PDB Chemical Component U2P
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 U2P
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O5' |
C5' |
1.441 |
1.429 |
| O5' |
H5' |
0.950 |
0.968 |
| C5' |
C4' |
1.513 |
1.530 |
| C5' |
H5'1 |
1.115 |
1.091 |
| C5' |
H5'2 |
1.115 |
1.090 |
| C4' |
O4' |
1.450 |
1.437 |
| C4' |
C3' |
1.520 |
1.541 |
| C4' |
H4' |
1.115 |
1.090 |
| O4' |
C1' |
1.421 |
1.444 |
| C1' |
N1 |
1.474 |
1.465 |
| C1' |
C2' |
1.534 |
1.550 |
| C1' |
H1' |
1.115 |
1.090 |
| N1 |
C6 |
1.377 |
1.368 |
| N1 |
C2 |
1.389 |
1.346 |
| C6 |
C5 |
1.337 |
1.351 |
| C6 |
H6 |
1.103 |
1.080 |
| C5 |
C4 |
1.429 |
1.416 |
| C5 |
H5 |
1.103 |
1.080 |
| C4 |
O4 |
1.231 |
1.218 |
| C4 |
N3 |
1.380 |
1.348 |
| N3 |
C2 |
1.373 |
1.346 |
| N3 |
HN3 |
1.020 |
0.970 |
| C2 |
O2 |
1.221 |
1.216 |
| C2' |
O2' |
1.420 |
1.430 |
| C2' |
C3' |
1.528 |
1.551 |
| C2' |
H2' |
1.115 |
1.089 |
| O2' |
P |
1.611 |
1.610 |
| P |
O1P |
1.521 |
1.480 |
| P |
O2P |
1.520 |
1.610 |
| P |
O3P |
1.522 |
1.610 |
| O2P |
H2P |
0.950 |
0.967 |
| O3P |
H3P |
0.950 |
0.967 |
| C3' |
O3' |
1.424 |
1.429 |
| C3' |
H3' |
1.115 |
1.090 |
| O3' |
H1 |
0.950 |
0.967 |
Bond Angles for U2P
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C5' |
O5' |
H5' |
110.5 |
106.8 |
| O5' |
C5' |
C4' |
110.4 |
109.5 |
| O5' |
C5' |
H5'1 |
111.8 |
109.5 |
| O5' |
C5' |
H5'2 |
111.9 |
109.5 |
| C4' |
C5' |
H5'1 |
111.9 |
109.5 |
| C4' |
C5' |
H5'2 |
111.8 |
109.5 |
| C5' |
C4' |
O4' |
109.6 |
109.9 |
| C5' |
C4' |
C3' |
116.0 |
109.9 |
| C5' |
C4' |
H4' |
103.4 |
109.9 |
| H5'1 |
C5' |
H5'2 |
98.6 |
109.5 |
| O4' |
C4' |
C3' |
104.4 |
107.4 |
| O4' |
C4' |
H4' |
115.1 |
109.9 |
| C4' |
O4' |
C1' |
109.8 |
107.0 |
| C3' |
C4' |
H4' |
108.7 |
109.8 |
| C4' |
C3' |
C2' |
102.1 |
104.0 |
| C4' |
C3' |
O3' |
110.1 |
110.8 |
| C4' |
C3' |
H3' |
115.0 |
110.5 |
| O4' |
C1' |
N1 |
107.9 |
110.6 |
| O4' |
C1' |
C2' |
107.2 |
103.5 |
| O4' |
C1' |
H1' |
114.5 |
110.6 |
| N1 |
C1' |
C2' |
116.1 |
110.8 |
| N1 |
C1' |
H1' |
105.3 |
110.6 |
| C1' |
N1 |
C6 |
121.3 |
