PDB Chemical Component BVD
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 BVD
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O5' |
C5' |
1.431 |
1.429 |
| O5' |
HO5' |
0.950 |
0.967 |
| C5' |
C4' |
1.553 |
1.530 |
| C5' |
H5'1 |
1.115 |
1.089 |
| C5' |
H5'2 |
1.115 |
1.091 |
| C4' |
O4' |
1.453 |
1.445 |
| C4' |
C3' |
1.527 |
1.548 |
| C4' |
H4' |
1.114 |
1.089 |
| O4' |
C1' |
1.465 |
1.437 |
| C1' |
N1 |
1.526 |
1.465 |
| C1' |
C2' |
1.516 |
1.541 |
| C1' |
H1' |
1.115 |
1.090 |
| N1 |
C6 |
1.372 |
1.365 |
| N1 |
C2 |
1.360 |
1.342 |
| C6 |
C5 |
1.322 |
1.366 |
| C6 |
H6 |
1.103 |
1.080 |
| C2 |
O2 |
1.225 |
1.215 |
| C2 |
N3 |
1.314 |
1.345 |
| N3 |
C4 |
1.364 |
1.349 |
| N3 |
HN3 |
1.020 |
0.970 |
| C4 |
O4 |
1.223 |
1.218 |
| C4 |
C5 |
1.419 |
1.470 |
| C5 |
C5A |
1.385 |
1.476 |
| C5A |
C5B |
1.358 |
1.327 |
| C5A |
H5A |
1.103 |
1.080 |
| C5B |
BR |
1.933 |
1.890 |
| C5B |
H5B |
1.103 |
1.081 |
| C2' |
C3' |
1.563 |
1.550 |
| C2' |
H2'1 |
1.115 |
1.090 |
| C2' |
H2'2 |
1.115 |
1.089 |
| C3' |
O3' |
1.403 |
1.429 |
| C3' |
H3' |
1.115 |
1.090 |
| O3' |
HO3' |
0.950 |
0.966 |
Bond Angles for BVD
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C5' |
O5' |
HO5' |
112.4 |
106.8 |
| O5' |
C5' |
C4' |
112.3 |
109.5 |
| O5' |
C5' |
H5'1 |
111.1 |
109.5 |
| O5' |
C5' |
H5'2 |
111.2 |
109.5 |
| C4' |
C5' |
H5'1 |
111.2 |
109.5 |
| C4' |
C5' |
H5'2 |
111.2 |
109.5 |
| C5' |
C4' |
O4' |
112.6 |
110.6 |
| C5' |
C4' |
C3' |
114.3 |
110.6 |
| C5' |
C4' |
H4' |
101.6 |
110.5 |
| H5'1 |
C5' |
H5'2 |
99.2 |
109.5 |
| O4' |
C4' |
C3' |
100.8 |
103.6 |
| O4' |
C4' |
H4' |
114.9 |
110.6 |
| C4' |
O4' |
C1' |
116.2 |
107.0 |
| C3' |
C4' |
H4' |
113.3 |
110.7 |
| C4' |
C3' |
C2' |
101.7 |
102.1 |
| C4' |
C3' |
O3' |
103.5 |
111.2 |
| C4' |
C3' |
H3' |
117.3 |
110.8 |
| O4' |
C1' |
N1 |
113.9 |
109.9 |
| O4' |
C1' |
C2' |
100.3 |
107.3 |
| O4' |
C1' |
H1' |
117.3 |
109.9 |
| N1 |
C1' |
C2' |
120.2 |
110.0 |
| N1 |
C1' |
H1' |
