PDB Chemical Component U3P
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 U3P
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N1 |
C2 |
1.379 |
1.344 |
| N1 |
C6 |
1.376 |
1.368 |
| N1 |
C1' |
1.462 |
1.465 |
| C2 |
N3 |
1.373 |
1.346 |
| C2 |
O2 |
1.212 |
1.215 |
| N3 |
C4 |
1.385 |
1.348 |
| N3 |
HN3 |
1.020 |
0.969 |
| C4 |
C5 |
1.447 |
1.416 |
| C4 |
O4 |
1.237 |
1.217 |
| C5 |
C6 |
1.347 |
1.349 |
| C5 |
H5 |
1.103 |
1.080 |
| C6 |
H6 |
1.103 |
1.081 |
| P |
O1P |
1.484 |
1.609 |
| P |
O2P |
1.478 |
1.478 |
| P |
O3P |
1.485 |
1.610 |
| P |
O3' |
1.599 |
1.610 |
| O1P |
HOP1 |
0.950 |
0.966 |
| O3P |
HOP3 |
0.950 |
0.967 |
| O5' |
C5' |
1.427 |
1.428 |
| O5' |
HO5' |
0.950 |
0.966 |
| C5' |
C4' |
1.535 |
1.530 |
| C5' |
H5'1 |
1.116 |
1.090 |
| C5' |
H5'2 |
1.115 |
1.091 |
| C4' |
O4' |
1.461 |
1.437 |
| C4' |
C3' |
1.531 |
1.540 |
| C4' |
H4' |
1.114 |
1.090 |
| O4' |
C1' |
1.423 |
1.444 |
| C3' |
O3' |
1.428 |
1.428 |
| C3' |
C2' |
1.535 |
1.551 |
| C3' |
H3' |
1.116 |
1.090 |
| C2' |
O2' |
1.425 |
1.428 |
| C2' |
C1' |
1.518 |
1.548 |
| C2' |
H2' |
1.116 |
1.090 |
| O2' |
HO2' |
0.951 |
0.966 |
| C1' |
H1' |
1.115 |
1.090 |
Bond Angles for U3P
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N1 |
C6 |
121.6 |
120.6 |
| C2 |
N1 |
C1' |
120.1 |
119.7 |
| N1 |
C2 |
N3 |
115.5 |
120.9 |
| N1 |
C2 |
O2 |
123.3 |
119.5 |
| C6 |
N1 |
C1' |
118.1 |
119.7 |
| N1 |
C6 |
C5 |
121.9 |
119.7 |
| N1 |
C6 |
H6 |
120.2 |
120.1 |
| N1 |
C1' |
O4' |
109.1 |
110.6 |
| N1 |
C1' |
C2' |
114.6 |
110.8 |
| N1 |
C1' |
H1' |
105.9 |
110.6 |
| N3 |
C2 |
O2 |
121.2 |
119.5 |
| C2 |
N3 |
C4 |
126.7 |
120.3 |
| C2 |
N3 |
HN3 |
116.2 |
119.9 |
| C4 |
N3 |
HN3 |
117.1 |
119.8 |
| N3 |
C4 |
C5 |
114.3 |
119.3 |
| N3 |
C4 |
O4 |
119.9 |
120.4 |
| C5 |
C4 |
O4 |
125.8 |
120.3 |
| C4 |
C5 |
C6 |
120.0 |
119.1 |
| C4 |
C5 |
H5 |
123.5 |
120.4 |
| C6 |
C5 |
H5 |
116.5 |
120.5 |
| C5 |
C6 |
H6 |
117.9 |
120.1 |
| O1P |
P |
O2P |
108.9 |
109.5 |
| O1P |
P |
O3P |
114.4 |
109.5 |
| O1P |
P |
O3' |
107.1 |
109.5 |
| P |
O1P |
HOP1 |
108.9 |
106.8 |
| O2P |
P |
O3P |
