PDB Chemical Component RBV
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 RBV
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N1 |
N2 |
1.359 |
1.288 |
| N1 |
C5 |
1.323 |
1.346 |
| N1 |
C1' |
1.451 |
1.466 |
| N2 |
C3 |
1.343 |
1.315 |
| C3 |
N4 |
1.366 |
1.345 |
| C3 |
C6 |
1.525 |
1.479 |
| N3 |
C6 |
1.428 |
1.347 |
| O3 |
C6 |
1.241 |
1.215 |
| N4 |
C5 |
1.364 |
1.308 |
| C1' |
C2' |
1.530 |
1.550 |
| C1' |
O4' |
1.412 |
1.444 |
| C2' |
O2' |
1.409 |
1.429 |
| C2' |
C3' |
1.531 |
1.548 |
| C3' |
O3' |
1.427 |
1.428 |
| C3' |
C4' |
1.529 |
1.542 |
| C4' |
O4' |
1.444 |
1.438 |
| C4' |
C5' |
1.509 |
1.530 |
| C5' |
O5' |
1.422 |
1.429 |
| N3 |
HN3 |
1.000 |
0.970 |
| N3 |
HN3A |
1.001 |
0.970 |
| C5 |
H5 |
1.080 |
1.080 |
| C1' |
H1' |
1.100 |
1.089 |
| C2' |
H2' |
1.100 |
1.090 |
| O2' |
HO2' |
0.950 |
0.967 |
| C3' |
H3' |
1.100 |
1.090 |
| O3' |
HO3' |
0.950 |
0.968 |
| C4' |
H4' |
1.100 |
1.090 |
| C5' |
H5' |
1.100 |
1.090 |
| C5' |
H5'A |
1.100 |
1.090 |
| O5' |
HO5' |
0.950 |
0.967 |
Bond Angles for RBV
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| N2 |
N1 |
C5 |
109.3 |
108.5 |
| N2 |
N1 |
C1' |
125.1 |
125.7 |
| N1 |
N2 |
C3 |
108.0 |
108.7 |
| C5 |
N1 |
C1' |
125.6 |
125.7 |
| N1 |
C5 |
N4 |
107.4 |
107.6 |
| N1 |
C5 |
H5 |
126.3 |
126.2 |
| N1 |
C1' |
C2' |
113.8 |
110.6 |
| N1 |
C1' |
O4' |
108.2 |
110.6 |
| N1 |
C1' |
H1' |
107.1 |
110.6 |
| N2 |
C3 |
N4 |
107.2 |
107.9 |
| N2 |
C3 |
C6 |
126.4 |
126.0 |
| N4 |
C3 |
C6 |
126.4 |
126.1 |
| C3 |
N4 |
C5 |
108.1 |
107.3 |
| C3 |
C6 |
N3 |
120.5 |
120.0 |
| C3 |
C6 |
O3 |
120.4 |
120.0 |
| N3 |
C6 |
O3 |
119.1 |
120.0 |
| C6 |
N3 |
HN3 |
120.0 |
120.0 |
| C6 |
N3 |
HN3A |
120.0 |
120.0 |
| N4 |
C5 |
H5 |
126.3 |
126.3 |
| C2' |
C1' |
O4' |
108.7 |
103.5 |
| C1' |
C2' |
O2' |
110.9 |
110.9 |
| C1' |
C2' |
C3' |
105.5 |
102.1 |
| C2' |
C1' |
H1' |
106.7 |
110.6 |
| C1' |
C2' |
H2' |
112.7 |
110.9 |
| C1' |
O4' |
C4' |
111.5 |
107.0 |
| O4' |
C1' |
H1' |
112.5 |
110.7 |
| O2' |
C2' |
C3' |
113.7 |
110.9 |
| O2' |
C2' |
H2' |
104.3 |
110.7 |
| C2' |
O2' |
HO2' |
109.5 |
