PDB Chemical Component URI
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 URI
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N1 |
C2 |
1.383 |
1.344 |
| N1 |
C6 |
1.380 |
1.369 |
| N1 |
C1' |
1.471 |
1.463 |
| C2 |
N3 |
1.374 |
1.346 |
| C2 |
O2 |
1.222 |
1.215 |
| N3 |
C4 |
1.380 |
1.348 |
| N3 |
H3 |
1.020 |
0.970 |
| C4 |
C5 |
1.433 |
1.416 |
| C4 |
O4 |
1.232 |
1.217 |
| C5 |
C6 |
1.338 |
1.350 |
| C5 |
H5 |
1.103 |
1.080 |
| C6 |
H6 |
1.102 |
1.080 |
| C1' |
C2' |
1.529 |
1.549 |
| C1' |
O4' |
1.406 |
1.443 |
| C1' |
H1' |
1.115 |
1.090 |
| C2' |
C3' |
1.527 |
1.552 |
| C2' |
O2' |
1.412 |
1.429 |
| C2' |
H2' |
1.115 |
1.091 |
| C3' |
C4' |
1.524 |
1.539 |
| C3' |
O3' |
1.420 |
1.428 |
| C3' |
H3' |
1.115 |
1.090 |
| C4' |
O4' |
1.446 |
1.438 |
| C4' |
C5' |
1.508 |
1.530 |
| C4' |
H4' |
1.115 |
1.090 |
| O2' |
HO2' |
0.950 |
0.967 |
| O3' |
HO3' |
0.950 |
0.967 |
| C5' |
O5' |
1.433 |
1.428 |
| C5' |
H5'1 |
1.115 |
1.090 |
| C5' |
H5'2 |
1.116 |
1.090 |
| O5' |
HO5' |
0.950 |
0.968 |
Bond Angles for URI
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N1 |
C6 |
121.0 |
120.6 |
| C2 |
N1 |
C1' |
117.2 |
119.7 |
| N1 |
C2 |
N3 |
114.9 |
120.9 |
| N1 |
C2 |
O2 |
122.7 |
119.5 |
| C6 |
N1 |
C1' |
121.7 |
119.6 |
| N1 |
C6 |
C5 |
122.6 |
119.7 |
| N1 |
C6 |
H6 |
120.4 |
120.2 |
| N1 |
C1' |
C2' |
113.2 |
110.7 |
| N1 |
C1' |
O4' |
108.8 |
110.6 |
| N1 |
C1' |
H1' |
107.0 |
110.6 |
| N3 |
C2 |
O2 |
122.3 |
119.5 |
| C2 |
N3 |
C4 |
127.1 |
120.3 |
| C2 |
N3 |
H3 |
116.3 |
119.8 |
| C4 |
N3 |
H3 |
116.7 |
119.8 |
| N3 |
C4 |
C5 |
114.7 |
119.3 |
| N3 |
C4 |
O4 |
119.3 |
120.4 |
| C5 |
C4 |
O4 |
126.0 |
120.3 |
| C4 |
C5 |
C6 |
119.7 |
119.2 |
| C4 |
C5 |
H5 |
123.5 |
120.4 |
| C6 |
C5 |
H5 |
116.8 |
120.4 |
| C5 |
C6 |
H6 |
117.0 |
120.2 |
| C2' |
C1' |
O4' |
108.3 |
103.5 |
| C2' |
C1' |
H1' |
107.5 |
110.6 |
| C1' |
C2' |
C3' |
103.4 |
102.1 |
| C1' |
C2' |
O2' |
110.6 |
111.0 |
| C1' |
C2' |
H2' |
114.0 |
110.9 |
| O4' |
C1' |
H1' |
112.0 |
110.6 |
| C1' |
O4' |
C4' |
110.3 |
107.0 |
| C3' |
C2' |
O2' |
113.2 |
110.8 |
| C3' |
C2' |
H2' |
111.5 |
110.9 |
| C2' |
C3' |
C4' |
104.4 |
104.0 |
| C2' |
C3' |
O3' |
102.7 |
110.5 |
| C2' |
C3' |
H3' |
116.4 |
110.5 |
| O2' |
C2' |
H2' |