113.9 |
109.4 |
| O2P |
P |
O3' |
108.5 |
109.5 |
| O3P |
P |
O3' |
103.6 |
109.4 |
| P |
O3P |
HOP3 |
114.4 |
106.8 |
| P |
O3' |
C3' |
120.7 |
106.9 |
| C5' |
O5' |
HO5' |
113.4 |
106.8 |
| O5' |
C5' |
C4' |
113.4 |
109.6 |
| O5' |
C5' |
H5'1 |
110.7 |
109.5 |
| O5' |
C5' |
H5'2 |
110.8 |
109.5 |
| C4' |
C5' |
H5'1 |
110.7 |
109.4 |
| C4' |
C5' |
H5'2 |
110.8 |
109.4 |
| C5' |
C4' |
O4' |
111.5 |
109.9 |
| C5' |
C4' |
C3' |
112.8 |
110.0 |
| C5' |
C4' |
H4' |
104.3 |
109.8 |
| H5'1 |
C5' |
H5'2 |
99.5 |
109.4 |
| O4' |
C4' |
C3' |
104.4 |
107.4 |
| O4' |
C4' |
H4' |
112.7 |
109.9 |
| C4' |
O4' |
C1' |
110.3 |
106.9 |
| C3' |
C4' |
H4' |
111.3 |
109.9 |
| C4' |
C3' |
O3' |
109.0 |
110.8 |
| C4' |
C3' |
C2' |
104.3 |
104.0 |
| C4' |
C3' |
H3' |
113.8 |
110.4 |
| O4' |
C1' |
C2' |
108.8 |
103.5 |
| O4' |
C1' |
H1' |
112.1 |
110.5 |
| O3' |
C3' |
C2' |
111.4 |
110.5 |
| O3' |
C3' |
H3' |
106.9 |
110.4 |
| C2' |
C3' |
H3' |
111.5 |
110.5 |
| C3' |
C2' |
O2' |
113.0 |
110.9 |
| C3' |
C2' |
C1' |
102.2 |
102.1 |
| C3' |
C2' |
H2' |
111.2 |
110.9 |
| O2' |
C2' |
C1' |
107.1 |
111.0 |
| O2' |
C2' |
H2' |
106.7 |
110.8 |
| C2' |
O2' |
HO2' |
112.9 |
106.9 |
| C1' |
C2' |
H2' |
116.7 |
110.9 |
| C2' |
C1' |
H1' |
106.3 |
110.6 |
Torsion Angles for U3P
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C6 |
N1 |
C2 |
C1' |
184.5 |
179.8 |
| C2 |
N1 |
C6 |
C5 |
358.6 |
0.2 |
| C2 |
N1 |
C6 |
H6 |
178.6 |
180.2 |
| C2 |
N1 |
C1' |
O4' |
204.3 |
58.4 |
| C2 |
N1 |
C1' |
C2' |
82.0 |
304.2 |
| C2 |
N1 |
C1' |
H1' |
325.2 |
181.1 |
| N3 |
C2 |
N1 |
O2 |
179.0 |
179.5 |
| N1 |
C2 |
N3 |
C4 |
2.1 |
0.6 |
| N1 |
C2 |
N3 |
HN3 |
182.0 |
180.3 |
| C2 |
N1 |
C6 |
C1' |
175.6 |
180.2 |
| C6 |
N1 |
C2 |
N3 |
0.2 |
359.5 |
| C6 |
N1 |
C2 |
O2 |
181.2 |
180.0 |
| C6 |
N1 |
C1' |
O4' |
19.9 |
238.6 |
| C6 |
N1 |
C1' |
C2' |
257.7 |
124.4 |
| C6 |
N1 |
C1' |
H1' |
140.8 |
1.3 |
| C4 |
C5 |
C6 |
N1 |
0.5 |
360.0 |
| N1 |
C6 |
C5 |
H5 |
180.5 |
180.0 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
180.1 |
| C2 |
N1 |
C1' |
C6 |
184.4 |
179.8 |
| C1' |
N1 |
C2 |
N3 |
175.7 |