95.8 |
109.9 |
| C1' |
N1 |
C6 |
120.6 |
119.3 |
| C1' |
N1 |
C2 |
119.5 |
119.3 |
| C2' |
C1' |
H1' |
110.5 |
109.8 |
| C1' |
C2' |
C3' |
104.1 |
104.2 |
| C1' |
C2' |
H2'1 |
114.2 |
110.5 |
| C1' |
C2' |
H2'2 |
114.2 |
110.5 |
| C6 |
N1 |
C2 |
119.9 |
121.4 |
| N1 |
C6 |
C5 |
124.5 |
119.5 |
| N1 |
C6 |
H6 |
119.8 |
120.3 |
| N1 |
C2 |
O2 |
125.1 |
119.1 |
| N1 |
C2 |
N3 |
115.6 |
121.9 |
| C5 |
C6 |
H6 |
115.7 |
120.2 |
| C6 |
C5 |
C4 |
115.6 |
118.2 |
| C6 |
C5 |
C5A |
118.7 |
120.9 |
| O2 |
C2 |
N3 |
119.3 |
119.0 |
| C2 |
N3 |
C4 |
126.5 |
120.3 |
| C2 |
N3 |
HN3 |
114.7 |
119.8 |
| C4 |
N3 |
HN3 |
118.9 |
119.9 |
| N3 |
C4 |
O4 |
118.3 |
120.6 |
| N3 |
C4 |
C5 |
116.6 |
118.7 |
| O4 |
C4 |
C5 |
125.1 |
120.6 |
| C4 |
C5 |
C5A |
125.0 |
120.9 |
| C5 |
C5A |
C5B |
121.8 |
120.1 |
| C5 |
C5A |
H5A |
120.1 |
120.0 |
| C5B |
C5A |
H5A |
118.0 |
119.9 |
| C5A |
C5B |
BR |
122.1 |
120.1 |
| C5A |
C5B |
H5B |
101.4 |
119.9 |
| BR |
C5B |
H5B |
136.5 |
120.0 |
| C3' |
C2' |
H2'1 |
114.3 |
110.3 |
| C3' |
C2' |
H2'2 |
114.3 |
110.6 |
| C2' |
C3' |
O3' |
108.0 |
110.9 |
| C2' |
C3' |
H3' |
113.4 |
110.8 |
| H2'1 |
C2' |
H2'2 |
96.2 |
110.6 |
| O3' |
C3' |
H3' |
111.9 |
110.8 |
| C3' |
O3' |
HO3' |
103.5 |
106.8 |
Torsion Angles for BVD
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C4' |
C5' |
O5' |
H5'1 |
234.7 |
240.0 |
| C4' |
C5' |
O5' |
H5'2 |
125.3 |
120.0 |
| O5' |
C5' |
C4' |
O4' |
301.7 |
63.6 |
| O5' |
C5' |
C4' |
C3' |
56.0 |
177.8 |
| O5' |
C5' |
C4' |
H4' |
178.3 |
300.7 |
| H5'1 |
C5' |
O5' |
H5'2 |
250.5 |
240.0 |
| HO5' |
O5' |
C5' |
C4' |
180.0 |
180.0 |
| HO5' |
O5' |
C5' |
H5'1 |
305.3 |
300.0 |
| HO5' |
O5' |
C5' |
H5'2 |
54.7 |
60.0 |
| C4' |
C5' |
O5' |
HO5' |
180.0 |
180.0 |
| O5' |
C5' |
C4' |
H5'1 |
125.2 |
120.0 |
| O5' |
C5' |
C4' |
H5'2 |
234.7 |
240.0 |
| H5'1 |
C5' |
C4' |
H5'2 |
109.5 |
120.0 |
| O4' |
C4' |
C5' |
C3' |
245.7 |
245.8 |
| O4' |
C4' |
C5' |
H4' |
123.4 |
122.9 |
| C5' |
C4' |
O4' |
