PDB Chemical Component DDU
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 DDU
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N1 |
C2 |
1.395 |
1.345 |
| N1 |
C6 |
1.314 |
1.368 |
| N1 |
C1' |
1.491 |
1.465 |
| C2 |
N3 |
1.387 |
1.346 |
| C2 |
O2 |
1.216 |
1.215 |
| N3 |
C4 |
1.390 |
1.348 |
| N3 |
HN3 |
1.020 |
0.970 |
| C4 |
C5 |
1.463 |
1.414 |
| C4 |
O4 |
1.234 |
1.217 |
| C5 |
C6 |
1.404 |
1.351 |
| C5 |
H5 |
1.104 |
1.080 |
| C6 |
H6 |
1.103 |
1.080 |
| C1' |
C2' |
1.531 |
1.549 |
| C1' |
O4' |
1.517 |
1.443 |
| C1' |
H1' |
1.114 |
1.090 |
| C2' |
C3' |
1.523 |
1.552 |
| C2' |
H2'1 |
1.114 |
1.090 |
| C2' |
H2'2 |
1.116 |
1.089 |
| C3' |
C4' |
1.550 |
1.540 |
| C3' |
O3' |
1.431 |
1.430 |
| C3' |
H3' |
1.115 |
1.090 |
| C4' |
O4' |
1.495 |
1.438 |
| C4' |
C5' |
1.530 |
1.530 |
| C4' |
H4' |
1.114 |
1.090 |
| O3' |
HO3' |
0.949 |
0.966 |
| C5' |
H5'1 |
1.115 |
1.091 |
| C5' |
H5'2 |
1.115 |
1.090 |
| C5' |
H5'3 |
1.115 |
1.090 |
Bond Angles for DDU
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N1 |
C6 |
122.9 |
120.7 |
| C2 |
N1 |
C1' |
119.4 |
119.7 |
| N1 |
C2 |
N3 |
117.1 |
120.9 |
| N1 |
C2 |
O2 |
123.8 |
119.5 |
| C6 |
N1 |
C1' |
117.7 |
119.7 |
| N1 |
C6 |
C5 |
120.4 |
119.7 |
| N1 |
C6 |
H6 |
116.5 |
120.2 |
| N1 |
C1' |
C2' |
114.0 |
110.8 |
| N1 |
C1' |
O4' |
121.6 |
110.6 |
| N1 |
C1' |
H1' |
95.0 |
110.5 |
| N3 |
C2 |
O2 |
119.2 |
119.6 |
| C2 |
N3 |
C4 |
125.1 |
120.3 |
| C2 |
N3 |
HN3 |
117.4 |
119.8 |
| C4 |
N3 |
HN3 |
117.6 |
119.9 |
| N3 |
C4 |
C5 |
113.7 |
119.4 |
| N3 |
C4 |
O4 |
121.1 |
120.3 |
| C5 |
C4 |
O4 |
125.2 |
120.3 |
| C4 |
C5 |
C6 |
120.8 |
119.1 |
| C4 |
C5 |
H5 |
121.7 |
120.4 |
| C6 |
C5 |
H5 |
117.5 |
120.4 |
| C5 |
C6 |
H6 |
123.1 |
120.1 |
| C2' |
C1' |
O4' |
104.0 |
103.5 |
| C2' |
C1' |
H1' |
115.8 |
110.7 |
| C1' |
C2' |
C3' |
103.9 |
102.1 |
| C1' |
C2' |
H2'1 |
114.3 |
110.9 |
| C1' |
C2' |
H2'2 |
114.3 |
110.9 |
| O4' |
C1' |
H1' |
106.8 |
110.6 |
| C1' |
O4' |
C4' |
107.5 |
107.0 |
| C3' |
C2' |
H2'1 |
114.4 |
110.8 |
| C3' |
C2' |
H2'2 |
114.3 |
111.0 |
| C2' |
C3' |
C4' |
99.4 |
104.0 |
| C2' |
C3' |
O3' |
110.5 |
110.5 |
| C2' |
C3' |
H3' |