179.7 |
| C1' |
N1 |
C2 |
O2 |
356.7 |
0.2 |
| C1' |
N1 |
C6 |
C5 |
183.0 |
180.0 |
| C1' |
N1 |
C6 |
H6 |
3.0 |
360.0 |
| C4' |
O4' |
C1' |
N1 |
237.4 |
201.3 |
| O4' |
C1' |
N1 |
C2' |
122.3 |
114.2 |
| O4' |
C1' |
N1 |
H1' |
239.1 |
237.2 |
| C3' |
C2' |
C1' |
N1 |
101.2 |
155.6 |
| O2' |
C2' |
C1' |
N1 |
220.1 |
273.8 |
| N1 |
C1' |
C2' |
H2' |
339.6 |
37.4 |
| C2' |
C1' |
N1 |
H1' |
116.9 |
123.1 |
| N3 |
C2 |
N1 |
C6 |
0.2 |
359.5 |
| N3 |
C2 |
N1 |
C1' |
175.7 |
179.7 |
| N1 |
C2 |
N3 |
O2 |
181.0 |
180.5 |
| C4 |
N3 |
C2 |
HN3 |
180.1 |
180.3 |
| C2 |
N3 |
C4 |
C5 |
357.1 |
359.7 |
| C2 |
N3 |
C4 |
O4 |
177.2 |
179.7 |
| O2 |
C2 |
N1 |
C6 |
181.2 |
180.0 |
| O2 |
C2 |
N1 |
C1' |
356.7 |
0.2 |
| N1 |
C2 |
O2 |
N3 |
178.9 |
179.5 |
| O2 |
C2 |
N3 |
C4 |
181.1 |
180.0 |
| O2 |
C2 |
N3 |
HN3 |
1.0 |
359.7 |
| C4 |
N3 |
C2 |
O2 |
181.1 |
180.0 |
| C2 |
N3 |
C4 |
HN3 |
179.9 |
179.7 |
| C5 |
C4 |
N3 |
O4 |
179.9 |
179.9 |
| N3 |
C4 |
C5 |
C6 |
1.5 |
0.1 |
| N3 |
C4 |
C5 |
H5 |
181.5 |
180.1 |
| HN3 |
N3 |
C2 |
O2 |
1.0 |
359.7 |
| C2 |
N3 |
HN3 |
C4 |
180.1 |
180.3 |
| HN3 |
N3 |
C4 |
C5 |
177.1 |
180.0 |
| HN3 |
N3 |
C4 |
O4 |
357.3 |
0.0 |
| N1 |
C6 |
C5 |
C4 |
0.5 |
360.0 |
| C5 |
C4 |
N3 |
HN3 |
177.1 |
180.0 |
| N3 |
C4 |
C5 |
O4 |
180.1 |
180.1 |
| C6 |
C5 |
C4 |
H5 |
180.1 |
180.0 |
| C4 |
C5 |
C6 |
H6 |
180.4 |
180.0 |
| O4 |
C4 |
N3 |
HN3 |
357.3 |
0.0 |
| N3 |
C4 |
O4 |
C5 |
179.8 |
179.9 |
| O4 |
C4 |
C5 |
C6 |
181.4 |
180.0 |
| O4 |
C4 |
C5 |
H5 |
1.3 |
0.0 |
| C5 |
C6 |
N1 |
C1' |
183.0 |
180.0 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
179.9 |
| C6 |
C5 |
C4 |
O4 |
181.4 |
180.0 |
| C4 |
C5 |
C6 |
H5 |
179.9 |
180.0 |
| H5 |
C5 |
C4 |
O4 |
1.3 |
0.0 |
| C4 |
C5 |
H5 |
C6 |
180.1 |
180.0 |
| H5 |
C5 |
C6 |
H6 |
0.5 |
0.0 |
| H6 |
C6 |
N1 |
C1' |
3.0 |
360.0 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
180.1 |
| H6 |
C6 |
C5 |
H5 |
0.5 |
0.0 |
| O2P |
P |
O1P |
O3P |
231.3 |
240.0 |
| O2P |
P |
O1P |
O3' |
117.1 |
120.1 |
| O3P |
P |
O1P |
O3' |
245.8 |
240.0 |
| O1P |
P |
O3P |
HOP3 |
180.0 |
60.0 |
| O1P |
P |
O3' |
