PDB Chemical Component URD
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 URD
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O5' |
C5' |
1.422 |
1.430 |
| O5' |
HO5' |
0.950 |
0.966 |
| C5' |
C4' |
1.510 |
1.529 |
| C5' |
H5' |
1.099 |
1.090 |
| C5' |
H5'' |
1.100 |
1.090 |
| C4' |
O4' |
1.455 |
1.437 |
| C4' |
C3' |
1.522 |
1.542 |
| C4' |
H4' |
1.100 |
1.090 |
| O4' |
C1' |
1.414 |
1.444 |
| C1' |
N1 |
1.471 |
1.465 |
| C1' |
C2' |
1.523 |
1.550 |
| C1' |
H1' |
1.100 |
1.090 |
| N1 |
C6 |
1.376 |
1.360 |
| N1 |
C2 |
1.388 |
1.347 |
| C6 |
C5 |
1.338 |
1.345 |
| C6 |
H6 |
1.080 |
1.081 |
| C2 |
O2 |
1.219 |
1.212 |
| C2 |
C3 |
1.374 |
1.516 |
| C3 |
C4 |
1.381 |
1.517 |
| C3 |
H31 |
1.100 |
1.090 |
| C3 |
H32 |
1.100 |
1.090 |
| C4 |
O4 |
1.236 |
1.214 |
| C4 |
C5 |
1.435 |
1.409 |
| C5 |
H5 |
1.080 |
1.079 |
| C2' |
O2' |
1.414 |
1.429 |
| C2' |
C3' |
1.527 |
1.551 |
| C2' |
H2' |
1.100 |
1.090 |
| O2' |
HO2' |
0.950 |
0.966 |
| C3' |
O3' |
1.421 |
1.429 |
| C3' |
H3' |
1.100 |
1.089 |
| O3' |
HO3' |
0.950 |
0.967 |
Bond Angles for URD
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C5' |
O5' |
HO5' |
109.5 |
106.8 |
| O5' |
C5' |
C4' |
110.2 |
109.4 |
| O5' |
C5' |
H5' |
109.1 |
109.4 |
| O5' |
C5' |
H5'' |
109.2 |
109.5 |
| C4' |
C5' |
H5' |
109.1 |
109.5 |
| C4' |
C5' |
H5'' |
109.2 |
109.5 |
| C5' |
C4' |
O4' |
109.2 |
109.9 |
| C5' |
C4' |
C3' |
115.3 |
109.9 |
| C5' |
C4' |
H4' |
104.5 |
109.9 |
| H5' |
C5' |
H5'' |
110.0 |
109.5 |
| O4' |
C4' |
C3' |
105.7 |
107.4 |
| O4' |
C4' |
H4' |
114.3 |
109.9 |
| C4' |
O4' |
C1' |
109.8 |
107.0 |
| C3' |
C4' |
H4' |
108.2 |
109.8 |
| C4' |
C3' |
C2' |
102.2 |
104.0 |
| C4' |
C3' |
O3' |
109.2 |
110.8 |
| C4' |
C3' |
H3' |
115.1 |
110.4 |
| O4' |
C1' |
N1 |
108.3 |
110.6 |
| O4' |
C1' |
C2' |
104.8 |
103.5 |
| O4' |
C1' |
H1' |
114.8 |
110.6 |
| N1 |
C1' |
C2' |
113.9 |
110.8 |
| N1 |
C1' |
H1' |
105.9 |
110.6 |
| C1' |
N1 |
C6 |
121.4 |
118.7 |
| C1' |
N1 |
C2 |
117.8 |
118.7 |
| C2' |
C1' |
H1' |
109.3 |
110.6 |
| C1' |
C2' |
O2' |
111.6 |
110.9 |
| C1' |
C2' |
C3' |
100.8 |
102.1 |
| C1' |
C2' |
H2' |
116.1 |
110.9 |
| C6 |
N1 |
C2 |
120.8 |
122.6 |
| N1 |
C6 |
C5 |
122.8 |
124.3 |
| N1 |
C6 |
H6 |
118.6 |
117.9 |
| N1 |
C2 |
O2 |
122.9 |
120.9 |
| N1 |
C2 |
C3 |
115.0 |
118.3 |
| C5 |
C6 |
H6 |
118.6 |
117.8 |
| C6 |
C5 |
C4 |
120.0 |