114.0 |
| C2' |
C3' |
O3' |
109.0 |
110.5 |
| C2' |
C3' |
C4' |
105.9 |
104.2 |
| C3' |
C2' |
H2' |
109.9 |
110.9 |
| C2' |
C3' |
H3' |
112.1 |
110.5 |
| O3' |
C3' |
C4' |
109.5 |
110.5 |
| O3' |
C3' |
H3' |
108.6 |
110.5 |
| C3' |
O3' |
HO3' |
109.5 |
114.0 |
| C3' |
C4' |
O4' |
107.7 |
107.3 |
| C3' |
C4' |
C5' |
115.0 |
109.9 |
| C4' |
C3' |
H3' |
111.6 |
110.6 |
| C3' |
C4' |
H4' |
106.7 |
109.9 |
| O4' |
C4' |
C5' |
108.6 |
109.9 |
| O4' |
C4' |
H4' |
113.3 |
109.9 |
| C4' |
C5' |
O5' |
111.8 |
109.4 |
| C5' |
C4' |
H4' |
105.7 |
110.0 |
| C4' |
C5' |
H5' |
108.7 |
109.4 |
| C4' |
C5' |
H5'A |
108.7 |
109.5 |
| O5' |
C5' |
H5' |
108.7 |
109.4 |
| O5' |
C5' |
H5'A |
108.7 |
109.5 |
| C5' |
O5' |
HO5' |
109.5 |
114.0 |
| HN3 |
N3 |
HN3A |
120.0 |
120.0 |
| H5' |
C5' |
H5'A |
110.2 |
109.5 |
Torsion Angles for RBV
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C5 |
N1 |
N2 |
C1' |
180.3 |
180.3 |
| N2 |
N1 |
C5 |
N4 |
359.8 |
360.0 |
| N2 |
N1 |
C5 |
H5 |
179.8 |
180.0 |
| N2 |
N1 |
C1' |
C2' |
150.5 |
305.1 |
| N2 |
N1 |
C1' |
O4' |
271.3 |
59.1 |
| N2 |
N1 |
C1' |
H1' |
32.8 |
182.2 |
| N1 |
N2 |
C3 |
N4 |
359.6 |
360.0 |
| N1 |
N2 |
C3 |
C6 |
179.7 |
180.0 |
| N2 |
N1 |
C5 |
C1' |
179.7 |
179.7 |
| C5 |
N1 |
N2 |
C3 |
0.4 |
0.1 |
| C5 |
N1 |
C1' |
C2' |
330.1 |
124.7 |
| C5 |
N1 |
C1' |
O4' |
91.0 |
238.7 |
| C5 |
N1 |
C1' |
H1' |
212.4 |
1.8 |
| C3 |
N4 |
C5 |
N1 |
359.9 |
0.0 |
| N4 |
C5 |
N1 |
H5 |
180.0 |
180.0 |
| N2 |
N1 |
C1' |
C5 |
180.4 |
180.4 |
| C1' |
N1 |
N2 |
C3 |
180.1 |
179.7 |
| C1' |
N1 |
C5 |
N4 |
180.1 |
180.3 |
| C1' |
N1 |
C5 |
H5 |
0.1 |
0.3 |
| C2' |
C1' |
N1 |
O4' |
239.1 |
245.9 |
| N1 |
C1' |
C2' |
O2' |
237.7 |
273.7 |
| N1 |
C1' |
C2' |
C3' |
114.1 |
155.5 |
| C2' |
C1' |
N1 |
H1' |
117.7 |
122.9 |
| N1 |
C1' |
C2' |
H2' |
354.2 |
37.2 |
| N1 |
C1' |
O4' |
C4' |
244.6 |
201.4 |
| O4' |
C1' |
N1 |
H1' |
238.5 |
237.0 |
| C3 |
N2 |
N1 |
C5 |
0.4 |
0.1 |
| C3 |
N2 |
N1 |
C1' |
180.1 |
179.7 |
| N4 |
C3 |
N2 |
C6 |
179.9 |
180.0 |
| N2 |
C3 |
N4 |
C5 |
0.3 |
0.0 |
| N2 |
C3 |
C6 |
N3 |
48.7 |
180.0 |
| N2 |
C3 |