C1' |
105.8 |
158.6 |
| C3' |
C4' |
C5' |
H4' |
237.7 |
237.1 |
| C5' |
C4' |
C3' |
C2' |
272.9 |
204.7 |
| C5' |
C4' |
C3' |
O3' |
161.0 |
86.4 |
| C5' |
C4' |
C3' |
H3' |
37.2 |
322.7 |
| H5'1 |
C5' |
O5' |
HO5' |
305.3 |
300.0 |
| O5' |
C5' |
H5'1 |
C4' |
234.1 |
240.0 |
| O5' |
C5' |
H5'1 |
H5'2 |
117.0 |
120.0 |
| C4' |
C5' |
H5'1 |
H5'2 |
242.9 |
240.0 |
| H5'1 |
C5' |
C4' |
O4' |
176.5 |
303.6 |
| H5'1 |
C5' |
C4' |
C3' |
290.8 |
57.8 |
| H5'1 |
C5' |
C4' |
H4' |
53.1 |
180.7 |
| H5'2 |
C5' |
O5' |
HO5' |
54.7 |
60.0 |
| O5' |
C5' |
H5'2 |
C4' |
125.9 |
120.0 |
| O5' |
C5' |
H5'2 |
H5'1 |
243.0 |
240.0 |
| C4' |
C5' |
H5'2 |
H5'1 |
117.1 |
120.0 |
| H5'2 |
C5' |
C4' |
O4' |
67.0 |
183.6 |
| H5'2 |
C5' |
C4' |
C3' |
181.2 |
297.8 |
| H5'2 |
C5' |
C4' |
H4' |
303.6 |
60.7 |
| O4' |
C4' |
C5' |
H5'1 |
176.5 |
303.6 |
| O4' |
C4' |
C5' |
H5'2 |
67.0 |
183.6 |
| C5' |
C4' |
O4' |
C3' |
122.2 |
118.5 |
| C5' |
C4' |
O4' |
H4' |
244.3 |
237.2 |
| C3' |
C4' |
O4' |
H4' |
122.1 |
118.6 |
| O4' |
C4' |
C3' |
C2' |
34.0 |
323.2 |
| O4' |
C4' |
C3' |
O3' |
282.0 |
204.9 |
| O4' |
C4' |
C3' |
H3' |
158.2 |
81.2 |
| C4' |
O4' |
C1' |
N1 |
221.0 |
213.9 |
| C4' |
O4' |
C1' |
C2' |
350.7 |
333.5 |
| C4' |
O4' |
C1' |
H1' |
110.4 |
92.8 |
| C3' |
C4' |
C5' |
H5'1 |
290.8 |
57.8 |
| C3' |
C4' |
C5' |
H5'2 |
181.2 |
297.8 |
| C5' |
C4' |
C3' |
O4' |
239.0 |
241.5 |
| C5' |
C4' |
C3' |
H4' |
115.7 |
122.9 |
| O4' |
C4' |
C3' |
H4' |
236.8 |
241.4 |
| C3' |
C4' |
O4' |
C1' |
343.6 |
40.0 |
| C1' |
C2' |
C3' |
C4' |
318.3 |
20.7 |
| C4' |
C3' |
C2' |
H2'1 |
193.1 |
262.1 |
| C4' |
C3' |
C2' |
H2'2 |
83.6 |
139.4 |
| C2' |
C3' |
C4' |
O3' |
112.0 |
118.3 |
| C2' |
C3' |
C4' |
H3' |
235.8 |
242.0 |
| O3' |
C3' |
C4' |
H3' |
123.8 |
123.7 |
| C4' |
C3' |
O3' |
HO3' |
180.0 |
174.2 |
| H4' |
C4' |
C5' |
H5'1 |
53.1 |
180.7 |
| H4' |
C4' |
C5' |
H5'2 |
303.6 |
60.7 |
| C5' |
C4' |
H4' |
O4' |
121.8 |
122.8 |
| C5' |
C4' |
H4' |
C3' |
237.0 |
237.1 |