121.0 |
| C6 |
C5 |
H5 |
120.0 |
119.5 |
| O2 |
C2 |
C3 |
122.1 |
120.8 |
| C2 |
C3 |
C4 |
127.2 |
116.6 |
| C2 |
C3 |
H31 |
99.8 |
108.2 |
| C2 |
C3 |
H32 |
103.9 |
107.8 |
| C4 |
C3 |
H31 |
99.7 |
108.1 |
| C4 |
C3 |
H32 |
103.9 |
108.1 |
| C3 |
C4 |
O4 |
118.7 |
121.4 |
| C3 |
C4 |
C5 |
114.3 |
117.3 |
| H31 |
C3 |
H32 |
124.8 |
107.8 |
| O4 |
C4 |
C5 |
125.4 |
121.4 |
| C4 |
C5 |
H5 |
120.0 |
119.5 |
| O2' |
C2' |
C3' |
115.7 |
110.9 |
| O2' |
C2' |
H2' |
101.3 |
110.8 |
| C2' |
O2' |
HO2' |
109.5 |
106.8 |
| C3' |
C2' |
H2' |
112.1 |
111.0 |
| C2' |
C3' |
O3' |
111.9 |
110.5 |
| C2' |
C3' |
H3' |
112.6 |
110.5 |
| O3' |
C3' |
H3' |
106.0 |
110.5 |
| C3' |
O3' |
HO3' |
109.5 |
106.8 |
Torsion Angles for URD
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C4' |
C5' |
O5' |
H5' |
119.7 |
240.0 |
| C4' |
C5' |
O5' |
H5'' |
240.0 |
120.0 |
| O5' |
C5' |
C4' |
O4' |
285.3 |
66.7 |
| O5' |
C5' |
C4' |
C3' |
44.0 |
184.7 |
| O5' |
C5' |
C4' |
H4' |
162.6 |
305.7 |
| H5' |
C5' |
O5' |
H5'' |
120.3 |
240.0 |
| HO5' |
O5' |
C5' |
C4' |
193.9 |
180.0 |
| HO5' |
O5' |
C5' |
H5' |
74.2 |
300.0 |
| HO5' |
O5' |
C5' |
H5'' |
313.9 |
60.0 |
| C4' |
C5' |
O5' |
HO5' |
193.9 |
180.0 |
| O5' |
C5' |
C4' |
H5' |
240.3 |
120.0 |
| O5' |
C5' |
C4' |
H5'' |
120.0 |
240.0 |
| H5' |
C5' |
C4' |
H5'' |
239.7 |
120.0 |
| O4' |
C4' |
C5' |
C3' |
241.3 |
242.0 |
| O4' |
C4' |
C5' |
H4' |
122.7 |
121.0 |
| C5' |
C4' |
O4' |
C1' |
123.1 |
145.9 |
| C3' |
C4' |
C5' |
H4' |
241.4 |
239.0 |
| C5' |
C4' |
C3' |
C2' |
264.9 |
238.6 |
| C5' |
C4' |
C3' |
O3' |
146.3 |
119.9 |
| C5' |
C4' |
C3' |
H3' |
27.3 |
357.2 |
| H5' |
C5' |
O5' |
HO5' |
74.2 |
300.0 |
| O5' |
C5' |
H5' |
C4' |
120.4 |
240.0 |
| O5' |
C5' |
H5' |
H5'' |
240.2 |
120.0 |
| C4' |
C5' |
H5' |
H5'' |
119.8 |
240.0 |
| H5' |
C5' |
C4' |
O4' |
45.0 |
306.7 |
| H5' |
C5' |
C4' |
C3' |
163.7 |
64.7 |
| H5' |
C5' |
C4' |
H4' |
282.3 |
185.7 |
| H5'' |
C5' |
O5' |
HO5' |
313.9 |
60.0 |
| O5' |
C5' |
H5'' |
C4' |
239.5 |
120.0 |
| O5' |
C5' |
H5'' |
H5' |
119.7 |
240.0 |
| C4' |
C5' |
H5'' |
H5' |
240.3 |
120.1 |
| H5'' |
C5' |
C4' |
O4' |
165.3 |
186.7 |
| H5'' |
C5' |
C4' |
C3' |
284.0 |
304.7 |
| H5'' |
C5' |
C4' |
H4' |
42.6 |
65.7 |
| O4' |
C4' |
C5' |
H5' |
45.0 |
306.7 |
| O4' |
C4' |
C5' |
H5'' |
165.3 |
186.7 |
| C5' |
C4' |
O4' |
C3' |
124.5 |
119.5 |
| C5' |
C4' |
