PDB Chemical Component DNB
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 DNB
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O2' |
C2' |
1.467 |
1.429 |
| O2' |
HO2' |
0.950 |
0.967 |
| C2' |
C3' |
1.531 |
1.546 |
| C2' |
C1' |
1.535 |
1.549 |
| C2' |
H2' |
1.100 |
1.090 |
| C3' |
O3' |
1.435 |
1.429 |
| C3' |
C4' |
1.534 |
1.540 |
| C3' |
H3' |
1.100 |
1.090 |
| O3' |
HO3' |
0.950 |
0.967 |
| C1' |
N4' |
1.453 |
1.486 |
| C1' |
C1 |
1.485 |
1.507 |
| C1' |
H1' |
1.100 |
1.090 |
| N4' |
C4' |
1.451 |
1.479 |
| N4' |
HN4' |
1.000 |
1.009 |
| C4' |
C5' |
1.559 |
1.530 |
| C4' |
H4' |
1.100 |
1.090 |
| C5' |
O5' |
1.451 |
1.429 |
| C5' |
H5' |
1.100 |
1.090 |
| C5' |
H5'A |
1.100 |
1.090 |
| O5' |
HO5' |
0.950 |
0.967 |
| C1 |
C6 |
1.397 |
1.382 |
| C1 |
C2 |
1.406 |
1.383 |
| C6 |
C5 |
1.409 |
1.383 |
| C6 |
H6 |
1.080 |
1.080 |
| C5 |
C4 |
1.397 |
1.386 |
| C5 |
H5 |
1.080 |
1.080 |
| C4 |
C3 |
1.405 |
1.395 |
| C3 |
N3 |
1.356 |
1.401 |
| C3 |
C2 |
1.388 |
1.386 |
| N3 |
HN3 |
1.000 |
0.970 |
| N3 |
HN3A |
1.000 |
0.970 |
| C2 |
H2 |
1.080 |
1.080 |
| C4 |
N4 |
1.469 |
1.400 |
| N4 |
HN4 |
1.000 |
0.971 |
| N4 |
HN4A |
1.000 |
0.970 |
Bond Angles for DNB
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2' |
O2' |
HO2' |
109.5 |
114.0 |
| O2' |
C2' |
C3' |
109.2 |
110.7 |
| O2' |
C2' |
C1' |
112.3 |
110.7 |
| O2' |
C2' |
H2' |
106.5 |
110.6 |
| C3' |
C2' |
C1' |
105.5 |
102.9 |
| C3' |
C2' |
H2' |
113.2 |
110.7 |
| C2' |
C3' |
O3' |
109.7 |
110.3 |
| C2' |
C3' |
C4' |
108.4 |
105.2 |
| C2' |
C3' |
H3' |
110.1 |
110.3 |
| C1' |
C2' |
H2' |
110.2 |
110.9 |
| C2' |
C1' |
N4' |
103.7 |
103.2 |
| C2' |
C1' |
C1 |
116.9 |
110.7 |
| C2' |
C1' |
H1' |
106.8 |
110.7 |
| O3' |
C3' |
C4' |
109.5 |
110.3 |
| O3' |
C3' |
H3' |
108.9 |
110.3 |
| C3' |
O3' |
HO3' |
109.5 |
114.0 |
| C4' |
C3' |
H3' |
110.3 |
110.4 |
| C3' |
C4' |
N4' |
100.3 |
107.0 |
| C3' |
C4' |
C5' |
115.0 |
109.9 |
| C3' |
C4' |
H4' |
113.1 |
109.9 |
| N4' |
C1' |
C1 |
103.5 |
110.7 |
| N4' |
C1' |
H1' |
119.5 |
110.7 |
| C1' |
N4' |
C4' |
114.4 |
105.8 |
| C1' |
N4' |
HN4' |
107.9 |
111.0 |