| O4' |
C4' |
H4' |
C3' |
115.1 |
114.3 |
| H4' |
C4' |
O4' |
C1' |
221.4 |
281.4 |
| H4' |
C4' |
C3' |
C2' |
157.2 |
81.8 |
| H4' |
C4' |
C3' |
O3' |
45.3 |
323.5 |
| H4' |
C4' |
C3' |
H3' |
281.5 |
199.8 |
| C1' |
O4' |
C4' |
C3' |
343.6 |
40.0 |
| C1' |
O4' |
C4' |
H4' |
221.4 |
281.4 |
| N1 |
C1' |
O4' |
C2' |
230.3 |
240.4 |
| N1 |
C1' |
O4' |
H1' |
110.7 |
121.1 |
| O4' |
C1' |
N1 |
C6 |
61.8 |
238.5 |
| O4' |
C1' |
N1 |
C2 |
244.7 |
58.3 |
| C2' |
C1' |
O4' |
H1' |
240.4 |
240.6 |
| O4' |
C1' |
C2' |
C3' |
30.7 |
2.2 |
| O4' |
C1' |
C2' |
H2'1 |
156.0 |
120.7 |
| O4' |
C1' |
C2' |
H2'2 |
265.4 |
243.4 |
| O4' |
C1' |
N1 |
C2' |
118.8 |
117.9 |
| O4' |
C1' |
N1 |
H1' |
236.7 |
238.9 |
| C2' |
C1' |
N1 |
H1' |
117.8 |
121.0 |
| N1 |
C1' |
C2' |
C3' |
156.2 |
121.7 |
| N1 |
C1' |
C2' |
H2'1 |
281.5 |
240.2 |
| N1 |
C1' |
C2' |
H2'2 |
30.9 |
2.9 |
| C6 |
N1 |
C1' |
C2 |
177.1 |
180.2 |
| C1' |
N1 |
C6 |
C5 |
187.6 |
180.0 |
| C1' |
N1 |
C6 |
H6 |
7.6 |
359.9 |
| C1' |
N1 |
C2 |
O2 |
350.7 |
0.2 |
| C1' |
N1 |
C2 |
N3 |
172.5 |
179.8 |
| C4' |
C3' |
C2' |
C1' |
318.3 |
20.7 |
| O4' |
C1' |
C2' |
N1 |
234.5 |
240.5 |
| O4' |
C1' |
C2' |
H1' |
124.5 |
119.4 |
| N1 |
C1' |
C2' |
H1' |
249.9 |
238.9 |
| C2' |
C1' |
N1 |
C6 |
303.0 |
120.6 |
| C2' |
C1' |
N1 |
C2 |
125.9 |
300.4 |
| C3' |
C2' |
C1' |
H2'1 |
234.7 |
241.5 |
| C3' |
C2' |
C1' |
H2'2 |
125.3 |
118.8 |
| C1' |
C2' |
C3' |
O3' |
66.9 |
139.2 |
| C1' |
C2' |
C3' |
H3' |
191.5 |
262.7 |
| H2'1 |
C2' |
C1' |
H2'2 |
250.6 |
237.3 |
| O4' |
C1' |
H1' |
N1 |
120.7 |
121.1 |
| O4' |
C1' |
H1' |
C2' |
245.9 |
242.2 |
| N1 |
C1' |
H1' |
C2' |
125.3 |
121.1 |
| H1' |
C1' |
N1 |
C6 |
185.1 |
359.6 |
| H1' |
C1' |
N1 |
C2 |
8.1 |
179.3 |
| H1' |
C1' |
C2' |
C3' |
266.2 |
242.8 |
| H1' |
C1' |
C2' |
H2'1 |
31.5 |
1.3 |
| H1' |
C1' |
C2' |
H2'2 |
140.9 |
123.9 |
| C6 |
N1 |
C1' |
C2' |
303.0 |
120.6 |
| C6 |
N1 |
C1' |
H1' |
185.1 |
359.6 |
| C1' |
N1 |
C6 |
C2 |
182.9 |
179.7 |
| C6 |