104.4 |
110.8 |
| C2' |
O2' |
HO2' |
110.6 |
106.8 |
| C4' |
C3' |
O3' |
108.6 |
110.8 |
| C4' |
C3' |
H3' |
111.2 |
110.4 |
| C3' |
C4' |
O4' |
107.5 |
107.4 |
| C3' |
C4' |
C5' |
116.7 |
109.9 |
| C3' |
C4' |
H4' |
105.8 |
109.9 |
| O3' |
C3' |
H3' |
112.7 |
110.4 |
| C3' |
O3' |
HO3' |
102.7 |
106.8 |
| O4' |
C4' |
C5' |
109.2 |
109.9 |
| O4' |
C4' |
H4' |
113.8 |
109.9 |
| C5' |
C4' |
H4' |
104.0 |
109.8 |
| C4' |
C5' |
O5' |
113.1 |
109.5 |
| C4' |
C5' |
H5'1 |
110.9 |
109.5 |
| C4' |
C5' |
H5'2 |
110.9 |
109.5 |
| O5' |
C5' |
H5'1 |
110.9 |
109.4 |
| O5' |
C5' |
H5'2 |
110.8 |
109.5 |
| C5' |
O5' |
HO5' |
113.1 |
106.8 |
| H5'1 |
C5' |
H5'2 |
99.4 |
109.5 |
Torsion Angles for URI
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C6 |
N1 |
C2 |
C1' |
177.9 |
179.7 |
| C2 |
N1 |
C6 |
C5 |
357.5 |
0.3 |
| C2 |
N1 |
C6 |
H6 |
177.5 |
180.3 |
| C2 |
N1 |
C1' |
C2' |
161.6 |
304.1 |
| C2 |
N1 |
C1' |
O4' |
282.1 |
58.2 |
| C2 |
N1 |
C1' |
H1' |
43.3 |
181.1 |
| N3 |
C2 |
N1 |
O2 |
179.6 |
179.5 |
| N1 |
C2 |
N3 |
C4 |
359.2 |
0.5 |
| N1 |
C2 |
N3 |
H3 |
179.2 |
180.3 |
| C2 |
N1 |
C6 |
C1' |
182.2 |
180.3 |
| C6 |
N1 |
C2 |
N3 |
2.4 |
359.5 |
| C6 |
N1 |
C2 |
O2 |
182.8 |
180.0 |
| C6 |
N1 |
C1' |
C2' |
343.7 |
124.4 |
| C6 |
N1 |
C1' |
O4' |
104.2 |
238.5 |
| C6 |
N1 |
C1' |
H1' |
225.4 |
1.5 |
| C4 |
C5 |
C6 |
N1 |
0.8 |
0.1 |
| N1 |
C6 |
C5 |
H5 |
180.8 |
179.9 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
180.0 |
| C2 |
N1 |
C1' |
C6 |
177.8 |
179.7 |
| C1' |
N1 |
C2 |
N3 |
184.6 |
179.8 |
| C1' |
N1 |
C2 |
O2 |
4.9 |
0.3 |
| C1' |
N1 |
C6 |
C5 |
175.3 |
179.9 |
| C1' |
N1 |
C6 |
H6 |
355.2 |
360.0 |
| C2' |
C1' |
N1 |
O4' |
239.5 |
245.9 |
| C2' |
C1' |
N1 |
H1' |
118.3 |
122.9 |
| N1 |
C1' |
C2' |
C3' |
143.7 |
155.7 |
| N1 |
C1' |
C2' |
O2' |
265.2 |
273.8 |
| N1 |
C1' |
C2' |
H2' |
22.5 |
37.4 |
| O4' |
C1' |
N1 |
H1' |
238.8 |
237.1 |
| N1 |
C1' |
O4' |
C4' |
224.1 |
201.3 |
| N3 |
C2 |
N1 |
C6 |
2.4 |
359.5 |
| N3 |
C2 |
N1 |
C1' |
184.6 |
179.8 |
| N1 |
C2 |
N3 |
O2 |
180.4 |
180.5 |
| C4 |
N3 |
C2 |
H3 |
180.0 |
180.2 |
| C2 |
N3 |
C4 |
C5 |
359.2 |
359.8 |
| C2 |
N3 |
C4 |
O4 |
179.3 |
179.7 |
| O2 |
C2 |
N1 |
C6 |
182.8 |
180.0 |
| O2 |
C2 |
N1 |
C1' |
4.9 |
0.3 |
| N1 |
C2 |
O2 |