O4' |
H4' |
243.3 |
238.9 |
| C3' |
C4' |
O4' |
H4' |
118.8 |
119.4 |
| O4' |
C4' |
C3' |
C2' |
25.6 |
358.1 |
| O4' |
C4' |
C3' |
O3' |
266.9 |
239.4 |
| O4' |
C4' |
C3' |
H3' |
147.9 |
116.7 |
| C4' |
O4' |
C1' |
N1 |
214.4 |
201.3 |
| C4' |
O4' |
C1' |
C2' |
336.3 |
319.9 |
| C4' |
O4' |
C1' |
H1' |
96.3 |
78.4 |
| C3' |
C4' |
C5' |
H5' |
163.7 |
64.7 |
| C3' |
C4' |
C5' |
H5'' |
284.0 |
304.7 |
| C5' |
C4' |
C3' |
O4' |
239.4 |
240.5 |
| C5' |
C4' |
C3' |
H4' |
116.5 |
121.1 |
| O4' |
C4' |
C3' |
H4' |
237.2 |
240.5 |
| C3' |
C4' |
O4' |
C1' |
358.6 |
26.5 |
| C1' |
C2' |
C3' |
C4' |
321.6 |
339.0 |
| O2' |
C2' |
C3' |
C4' |
201.2 |
220.8 |
| C4' |
C3' |
C2' |
H2' |
85.7 |
97.2 |
| C2' |
C3' |
C4' |
O3' |
118.7 |
118.7 |
| C2' |
C3' |
C4' |
H3' |
237.6 |
241.4 |
| O3' |
C3' |
C4' |
H3' |
119.0 |
122.7 |
| C4' |
C3' |
O3' |
HO3' |
119.0 |
294.7 |
| H4' |
C4' |
C5' |
H5' |
282.3 |
185.7 |
| H4' |
C4' |
C5' |
H5'' |
42.6 |
65.7 |
| C5' |
C4' |
H4' |
O4' |
119.3 |
121.1 |
| C5' |
C4' |
H4' |
C3' |
236.7 |
239.0 |
| O4' |
C4' |
H4' |
C3' |
117.4 |
117.9 |
| H4' |
C4' |
O4' |
C1' |
239.8 |
267.0 |
| H4' |
C4' |
C3' |
C2' |
148.4 |
117.5 |
| H4' |
C4' |
C3' |
O3' |
29.7 |
358.8 |
| H4' |
C4' |
C3' |
H3' |
270.7 |
236.1 |
| C1' |
O4' |
C4' |
C3' |
358.6 |
26.5 |
| C1' |
O4' |
C4' |
H4' |
239.8 |
267.0 |
| N1 |
C1' |
O4' |
C2' |
238.0 |
241.3 |
| N1 |
C1' |
O4' |
H1' |
118.1 |
122.9 |
| O4' |
C1' |
N1 |
C6 |
39.6 |
53.5 |
| O4' |
C1' |
N1 |
C2 |
220.2 |
233.3 |
| C2' |
C1' |
O4' |
H1' |
240.1 |
241.5 |
| O4' |
C1' |
C2' |
O2' |
162.0 |
155.3 |
| O4' |
C1' |
C2' |
C3' |
38.6 |
37.1 |
| O4' |
C1' |
C2' |
H2' |
277.4 |
278.8 |
| O4' |
C1' |
N1 |
C2' |
116.2 |
114.1 |
| O4' |
C1' |
N1 |
H1' |
236.3 |
237.1 |
| C2' |
C1' |
N1 |
H1' |
120.1 |
123.0 |
| N1 |
C1' |
C2' |
O2' |
280.2 |
273.8 |
| N1 |
C1' |
C2' |
C3' |
156.9 |
155.7 |
| N1 |
C1' |
C2' |
H2' |
35.6 |
37.4 |
| C6 |
N1 |
C1' |
C2 |
179.4 |
180.2 |
| C1' |
N1 |
C6 |
C5 |
181.6 |
180.0 |
| C1' |
N1 |
C6 |
H6 |
1.5 |
360.0 |
| C1' |
N1 |
C2 |
O2 |
358.2 |
0.2 |
| C1' |
N1 |
C2 |
C3 |
178.3 |
179.8 |
| C4' |
C3' |
C2' |
C1' |
321.6 |
339.0 |
| O4' |
C1' |
C2' |
N1 |
241.8 |
241.4 |
| O4' |
C1' |
C2' |
H1' |
123.6 |
118.5 |
| N1 |
C1' |
C2' |
H1' |
241.8 |
237.0 |
| C2' |
C1' |
N1 |
C6 |
283.4 |
299.4 |
| C2' |
C1' |
N1 |
C2 |
103.9 |
119.2 |
| O2' |
C2' |
C1' |