| C1 |
C1' |
H1' |
107.0 |
110.7 |
| C1' |
C1 |
C6 |
123.2 |
119.9 |
| C1' |
C1 |
C2 |
117.1 |
119.9 |
| C4' |
N4' |
HN4' |
107.8 |
111.0 |
| N4' |
C4' |
C5' |
112.6 |
109.9 |
| N4' |
C4' |
H4' |
115.6 |
109.9 |
| C5' |
C4' |
H4' |
100.9 |
110.1 |
| C4' |
C5' |
O5' |
111.1 |
109.5 |
| C4' |
C5' |
H5' |
108.9 |
109.4 |
| C4' |
C5' |
H5'A |
108.6 |
109.5 |
| O5' |
C5' |
H5' |
108.9 |
109.5 |
| O5' |
C5' |
H5'A |
108.6 |
109.5 |
| C5' |
O5' |
HO5' |
109.5 |
114.0 |
| H5' |
C5' |
H5'A |
110.7 |
109.5 |
| C6 |
C1 |
C2 |
119.7 |
120.2 |
| C1 |
C6 |
C5 |
120.5 |
120.2 |
| C1 |
C6 |
H6 |
119.8 |
119.9 |
| C1 |
C2 |
C3 |
119.7 |
120.0 |
| C1 |
C2 |
H2 |
120.1 |
120.0 |
| C5 |
C6 |
H6 |
119.8 |
119.9 |
| C6 |
C5 |
C4 |
119.6 |
120.0 |
| C6 |
C5 |
H5 |
120.2 |
120.0 |
| C4 |
C5 |
H5 |
120.2 |
120.0 |
| C5 |
C4 |
C3 |
119.6 |
119.8 |
| C5 |
C4 |
N4 |
133.7 |
120.1 |
| C4 |
C3 |
N3 |
120.1 |
120.1 |
| C4 |
C3 |
C2 |
120.9 |
119.8 |
| C3 |
C4 |
N4 |
103.9 |
120.1 |
| N3 |
C3 |
C2 |
119.0 |
120.1 |
| C3 |
N3 |
HN3 |
109.5 |
120.0 |
| C3 |
N3 |
HN3A |
109.5 |
120.0 |
| C3 |
C2 |
H2 |
120.1 |
120.0 |
| HN3 |
N3 |
HN3A |
109.4 |
120.0 |
| C4 |
N4 |
HN4 |
109.5 |
120.0 |
| C4 |
N4 |
HN4A |
109.5 |
120.0 |
| HN4 |
N4 |
HN4A |
109.4 |
120.0 |
Torsion Angles for DNB
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C3' |
C2' |
O2' |
C1' |
116.7 |
113.5 |
| C3' |
C2' |
O2' |
H2' |
237.4 |
236.9 |
| O2' |
C2' |
C3' |
O3' |
346.9 |
338.6 |
| O2' |
C2' |
C3' |
C4' |
227.4 |
219.7 |
| O2' |
C2' |
C3' |
H3' |
106.7 |
100.7 |
| C1' |
C2' |
O2' |
H2' |
120.7 |
123.4 |
| O2' |
C2' |
C1' |
N4' |
113.6 |
155.8 |
| O2' |
C2' |
C1' |
C1 |
226.7 |
274.2 |
| O2' |
C2' |
C1' |
H1' |
346.5 |
37.3 |
| HO2' |
O2' |
C2' |
C3' |
269.2 |
298.6 |
| HO2' |
O2' |
C2' |
C1' |
152.6 |
185.0 |
| HO2' |
O2' |
C2' |
H2' |
31.9 |
61.7 |
| C3' |
C2' |
O2' |
HO2' |
269.2 |
298.6 |
| O2' |
C2' |
C3' |
C1' |
239.1 |
241.6 |
| O2' |
C2' |
C3' |
H2' |
118.5 |
123.1 |
| C1' |
C2' |
C3' |
H2' |
239.4 |
241.5 |
| C3' |
C2' |
C1' |
N4' |
354.7 |
37.4 |
| C3' |
C2' |
C1' |
C1 |
107.9 |
155.9 |
| C3' |
C2' |
C1' |
H1' |