N3 |
179.6 |
179.5 |
| O2 |
C2 |
N3 |
C4 |
178.8 |
180.0 |
| O2 |
C2 |
N3 |
H3 |
358.8 |
359.7 |
| C4 |
N3 |
C2 |
O2 |
178.8 |
180.0 |
| C2 |
N3 |
C4 |
H3 |
180.0 |
179.8 |
| C5 |
C4 |
N3 |
O4 |
180.0 |
180.1 |
| N3 |
C4 |
C5 |
C6 |
0.8 |
359.9 |
| N3 |
C4 |
C5 |
H5 |
180.8 |
180.0 |
| H3 |
N3 |
C2 |
O2 |
358.8 |
359.7 |
| C2 |
N3 |
H3 |
C4 |
180.0 |
180.2 |
| H3 |
N3 |
C4 |
C5 |
179.2 |
180.1 |
| H3 |
N3 |
C4 |
O4 |
359.2 |
359.9 |
| N1 |
C6 |
C5 |
C4 |
0.8 |
0.1 |
| C5 |
C4 |
N3 |
H3 |
179.2 |
180.1 |
| N3 |
C4 |
C5 |
O4 |
180.0 |
179.9 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
179.9 |
| C4 |
C5 |
C6 |
H6 |
180.8 |
180.0 |
| O4 |
C4 |
N3 |
H3 |
359.2 |
359.9 |
| N3 |
C4 |
O4 |
C5 |
180.0 |
180.1 |
| O4 |
C4 |
C5 |
C6 |
180.7 |
180.0 |
| O4 |
C4 |
C5 |
H5 |
0.8 |
0.2 |
| C5 |
C6 |
N1 |
C1' |
175.3 |
179.9 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.0 |
| C6 |
C5 |
C4 |
O4 |
180.7 |
180.0 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
180.1 |
| H5 |
C5 |
C4 |
O4 |
0.8 |
0.2 |
| C4 |
C5 |
H5 |
C6 |
180.0 |
179.9 |
| H5 |
C5 |
C6 |
H6 |
0.8 |
359.9 |
| H6 |
C6 |
N1 |
C1' |
355.2 |
360.0 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
180.0 |
| H6 |
C6 |
C5 |
H5 |
0.8 |
359.9 |
| N1 |
C1' |
C2' |
O4' |
120.8 |
118.6 |
| N1 |
C1' |
C2' |
H1' |
242.0 |
237.1 |
| O4' |
C1' |
C2' |
H1' |
121.2 |
118.5 |
| C2' |
C1' |
O4' |
C4' |
347.5 |
320.0 |
| C3' |
C2' |
C1' |
O2' |
238.6 |
241.8 |
| C3' |
C2' |
C1' |
H2' |
121.2 |
118.2 |
| C1' |
C2' |
C3' |
C4' |
336.1 |
339.0 |
| C1' |
C2' |
C3' |
O3' |
89.4 |
98.0 |
| C1' |
C2' |
C3' |
H3' |
213.1 |
220.5 |
| O2' |
C2' |
C1' |
H2' |
242.7 |
236.4 |
| C1' |
C2' |
O2' |
HO2' |
180.0 |
180.0 |
| N1 |
C1' |
O4' |
C2' |
236.6 |
241.4 |
| N1 |
C1' |
O4' |
H1' |
118.1 |
122.9 |
| C2' |
C1' |
O4' |
H1' |
241.6 |
241.6 |
| O4' |
C1' |
C2' |
C3' |
22.9 |
37.1 |
| O4' |
C1' |
C2' |
O2' |
144.4 |
155.2 |
| O4' |
C1' |
C2' |
H2' |
261.7 |
278.8 |
| C3' |
C4' |
O4' |
C1' |
356.6 |
26.4 |
| C1' |
O4' |
C4' |
C5' |
124.1 |
146.0 |
| C1' |
O4' |
C4' |
H4' |
239.8 |
266.9 |
| N1 |
C1' |
H1' |
C2' |
121.9 |
123.0 |
| N1 |
C1' |
H1' |
O4' |
240.8 |
237.0 |
| C2' |
C1' |
H1' |
O4' |
118.9 |
114.0 |
| H1' |
C1' |
C2' |
C3' |
261.7 |
278.6 |
| H1' |
C1' |