119.7 |
| C1' |
N1 |
C2 |
118.0 |
119.7 |
| C2' |
C1' |
H1' |
106.1 |
110.6 |
| C1' |
C2' |
O2' |
106.8 |
110.8 |
| C1' |
C2' |
C3' |
100.9 |
102.1 |
| C1' |
C2' |
H2' |
117.8 |
110.9 |
| C6 |
N1 |
C2 |
120.7 |
120.6 |
| N1 |
C6 |
C5 |
122.8 |
119.7 |
| N1 |
C6 |
H6 |
120.1 |
120.1 |
| N1 |
C2 |
N3 |
114.9 |
120.9 |
| N1 |
C2 |
O2 |
123.2 |
119.5 |
| C5 |
C6 |
H6 |
117.0 |
120.2 |
| C6 |
C5 |
C4 |
119.8 |
119.1 |
| C6 |
C5 |
H5 |
116.9 |
120.5 |
| C4 |
C5 |
H5 |
123.4 |
120.4 |
| C5 |
C4 |
O4 |
125.8 |
120.3 |
| C5 |
C4 |
N3 |
114.7 |
119.4 |
| O4 |
C4 |
N3 |
119.5 |
120.3 |
| C4 |
N3 |
C2 |
127.1 |
120.3 |
| C4 |
N3 |
HN3 |
116.8 |
119.9 |
| C2 |
N3 |
HN3 |
116.1 |
119.9 |
| N3 |
C2 |
O2 |
121.9 |
119.5 |
| O2' |
C2' |
C3' |
113.3 |
110.9 |
| O2' |
C2' |
H2' |
106.4 |
110.8 |
| C2' |
O2' |
P |
120.7 |
106.8 |
| C3' |
C2' |
H2' |
111.8 |
111.0 |
| C2' |
C3' |
O3' |
113.0 |
110.5 |
| C2' |
C3' |
H3' |
112.3 |
110.5 |
| O2' |
P |
O1P |
107.4 |
109.4 |
| O2' |
P |
O2P |
104.5 |
109.5 |
| O2' |
P |
O3P |
107.1 |
109.5 |
| O1P |
P |
O2P |
112.2 |
109.5 |
| O1P |
P |
O3P |
112.9 |
109.5 |
| O2P |
P |
O3P |
112.2 |
109.5 |
| P |
O2P |
H2P |
104.5 |
106.8 |
| P |
O3P |
H3P |
107.2 |
106.8 |
| O3' |
C3' |
H3' |
104.6 |
110.4 |
| C3' |
O3' |
H1 |
110.1 |
106.8 |
Torsion Angles for U2P
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C4' |
C5' |
O5' |
H5'1 |
125.3 |
240.0 |
| C4' |
C5' |
O5' |
H5'2 |
234.8 |
120.0 |
| O5' |
C5' |
C4' |
O4' |
302.4 |
66.7 |
| O5' |
C5' |
C4' |
C3' |
60.2 |
184.7 |
| O5' |
C5' |
C4' |
H4' |
179.1 |
305.7 |
| H5'1 |
C5' |
O5' |
H5'2 |
109.5 |
240.0 |
| H5' |
O5' |
C5' |
C4' |
180.0 |
180.0 |
| H5' |
O5' |
C5' |
H5'1 |
54.7 |
300.0 |
| H5' |
O5' |
C5' |
H5'2 |
305.2 |
60.0 |
| C4' |
C5' |
O5' |
H5' |
180.0 |
180.0 |
| O5' |
C5' |
C4' |
H5'1 |
234.7 |
120.0 |
| O5' |
C5' |
C4' |
H5'2 |
125.3 |
240.0 |
| H5'1 |
C5' |
C4' |
H5'2 |
250.5 |
120.0 |
| O4' |
C4' |
C5' |
C3' |
242.2 |
242.0 |
| O4' |
C4' |
C5' |
H4' |
123.3 |
121.1 |
| C5' |
C4' |
O4' |
C1' |
144.1 |
145.9 |
| C3' |
C4' |
C5' |