227.6 |
279.0 |
| O3' |
C3' |
C2' |
C4' |
119.6 |
118.9 |
| O3' |
C3' |
C2' |
H3' |
240.2 |
237.9 |
| C2' |
C3' |
O3' |
HO3' |
86.7 |
61.5 |
| C4' |
C3' |
C2' |
H3' |
120.6 |
119.0 |
| C2' |
C3' |
C4' |
N4' |
23.6 |
358.8 |
| C2' |
C3' |
C4' |
C5' |
262.5 |
239.5 |
| C2' |
C3' |
C4' |
H4' |
147.2 |
118.1 |
| C1' |
C2' |
O2' |
HO2' |
152.6 |
185.0 |
| O2' |
C2' |
C1' |
C3' |
118.9 |
118.3 |
| O2' |
C2' |
C1' |
H2' |
241.4 |
236.8 |
| C3' |
C2' |
C1' |
H2' |
122.6 |
118.4 |
| C1' |
C2' |
C3' |
O3' |
107.9 |
97.0 |
| C1' |
C2' |
C3' |
C4' |
348.3 |
338.0 |
| C1' |
C2' |
C3' |
H3' |
227.7 |
219.1 |
| N4' |
C1' |
C2' |
C1 |
246.9 |
241.5 |
| N4' |
C1' |
C2' |
H1' |
127.1 |
118.4 |
| C2' |
C1' |
N4' |
C4' |
22.6 |
320.8 |
| C2' |
C1' |
N4' |
HN4' |
142.6 |
81.3 |
| C1 |
C1' |
C2' |
H1' |
240.3 |
236.9 |
| C2' |
C1' |
C1 |
C6 |
9.1 |
280.0 |
| C2' |
C1' |
C1 |
C2 |
190.3 |
99.7 |
| H2' |
C2' |
O2' |
HO2' |
31.9 |
61.7 |
| O2' |
C2' |
H2' |
C3' |
239.9 |
236.9 |
| O2' |
C2' |
H2' |
C1' |
122.1 |
123.3 |
| C3' |
C2' |
H2' |
C1' |
242.1 |
246.4 |
| H2' |
C2' |
C3' |
O3' |
228.4 |
215.5 |
| H2' |
C2' |
C3' |
C4' |
108.9 |
96.6 |
| H2' |
C2' |
C3' |
H3' |
348.2 |
337.6 |
| H2' |
C2' |
C1' |
N4' |
232.2 |
279.0 |
| H2' |
C2' |
C1' |
C1 |
345.3 |
37.5 |
| H2' |
C2' |
C1' |
H1' |
105.0 |
160.6 |
| O3' |
C3' |
C2' |
C1' |
107.9 |
97.0 |
| O3' |
C3' |
C2' |
H2' |
228.4 |
215.5 |
| C2' |
C3' |
O3' |
C4' |
241.2 |
244.3 |
| C2' |
C3' |
O3' |
H3' |
120.5 |
122.1 |
| C4' |
C3' |
O3' |
H3' |
239.4 |
237.8 |
| O3' |
C3' |
C4' |
N4' |
263.8 |
239.9 |
| O3' |
C3' |
C4' |
C5' |
142.8 |
120.5 |
| O3' |
C3' |
C4' |
H4' |
27.5 |
359.2 |
| C4' |
C3' |
C2' |
C1' |
348.3 |
338.0 |
| C4' |
C3' |
C2' |
H2' |
108.9 |
96.6 |
| C2' |
C3' |
C4' |
O3' |
119.7 |
118.9 |
| C2' |
C3' |
C4' |
H3' |
239.5 |
241.1 |
| O3' |
C3' |
C4' |
H3' |
119.8 |
122.2 |
| C4' |
C3' |
O3' |
HO3' |
205.5 |
177.2 |
| C1' |
N4' |
C4' |
C3' |
330.9 |
25.3 |
| C3' |
C4' |
N4' |
HN4' |
210.9 |
264.8 |
| N4' |
C4' |
C3' |
C5' |
121.0 |
119.3 |
| N4' |
C4' |
C3' |
H4' |
236.3 |
240.7 |
| C5' |
C4' |
C3' |
H4' |
115.3 |
121.4 |