C3' |
123.3 |
118.2 |
| O2' |
C2' |
C1' |
H2' |
244.6 |
236.4 |
| C1' |
C2' |
O2' |
HO2' |
349.9 |
180.0 |
| C3' |
C2' |
C1' |
H2' |
121.3 |
118.3 |
| C1' |
C2' |
C3' |
O3' |
78.4 |
97.9 |
| C1' |
C2' |
C3' |
H3' |
197.6 |
220.5 |
| O4' |
C1' |
H1' |
N1 |
119.4 |
122.9 |
| O4' |
C1' |
H1' |
C2' |
242.6 |
246.0 |
| N1 |
C1' |
H1' |
C2' |
123.1 |
123.1 |
| H1' |
C1' |
N1 |
C6 |
163.2 |
176.4 |
| H1' |
C1' |
N1 |
C2 |
343.8 |
356.2 |
| H1' |
C1' |
C2' |
O2' |
38.4 |
36.8 |
| H1' |
C1' |
C2' |
C3' |
275.1 |
278.6 |
| H1' |
C1' |
C2' |
H2' |
153.8 |
160.3 |
| C6 |
N1 |
C1' |
C2' |
283.4 |
299.4 |
| C6 |
N1 |
C1' |
H1' |
163.2 |
176.4 |
| C1' |
N1 |
C6 |
C2 |
180.6 |
179.7 |
| C6 |
N1 |
C2 |
O2 |
178.8 |
179.9 |
| C6 |
N1 |
C2 |
C3 |
358.9 |
359.5 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
180.0 |
| N1 |
C6 |
C5 |
C4 |
0.1 |
360.0 |
| N1 |
C6 |
C5 |
H5 |
180.1 |
180.0 |
| C2 |
N1 |
C1' |
C2' |
103.9 |
119.2 |
| C2 |
N1 |
C1' |
H1' |
343.8 |
356.2 |
| C1' |
N1 |
C2 |
C6 |
179.4 |
180.3 |
| C2 |
N1 |
C6 |
C5 |
0.9 |
0.3 |
| C2 |
N1 |
C6 |
H6 |
180.9 |
180.2 |
| O2 |
C2 |
N1 |
C3 |
179.9 |
180.4 |
| N1 |
C2 |
C3 |
C4 |
0.4 |
0.4 |
| N1 |
C2 |
C3 |
H31 |
250.1 |
238.5 |
| N1 |
C2 |
C3 |
H32 |
120.4 |
122.1 |
| C5 |
C6 |
N1 |
C2 |
0.9 |
0.3 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.0 |
| C3 |
C4 |
C5 |
C6 |
359.2 |
0.0 |
| O4 |
C4 |
C5 |
C6 |
164.0 |
180.0 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
180.0 |
| H6 |
C6 |
N1 |
C2 |
180.9 |
180.2 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
180.0 |
| H6 |
C6 |
C5 |
C4 |
180.1 |
180.0 |
| H6 |
C6 |
C5 |
H5 |
0.1 |
0.0 |
| N1 |
C2 |
O2 |
C3 |
180.1 |
179.6 |
| O2 |
C2 |
C3 |
C4 |
180.4 |
180.1 |
| O2 |
C2 |
C3 |
H31 |
70.2 |
58.1 |
| O2 |
C2 |
C3 |
H32 |
300.5 |
301.8 |
| N1 |
C2 |
C3 |
O2 |
179.9 |
180.4 |
| C4 |
C3 |
C2 |
H31 |
110.3 |
122.0 |
| C4 |
C3 |
C2 |
H32 |
240.0 |
238.3 |
| C2 |
C3 |
C4 |
O4 |
194.7 |
179.8 |
| C2 |
C3 |
C4 |
C5 |
0.6 |
359.8 |
| H31 |
C3 |
C2 |
H32 |
129.7 |
116.4 |
| C6 |
C5 |
C4 |
C3 |
359.2 |
0.0 |
| C2 |
C3 |
C4 |
H31 |
249.7 |
238.0 |
| C2 |
C3 |
C4 |
H32 |
120.0 |
121.6 |
| H31 |
C3 |
C4 |
H32 |
230.3 |
243.5 |
| O4 |
C4 |
C3 |
C5 |
194.2 |
180.1 |
| C3 |
C4 |
C5 |
H5 |
179.2 |
180.0 |
| C2 |
C3 |
H31 |
C4 |
130.7 |
127.0 |
| C2 |
C3 |
H31 |
H32 |
245.3 |
243.6 |
| C4 |
C3 |
H31 |
H32 |
114.6 |