H4' |
241.1 |
239.0 |
| C5' |
C4' |
C3' |
C2' |
203.2 |
238.6 |
| C5' |
C4' |
C3' |
O3' |
83.0 |
119.9 |
| C5' |
C4' |
C3' |
H3' |
325.1 |
357.2 |
| H5'1 |
C5' |
O5' |
H5' |
54.7 |
300.0 |
| O5' |
C5' |
H5'1 |
C4' |
124.5 |
240.0 |
| O5' |
C5' |
H5'1 |
H5'2 |
242.2 |
120.0 |
| C4' |
C5' |
H5'1 |
H5'2 |
117.7 |
240.0 |
| H5'1 |
C5' |
C4' |
O4' |
67.6 |
306.7 |
| H5'1 |
C5' |
C4' |
C3' |
185.5 |
64.7 |
| H5'1 |
C5' |
C4' |
H4' |
304.3 |
185.7 |
| H5'2 |
C5' |
O5' |
H5' |
305.2 |
60.0 |
| O5' |
C5' |
H5'2 |
C4' |
235.5 |
120.0 |
| O5' |
C5' |
H5'2 |
H5'1 |
117.8 |
240.0 |
| C4' |
C5' |
H5'2 |
H5'1 |
242.2 |
120.0 |
| H5'2 |
C5' |
C4' |
O4' |
177.1 |
186.7 |
| H5'2 |
C5' |
C4' |
C3' |
295.0 |
304.7 |
| H5'2 |
C5' |
C4' |
H4' |
53.8 |
65.7 |
| O4' |
C4' |
C5' |
H5'1 |
67.6 |
306.7 |
| O4' |
C4' |
C5' |
H5'2 |
177.1 |
186.7 |
| C5' |
C4' |
O4' |
C3' |
124.9 |
119.5 |
| C5' |
C4' |
O4' |
H4' |
243.9 |
238.9 |
| C3' |
C4' |
O4' |
H4' |
119.1 |
119.4 |
| O4' |
C4' |
C3' |
C2' |
323.9 |
358.1 |
| O4' |
C4' |
C3' |
O3' |
203.7 |
239.4 |
| O4' |
C4' |
C3' |
H3' |
85.8 |
116.7 |
| C4' |
O4' |
C1' |
N1 |
240.0 |
201.3 |
| C4' |
O4' |
C1' |
C2' |
5.6 |
319.9 |
| C4' |
O4' |
C1' |
H1' |
123.0 |
78.4 |
| C3' |
C4' |
C5' |
H5'1 |
185.5 |
64.7 |
| C3' |
C4' |
C5' |
H5'2 |
295.0 |
304.7 |
| C5' |
C4' |
C3' |
O4' |
239.3 |
240.5 |
| C5' |
C4' |
C3' |
H4' |
115.9 |
121.0 |
| O4' |
C4' |
C3' |
H4' |
236.6 |
240.5 |
| C3' |
C4' |
O4' |
C1' |
19.3 |
26.4 |
| C1' |
C2' |
C3' |
C4' |
38.1 |
339.0 |
| O2' |
C2' |
C3' |
C4' |
284.4 |
220.9 |
| C4' |
C3' |
C2' |
H2' |
164.2 |
97.3 |
| C2' |
C3' |
C4' |
O3' |
120.3 |
118.7 |
| C2' |
C3' |
C4' |
H3' |
238.1 |
241.4 |
| O3' |
C3' |
C4' |
H3' |
117.8 |
122.7 |
| C4' |
C3' |
O3' |
H1 |
180.0 |
294.7 |
| H4' |
C4' |
C5' |
H5'1 |
304.3 |
185.7 |
| H4' |
C4' |
C5' |
H5'2 |
53.8 |
65.7 |
| C5' |
C4' |
H4' |
O4' |
119.5 |
121.1 |
| C5' |
C4' |
H4' |
C3' |
236.2 |
239.0 |
| O4' |
C4' |
H4' |
C3' |
116.7 |
117.9 |
| H4' |
C4' |
O4' |
C1' |
260.2 |
267.0 |
| H4' |
C4' |
C3' |
C2' |
87.3 |
117.6 |
| H4' |