| C3' |
C4' |
C5' |
O5' |
163.0 |
185.0 |
| C3' |
C4' |
C5' |
H5' |
283.0 |
304.9 |
| C3' |
C4' |
C5' |
H5'A |
43.6 |
65.0 |
| H3' |
C3' |
C2' |
C1' |
227.7 |
219.1 |
| H3' |
C3' |
C2' |
H2' |
348.2 |
337.6 |
| C2' |
C3' |
H3' |
O3' |
239.7 |
237.9 |
| C2' |
C3' |
H3' |
C4' |
119.5 |
115.7 |
| O3' |
C3' |
H3' |
C4' |
239.8 |
237.8 |
| H3' |
C3' |
O3' |
HO3' |
326.2 |
299.4 |
| H3' |
C3' |
C4' |
N4' |
144.1 |
117.7 |
| H3' |
C3' |
C4' |
C5' |
23.0 |
358.4 |
| H3' |
C3' |
C4' |
H4' |
267.7 |
237.0 |
| HO3' |
O3' |
C3' |
C4' |
205.5 |
177.2 |
| HO3' |
O3' |
C3' |
H3' |
326.2 |
299.4 |
| N4' |
C1' |
C2' |
H2' |
232.2 |
279.0 |
| C2' |
C1' |
N4' |
C1 |
122.5 |
118.5 |
| C2' |
C1' |
N4' |
H1' |
241.3 |
241.6 |
| C3' |
C4' |
N4' |
C1' |
330.9 |
25.3 |
| C1 |
C1' |
N4' |
H1' |
118.8 |
123.1 |
| N4' |
C1' |
C1 |
C6 |
122.4 |
33.9 |
| N4' |
C1' |
C1 |
C2 |
303.6 |
213.5 |
| C4' |
N4' |
C1' |
HN4' |
240.0 |
239.5 |
| C1' |
N4' |
C4' |
C5' |
93.7 |
144.7 |
| C1' |
N4' |
C4' |
H4' |
209.0 |
266.0 |
| C1 |
C1' |
C2' |
H2' |
345.3 |
37.5 |
| C2' |
C1' |
C1 |
N4' |
246.7 |
246.2 |
| C2' |
C1' |
C1 |
H1' |
119.6 |
123.1 |
| N4' |
C1' |
C1 |
H1' |
232.9 |
236.9 |
| C1 |
C1' |
N4' |
C4' |
260.1 |
202.3 |
| C1 |
C1' |
N4' |
HN4' |
20.0 |
322.9 |
| C6 |
C1 |
C1' |
C2 |
178.8 |
180.3 |
| C1' |
C1 |
C6 |
C5 |
180.5 |
180.0 |
| C1' |
C1 |
C6 |
H6 |
0.5 |
359.8 |
| C1' |
C1 |
C2 |
C3 |
179.0 |
179.8 |
| C1' |
C1 |
C2 |
H2 |
359.0 |
0.0 |
| H1' |
C1' |
C2' |
H2' |
105.0 |
160.6 |
| C2' |
C1' |
H1' |
N4' |
117.1 |
113.8 |
| C2' |
C1' |
H1' |
C1 |
234.1 |
236.9 |
| N4' |
C1' |
H1' |
C1 |
117.0 |
123.1 |
| H1' |
C1' |
N4' |
C4' |
141.3 |
79.2 |
| H1' |
C1' |
N4' |
HN4' |
261.2 |
199.8 |
| H1' |
C1' |
C1 |
C6 |
249.5 |
157.0 |
| H1' |
C1' |
C1 |
C2 |
70.7 |
336.6 |
| N4' |
C4' |
C3' |
H3' |
144.1 |
117.7 |
| C3' |
C4' |
N4' |
C5' |
237.2 |
240.7 |
| C3' |
C4' |
N4' |
H4' |
122.0 |
119.3 |
| C4' |
N4' |
C1' |
C1 |
260.1 |
202.3 |
| C4' |
N4' |
C1' |
H1' |
141.3 |
79.2 |
| C1' |
N4' |
C4' |
HN4' |
120.0 |
120.5 |
| C5' |
C4' |
N4' |
H4' |
244.7 |
238.7 |
| N4' |
C4' |
C5' |
O5' |
48.9 |
67.4 |