116.6 |
| H31 |
C3 |
C4 |
O4 |
305.0 |
301.8 |
| H31 |
C3 |
C4 |
C5 |
110.9 |
121.8 |
| C2 |
C3 |
H32 |
C4 |
225.3 |
233.2 |
| C2 |
C3 |
H32 |
H31 |
112.7 |
116.6 |
| C4 |
C3 |
H32 |
H31 |
247.4 |
243.4 |
| H32 |
C3 |
C4 |
O4 |
74.7 |
58.3 |
| H32 |
C3 |
C4 |
C5 |
240.5 |
238.2 |
| C6 |
C5 |
C4 |
O4 |
164.0 |
180.0 |
| O4 |
C4 |
C3 |
H31 |
305.0 |
301.8 |
| O4 |
C4 |
C3 |
H32 |
74.7 |
58.3 |
| C3 |
C4 |
O4 |
C5 |
164.1 |
179.9 |
| O4 |
C4 |
C5 |
H5 |
344.0 |
359.9 |
| C4 |
C5 |
C6 |
H6 |
180.1 |
180.0 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
180.0 |
| C5 |
C4 |
C3 |
H31 |
110.9 |
121.8 |
| C5 |
C4 |
C3 |
H32 |
240.5 |
238.2 |
| C3 |
C4 |
C5 |
O4 |
195.3 |
180.1 |
| H5 |
C5 |
C6 |
H6 |
0.1 |
0.0 |
| C6 |
C5 |
H5 |
C4 |
180.0 |
180.0 |
| C4' |
C3' |
C2' |
O2' |
201.2 |
220.8 |
| O2' |
C2' |
C1' |
H1' |
38.4 |
36.8 |
| C1' |
C2' |
O2' |
C3' |
245.6 |
247.3 |
| C1' |
C2' |
O2' |
H2' |
124.2 |
123.6 |
| C3' |
C2' |
O2' |
H2' |
238.6 |
236.3 |
| O2' |
C2' |
C3' |
O3' |
317.9 |
339.7 |
| O2' |
C2' |
C3' |
H3' |
77.1 |
102.2 |
| C2' |
C3' |
C4' |
H4' |
148.4 |
117.5 |
| C4' |
C3' |
C2' |
O3' |
243.2 |
241.1 |
| C4' |
C3' |
C2' |
H3' |
124.0 |
118.5 |
| C3' |
C2' |
C1' |
H1' |
275.1 |
278.6 |
| C1' |
C2' |
C3' |
O2' |
120.5 |
118.2 |
| C1' |
C2' |
C3' |
H2' |
235.9 |
241.8 |
| O2' |
C2' |
C3' |
H2' |
115.5 |
123.6 |
| C3' |
C2' |
O2' |
HO2' |
104.3 |
292.7 |
| O3' |
C3' |
C2' |
H3' |
240.8 |
237.4 |
| C2' |
C3' |
O3' |
HO3' |
6.6 |
180.0 |
| H2' |
C2' |
C1' |
H1' |
153.8 |
160.3 |
| C1' |
C2' |
H2' |
O2' |
238.9 |
236.4 |
| C1' |
C2' |
H2' |
C3' |
115.0 |
112.8 |
| O2' |
C2' |
H2' |
C3' |
236.1 |
236.4 |
| H2' |
C2' |
O2' |
HO2' |
225.7 |
56.4 |
| H2' |
C2' |
C3' |
O3' |
202.4 |
216.1 |
| H2' |
C2' |
C3' |
H3' |
321.7 |
338.7 |
| HO2' |
O2' |
C2' |
C3' |
104.3 |
292.7 |
| HO2' |
O2' |
C2' |
H2' |
225.7 |
56.4 |
| O3' |
C3' |
C4' |
H4' |
29.7 |
358.8 |
| C4' |
C3' |
O3' |
C2' |
112.4 |
114.7 |
| C4' |
C3' |
O3' |
H3' |
235.5 |
237.3 |
| O3' |
C3' |
C2' |
H2' |
202.4 |
216.1 |
| C2' |
C3' |
O3' |
H3' |
123.1 |
122.6 |
| H3' |
C3' |
C4' |
H4' |
270.7 |
236.1 |
| C4' |
C3' |
H3' |
C2' |
243.4 |
245.5 |
| C4' |
C3' |
H3' |
O3' |
120.8 |
122.9 |
| H3' |
C3' |
C2' |
H2' |
321.7 |
338.7 |
| C2' |
C3' |
H3' |
O3' |
237.4 |
237.4 |
| H3' |
C3' |
O3' |
HO3' |
243.6 |
57.4 |
| HO3' |
O3' |
C3' |
H3' |
243.6 |
57.4 |