C4' |
C3' |
O3' |
327.0 |
358.9 |
| H4' |
C4' |
C3' |
H3' |
209.2 |
236.2 |
| C1' |
O4' |
C4' |
C3' |
19.3 |
26.4 |
| C1' |
O4' |
C4' |
H4' |
260.2 |
267.0 |
| N1 |
C1' |
O4' |
C2' |
234.3 |
241.4 |
| N1 |
C1' |
O4' |
H1' |
116.9 |
122.9 |
| O4' |
C1' |
N1 |
C6 |
42.3 |
233.5 |
| O4' |
C1' |
N1 |
C2 |
223.2 |
53.3 |
| C2' |
C1' |
O4' |
H1' |
242.6 |
241.5 |
| O4' |
C1' |
C2' |
O2' |
90.9 |
155.2 |
| O4' |
C1' |
C2' |
C3' |
332.3 |
37.1 |
| O4' |
C1' |
C2' |
H2' |
210.3 |
278.7 |
| O4' |
C1' |
N1 |
C2' |
120.2 |
114.1 |
| O4' |
C1' |
N1 |
H1' |
237.3 |
237.1 |
| C2' |
C1' |
N1 |
H1' |
117.0 |
123.0 |
| N1 |
C1' |
C2' |
O2' |
211.5 |
273.8 |
| N1 |
C1' |
C2' |
C3' |
92.9 |
155.6 |
| N1 |
C1' |
C2' |
H2' |
331.0 |
37.3 |
| C6 |
N1 |
C1' |
C2 |
179.2 |
180.2 |
| C1' |
N1 |
C6 |
C5 |
182.2 |
180.0 |
| C1' |
N1 |
C6 |
H6 |
2.2 |
0.0 |
| C1' |
N1 |
C2 |
N3 |
177.6 |
179.7 |
| C1' |
N1 |
C2 |
O2 |
357.4 |
0.3 |
| C4' |
C3' |
C2' |
C1' |
38.1 |
339.0 |
| O4' |
C1' |
C2' |
N1 |
239.4 |
241.4 |
| O4' |
C1' |
C2' |
H1' |
122.8 |
118.5 |
| N1 |
C1' |
C2' |
H1' |
243.4 |
237.1 |
| C2' |
C1' |
N1 |
C6 |
282.1 |
119.4 |
| C2' |
C1' |
N1 |
C2 |
102.9 |
299.2 |
| O2' |
C2' |
C1' |
C3' |
118.6 |
118.1 |
| O2' |
C2' |
C1' |
H2' |
240.5 |
236.5 |
| C1' |
C2' |
O2' |
P |
157.0 |
120.0 |
| C3' |
C2' |
C1' |
H2' |
121.9 |
118.4 |
| C1' |
C2' |
C3' |
O3' |
156.4 |
97.9 |
| C1' |
C2' |
C3' |
H3' |
274.4 |
220.4 |
| O4' |
C1' |
H1' |
N1 |
118.4 |
122.9 |
| O4' |
C1' |
H1' |
C2' |
242.0 |
246.0 |
| N1 |
C1' |
H1' |
C2' |
123.6 |
123.1 |
| H1' |
C1' |
N1 |
C6 |
165.1 |
356.4 |
| H1' |
C1' |
N1 |
C2 |
345.9 |
176.2 |
| H1' |
C1' |
C2' |
O2' |
328.1 |
36.7 |
| H1' |
C1' |
C2' |
C3' |
209.5 |
278.6 |
| H1' |
C1' |
C2' |
H2' |
87.6 |
160.2 |
| C6 |
N1 |
C1' |
C2' |
282.1 |
119.4 |
| C6 |
N1 |
C1' |
H1' |
165.1 |
356.4 |
| C1' |
N1 |
C6 |
C2 |
180.9 |
179.8 |
| C6 |
N1 |
C2 |
N3 |
358.4 |
359.5 |
| C6 |
N1 |
C2 |
O2 |
178.3 |
180.1 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
179.9 |
| N1 |
C6 |
C5 |
C4 |
359.9 |
0.1 |
| N1 |
C6 |
C5 |