N1 |
C2 |
O2 |
173.6 |
180.0 |
| C6 |
N1 |
C2 |
N3 |
355.4 |
359.5 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
180.0 |
| N1 |
C6 |
C5 |
C4 |
351.8 |
0.0 |
| N1 |
C6 |
C5 |
C5A |
181.1 |
180.0 |
| C2 |
N1 |
C1' |
C2' |
125.9 |
300.4 |
| C2 |
N1 |
C1' |
H1' |
8.1 |
179.3 |
| C1' |
N1 |
C2 |
C6 |
177.1 |
180.3 |
| C2 |
N1 |
C6 |
C5 |
4.6 |
0.2 |
| C2 |
N1 |
C6 |
H6 |
184.6 |
180.2 |
| O2 |
C2 |
N1 |
N3 |
178.2 |
180.4 |
| N1 |
C2 |
N3 |
C4 |
9.8 |
0.4 |
| N1 |
C2 |
N3 |
HN3 |
189.8 |
180.3 |
| C5 |
C6 |
N1 |
C2 |
4.6 |
0.2 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.0 |
| N3 |
C4 |
C5 |
C6 |
11.8 |
360.0 |
| O4 |
C4 |
C5 |
C6 |
194.3 |
180.0 |
| C4 |
C5 |
C6 |
C5A |
170.8 |
180.0 |
| C6 |
C5 |
C5A |
C5B |
197.3 |
174.4 |
| C6 |
C5 |
C5A |
H5A |
17.3 |
354.4 |
| H6 |
C6 |
N1 |
C2 |
184.6 |
180.2 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
180.0 |
| H6 |
C6 |
C5 |
C4 |
171.8 |
180.0 |
| H6 |
C6 |
C5 |
C5A |
1.1 |
0.1 |
| N1 |
C2 |
O2 |
N3 |
181.8 |
179.6 |
| O2 |
C2 |
N3 |
C4 |
191.4 |
180.0 |
| O2 |
C2 |
N3 |
HN3 |
11.4 |
359.8 |
| N1 |
C2 |
N3 |
O2 |
178.3 |
180.4 |
| C4 |
N3 |
C2 |
HN3 |
180.0 |
180.2 |
| C2 |
N3 |
C4 |
O4 |
164.0 |
179.7 |
| C2 |
N3 |
C4 |
C5 |
346.4 |
359.8 |
| C6 |
C5 |
C4 |
N3 |
11.8 |
360.0 |
| C2 |
N3 |
C4 |
HN3 |
180.0 |
179.8 |
| O4 |
C4 |
N3 |
C5 |
177.6 |
179.9 |
| N3 |
C4 |
C5 |
C5A |
181.9 |
179.9 |
| C2 |
N3 |
HN3 |
C4 |
180.0 |
180.2 |
| HN3 |
N3 |
C4 |
O4 |
344.0 |
359.9 |
| HN3 |
N3 |
C4 |
C5 |
166.4 |
180.0 |
| C6 |
C5 |
C4 |
O4 |
194.3 |
180.0 |
| O4 |
C4 |
N3 |
HN3 |
344.0 |
359.9 |
| N3 |
C4 |
O4 |
C5 |
182.6 |
180.1 |
| O4 |
C4 |
C5 |
C5A |
4.4 |
0.0 |
| C4 |
C5 |
C6 |
H6 |
171.8 |
180.0 |
| C6 |
C5 |
C4 |
C5A |
189.9 |
180.0 |
| C5 |
C4 |
N3 |
HN3 |
166.4 |
180.0 |
| N3 |
C4 |
C5 |
O4 |
177.4 |
179.9 |
| C4 |
C5 |
C5A |
C5B |
27.4 |
354.4 |
| C4 |
C5 |
C5A |
H5A |
207.5 |
174.4 |
| C5A |
C5 |
C6 |
H6 |
1.1 |
0.1 |
| C6 |
C5 |
C5A |
C4 |
169.8 |
180.0 |
| C5B |