C2' |
O2' |
23.2 |
36.8 |
| H1' |
C1' |
C2' |
H2' |
140.5 |
160.4 |
| H1' |
C1' |
O4' |
C4' |
106.0 |
78.4 |
| C3' |
C2' |
C1' |
O4' |
22.9 |
37.1 |
| C3' |
C2' |
C1' |
H1' |
261.7 |
278.6 |
| C1' |
C2' |
C3' |
O2' |
119.7 |
118.2 |
| C1' |
C2' |
C3' |
H2' |
237.1 |
241.8 |
| O2' |
C2' |
C3' |
H2' |
117.4 |
123.6 |
| C3' |
C2' |
O2' |
HO2' |
295.4 |
292.7 |
| C4' |
C3' |
C2' |
O3' |
246.7 |
241.0 |
| C4' |
C3' |
C2' |
H3' |
123.0 |
118.5 |
| C2' |
C3' |
C4' |
O4' |
17.6 |
358.1 |
| C2' |
C3' |
C4' |
C5' |
254.6 |
238.6 |
| C2' |
C3' |
C4' |
H4' |
139.5 |
117.6 |
| O3' |
C3' |
C2' |
H3' |
236.3 |
237.5 |
| C2' |
C3' |
O3' |
HO3' |
180.1 |
180.0 |
| O2' |
C2' |
C1' |
O4' |
144.4 |
155.2 |
| O2' |
C2' |
C1' |
H1' |
23.2 |
36.8 |
| C1' |
C2' |
O2' |
C3' |
244.6 |
247.3 |
| C1' |
C2' |
O2' |
H2' |
123.1 |
123.6 |
| C3' |
C2' |
O2' |
H2' |
238.5 |
236.4 |
| O2' |
C2' |
C3' |
C4' |
216.4 |
220.8 |
| O2' |
C2' |
C3' |
O3' |
329.7 |
339.8 |
| O2' |
C2' |
C3' |
H3' |
93.4 |
102.3 |
| H2' |
C2' |
C1' |
O4' |
261.7 |
278.8 |
| H2' |
C2' |
C1' |
H1' |
140.5 |
160.4 |
| C1' |
C2' |
H2' |
C3' |
116.6 |
112.7 |
| C1' |
C2' |
H2' |
O2' |
239.2 |
236.3 |
| C3' |
C2' |
H2' |
O2' |
122.6 |
123.6 |
| H2' |
C2' |
C3' |
C4' |
99.0 |
97.2 |
| H2' |
C2' |
C3' |
O3' |
212.3 |
216.2 |
| H2' |
C2' |
C3' |
H3' |
336.0 |
338.7 |
| H2' |
C2' |
O2' |
HO2' |
56.9 |
56.3 |
| C1' |
O4' |
C4' |
C3' |
356.6 |
26.4 |
| C4' |
C3' |
C2' |
O2' |
216.4 |
220.8 |
| C4' |
C3' |
C2' |
H2' |
99.0 |
97.2 |
| C2' |
C3' |
C4' |
O3' |
109.1 |
118.7 |
| C2' |
C3' |
C4' |
H3' |
233.7 |
241.4 |
| O3' |
C3' |
C4' |
H3' |
124.6 |
122.7 |
| C4' |
C3' |
O3' |
HO3' |
290.2 |
294.7 |
| O4' |
C4' |
C3' |
C5' |
123.0 |
119.5 |
| O4' |
C4' |
C3' |
H4' |
238.1 |
240.5 |
| C5' |
C4' |
C3' |
H4' |
115.1 |
121.0 |
| C3' |
C4' |
C5' |
O5' |
279.9 |
179.7 |
| C3' |
C4' |
C5' |
H5'1 |
45.3 |
59.7 |
| C3' |
C4' |
C5' |
H5'2 |
154.7 |
299.7 |
| O3' |
C3' |
C2' |
O2' |
329.7 |
339.8 |
| O3' |
C3' |
C2' |
H2' |
212.3 |
216.2 |
| C2' |
C3' |
O3' |
C4' |
249.8 |
245.2 |
| C2' |
C3' |
O3' |
H3' |
126.1 |
122.5 |
| C4' |
C3' |
O3' |
H3' |
236.3 |
237.3 |
| O3' |
C3' |
C4' |
O4' |
268.5 |
239.4 |
| O3' |
C3' |
C4' |
C5' |
145.5 |
119.8 |
| O3' |
C3' |
C4' |
H4' |
30.5 |
358.8 |
