PDB Chemical Component U5P
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 U5P
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N1 |
C2 |
1.403 |
1.345 |
| N1 |
C6 |
1.398 |
1.368 |
| N1 |
C1' |
1.471 |
1.465 |
| C2 |
N3 |
1.368 |
1.345 |
| C2 |
O2 |
1.225 |
1.216 |
| N3 |
C4 |
1.400 |
1.349 |
| N3 |
HN3 |
1.000 |
0.970 |
| C4 |
C5 |
1.436 |
1.416 |
| C4 |
O4 |
1.205 |
1.218 |
| C5 |
C6 |
1.327 |
1.350 |
| C5 |
H5 |
1.080 |
1.080 |
| C6 |
H6 |
1.080 |
1.081 |
| C1' |
C2' |
1.516 |
1.545 |
| C1' |
O4' |
1.414 |
1.444 |
| C1' |
H1' |
1.100 |
1.091 |
| C2' |
O2' |
1.436 |
1.429 |
| C2' |
C3' |
1.535 |
1.545 |
| C2' |
H2' |
1.100 |
1.090 |
| O2' |
HO2' |
0.950 |
0.967 |
| C3' |
C4' |
1.518 |
1.545 |
| C3' |
O3' |
1.454 |
1.429 |
| C3' |
H3' |
1.100 |
1.089 |
| C4' |
O4' |
1.463 |
1.446 |
| C4' |
C5' |
1.522 |
1.530 |
| C4' |
H4' |
1.100 |
1.090 |
| O3' |
HO3' |
0.950 |
0.967 |
| C5' |
O5' |
1.435 |
1.429 |
| C5' |
H5'1 |
1.100 |
1.090 |
| C5' |
H5'2 |
1.100 |
1.090 |
| O5' |
P |
1.608 |
1.610 |
| P |
O1P |
1.507 |
1.480 |
| P |
O2P |
1.491 |
1.609 |
| P |
O3P |
1.644 |
1.610 |
| O2P |
HOP2 |
0.950 |
0.967 |
| O3P |
HOP3 |
0.950 |
0.967 |
Bond Angles for U5P
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N1 |
C6 |
120.3 |
120.6 |
| C2 |
N1 |
C1' |
116.6 |
119.7 |
| N1 |
C2 |
N3 |
115.3 |
120.9 |
| N1 |
C2 |
O2 |
120.8 |
119.5 |
| C6 |
N1 |
C1' |
123.1 |
119.7 |
| N1 |
C6 |
C5 |
122.6 |
119.7 |
| N1 |
C6 |
H6 |
118.7 |
120.2 |
| N1 |
C1' |
C2' |
118.0 |
110.4 |
| N1 |
C1' |
O4' |
114.0 |
110.5 |
| N1 |
C1' |
H1' |
98.6 |
110.4 |
| N3 |
C2 |
O2 |
123.9 |
119.5 |
| C2 |
N3 |
C4 |
126.8 |
120.3 |
| C2 |
N3 |
HN3 |
116.6 |
119.9 |
| C4 |
N3 |
HN3 |
116.6 |
119.9 |
| N3 |
C4 |
C5 |
114.5 |
119.4 |
| N3 |
C4 |
O4 |
117.9 |
120.3 |
| C5 |
C4 |
O4 |
127.5 |
120.3 |
| C4 |
C5 |
C6 |
120.4 |
119.1 |
| C4 |
C5 |
H5 |
119.8 |
120.4 |
| C6 |
C5 |
H5 |
119.8 |
120.5 |
| C5 |
C6 |
H6 |
118.7 |
120.1 |
| C2' |
C1' |
O4' |
106.4 |
104.8 |
| C2' |
C1' |
H1' |
107.5 |
110.3 |
| C1' |
C2' |
O2' |
113.2 |
110.7 |
| C1' |
C2' |
C3' |
104.1 |
104.1 |