114.7 |
110.5 |
| H2'1 |
C2' |
H2'2 |
96.1 |
110.9 |
| C4' |
C3' |
O3' |
108.0 |
110.8 |
| C4' |
C3' |
H3' |
116.9 |
110.5 |
| C3' |
C4' |
O4' |
104.5 |
107.4 |
| C3' |
C4' |
C5' |
112.2 |
109.9 |
| C3' |
C4' |
H4' |
110.7 |
109.9 |
| O3' |
C3' |
H3' |
107.1 |
110.4 |
| C3' |
O3' |
HO3' |
110.4 |
106.8 |
| O4' |
C4' |
C5' |
108.5 |
109.9 |
| O4' |
C4' |
H4' |
114.3 |
109.9 |
| C5' |
C4' |
H4' |
106.8 |
109.9 |
| C4' |
C5' |
H5'1 |
112.2 |
109.5 |
| C4' |
C5' |
H5'2 |
111.2 |
109.5 |
| C4' |
C5' |
H5'3 |
111.2 |
109.5 |
| H5'1 |
C5' |
H5'2 |
111.2 |
109.5 |
| H5'1 |
C5' |
H5'3 |
111.2 |
109.4 |
| H5'2 |
C5' |
H5'3 |
99.1 |
109.5 |
Torsion Angles for DDU
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C6 |
N1 |
C2 |
C1' |
182.1 |
179.8 |
| C2 |
N1 |
C6 |
C5 |
359.5 |
0.2 |
| C2 |
N1 |
C6 |
H6 |
179.5 |
180.2 |
| C2 |
N1 |
C1' |
C2' |
77.1 |
304.2 |
| C2 |
N1 |
C1' |
O4' |
202.9 |
58.3 |
| C2 |
N1 |
C1' |
H1' |
316.0 |
181.1 |
| N3 |
C2 |
N1 |
O2 |
181.4 |
179.5 |
| N1 |
C2 |
N3 |
C4 |
359.2 |
0.6 |
| N1 |
C2 |
N3 |
HN3 |
179.2 |
180.2 |
| C2 |
N1 |
C6 |
C1' |
177.9 |
180.2 |
| C6 |
N1 |
C2 |
N3 |
0.6 |
359.5 |
| C6 |
N1 |
C2 |
O2 |
179.2 |
180.0 |
| C6 |
N1 |
C1' |
C2' |
255.1 |
124.4 |
| C6 |
N1 |
C1' |
O4' |
20.9 |
238.6 |
| C6 |
N1 |
C1' |
H1' |
134.1 |
1.4 |
| C4 |
C5 |
C6 |
N1 |
0.6 |
0.0 |
| N1 |
C6 |
C5 |
H5 |
180.7 |
180.0 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
180.0 |
| C2 |
N1 |
C1' |
C6 |
182.0 |
179.8 |
| C1' |
N1 |
C2 |
N3 |
178.5 |
179.7 |
| C1' |
N1 |
C2 |
O2 |
357.1 |
0.2 |
| C1' |
N1 |
C6 |
C5 |
181.5 |
180.0 |
| C1' |
N1 |
C6 |
H6 |
1.5 |
360.0 |
| C2' |
C1' |
N1 |
O4' |
234.2 |
245.8 |
| C2' |
C1' |
N1 |
H1' |
121.0 |
123.0 |
| N1 |
C1' |
C2' |
C3' |
166.7 |
155.7 |
| N1 |
C1' |
C2' |
H2'1 |
292.0 |
273.7 |
| N1 |
C1' |
C2' |
H2'2 |
41.4 |
37.4 |
| O4' |
C1' |
N1 |
H1' |
246.8 |
237.2 |
| N1 |
C1' |
O4' |
C4' |
223.7 |
201.3 |
| N3 |
C2 |
N1 |
C6 |
0.6 |
359.5 |
| N3 |
C2 |
N1 |
C1' |
178.5 |
179.7 |
| N1 |
C2 |
N3 |
O2 |
178.7 |
180.5 |
| C4 |
N3 |
C2 |
HN3 |
180.0 |
180.4 |
| C2 |
N3 |
C4 |
C5 |
0.9 |
359.7 |
| C2 |
N3 |
C4 |
O4 |
181.0 |
179.7 |
| O2 |
C2 |
N1 |
C6 |
179.2 |