C6 |
O3 |
230.1 |
360.0 |
| N1 |
C5 |
N4 |
C3 |
359.9 |
0.0 |
| N2 |
C3 |
N4 |
C6 |
180.1 |
180.0 |
| N4 |
C3 |
C6 |
N3 |
228.8 |
0.0 |
| N4 |
C3 |
C6 |
O3 |
50.2 |
180.0 |
| C3 |
N4 |
C5 |
H5 |
180.0 |
180.0 |
| N2 |
C3 |
C6 |
N4 |
179.9 |
180.0 |
| C6 |
C3 |
N4 |
C5 |
180.2 |
180.0 |
| N3 |
C6 |
C3 |
O3 |
178.6 |
180.0 |
| C3 |
C6 |
N3 |
HN3 |
181.4 |
359.9 |
| C3 |
C6 |
N3 |
HN3A |
1.4 |
180.0 |
| C3 |
C6 |
N3 |
O3 |
181.4 |
180.0 |
| HN3 |
N3 |
C6 |
HN3A |
180.0 |
180.0 |
| C3 |
C6 |
O3 |
N3 |
178.6 |
180.0 |
| O3 |
C6 |
N3 |
HN3 |
0.0 |
180.0 |
| O3 |
C6 |
N3 |
HN3A |
180.0 |
0.0 |
| N4 |
C5 |
N1 |
C1' |
180.1 |
180.3 |
| N1 |
C5 |
N4 |
H5 |
180.0 |
180.0 |
| C5 |
N4 |
C3 |
C6 |
180.2 |
180.0 |
| N1 |
C1' |
C2' |
O4' |
120.6 |
118.5 |
| N1 |
C1' |
C2' |
H1' |
242.1 |
237.1 |
| C2' |
C1' |
O4' |
C4' |
8.6 |
319.9 |
| O4' |
C1' |
C2' |
H1' |
121.5 |
118.6 |
| O2' |
C2' |
C1' |
C3' |
123.6 |
118.2 |
| O2' |
C2' |
C1' |
H2' |
243.4 |
236.5 |
| C1' |
C2' |
O2' |
HO2' |
180.0 |
180.0 |
| C1' |
C2' |
C3' |
O3' |
120.0 |
97.8 |
| C1' |
C2' |
C3' |
C4' |
2.2 |
339.1 |
| C3' |
C2' |
C1' |
H2' |
119.9 |
118.3 |
| C1' |
C2' |
C3' |
H3' |
240.3 |
220.3 |
| N1 |
C1' |
O4' |
C2' |
236.0 |
241.5 |
| N1 |
C1' |
O4' |
H1' |
118.1 |
122.9 |
| O4' |
C1' |
C2' |
O2' |
117.1 |
155.2 |
| O4' |
C1' |
C2' |
C3' |
353.5 |
37.0 |
| C2' |
C1' |
O4' |
H1' |
242.1 |
241.4 |
| O4' |
C1' |
C2' |
H2' |
233.6 |
278.8 |
| C3' |
C4' |
O4' |
C1' |
352.9 |
26.5 |
| C1' |
O4' |
C4' |
C5' |
118.0 |
145.9 |
| C1' |
O4' |
C4' |
H4' |
235.2 |
267.1 |
| O2' |
C2' |
C1' |
O4' |
117.1 |
155.2 |
| C1' |
C2' |
O2' |
C3' |
241.3 |
247.3 |
| O2' |
C2' |
C1' |
H1' |
355.6 |
36.6 |
| C1' |
C2' |
O2' |
H2' |
121.6 |
123.6 |
| O2' |
C2' |
C3' |
O3' |
358.3 |
339.5 |
| O2' |
C2' |
C3' |
C4' |
240.5 |
220.9 |
| C3' |
C2' |
O2' |
H2' |
240.3 |
236.4 |
| O2' |
C2' |
C3' |
H3' |
118.6 |
102.1 |
| C3' |
C2' |
C1' |
O4' |
353.5 |
37.0 |
| C1' |
C2' |
C3' |
O2' |
121.7 |
118.2 |
| C3' |
C2' |
C1' |
H1' |
232.0 |
278.4 |
| C1' |
C2' |
C3' |
H2' |
238.3 |
241.7 |
| O2' |
C2' |
C3' |
H2' |
116.5 |
123.5 |