| N4' |
C4' |
C5' |
H5' |
168.9 |
187.4 |
| N4' |
C4' |
C5' |
H5'A |
289.6 |
307.4 |
| HN4' |
N4' |
C1' |
C1 |
20.0 |
322.9 |
| HN4' |
N4' |
C1' |
H1' |
261.2 |
199.8 |
| C1' |
N4' |
HN4' |
C4' |
235.9 |
242.6 |
| HN4' |
N4' |
C4' |
C5' |
333.7 |
24.2 |
| HN4' |
N4' |
C4' |
H4' |
89.0 |
145.5 |
| C5' |
C4' |
C3' |
H3' |
23.0 |
358.4 |
| C3' |
C4' |
C5' |
N4' |
114.1 |
117.6 |
| C3' |
C4' |
C5' |
H4' |
237.9 |
238.8 |
| C5' |
C4' |
N4' |
HN4' |
333.7 |
24.2 |
| N4' |
C4' |
C5' |
H4' |
123.8 |
121.2 |
| O5' |
C5' |
C4' |
H5' |
240.0 |
240.1 |
| O5' |
C5' |
C4' |
H5'A |
119.3 |
120.0 |
| C4' |
C5' |
O5' |
HO5' |
7.7 |
180.0 |
| H5' |
C5' |
C4' |
H5'A |
239.3 |
239.9 |
| H4' |
C4' |
C3' |
H3' |
267.7 |
237.0 |
| C3' |
C4' |
H4' |
N4' |
245.2 |
242.4 |
| C3' |
C4' |
H4' |
C5' |
123.5 |
121.2 |
| H4' |
C4' |
N4' |
HN4' |
89.0 |
145.5 |
| N4' |
C4' |
H4' |
C5' |
238.3 |
238.8 |
| H4' |
C4' |
C5' |
O5' |
285.1 |
306.2 |
| H4' |
C4' |
C5' |
H5' |
45.1 |
66.2 |
| H4' |
C4' |
C5' |
H5'A |
165.8 |
186.2 |
| O5' |
C5' |
C4' |
H4' |
285.1 |
306.2 |
| C4' |
C5' |
O5' |
H5' |
120.0 |
119.9 |
| C4' |
C5' |
O5' |
H5'A |
240.7 |
240.0 |
| H5' |
C5' |
O5' |
H5'A |
120.7 |
120.0 |
| H5' |
C5' |
C4' |
H4' |
45.1 |
66.2 |
| C4' |
C5' |
H5' |
O5' |
238.7 |
240.1 |
| C4' |
C5' |
H5' |
H5'A |
119.3 |
120.1 |
| O5' |
C5' |
H5' |
H5'A |
240.7 |
240.0 |
| H5' |
C5' |
O5' |
HO5' |
247.7 |
60.0 |
| H5'A |
C5' |
C4' |
H4' |
165.8 |
186.2 |
| C4' |
C5' |
H5'A |
O5' |
120.9 |
120.0 |
| C4' |
C5' |
H5'A |
H5' |
240.5 |
240.0 |
| O5' |
C5' |
H5'A |
H5' |
119.6 |
120.0 |
| H5'A |
C5' |
O5' |
HO5' |
127.0 |
300.0 |
| HO5' |
O5' |
C5' |
H5' |
247.7 |
60.0 |
| HO5' |
O5' |
C5' |
H5'A |
127.0 |
300.0 |
| C6 |
C1 |
C1' |
H1' |
249.5 |
157.0 |
| C1' |
C1 |
C6 |
C2 |
181.2 |
179.7 |
| C6 |
C1 |
C2 |
C3 |
0.2 |
359.5 |
| C6 |
C1 |
C2 |
H2 |
180.2 |
179.7 |
| C5 |
C6 |
C1 |
H6 |
180.0 |
180.1 |
| C1 |
C6 |
C5 |
C4 |
0.6 |
359.9 |
| C1 |
C6 |
C5 |
H5 |
180.7 |
179.9 |
| C2 |
C1 |
C1' |
H1' |
70.7 |
336.6 |
| C1' |
C1 |
C2 |
C6 |
178.8 |
180.3 |
| C2 |
C1 |
C6 |
C5 |
359.3 |
0.3 |
| C2 |
C1 |
C6 |
H6 |