180.0 |
| O2 |
C2 |
N1 |
C1' |
357.1 |
0.2 |
| N1 |
C2 |
O2 |
N3 |
181.4 |
179.5 |
| O2 |
C2 |
N3 |
C4 |
180.5 |
180.0 |
| O2 |
C2 |
N3 |
HN3 |
0.5 |
359.7 |
| C4 |
N3 |
C2 |
O2 |
180.5 |
180.0 |
| C2 |
N3 |
C4 |
HN3 |
180.0 |
179.6 |
| C5 |
C4 |
N3 |
O4 |
179.8 |
180.0 |
| N3 |
C4 |
C5 |
C6 |
359.3 |
0.0 |
| N3 |
C4 |
C5 |
H5 |
179.2 |
180.1 |
| HN3 |
N3 |
C2 |
O2 |
0.5 |
359.7 |
| C2 |
N3 |
HN3 |
C4 |
180.0 |
180.4 |
| HN3 |
N3 |
C4 |
C5 |
180.9 |
180.1 |
| HN3 |
N3 |
C4 |
O4 |
1.1 |
0.1 |
| N1 |
C6 |
C5 |
C4 |
0.6 |
0.0 |
| C5 |
C4 |
N3 |
HN3 |
180.9 |
180.1 |
| N3 |
C4 |
C5 |
O4 |
180.2 |
180.0 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
179.9 |
| C4 |
C5 |
C6 |
H6 |
180.6 |
180.0 |
| O4 |
C4 |
N3 |
HN3 |
1.1 |
0.1 |
| N3 |
C4 |
O4 |
C5 |
179.8 |
180.0 |
| O4 |
C4 |
C5 |
C6 |
179.1 |
180.0 |
| O4 |
C4 |
C5 |
H5 |
359.0 |
0.1 |
| C5 |
C6 |
N1 |
C1' |
181.5 |
180.0 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.0 |
| C6 |
C5 |
C4 |
O4 |
179.1 |
180.0 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
180.1 |
| H5 |
C5 |
C4 |
O4 |
359.0 |
0.1 |
| C4 |
C5 |
H5 |
C6 |
180.0 |
179.9 |
| H5 |
C5 |
C6 |
H6 |
0.6 |
360.0 |
| H6 |
C6 |
N1 |
C1' |
1.5 |
360.0 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
180.0 |
| H6 |
C6 |
C5 |
H5 |
0.6 |
360.0 |
| N1 |
C1' |
C2' |
O4' |
134.5 |
118.6 |
| N1 |
C1' |
C2' |
H1' |
251.4 |
237.1 |
| O4' |
C1' |
C2' |
H1' |
116.8 |
118.5 |
| C2' |
C1' |
O4' |
C4' |
353.9 |
320.0 |
| C3' |
C2' |
C1' |
H2'1 |
234.7 |
241.9 |
| C3' |
C2' |
C1' |
H2'2 |
125.3 |
118.3 |
| C1' |
C2' |
C3' |
C4' |
315.6 |
339.0 |
| C1' |
C2' |
C3' |
O3' |
69.0 |
97.9 |
| C1' |
C2' |
C3' |
H3' |
190.1 |
220.4 |
| H2'1 |
C2' |
C1' |
H2'2 |
250.6 |
236.4 |
| N1 |
C1' |
O4' |
C2' |
229.9 |
241.3 |
| N1 |
C1' |
O4' |
H1' |
106.9 |
122.8 |
| C2' |
C1' |
O4' |
H1' |
237.1 |
241.4 |
| O4' |
C1' |
C2' |
C3' |
32.1 |
37.1 |
| O4' |
C1' |
C2' |
H2'1 |
157.5 |
155.2 |
| O4' |
C1' |
C2' |
H2'2 |
266.9 |
278.8 |
| C3' |
C4' |
O4' |
C1' |
338.3 |
26.4 |
| C1' |
O4' |
C4' |
C5' |
98.2 |
145.9 |
| C1' |
O4' |
C4' |
H4' |
217.2 |
266.9 |
| N1 |
C1' |
H1' |
C2' |
119.6 |
123.1 |
| N1 |
C1' |
H1' |
O4' |