| C3' |
C2' |
O2' |
HO2' |
298.7 |
292.7 |
| O3' |
C3' |
C2' |
C4' |
117.8 |
118.6 |
| O3' |
C3' |
C2' |
H3' |
239.7 |
237.4 |
| C2' |
C3' |
O3' |
HO3' |
180.0 |
61.5 |
| C2' |
C3' |
C4' |
O4' |
2.6 |
358.0 |
| C2' |
C3' |
C4' |
C5' |
241.4 |
238.6 |
| C4' |
C3' |
C2' |
H3' |
121.9 |
118.8 |
| C2' |
C3' |
C4' |
H4' |
124.6 |
117.4 |
| C2' |
C3' |
O3' |
C4' |
244.5 |
245.2 |
| O3' |
C3' |
C2' |
H2' |
241.8 |
216.0 |
| C2' |
C3' |
O3' |
H3' |
122.4 |
122.6 |
| O3' |
C3' |
C4' |
O4' |
245.2 |
239.3 |
| O3' |
C3' |
C4' |
C5' |
124.0 |
119.9 |
| C4' |
C3' |
O3' |
H3' |
237.9 |
237.4 |
| O3' |
C3' |
C4' |
H4' |
7.1 |
358.7 |
| C1' |
O4' |
C4' |
C3' |
352.9 |
26.5 |
| C2' |
C3' |
C4' |
O3' |
117.5 |
118.7 |
| C4' |
C3' |
C2' |
H2' |
124.0 |
97.4 |
| C2' |
C3' |
C4' |
H3' |
237.8 |
241.3 |
| O3' |
C3' |
C4' |
H3' |
120.3 |
122.6 |
| C4' |
C3' |
O3' |
HO3' |
295.5 |
176.3 |
| O4' |
C4' |
C3' |
C5' |
121.2 |
119.4 |
| O4' |
C4' |
C3' |
H4' |
238.1 |
240.6 |
| C3' |
C4' |
C5' |
O5' |
162.8 |
185.0 |
| C5' |
C4' |
C3' |
H4' |
116.8 |
121.2 |
| C3' |
C4' |
C5' |
H5' |
282.8 |
304.9 |
| C3' |
C4' |
C5' |
H5'A |
42.8 |
65.0 |
| C4' |
O4' |
C1' |
H1' |
126.4 |
78.5 |
| C3' |
C4' |
O4' |
C5' |
234.9 |
240.6 |
| O4' |
C4' |
C3' |
H3' |
124.8 |
116.7 |
| C3' |
C4' |
O4' |
H4' |
117.8 |
119.4 |
| O4' |
C4' |
C5' |
O5' |
42.1 |
67.2 |
| C5' |
C4' |
O4' |
H4' |
242.9 |
238.8 |
| O4' |
C4' |
C5' |
H5' |
162.1 |
187.1 |
| O4' |
C4' |
C5' |
H5'A |
282.1 |
307.2 |
| C3' |
C4' |
C5' |
O4' |
120.7 |
117.8 |
| C5' |
C4' |
C3' |
H3' |
3.6 |
357.3 |
| C3' |
C4' |
C5' |
H4' |
242.6 |
238.9 |
| O4' |
C4' |
C5' |
H4' |
121.9 |
121.1 |
| O5' |
C5' |
C4' |
H5' |
240.0 |
240.1 |
| O5' |
C5' |
C4' |
H5'A |
120.0 |
120.0 |
| C4' |
C5' |
O5' |
HO5' |
180.0 |
180.0 |
| H5' |
C5' |
C4' |
H5'A |
240.0 |
240.0 |
| O5' |
C5' |
C4' |
H4' |
280.2 |
306.1 |
| C4' |
C5' |
O5' |
H5' |
120.0 |
119.9 |
| C4' |
C5' |
O5' |
H5'A |
240.0 |
240.0 |
| H5' |
C5' |
O5' |
H5'A |
120.0 |
120.0 |
| HN3 |
N3 |
C6 |
O3 |
0.0 |
180.0 |
| C6 |
N3 |
HN3 |
HN3A |
180.0 |
180.0 |
| HN3A |
N3 |
C6 |
O3 |
180.0 |
0.0 |