C5A |
C5 |
H5A |
180.0 |
180.1 |
| C5 |
C5A |
C5B |
BR |
174.8 |
185.1 |
| C5 |
C5A |
C5B |
H5B |
354.8 |
5.0 |
| C5 |
C5A |
C5B |
H5A |
180.0 |
179.9 |
| BR |
C5B |
C5A |
H5B |
180.0 |
180.0 |
| C5 |
C5A |
H5A |
C5B |
180.0 |
180.1 |
| H5A |
C5A |
C5B |
BR |
354.8 |
5.1 |
| H5A |
C5A |
C5B |
H5B |
174.8 |
185.1 |
| BR |
C5B |
C5A |
H5A |
354.8 |
5.1 |
| C5A |
C5B |
BR |
H5B |
180.0 |
180.0 |
| H5B |
C5B |
C5A |
H5A |
174.8 |
185.1 |
| C5A |
C5B |
H5B |
BR |
180.0 |
180.0 |
| C2' |
C3' |
C4' |
H4' |
157.2 |
81.8 |
| C4' |
C3' |
C2' |
O3' |
251.5 |
241.5 |
| C4' |
C3' |
C2' |
H3' |
126.8 |
118.0 |
| C3' |
C2' |
C1' |
H1' |
266.2 |
242.8 |
| C1' |
C2' |
C3' |
H2'1 |
125.3 |
118.6 |
| C1' |
C2' |
C3' |
H2'2 |
234.8 |
241.2 |
| H2'1 |
C2' |
C3' |
H2'2 |
109.5 |
122.6 |
| O3' |
C3' |
C2' |
H3' |
235.4 |
236.5 |
| C2' |
C3' |
O3' |
HO3' |
72.7 |
61.4 |
| H2'1 |
C2' |
C1' |
H1' |
31.5 |
1.3 |
| C1' |
C2' |
H2'1 |
C3' |
240.2 |
245.3 |
| C1' |
C2' |
H2'1 |
H2'2 |
120.0 |
122.7 |
| C3' |
C2' |
H2'1 |
H2'2 |
239.8 |
237.4 |
| H2'1 |
C2' |
C3' |
O3' |
301.6 |
20.6 |
| H2'1 |
C2' |
C3' |
H3' |
66.2 |
144.1 |
| H2'2 |
C2' |
C1' |
H1' |
140.9 |
123.9 |
| C1' |
C2' |
H2'2 |
C3' |
119.7 |
114.9 |
| C1' |
C2' |
H2'2 |
H2'1 |
239.9 |
237.3 |
| C3' |
C2' |
H2'2 |
H2'1 |
120.2 |
122.5 |
| H2'2 |
C2' |
C3' |
O3' |
192.1 |
258.0 |
| H2'2 |
C2' |
C3' |
H3' |
316.7 |
21.4 |
| O3' |
C3' |
C4' |
H4' |
45.3 |
323.5 |
| C4' |
C3' |
O3' |
C2' |
107.3 |
112.8 |
| C4' |
C3' |
O3' |
H3' |
232.8 |
236.3 |
| O3' |
C3' |
C2' |
H2'1 |
301.6 |
20.6 |
| O3' |
C3' |
C2' |
H2'2 |
192.1 |
258.0 |
| C2' |
C3' |
O3' |
H3' |
125.5 |
123.5 |
| H3' |
C3' |
C4' |
H4' |
281.5 |
199.8 |
| C4' |
C3' |
H3' |
C2' |
241.9 |
247.5 |
| C4' |
C3' |
H3' |
O3' |
119.4 |
123.9 |
| H3' |
C3' |
C2' |
H2'1 |
66.2 |
144.1 |
| H3' |
C3' |
C2' |
H2'2 |
316.7 |
21.4 |
| C2' |
C3' |
H3' |
O3' |
237.6 |
236.4 |
| H3' |
C3' |
O3' |
HO3' |
307.2 |
297.8 |
| HO3' |
O3' |
C3' |
H3' |
307.2 |
297.8 |