C3' |
42.2 |
180.0 |
| O1P |
P |
O2P |
O3P |
128.9 |
120.0 |
| O1P |
P |
O2P |
O3' |
243.7 |
239.9 |
| O2P |
P |
O1P |
HOP1 |
180.0 |
300.0 |
| O3P |
P |
O2P |
O3' |
114.8 |
119.9 |
| O2P |
P |
O3P |
HOP3 |
306.2 |
180.0 |
| O2P |
P |
O3' |
C3' |
284.7 |
60.0 |
| O1P |
P |
O3P |
O2P |
233.9 |
240.0 |
| O1P |
P |
O3P |
O3' |
116.3 |
120.0 |
| O3P |
P |
O1P |
HOP1 |
308.7 |
60.0 |
| O2P |
P |
O3P |
O3' |
242.4 |
240.0 |
| O3P |
P |
O3' |
C3' |
163.4 |
300.0 |
| O1P |
P |
O3' |
O2P |
117.4 |
120.1 |
| O1P |
P |
O3' |
O3P |
238.7 |
240.0 |
| O3' |
P |
O1P |
HOP1 |
62.9 |
179.9 |
| O2P |
P |
O3' |
O3P |
121.3 |
119.9 |
| O3' |
P |
O3P |
HOP3 |
63.8 |
299.9 |
| C4' |
C3' |
O3' |
P |
177.9 |
234.8 |
| P |
O3' |
C3' |
C2' |
63.4 |
120.1 |
| P |
O3' |
C3' |
H3' |
301.3 |
357.5 |
| HOP1 |
O1P |
P |
O2P |
180.0 |
300.0 |
| HOP1 |
O1P |
P |
O3P |
308.7 |
60.0 |
| HOP1 |
O1P |
P |
O3' |
62.9 |
179.9 |
| HOP3 |
O3P |
P |
O3' |
63.8 |
299.9 |
| C4' |
C5' |
O5' |
H5'1 |
234.8 |
240.0 |
| C4' |
C5' |
O5' |
H5'2 |
125.3 |
120.0 |
| O5' |
C5' |
C4' |
O4' |
57.6 |
61.6 |
| O5' |
C5' |
C4' |
C3' |
174.7 |
179.7 |
| O5' |
C5' |
C4' |
H4' |
295.7 |
300.7 |
| H5'1 |
C5' |
O5' |
H5'2 |
250.5 |
240.0 |
| HO5' |
O5' |
C5' |
C4' |
180.0 |
180.0 |
| HO5' |
O5' |
C5' |
H5'1 |
305.3 |
300.0 |
| HO5' |
O5' |
C5' |
H5'2 |
54.7 |
60.0 |
| C4' |
C5' |
O5' |
HO5' |
180.0 |
180.0 |
| O5' |
C5' |
C4' |
H5'1 |
125.2 |
120.0 |
| O5' |
C5' |
C4' |
H5'2 |
234.7 |
239.9 |
| H5'1 |
C5' |
C4' |
H5'2 |
109.4 |
119.9 |
| O4' |
C4' |
C5' |
C3' |
242.9 |
241.9 |
| O4' |
C4' |
C5' |
H4' |
121.9 |
120.9 |
| C5' |
C4' |
O4' |
C1' |
138.8 |
146.0 |
| C3' |
C4' |
C5' |
H4' |
239.0 |
239.0 |
| C5' |
C4' |
C3' |
O3' |
90.2 |
119.8 |
| C5' |
C4' |
C3' |
C2' |
209.3 |
238.6 |
| C5' |
C4' |
C3' |
H3' |
331.0 |
357.2 |
| H5'1 |
C5' |
O5' |
HO5' |
305.3 |
300.0 |
| O5' |
C5' |
H5'1 |
C4' |
233.3 |
239.9 |
| O5' |
C5' |
H5'1 |
H5'2 |
116.6 |
120.0 |
| C4' |
C5' |
H5'1 |
H5'2 |
243.4 |
240.1 |
| H5'1 |
C5' |
C4' |
O4' |
292.4 |
301.6 |
| H5'1 |
C5' |
C4' |
C3' |
49.5 |
59.7 |
| H5'1 |
C5' |
C4' |
H4' |
170.5 |
180.7 |
