0 |
180.0 |
| HG3 |
CG |
CD |
HD3 |
303.0 |
300.0 |
| CB |
CG |
HG3 |
HG2 |
119.3 |
120.0 |
| HG3 |
CG |
CB |
CA |
306.0 |
300.0 |
| HG3 |
CG |
CB |
HB2 |
66.0 |
60.0 |
| HG3 |
CG |
CB |
HB3 |
186.0 |
180.0 |
| NH2 |
CZ |
NE |
CD |
356.1 |
6.2 |
| NE |
CD |
CG |
CB |
183.0 |
180.0 |
| NE |
CD |
CG |
HG2 |
303.0 |
300.0 |
| NE |
CD |
CG |
HG3 |
63.0 |
60.0 |
| CG |
CD |
NE |
HD2 |
120.0 |
120.0 |
| CG |
CD |
NE |
HD3 |
240.0 |
240.0 |
| HD2 |
CD |
NE |
HD3 |
120.0 |
120.1 |
| CZ |
NE |
CD |
HE |
180.0 |
179.9 |
| CD |
NE |
CZ |
NH1 |
180.5 |
186.2 |
| HD2 |
CD |
CG |
CB |
303.0 |
300.0 |
| HD2 |
CD |
CG |
HG2 |
63.0 |
60.1 |
| HD2 |
CD |
CG |
HG3 |
183.0 |
180.0 |
| CG |
CD |
HD2 |
NE |
240.6 |
240.0 |
| CG |
CD |
HD2 |
HD3 |
120.3 |
120.0 |
| NE |
CD |
HD2 |
HD3 |
239.7 |
239.9 |
| HD2 |
CD |
NE |
CZ |
356.1 |
60.0 |
| HD2 |
CD |
NE |
HE |
176.0 |
240.1 |
| HD3 |
CD |
CG |
CB |
63.0 |
60.0 |
| HD3 |
CD |
CG |
HG2 |
183.0 |
180.0 |
| HD3 |
CD |
CG |
HG3 |
303.0 |
300.0 |
| CG |
CD |
HD3 |
NE |
119.4 |
120.0 |
| CG |
CD |
HD3 |
HD2 |
239.7 |
240.1 |
| NE |
CD |
HD3 |
HD2 |
120.3 |
120.1 |
| HD3 |
CD |
NE |
CZ |
236.0 |
299.9 |
| HD3 |
CD |
NE |
HE |
56.0 |
120.0 |
| O |
C |
CA |
CB |
73.4 |
100.0 |
| CA |
CB |
CG |
HG2 |
65.9 |
60.0 |
| CA |
CB |
CG |
HG3 |
306.0 |
300.0 |
| CG |
CB |
CA |
HB2 |
120.0 |
120.0 |
| CG |
CB |
CA |
HB3 |
240.0 |
240.0 |
| HB2 |
CB |
CA |
HB3 |
120.0 |
120.0 |
| CB |
CA |
N |
H2 |
180.0 |
300.0 |
| CB |
CA |
N |
H |
300.0 |
64.0 |
| N |
CA |
CB |
C |
119.2 |
120.0 |
| N |
CA |
CB |
HA |
239.6 |
240.0 |
| CB |
CA |
C |
OXT |
253.4 |
280.0 |
| C |
CA |
CB |
HA |
120.4 |
120.0 |
| HB2 |
CB |
CG |
HG2 |
186.0 |
180.0 |
| HB2 |
CB |
CG |
HG3 |
66.0 |
60.0 |
| CG |
CB |
HB2 |
CA |
238.6 |
240.0 |
| CG |
CB |
HB2 |
HB3 |
119.3 |
120.0 |
| CA |
CB |
HB2 |
HB3 |
240.7 |
240.0 |
| HB2 |
CB |
CA |
N |
184.4 |
175.0 |
| HB2 |
CB |
CA |
C |
65.2 |
55.0 |
| HB2 |
CB |
CA |
HA |
304.8 |
295.0 |
| HB3 |
CB |
CG |
HG2 |
305.9 |
300.0 |
| HB3 |
CB |
CG |
HG3 |
186.0 |
180.0 |
| CG |
CB |
HB3 |
CA |
121.3 |
120.0 |
| CG |
CB |
HB3 |
HB2 |
240.7 |
240.0 |
| CA |
CB |
HB3 |
HB2 |
119.4 |
120.0 |
| HB3 |
CB |
CA |
N |
64.4 |
55.0 |
| HB3 |
CB |
CA |
C |
305.2 |
295.0 |
| HB3 |
CB |
CA |
HA |
184.8 |
175.1 |
| C6 |
NH3 |
C1 |
H5 |
180.0 |
180.0 |
| C6 |
NH3 |
C1 |
H4 |
300.0 |
300.0 |
| C6 |
NH3 |
C1 |
H3 |
60.0 |
60.0 |
| C1 |