| C1' |
C2' |
H2' |
112.7 |
110.5 |
| O4' |
C1' |
H1' |
112.2 |
110.4 |
| C1' |
O4' |
C4' |
110.3 |
105.4 |
| O2' |
C2' |
C3' |
114.8 |
110.5 |
| O2' |
C2' |
H2' |
101.4 |
110.5 |
| C2' |
O2' |
HO2' |
109.5 |
106.8 |
| C3' |
C2' |
H2' |
110.9 |
110.5 |
| C2' |
C3' |
C4' |
100.9 |
104.2 |
| C2' |
C3' |
O3' |
111.8 |
110.5 |
| C2' |
C3' |
H3' |
115.6 |
110.5 |
| C4' |
C3' |
O3' |
115.1 |
110.5 |
| C4' |
C3' |
H3' |
112.4 |
110.6 |
| C3' |
C4' |
O4' |
105.7 |
104.7 |
| C3' |
C4' |
C5' |
119.0 |
110.6 |
| C3' |
C4' |
H4' |
104.6 |
110.3 |
| O3' |
C3' |
H3' |
101.6 |
110.4 |
| C3' |
O3' |
HO3' |
109.5 |
106.8 |
| O4' |
C4' |
C5' |
106.1 |
110.4 |
| O4' |
C4' |
H4' |
117.9 |
110.4 |
| C5' |
C4' |
H4' |
104.2 |
110.3 |
| C4' |
C5' |
O5' |
113.1 |
109.5 |
| C4' |
C5' |
H5'1 |
108.3 |
109.5 |
| C4' |
C5' |
H5'2 |
107.5 |
109.4 |
| O5' |
C5' |
H5'1 |
108.2 |
109.5 |
| O5' |
C5' |
H5'2 |
107.4 |
109.5 |
| C5' |
O5' |
P |
121.9 |
106.8 |
| H5'1 |
C5' |
H5'2 |
112.4 |
109.5 |
| O5' |
P |
O1P |
117.2 |
109.5 |
| O5' |
P |
O2P |
110.5 |
109.5 |
| O5' |
P |
O3P |
100.4 |
109.5 |
| O1P |
P |
O2P |
105.1 |
109.5 |
| O1P |
P |
O3P |
115.6 |
109.5 |
| O2P |
P |
O3P |
107.8 |
109.5 |
| P |
O2P |
HOP2 |
109.5 |
106.8 |
| P |
O3P |
HOP3 |
109.5 |
106.8 |
Torsion Angles for U5P
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C6 |
N1 |
C2 |
C1' |
180.1 |
179.7 |
| C2 |
N1 |
C6 |
C5 |
0.1 |
0.2 |
| C2 |
N1 |
C6 |
H6 |
180.1 |
180.2 |
| C2 |
N1 |
C1' |
C2' |
119.9 |
294.7 |
| C2 |
N1 |
C1' |
O4' |
245.8 |
50.2 |
| C2 |
N1 |
C1' |
H1' |
4.8 |
172.5 |
| N3 |
C2 |
N1 |
O2 |
179.8 |
179.6 |
| N1 |
C2 |
N3 |
C4 |
0.1 |
0.5 |
| N1 |
C2 |
N3 |
HN3 |
180.0 |
180.3 |
| C2 |
N1 |
C6 |
C1' |
179.9 |
180.3 |
| C6 |
N1 |
C2 |
N3 |
359.8 |
359.5 |
| C6 |
N1 |
C2 |
O2 |
179.9 |
180.0 |
| C6 |
N1 |
C1' |
C2' |
299.8 |
115.0 |
| C6 |
N1 |
C1' |
O4' |
65.7 |
230.4 |
| C6 |
N1 |
C1' |
H1' |
184.7 |
352.8 |
| C4 |
C5 |
C6 |
N1 |
0.1 |
360.0 |
| N1 |
C6 |
C5 |
H5 |
180.1 |
180.0 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
180.0 |
| C2 |
N1 |
C1' |
C6 |
180.1 |
179.7 |
| C1' |