179.3 |
180.2 |
| C4 |
C3 |
C2 |
C1 |
0.4 |
0.5 |
| N3 |
C3 |
C2 |
C1 |
180.9 |
180.3 |
| C3 |
C2 |
C1 |
H2 |
180.0 |
179.8 |
| C5 |
C6 |
C1 |
C2 |
359.3 |
0.3 |
| C1 |
C6 |
C5 |
H6 |
180.0 |
179.9 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
180.0 |
| C6 |
C5 |
C4 |
C3 |
360.0 |
0.0 |
| C6 |
C5 |
C4 |
N4 |
202.5 |
180.0 |
| H6 |
C6 |
C1 |
C2 |
179.3 |
180.2 |
| C1 |
C6 |
H6 |
C5 |
180.0 |
180.1 |
| H6 |
C6 |
C5 |
C4 |
180.7 |
180.1 |
| H6 |
C6 |
C5 |
H5 |
0.7 |
0.1 |
| C4 |
C5 |
C6 |
H6 |
180.7 |
180.1 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
180.0 |
| C5 |
C4 |
C3 |
N3 |
179.0 |
180.0 |
| C5 |
C4 |
C3 |
C2 |
359.5 |
359.8 |
| C3 |
C4 |
C5 |
N4 |
157.4 |
180.0 |
| C5 |
C4 |
N4 |
HN4 |
148.6 |
0.0 |
| C5 |
C4 |
N4 |
HN4A |
268.6 |
180.0 |
| H5 |
C5 |
C6 |
H6 |
0.7 |
0.1 |
| C6 |
C5 |
H5 |
C4 |
180.0 |
180.0 |
| H5 |
C5 |
C4 |
C3 |
179.9 |
180.0 |
| H5 |
C5 |
C4 |
N4 |
22.5 |
0.0 |
| C1 |
C2 |
C3 |
C4 |
0.4 |
0.5 |
| C3 |
C4 |
C5 |
H5 |
179.9 |
180.0 |
| C5 |
C4 |
C3 |
N4 |
196.6 |
180.0 |
| N3 |
C3 |
C4 |
C2 |
179.5 |
180.2 |
| C4 |
C3 |
N3 |
HN3 |
151.3 |
0.0 |
| C4 |
C3 |
N3 |
HN3A |
271.3 |
180.0 |
| C4 |
C3 |
C2 |
H2 |
180.4 |
180.3 |
| C3 |
C4 |
N4 |
HN4 |
348.8 |
180.0 |
| C3 |
C4 |
N4 |
HN4A |
108.7 |
359.9 |
| C1 |
C2 |
C3 |
N3 |
180.9 |
180.3 |
| C4 |
C3 |
N3 |
C2 |
180.5 |
179.8 |
| N3 |
C3 |
C4 |
N4 |
342.4 |
0.0 |
| N3 |
C3 |
C2 |
H2 |
0.9 |
0.0 |
| HN3 |
N3 |
C3 |
HN3A |
240.0 |
180.0 |
| C1 |
C2 |
C3 |
H2 |
180.0 |
180.2 |
| C4 |
C3 |
C2 |
N3 |
179.5 |
180.2 |
| C2 |
C3 |
C4 |
N4 |
162.9 |
179.8 |
| C2 |
C3 |
N3 |
HN3 |
330.9 |
180.3 |
| C2 |
C3 |
N3 |
HN3A |
90.8 |
0.2 |
| HN3 |
N3 |
C3 |
C2 |
330.9 |
180.3 |
| C3 |
N3 |
HN3 |
HN3A |
120.0 |
180.0 |
| HN3A |
N3 |
C3 |
C2 |
90.8 |
0.2 |
| C3 |
N3 |
HN3A |
HN3 |
240.0 |
180.0 |
| C1 |
C2 |
H2 |
C3 |
180.0 |
179.8 |
| N4 |
C4 |
C5 |
H5 |
22.5 |
0.0 |
| C5 |
C4 |
N4 |
C3 |
159.9 |
180.0 |
| N4 |
C4 |
C3 |
N3 |
342.4 |
0.0 |
| N4 |
C4 |
C3 |
C2 |
162.9 |
179.8 |
| HN4 |
N4 |
C4 |
HN4A |
240.0 |
180.1 |
| C4 |
N4 |
HN4 |
HN4A |
120.0 |
179.9 |
| C4 |
N4 |
HN4A |
HN4 |
240.0 |
180.1 |