| C6 |
N3 |
HN3A |
HN3 |
180.0 |
180.0 |
| H5 |
C5 |
N1 |
C1' |
0.1 |
0.3 |
| N1 |
C5 |
H5 |
N4 |
180.0 |
180.0 |
| N1 |
C1' |
H1' |
C2' |
122.2 |
122.9 |
| N1 |
C1' |
H1' |
O4' |
241.3 |
237.1 |
| C2' |
C1' |
H1' |
O4' |
119.0 |
114.1 |
| H1' |
C1' |
C2' |
O2' |
355.6 |
36.6 |
| H1' |
C1' |
C2' |
C3' |
232.0 |
278.4 |
| H1' |
C1' |
C2' |
H2' |
112.2 |
160.1 |
| H1' |
C1' |
O4' |
C4' |
126.4 |
78.5 |
| H2' |
C2' |
C1' |
O4' |
233.6 |
278.8 |
| C1' |
C2' |
H2' |
O2' |
239.6 |
236.4 |
| C1' |
C2' |
H2' |
C3' |
117.3 |
112.8 |
| H2' |
C2' |
C1' |
H1' |
112.2 |
160.1 |
| O2' |
C2' |
H2' |
C3' |
237.7 |
236.4 |
| H2' |
C2' |
O2' |
HO2' |
58.4 |
56.4 |
| H2' |
C2' |
C3' |
O3' |
241.8 |
216.0 |
| H2' |
C2' |
C3' |
C4' |
124.0 |
97.4 |
| H2' |
C2' |
C3' |
H3' |
2.1 |
338.6 |
| HO2' |
O2' |
C2' |
C3' |
298.7 |
292.7 |
| HO2' |
O2' |
C2' |
H2' |
58.4 |
56.4 |
| C2' |
C3' |
H3' |
O3' |
239.5 |
237.4 |
| C2' |
C3' |
H3' |
C4' |
118.6 |
114.8 |
| H3' |
C3' |
C2' |
H2' |
2.1 |
338.6 |
| O3' |
C3' |
H3' |
C4' |
239.1 |
237.4 |
| H3' |
C3' |
O3' |
HO3' |
57.6 |
298.9 |
| H3' |
C3' |
C4' |
O4' |
124.8 |
116.7 |
| H3' |
C3' |
C4' |
C5' |
3.6 |
357.3 |
| H3' |
C3' |
C4' |
H4' |
246.8 |
236.1 |
| HO3' |
O3' |
C3' |
C4' |
295.5 |
176.3 |
| HO3' |
O3' |
C3' |
H3' |
57.6 |
298.9 |
| C3' |
C4' |
H4' |
O4' |
241.6 |
242.2 |
| C3' |
C4' |
H4' |
C5' |
122.8 |
121.1 |
| H4' |
C4' |
C3' |
H3' |
246.8 |
236.1 |
| O4' |
C4' |
H4' |
C5' |
241.2 |
238.9 |
| H4' |
C4' |
C5' |
O5' |
280.2 |
306.1 |
| H4' |
C4' |
C5' |
H5' |
40.2 |
66.0 |
| H4' |
C4' |
C5' |
H5'A |
160.2 |
186.0 |
| C4' |
C5' |
H5' |
O5' |
238.1 |
240.1 |
| H5' |
C5' |
C4' |
H4' |
40.2 |
66.0 |
| C4' |
C5' |
H5' |
H5'A |
119.1 |
120.0 |
| O5' |
C5' |
H5' |
H5'A |
240.9 |
239.9 |
| H5' |
C5' |
O5' |
HO5' |
60.0 |
60.1 |
| C4' |
C5' |
H5'A |
O5' |
121.9 |
120.0 |
| H5'A |
C5' |
C4' |
H4' |
160.2 |
186.0 |
| C4' |
C5' |
H5'A |
H5' |
240.9 |
240.0 |
| O5' |
C5' |
H5'A |
H5' |
119.1 |
120.0 |
| H5'A |
C5' |
O5' |
HO5' |
300.0 |
300.0 |
| HO5' |
O5' |
C5' |
H5' |
60.0 |
60.1 |
| HO5' |
O5' |
C5' |
H5'A |
300.0 |
300.0 |