234.9 |
237.2 |
| C2' |
C1' |
H1' |
O4' |
115.3 |
114.1 |
| H1' |
C1' |
C2' |
C3' |
275.3 |
278.6 |
| H1' |
C1' |
C2' |
H2'1 |
40.6 |
36.6 |
| H1' |
C1' |
C2' |
H2'2 |
150.0 |
160.3 |
| H1' |
C1' |
O4' |
C4' |
116.8 |
78.5 |
| C3' |
C2' |
C1' |
O4' |
32.1 |
37.1 |
| C3' |
C2' |
C1' |
H1' |
275.3 |
278.6 |
| C1' |
C2' |
C3' |
H2'1 |
125.3 |
118.1 |
| C1' |
C2' |
C3' |
H2'2 |
234.7 |
241.7 |
| H2'1 |
C2' |
C3' |
H2'2 |
109.4 |
123.6 |
| C4' |
C3' |
C2' |
O3' |
246.6 |
241.1 |
| C4' |
C3' |
C2' |
H3' |
125.5 |
118.6 |
| C2' |
C3' |
C4' |
O4' |
40.5 |
358.1 |
| C2' |
C3' |
C4' |
C5' |
283.2 |
238.6 |
| C2' |
C3' |
C4' |
H4' |
164.0 |
117.6 |
| O3' |
C3' |
C2' |
H3' |
238.9 |
237.5 |
| C2' |
C3' |
O3' |
HO3' |
180.0 |
61.4 |
| H2'1 |
C2' |
C1' |
O4' |
157.5 |
155.2 |
| H2'1 |
C2' |
C1' |
H1' |
40.6 |
36.6 |
| C1' |
C2' |
H2'1 |
C3' |
240.4 |
247.4 |
| C1' |
C2' |
H2'1 |
H2'2 |
120.2 |
123.7 |
| C3' |
C2' |
H2'1 |
H2'2 |
239.8 |
236.3 |
| H2'1 |
C2' |
C3' |
C4' |
190.3 |
220.9 |
| H2'1 |
C2' |
C3' |
O3' |
303.7 |
339.8 |
| H2'1 |
C2' |
C3' |
H3' |
64.8 |
102.2 |
| H2'2 |
C2' |
C1' |
O4' |
266.9 |
278.8 |
| H2'2 |
C2' |
C1' |
H1' |
150.0 |
160.3 |
| C1' |
C2' |
H2'2 |
C3' |
119.6 |
112.8 |
| C1' |
C2' |
H2'2 |
H2'1 |
239.8 |
236.3 |
| C3' |
C2' |
H2'2 |
H2'1 |
120.2 |
123.6 |
| H2'2 |
C2' |
C3' |
C4' |
80.9 |
97.3 |
| H2'2 |
C2' |
C3' |
O3' |
194.3 |
216.2 |
| H2'2 |
C2' |
C3' |
H3' |
315.3 |
338.6 |
| C1' |
O4' |
C4' |
C3' |
338.3 |
26.4 |
| C4' |
C3' |
C2' |
H2'1 |
190.3 |
220.9 |
| C4' |
C3' |
C2' |
H2'2 |
80.9 |
97.3 |
| C2' |
C3' |
C4' |
O3' |
115.2 |
118.7 |
| C2' |
C3' |
C4' |
H3' |
236.0 |
241.4 |
| O3' |
C3' |
C4' |
H3' |
120.8 |
122.6 |
| C4' |
C3' |
O3' |
HO3' |
287.8 |
176.2 |
| O4' |
C4' |
C3' |
C5' |
117.3 |
119.5 |
| O4' |
C4' |
C3' |
H4' |
236.5 |
240.5 |
| C5' |
C4' |
C3' |
H4' |
119.2 |
121.0 |
| C3' |
C4' |
C5' |
H5'1 |
180.0 |
179.7 |
| C3' |
C4' |
C5' |
H5'2 |
305.3 |
299.6 |
| C3' |
C4' |
C5' |
H5'3 |
54.7 |
59.7 |
| O3' |
C3' |
C2' |
H2'1 |
303.7 |
339.8 |
| O3' |
C3' |
C2' |
H2'2 |
194.3 |
216.2 |
| C2' |
C3' |
O3' |
C4' |
252.2 |
245.3 |
| C2' |
C3' |
O3' |
H3' |
125.5 |
122.5 |
| C4' |
C3' |
O3' |