H5 |
179.9 |
180.0 |
| C2 |
N1 |
C1' |
C2' |
102.9 |
299.2 |
| C2 |
N1 |
C1' |
H1' |
345.9 |
176.2 |
| C1' |
N1 |
C2 |
C6 |
179.2 |
180.2 |
| C2 |
N1 |
C6 |
C5 |
1.3 |
0.2 |
| C2 |
N1 |
C6 |
H6 |
181.3 |
180.3 |
| C4 |
N3 |
C2 |
N1 |
0.8 |
0.6 |
| N1 |
C2 |
N3 |
HN3 |
180.8 |
180.2 |
| N3 |
C2 |
N1 |
O2 |
180.1 |
179.4 |
| C5 |
C6 |
N1 |
C2 |
1.3 |
0.2 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.1 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
180.1 |
| C6 |
C5 |
C4 |
O4 |
178.0 |
180.0 |
| C6 |
C5 |
C4 |
N3 |
359.3 |
360.0 |
| H6 |
C6 |
N1 |
C2 |
181.3 |
180.3 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
179.9 |
| H6 |
C6 |
C5 |
C4 |
180.0 |
180.0 |
| H6 |
C6 |
C5 |
H5 |
359.9 |
359.9 |
| C4 |
C5 |
C6 |
H6 |
180.0 |
180.0 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
179.9 |
| O4 |
C4 |
C5 |
N3 |
178.8 |
180.0 |
| C5 |
C4 |
N3 |
C2 |
0.4 |
359.7 |
| C5 |
C4 |
N3 |
HN3 |
180.4 |
180.0 |
| H5 |
C5 |
C6 |
H6 |
359.9 |
359.9 |
| C6 |
C5 |
H5 |
C4 |
180.0 |
180.1 |
| H5 |
C5 |
C4 |
O4 |
358.1 |
0.1 |
| H5 |
C5 |
C4 |
N3 |
179.3 |
180.0 |
| O4 |
C4 |
C5 |
H5 |
358.1 |
0.1 |
| C5 |
C4 |
O4 |
N3 |
181.3 |
180.0 |
| O4 |
C4 |
N3 |
C2 |
181.5 |
179.7 |
| O4 |
C4 |
N3 |
HN3 |
1.5 |
0.0 |
| N1 |
C2 |
N3 |
C4 |
0.8 |
0.6 |
| N3 |
C4 |
C5 |
H5 |
179.3 |
180.0 |
| C5 |
C4 |
N3 |
O4 |
178.9 |
180.0 |
| C2 |
N3 |
C4 |
HN3 |
180.0 |
179.7 |
| C4 |
N3 |
C2 |
O2 |
180.9 |
180.0 |
| N1 |
C2 |
N3 |
O2 |
179.9 |
180.6 |
| C4 |
N3 |
C2 |
HN3 |
180.0 |
180.3 |
| C4 |
N3 |
HN3 |
C2 |
180.0 |
179.7 |
| HN3 |
N3 |
C2 |
O2 |
0.9 |
359.7 |
| N1 |
C2 |
O2 |
N3 |
180.1 |
179.4 |
| O2 |
C2 |
N3 |
HN3 |
0.9 |
359.7 |
| C4' |
C3' |
C2' |
O2' |
284.4 |
220.9 |
| O2' |
C2' |
C1' |
H1' |
328.1 |
36.7 |
| C1' |
C2' |
O2' |
C3' |
249.9 |
247.3 |
| C1' |
C2' |
O2' |
H2' |
126.6 |
123.6 |
| C3' |
C2' |
O2' |
H2' |
236.8 |
236.3 |
| O2' |
C2' |
C3' |
O3' |
42.6 |
339.8 |
| O2' |
C2' |
C3' |
H3' |
160.6 |
102.3 |
| C2' |
O2' |
P |
O1P |
62.1 |
305.0 |
| C2' |
O2' |
P |
O2P |
181.3 |
64.9 |
| C2' |
O2' |
P |
O3P |
300.5 |