N1 |
C2 |
N3 |
179.7 |
179.8 |
| C1' |
N1 |
C2 |
O2 |
359.9 |
0.2 |
| C1' |
N1 |
C6 |
C5 |
180.2 |
180.0 |
| C1' |
N1 |
C6 |
H6 |
0.2 |
359.9 |
| C2' |
C1' |
N1 |
O4' |
234.2 |
244.6 |
| C2' |
C1' |
N1 |
H1' |
115.1 |
122.2 |
| N1 |
C1' |
C2' |
O2' |
280.1 |
261.6 |
| N1 |
C1' |
C2' |
C3' |
154.7 |
142.9 |
| N1 |
C1' |
C2' |
H2' |
34.4 |
24.3 |
| O4' |
C1' |
N1 |
H1' |
241.0 |
237.6 |
| N1 |
C1' |
O4' |
C4' |
223.3 |
200.7 |
| N3 |
C2 |
N1 |
C6 |
359.8 |
359.5 |
| N3 |
C2 |
N1 |
C1' |
179.7 |
179.8 |
| N1 |
C2 |
N3 |
O2 |
180.2 |
180.4 |
| C4 |
N3 |
C2 |
HN3 |
180.0 |
180.2 |
| C2 |
N3 |
C4 |
C5 |
0.2 |
359.8 |
| C2 |
N3 |
C4 |
O4 |
180.5 |
179.8 |
| O2 |
C2 |
N1 |
C6 |
179.9 |
180.0 |
| O2 |
C2 |
N1 |
C1' |
359.9 |
0.2 |
| N1 |
C2 |
O2 |
N3 |
179.8 |
179.6 |
| O2 |
C2 |
N3 |
C4 |
179.9 |
180.0 |
| O2 |
C2 |
N3 |
HN3 |
359.9 |
359.8 |
| C4 |
N3 |
C2 |
O2 |
179.9 |
180.0 |
| C2 |
N3 |
C4 |
HN3 |
180.0 |
179.8 |
| C5 |
C4 |
N3 |
O4 |
179.7 |
180.0 |
| N3 |
C4 |
C5 |
C6 |
359.7 |
0.0 |
| N3 |
C4 |
C5 |
H5 |
179.7 |
180.0 |
| HN3 |
N3 |
C2 |
O2 |
359.9 |
359.8 |
| C2 |
N3 |
HN3 |
C4 |
180.0 |
180.2 |
| HN3 |
N3 |
C4 |
C5 |
180.2 |
180.0 |
| HN3 |
N3 |
C4 |
O4 |
0.5 |
360.0 |
| N1 |
C6 |
C5 |
C4 |
0.1 |
360.0 |
| C5 |
C4 |
N3 |
HN3 |
180.2 |
180.0 |
| N3 |
C4 |
C5 |
O4 |
180.3 |
180.0 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
180.0 |
| C4 |
C5 |
C6 |
H6 |
180.1 |
180.0 |
| O4 |
C4 |
N3 |
HN3 |
0.5 |
360.0 |
| N3 |
C4 |
O4 |
C5 |
179.6 |
180.0 |
| O4 |
C4 |
C5 |
C6 |
179.4 |
180.0 |
| O4 |
C4 |
C5 |
H5 |
359.4 |
0.0 |
| C5 |
C6 |
N1 |
C1' |
180.2 |
180.0 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.0 |
| C6 |
C5 |
C4 |
O4 |
179.4 |
180.0 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
180.0 |
| H5 |
C5 |
C4 |
O4 |
359.4 |
0.0 |
| C4 |
C5 |
H5 |
C6 |
180.0 |
180.0 |
| H5 |
C5 |
C6 |
H6 |
0.1 |
0.0 |
| H6 |
C6 |
N1 |
C1' |
0.2 |
359.9 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
180.0 |
| H6 |
C6 |
C5 |
H5 |
0.1 |
0.0 |
| N1 |
C1' |
C2' |
O4' |
129.5 |
119.0 |
| N1 |
C1' |
C2' |
H1' |
249.8 |
237.8 |
| O4' |
C1' |