NH3 |
C6 |
HH33 |
180.0 |
180.1 |
| O1 |
C6 |
NH3 |
NH1 |
173.7 |
180.0 |
| CZ |
NH1 |
C6 |
NH3 |
181.6 |
175.3 |
| NH3 |
C6 |
NH1 |
HH11 |
1.6 |
355.3 |
| HH33 |
NH3 |
C1 |
H5 |
0.0 |
0.1 |
| HH33 |
NH3 |
C1 |
H4 |
120.0 |
120.1 |
| HH33 |
NH3 |
C1 |
H3 |
240.0 |
240.1 |
| C1 |
NH3 |
HH33 |
C6 |
180.0 |
179.9 |
| HH33 |
NH3 |
C6 |
NH1 |
0.2 |
359.9 |
| NE |
CZ |
NH2 |
HH22 |
184.5 |
174.9 |
| NH2 |
CZ |
NE |
NH1 |
175.6 |
180.0 |
| CZ |
NE |
CD |
HD2 |
356.1 |
60.0 |
| CZ |
NE |
CD |
HD3 |
236.0 |
299.9 |
| CD |
NE |
CZ |
HE |
180.0 |
180.1 |
| NE |
CZ |
NH1 |
C6 |
182.3 |
6.2 |
| NE |
CZ |
NH1 |
HH11 |
2.3 |
186.3 |
| HE |
NE |
CD |
HD2 |
176.0 |
240.1 |
| HE |
NE |
CD |
HD3 |
56.0 |
120.0 |
| CD |
NE |
HE |
CZ |
180.0 |
179.9 |
| HE |
NE |
CZ |
NH1 |
0.5 |
6.1 |
| NH1 |
CZ |
NH2 |
HH22 |
0.0 |
354.9 |
| NH2 |
CZ |
NH1 |
NE |
184.5 |
180.0 |
| O1 |
C6 |
NH1 |
CZ |
7.7 |
355.2 |
| NH3 |
C6 |
NH1 |
CZ |
181.6 |
175.3 |
| NH1 |
CZ |
NE |
HE |
0.5 |
6.1 |
| C6 |
NH1 |
CZ |
HH11 |
180.0 |
180.0 |
| O1 |
C6 |
NH1 |
NH3 |
186.1 |
180.0 |
| NH1 |
C6 |
NH3 |
HH33 |
0.2 |
359.9 |
| CZ |
NH1 |
C6 |
HH11 |
180.0 |
180.0 |
| CZ |
NH1 |
HH11 |
C6 |
180.0 |
180.0 |
| O |
C |
CA |
N |
314.1 |
340.0 |
| N |
CA |
CB |
HB2 |
184.4 |
175.0 |
| N |
CA |
CB |
HB3 |
64.4 |
55.0 |
| CB |
CA |
N |
C |
240.7 |
240.0 |
| CB |
CA |
N |
HA |
120.2 |
120.0 |
| H2 |
N |
CA |
H |
240.0 |
236.0 |
| N |
CA |
C |
OXT |
134.1 |
160.0 |
| C |
CA |
N |
HA |
239.6 |
240.0 |
| CA |
N |
H2 |
H |
120.0 |
124.0 |
| H2 |
N |
CA |
C |
299.3 |
60.0 |
| H2 |
N |
CA |
HA |
59.7 |
180.0 |
| CA |
N |
H |
H2 |
240.0 |
236.0 |
| H |
N |
CA |
C |
59.3 |
184.0 |
| H |
N |
CA |
HA |
179.7 |
304.0 |
| O |
C |
CA |
OXT |
180.0 |
180.0 |
| C |
CA |
CB |
HB2 |
65.2 |
55.0 |
| C |
CA |
CB |
HB3 |
305.2 |
295.0 |
| CB |
CA |
C |
N |
119.4 |
120.0 |
| CB |
CA |
C |
HA |
239.7 |
240.1 |
| C |
CA |
N |
H2 |
299.3 |
60.0 |
| C |
CA |
N |
H |
59.3 |
184.0 |
| N |
CA |
C |
HA |
120.4 |
120.1 |
| CA |
C |
OXT |
HXT |
180.0 |
180.0 |
| O |
C |
OXT |
CA |
180.0 |
180.0 |
| OXT |
C |
CA |
HA |
13.7 |
39.9 |
| HA |
CA |
CB |
HB2 |
304.8 |
295.0 |
| HA |
CA |
CB |
HB3 |
184.8 |
175.1 |
| CB |
CA |
HA |
N |
239.9 |
240.0 |
| CB |
CA |
HA |
C |
120.1 |
120.0 |
| HA |
CA |
N |
H2 |
59.7 |
180.0 |
| HA |
CA |
N |
H |
179.7 |
304.0 |
| N |
CA |
HA |
C |
240.1 |
240.0 |
| HA |
CA |
C |
OXT |
13.7 |
39.9 |