185.0 |
| C2' |
C3' |
C4' |
H4' |
87.3 |
117.6 |
| C4' |
C3' |
C2' |
O3' |
241.8 |
241.1 |
| C4' |
C3' |
C2' |
H3' |
123.8 |
118.6 |
| C3' |
C2' |
C1' |
H1' |
209.5 |
278.6 |
| C1' |
C2' |
C3' |
O2' |
113.7 |
118.1 |
| C1' |
C2' |
C3' |
H2' |
233.9 |
241.7 |
| O2' |
C2' |
C3' |
H2' |
120.2 |
123.6 |
| C3' |
C2' |
O2' |
P |
267.1 |
232.7 |
| O3' |
C3' |
C2' |
H3' |
242.0 |
237.5 |
| C2' |
C3' |
O3' |
H1 |
66.6 |
180.0 |
| H2' |
C2' |
C1' |
H1' |
87.6 |
160.2 |
| C1' |
C2' |
H2' |
O2' |
240.3 |
236.5 |
| C1' |
C2' |
H2' |
C3' |
116.2 |
112.8 |
| O2' |
C2' |
H2' |
C3' |
235.8 |
236.3 |
| H2' |
C2' |
O2' |
P |
30.4 |
356.4 |
| H2' |
C2' |
C3' |
O3' |
282.4 |
216.2 |
| H2' |
C2' |
C3' |
H3' |
40.4 |
338.7 |
| P |
O2' |
C2' |
C3' |
267.1 |
232.7 |
| P |
O2' |
C2' |
H2' |
30.4 |
356.4 |
| O1P |
P |
O2' |
O2P |
240.7 |
240.0 |
| O1P |
P |
O2' |
O3P |
121.6 |
120.0 |
| O2P |
P |
O2' |
O3P |
240.8 |
240.0 |
| O2' |
P |
O2P |
H2P |
180.0 |
60.0 |
| O2' |
P |
O3P |
H3P |
180.0 |
179.9 |
| O2' |
P |
O1P |
O2P |
114.2 |
120.0 |
| O2' |
P |
O1P |
O3P |
242.1 |
240.0 |
| O2P |
P |
O1P |
O3P |
127.9 |
120.0 |
| O1P |
P |
O2P |
H2P |
295.9 |
180.0 |
| O1P |
P |
O3P |
H3P |
62.0 |
60.0 |
| O2' |
P |
O2P |
O1P |
244.0 |
240.0 |
| O2' |
P |
O2P |
O3P |
115.7 |
120.0 |
| O1P |
P |
O2P |
O3P |
231.7 |
240.0 |
| O2P |
P |
O3P |
H3P |
294.1 |
300.0 |
| O2' |
P |
O3P |
O1P |
118.0 |
120.0 |
| O2' |
P |
O3P |
O2P |
245.9 |
240.0 |
| O1P |
P |
O3P |
O2P |
127.9 |
120.0 |
| O3P |
P |
O2P |
H2P |
64.3 |
300.0 |
| H2P |
O2P |
P |
O3P |
64.3 |
300.0 |
| O3' |
C3' |
C4' |
H4' |
327.0 |
358.9 |
| C4' |
C3' |
O3' |
C2' |
113.5 |
114.7 |
| C4' |
C3' |
O3' |
H3' |
235.9 |
237.3 |
| O3' |
C3' |
C2' |
H2' |
282.4 |
216.2 |
| C2' |
C3' |
O3' |
H3' |
122.4 |
122.5 |
| H3' |
C3' |
C4' |
H4' |
209.2 |
236.2 |
| C4' |
C3' |
H3' |
C2' |
243.8 |
245.4 |
| C4' |
C3' |
H3' |
O3' |
120.9 |
122.9 |
| H3' |
C3' |
C2' |
H2' |
40.4 |
338.7 |
| C2' |
C3' |
H3' |
O3' |
237.1 |
237.5 |
| H3' |
C3' |
O3' |
H1 |
304.1 |
57.4 |
| H1 |
O3' |
C3' |
H3' |
304.1 |
57.4 |