| H3' |
C3' |
C2' |
O2' |
93.4 |
102.3 |
| H3' |
C3' |
C2' |
H2' |
336.0 |
338.7 |
| C2' |
C3' |
H3' |
C4' |
119.4 |
114.5 |
| C2' |
C3' |
H3' |
O3' |
241.7 |
237.5 |
| C4' |
C3' |
H3' |
O3' |
122.3 |
122.9 |
| H3' |
C3' |
C4' |
O4' |
143.9 |
116.7 |
| H3' |
C3' |
C4' |
C5' |
20.9 |
357.1 |
| H3' |
C3' |
C4' |
H4' |
265.9 |
236.2 |
| H3' |
C3' |
O3' |
HO3' |
54.0 |
57.4 |
| C4' |
O4' |
C1' |
H1' |
106.0 |
78.4 |
| O4' |
C4' |
C3' |
O3' |
268.5 |
239.4 |
| O4' |
C4' |
C3' |
H3' |
143.9 |
116.7 |
| C3' |
C4' |
O4' |
C5' |
232.5 |
240.4 |
| C3' |
C4' |
O4' |
H4' |
116.8 |
119.5 |
| C5' |
C4' |
O4' |
H4' |
244.3 |
239.1 |
| O4' |
C4' |
C5' |
O5' |
157.8 |
61.6 |
| O4' |
C4' |
C5' |
H5'1 |
283.1 |
301.7 |
| O4' |
C4' |
C5' |
H5'2 |
32.6 |
181.7 |
| C5' |
C4' |
C3' |
O3' |
145.5 |
119.8 |
| C5' |
C4' |
C3' |
H3' |
20.9 |
357.1 |
| C3' |
C4' |
C5' |
O4' |
122.1 |
118.1 |
| C3' |
C4' |
C5' |
H4' |
243.9 |
239.0 |
| O4' |
C4' |
C5' |
H4' |
121.8 |
120.9 |
| O5' |
C5' |
C4' |
H5'1 |
234.7 |
120.0 |
| O5' |
C5' |
C4' |
H5'2 |
125.2 |
240.0 |
| C4' |
C5' |
O5' |
HO5' |
180.0 |
180.0 |
| H5'1 |
C5' |
C4' |
H5'2 |
250.5 |
120.0 |
| H4' |
C4' |
C3' |
O3' |
30.5 |
358.8 |
| H4' |
C4' |
C3' |
H3' |
265.9 |
236.2 |
| C3' |
C4' |
H4' |
O4' |
242.2 |
242.0 |
| C3' |
C4' |
H4' |
C5' |
123.5 |
121.0 |
| O4' |
C4' |
H4' |
C5' |
241.3 |
239.0 |
| H4' |
C4' |
C5' |
O5' |
36.0 |
300.7 |
| H4' |
C4' |
C5' |
H5'1 |
161.3 |
180.7 |
| H4' |
C4' |
C5' |
H5'2 |
270.8 |
60.7 |
| HO2' |
O2' |
C2' |
H2' |
56.9 |
56.3 |
| HO3' |
O3' |
C3' |
H3' |
54.0 |
57.4 |
| O5' |
C5' |
C4' |
H4' |
36.0 |
300.7 |
| C4' |
C5' |
O5' |
H5'1 |
125.3 |
240.0 |
| C4' |
C5' |
O5' |
H5'2 |
234.7 |
120.0 |
| H5'1 |
C5' |
O5' |
H5'2 |
109.5 |
240.0 |
| H5'1 |
C5' |
C4' |
H4' |
161.3 |
180.7 |
| C4' |
C5' |
H5'1 |
O5' |
233.4 |
120.0 |
| C4' |
C5' |
H5'1 |
H5'2 |
116.7 |
240.0 |
| O5' |
C5' |
H5'1 |
H5'2 |
243.3 |
120.0 |
| H5'1 |
C5' |
O5' |
HO5' |
54.7 |
300.0 |
| H5'2 |
C5' |
C4' |
H4' |
270.8 |
60.7 |
| C4' |
C5' |
H5'2 |
O5' |
126.5 |
239.9 |
| C4' |
C5' |
H5'2 |
H5'1 |
243.3 |
120.0 |
| O5' |
C5' |
H5'2 |
H5'1 |
116.8 |
240.0 |
| H5'2 |
C5' |
O5' |
HO5' |
305.3 |
59.9 |
| HO5' |
O5' |
C5' |
H5'1 |
54.7 |
300.0 |
| HO5' |
O5' |
C5' |
H5'2 |
305.3 |
59.9 |