H3' |
233.3 |
237.3 |
| O3' |
C3' |
C4' |
O4' |
285.3 |
239.4 |
| O3' |
C3' |
C4' |
C5' |
167.9 |
119.9 |
| O3' |
C3' |
C4' |
H4' |
48.7 |
358.9 |
| H3' |
C3' |
C2' |
H2'1 |
64.8 |
102.2 |
| H3' |
C3' |
C2' |
H2'2 |
315.3 |
338.6 |
| C2' |
C3' |
H3' |
C4' |
115.8 |
114.6 |
| C2' |
C3' |
H3' |
O3' |
237.1 |
237.5 |
| C4' |
C3' |
H3' |
O3' |
121.3 |
122.9 |
| H3' |
C3' |
C4' |
O4' |
164.5 |
116.7 |
| H3' |
C3' |
C4' |
C5' |
47.2 |
357.2 |
| H3' |
C3' |
C4' |
H4' |
288.0 |
236.2 |
| H3' |
C3' |
O3' |
HO3' |
54.5 |
298.9 |
| C4' |
O4' |
C1' |
H1' |
116.8 |
78.5 |
| O4' |
C4' |
C3' |
O3' |
285.3 |
239.4 |
| O4' |
C4' |
C3' |
H3' |
164.5 |
116.7 |
| C3' |
C4' |
O4' |
C5' |
240.2 |
240.5 |
| C3' |
C4' |
O4' |
H4' |
121.1 |
119.5 |
| C5' |
C4' |
O4' |
H4' |
241.0 |
239.0 |
| O4' |
C4' |
C5' |
H5'1 |
65.0 |
61.7 |
| O4' |
C4' |
C5' |
H5'2 |
190.3 |
181.7 |
| O4' |
C4' |
C5' |
H5'3 |
299.8 |
301.7 |
| C5' |
C4' |
C3' |
O3' |
167.9 |
119.9 |
| C5' |
C4' |
C3' |
H3' |
47.2 |
357.2 |
| C3' |
C4' |
C5' |
O4' |
115.0 |
118.0 |
| C3' |
C4' |
C5' |
H4' |
238.6 |
239.0 |
| O4' |
C4' |
C5' |
H4' |
123.6 |
121.0 |
| H5'1 |
C5' |
C4' |
H5'2 |
234.7 |
240.0 |
| H5'1 |
C5' |
C4' |
H5'3 |
125.2 |
120.0 |
| H5'2 |
C5' |
C4' |
H5'3 |
250.6 |
240.0 |
| H4' |
C4' |
C3' |
O3' |
48.7 |
358.9 |
| H4' |
C4' |
C3' |
H3' |
288.0 |
236.2 |
| C3' |
C4' |
H4' |
O4' |
242.3 |
242.0 |
| C3' |
C4' |
H4' |
C5' |
122.4 |
121.0 |
| O4' |
C4' |
H4' |
C5' |
240.1 |
239.0 |
| H4' |
C4' |
C5' |
H5'1 |
301.4 |
300.7 |
| H4' |
C4' |
C5' |
H5'2 |
66.7 |
60.7 |
| H4' |
C4' |
C5' |
H5'3 |
176.2 |
180.7 |
| HO3' |
O3' |
C3' |
H3' |
54.5 |
298.9 |
| H5'1 |
C5' |
C4' |
H4' |
301.4 |
300.7 |
| C4' |
C5' |
H5'1 |
H5'2 |
125.3 |
120.0 |
| C4' |
C5' |
H5'1 |
H5'3 |
234.7 |
240.0 |
| H5'2 |
C5' |
H5'1 |
H5'3 |
109.4 |
120.0 |
| H5'2 |
C5' |
C4' |
H4' |
66.7 |
60.7 |
| C4' |
C5' |
H5'2 |
H5'1 |
234.1 |
240.0 |
| C4' |
C5' |
H5'2 |
H5'3 |
117.1 |
120.1 |
| H5'1 |
C5' |
H5'2 |
H5'3 |
243.0 |
240.0 |
| H5'3 |
C5' |
C4' |
H4' |
176.2 |
180.7 |
| C4' |
C5' |
H5'3 |
H5'1 |
125.8 |
120.0 |
| C4' |
C5' |
H5'3 |
H5'2 |
242.9 |
240.0 |
| H5'1 |
C5' |
H5'3 |
H5'2 |
117.1 |
120.0 |