C2' |
H1' |
120.3 |
118.8 |
| C2' |
C1' |
O4' |
C4' |
355.1 |
319.6 |
| O2' |
C2' |
C1' |
C3' |
125.4 |
118.7 |
| O2' |
C2' |
C1' |
H2' |
245.7 |
237.3 |
| C1' |
C2' |
O2' |
HO2' |
327.8 |
183.8 |
| C3' |
C2' |
C1' |
H2' |
120.3 |
118.6 |
| C1' |
C2' |
C3' |
C4' |
325.4 |
360.0 |
| C1' |
C2' |
C3' |
O3' |
88.3 |
118.6 |
| C1' |
C2' |
C3' |
H3' |
203.9 |
241.2 |
| N1 |
C1' |
O4' |
C2' |
228.3 |
241.1 |
| N1 |
C1' |
O4' |
H1' |
111.0 |
122.4 |
| C2' |
C1' |
O4' |
H1' |
242.8 |
241.3 |
| O4' |
C1' |
C2' |
O2' |
150.7 |
142.7 |
| O4' |
C1' |
C2' |
C3' |
25.3 |
23.9 |
| O4' |
C1' |
C2' |
H2' |
265.0 |
265.3 |
| C3' |
C4' |
O4' |
C1' |
342.3 |
40.4 |
| C1' |
O4' |
C4' |
C5' |
109.5 |
159.5 |
| C1' |
O4' |
C4' |
H4' |
225.8 |
281.7 |
| N1 |
C1' |
H1' |
C2' |
123.1 |
122.3 |
| N1 |
C1' |
H1' |
O4' |
239.6 |
237.6 |
| C2' |
C1' |
H1' |
O4' |
116.6 |
115.3 |
| H1' |
C1' |
C2' |
O2' |
30.3 |
23.9 |
| H1' |
C1' |
C2' |
C3' |
265.0 |
265.1 |
| H1' |
C1' |
C2' |
H2' |
144.7 |
146.5 |
| H1' |
C1' |
O4' |
C4' |
112.3 |
78.3 |
| O2' |
C2' |
C1' |
O4' |
150.7 |
142.7 |
| O2' |
C2' |
C1' |
H1' |
30.3 |
23.9 |
| C1' |
C2' |
O2' |
C3' |
240.6 |
245.3 |
| C1' |
C2' |
O2' |
H2' |
121.0 |
122.7 |
| C3' |
C2' |
O2' |
H2' |
240.3 |
237.4 |
| O2' |
C2' |
C3' |
C4' |
201.1 |
241.2 |
| O2' |
C2' |
C3' |
O3' |
324.0 |
359.8 |
| O2' |
C2' |
C3' |
H3' |
79.6 |
122.4 |
| C3' |
C2' |
C1' |
O4' |
25.3 |
23.9 |
| C3' |
C2' |
C1' |
H1' |
265.0 |
265.1 |
| C1' |
C2' |
C3' |
O2' |
124.3 |
118.8 |
| C1' |
C2' |
C3' |
H2' |
238.5 |
241.4 |
| O2' |
C2' |
C3' |
H2' |
114.2 |
122.5 |
| C3' |
C2' |
O2' |
HO2' |
87.2 |
298.6 |
| C4' |
C3' |
C2' |
O3' |
237.2 |
241.3 |
| C4' |
C3' |
C2' |
H3' |
121.5 |
118.8 |
| C2' |
C3' |
C4' |
O4' |
32.0 |
336.1 |
| C2' |
C3' |
C4' |
C5' |
273.0 |
217.2 |
| C2' |
C3' |
C4' |
H4' |
157.1 |
94.9 |
| O3' |
C3' |
C2' |
H3' |
244.4 |
237.4 |
| C2' |
C3' |
O3' |
HO3' |
231.8 |
63.3 |
| H2' |
C2' |
C1' |
O4' |
265.0 |
265.3 |
| H2' |
C2' |
C1' |
H1' |
144.7 |
146.5 |
| C1' |
C2' |
H2' |
O2' |
238.7 |
237.2 |
| C1' |
C2' |
H2' |
C3' |
116.3 |
114.6 |
| O2' |