| H5'2 |
C5' |
O5' |
HO5' |
54.7 |
60.0 |
| O5' |
C5' |
H5'2 |
C4' |
126.8 |
120.1 |
| O5' |
C5' |
H5'2 |
H5'1 |
243.4 |
240.0 |
| C4' |
C5' |
H5'2 |
H5'1 |
116.6 |
119.9 |
| H5'2 |
C5' |
C4' |
O4' |
182.9 |
181.7 |
| H5'2 |
C5' |
C4' |
C3' |
300.1 |
299.7 |
| H5'2 |
C5' |
C4' |
H4' |
61.0 |
60.8 |
| N1 |
C1' |
O4' |
C4' |
237.4 |
201.3 |
| O4' |
C4' |
C5' |
H5'1 |
292.4 |
301.6 |
| O4' |
C4' |
C5' |
H5'2 |
182.9 |
181.7 |
| C5' |
C4' |
O4' |
C3' |
122.1 |
119.6 |
| C5' |
C4' |
O4' |
H4' |
243.1 |
239.1 |
| C3' |
C4' |
O4' |
H4' |
121.0 |
119.5 |
| O4' |
C4' |
C3' |
O3' |
211.4 |
239.3 |
| O4' |
C4' |
C3' |
C2' |
330.5 |
358.1 |
| O4' |
C4' |
C3' |
H3' |
92.2 |
116.7 |
| C4' |
O4' |
C1' |
C2' |
3.1 |
320.0 |
| C4' |
O4' |
C1' |
H1' |
120.4 |
78.5 |
| P |
O3' |
C3' |
C4' |
177.9 |
234.8 |
| C3' |
C4' |
C5' |
H5'1 |
49.5 |
59.7 |
| C3' |
C4' |
C5' |
H5'2 |
300.1 |
299.7 |
| C5' |
C4' |
C3' |
O4' |
238.8 |
240.5 |
| C5' |
C4' |
C3' |
H4' |
116.9 |
121.0 |
| O4' |
C4' |
C3' |
H4' |
238.1 |
240.5 |
| C3' |
C4' |
O4' |
C1' |
16.7 |
26.4 |
| O3' |
C3' |
C4' |
C2' |
240.9 |
241.2 |
| O3' |
C3' |
C4' |
H3' |
119.3 |
122.6 |
| C2' |
C3' |
C4' |
H3' |
238.4 |
241.4 |
| C4' |
C3' |
C2' |
O2' |
275.8 |
220.7 |
| C4' |
C3' |
C2' |
C1' |
30.6 |
339.0 |
| C4' |
C3' |
C2' |
H2' |
155.9 |
97.2 |
| H4' |
C4' |
C5' |
H5'1 |
170.5 |
180.7 |
| H4' |
C4' |
C5' |
H5'2 |
61.0 |
60.8 |
| C5' |
C4' |
H4' |
O4' |
121.1 |
121.0 |
| C5' |
C4' |
H4' |
C3' |
238.0 |
238.9 |
| O4' |
C4' |
H4' |
C3' |
117.0 |
118.0 |
| H4' |
C4' |
O4' |
C1' |
255.7 |
266.9 |
| H4' |
C4' |
C3' |
O3' |
333.3 |
358.8 |
| H4' |
C4' |
C3' |
C2' |
92.4 |
117.6 |
| H4' |
C4' |
C3' |
H3' |
214.1 |
236.2 |
| N1 |
C1' |
O4' |
C2' |
234.3 |
241.3 |
| N1 |
C1' |
O4' |
H1' |
117.0 |
122.8 |
| C1' |
O4' |
C4' |
C3' |
16.7 |
26.4 |
| C1' |
O4' |
C4' |
H4' |
255.7 |
266.9 |
| C3' |
C2' |
C1' |
O4' |
338.7 |
37.1 |
| O2' |
C2' |
C1' |
O4' |
97.7 |
155.3 |
| O4' |
C1' |
C2' |
H2' |
217.1 |
278.8 |
| C2' |
C1' |
O4' |
H1' |
242.7 |
241.5 |
| O3' |
C3' |
C4' |
H4' |
333.3 |
358.8 |
| C4' |
C3' |
O3' |
C2' |
114.5 |
114.7 |
| C4' |
C3' |
O3' |
H3' |
236.6 |
237.3 |
| C2' |
C3' |
O3' |
H3' |
122.0 |
122.6 |
| O3' |
C3' |
C2' |
O2' |
33.3 |
339.7 |
| O3' |
C3' |
C2' |
C1' |
148.0 |
97.9 |
| O3' |
C3' |
C2' |
H2' |
273.3 |
216.2 |
| N1 |
C1' |
C2' |
C3' |
101.2 |
155.6 |
| C2' |
C3' |
C4' |
H4' |
92.4 |
117.6 |
| C4' |
C3' |
C2' |
O3' |
242.6 |
241.1 |
| C4' |
C3' |
C2' |
H3' |
123.2 |
118.5 |
| O4' |
C1' |
C2' |
C3' |
338.7 |
37.1 |
| O3' |
C3' |
C2' |
H3' |
240.6 |
237.5 |
| O2' |
C2' |
C3' |
C1' |
245.2 |
241.7 |
| O2' |
C2' |
C3' |
H2' |
119.9 |
123.5 |
| C3' |
C2' |
O2' |
HO2' |
180.0 |
174.2 |
| C1' |
C2' |
C3' |
H2' |
234.7 |
241.8 |
| C3' |
C2' |
C1' |
H1' |
217.8 |
278.7 |
| H3' |
C3' |
C4' |
H4' |
214.1 |
236.2 |
| C4' |
C3' |
H3' |
O3' |
120.4 |
122.9 |
| C4' |
C3' |
H3' |
C2' |
242.4 |
245.5 |
| O3' |
C3' |
H3' |
C2' |
122.0 |
122.6 |
| H3' |
C3' |
C2' |
O2' |
152.6 |
102.2 |
| H3' |
C3' |
C2' |
C1' |
267.4 |
220.5 |
| H3' |
C3' |
C2' |
H2' |
32.7 |
338.7 |
| N1 |
C1' |
C2' |
O2' |
220.1 |
273.8 |
| O4' |
C1' |
C2' |
O2' |
97.7 |
155.3 |
| O2' |
C2' |
C3' |
H3' |
152.6 |
102.2 |
| C3' |
C2' |
O2' |
C1' |
111.8 |
112.8 |
| C3' |
C2' |
O2' |
H2' |
237.5 |
236.4 |
| C1' |
C2' |
O2' |
H2' |
125.7 |
123.6 |
| O2' |
C2' |
C1' |
H1' |
336.8 |
36.9 |
| N1 |
C1' |
C2' |
O4' |
122.5 |
118.6 |
| N1 |
C1' |
C2' |
H1' |
243.4 |
236.9 |
| O4' |
C1' |
C2' |
H1' |
120.9 |
118.4 |
| C1' |
C2' |
C3' |
H3' |
267.4 |
220.5 |
| C3' |
C2' |
C1' |
O2' |
241.0 |
241.8 |
| C3' |
C2' |
C1' |
H2' |
121.6 |
118.2 |
| O2' |
C2' |
C1' |
H2' |
240.6 |
236.4 |
| C1' |
C2' |
O2' |
HO2' |
68.2 |
61.4 |
| H2' |
C2' |
C3' |
H3' |
32.7 |
338.7 |
| C3' |
C2' |
H2' |
O2' |
123.6 |
123.5 |
| C3' |
C2' |
H2' |
C1' |
243.3 |
247.2 |
| O2' |
C2' |
H2' |
C1' |
119.7 |
123.7 |
| H2' |
C2' |
O2' |
HO2' |
302.5 |
297.7 |
| H2' |
C2' |
C1' |
H1' |
96.2 |
160.5 |
| HO2' |
O2' |
C2' |
C1' |
68.2 |
61.4 |
| HO2' |
O2' |
C2' |
H2' |
302.5 |
297.7 |
| N1 |
C1' |
H1' |
O4' |
241.1 |
237.2 |
| N1 |
C1' |
H1' |
C2' |
122.3 |
123.2 |
| O4' |
C1' |
H1' |
C2' |
241.2 |
246.0 |
| H1' |
C1' |
C2' |
H2' |
96.2 |
160.5 |