C2' |
H2' |
C3' |
237.6 |
237.4 |
| H2' |
C2' |
O2' |
HO2' |
206.8 |
61.1 |
| H2' |
C2' |
C3' |
C4' |
86.9 |
118.6 |
| H2' |
C2' |
C3' |
O3' |
209.8 |
237.3 |
| H2' |
C2' |
C3' |
H3' |
325.4 |
359.9 |
| HO2' |
O2' |
C2' |
C3' |
87.2 |
298.6 |
| HO2' |
O2' |
C2' |
H2' |
206.8 |
61.1 |
| C1' |
O4' |
C4' |
C3' |
342.3 |
40.4 |
| C4' |
C3' |
C2' |
H2' |
86.9 |
118.6 |
| C2' |
C3' |
C4' |
O3' |
120.5 |
118.7 |
| C2' |
C3' |
C4' |
H3' |
236.2 |
241.2 |
| O3' |
C3' |
C4' |
H3' |
115.7 |
122.5 |
| C4' |
C3' |
O3' |
HO3' |
346.1 |
178.1 |
| O4' |
C4' |
C3' |
C5' |
119.0 |
118.9 |
| O4' |
C4' |
C3' |
H4' |
234.8 |
241.2 |
| C5' |
C4' |
C3' |
H4' |
115.8 |
122.3 |
| C3' |
C4' |
C5' |
O5' |
185.9 |
181.8 |
| C3' |
C4' |
C5' |
H5'1 |
305.8 |
301.9 |
| C3' |
C4' |
C5' |
H5'2 |
67.4 |
61.8 |
| O3' |
C3' |
C2' |
H2' |
209.8 |
237.3 |
| C2' |
C3' |
O3' |
C4' |
245.6 |
245.2 |
| C2' |
C3' |
O3' |
H3' |
123.9 |
122.6 |
| C4' |
C3' |
O3' |
H3' |
238.3 |
237.4 |
| O3' |
C3' |
C4' |
O4' |
271.4 |
217.4 |
| O3' |
C3' |
C4' |
C5' |
152.4 |
98.6 |
| O3' |
C3' |
C4' |
H4' |
36.6 |
336.2 |
| H3' |
C3' |
C2' |
H2' |
325.4 |
359.9 |
| C2' |
C3' |
H3' |
C4' |
115.1 |
114.8 |
| C2' |
C3' |
H3' |
O3' |
238.7 |
237.4 |
| C4' |
C3' |
H3' |
O3' |
123.6 |
122.6 |
| H3' |
C3' |
C4' |
O4' |
155.7 |
94.9 |
| H3' |
C3' |
C4' |
C5' |
36.7 |
336.0 |
| H3' |
C3' |
C4' |
H4' |
280.9 |
213.7 |
| H3' |
C3' |
O3' |
HO3' |
107.9 |
300.7 |
| C4' |
O4' |
C1' |
H1' |
112.3 |
78.3 |
| O4' |
C4' |
C3' |
O3' |
271.4 |
217.4 |
| O4' |
C4' |
C3' |
H3' |
155.7 |
94.9 |
| C3' |
C4' |
O4' |
C5' |
232.7 |
240.9 |
| C3' |
C4' |
O4' |
H4' |
116.5 |
118.7 |
| C5' |
C4' |
O4' |
H4' |
243.7 |
237.8 |
| O4' |
C4' |
C5' |
O5' |
67.1 |
66.5 |
| O4' |
C4' |
C5' |
H5'1 |
187.1 |
186.5 |
| O4' |
C4' |
C5' |
H5'2 |
308.7 |
306.5 |
| C5' |
C4' |
C3' |
O3' |
152.4 |
98.6 |
| C5' |
C4' |
C3' |
H3' |
36.7 |
336.0 |
| C3' |
C4' |
C5' |
O4' |
118.8 |
115.4 |
| C3' |
C4' |
C5' |
H4' |
244.0 |
237.7 |
| O4' |
C4' |
C5' |
H4' |
125.2 |
122.3 |
| O5' |
C5' |
C4' |
H5'1 |
240.0 |
240.0 |
| O5' |
C5' |
C4' |
H5'2 |
118.4 |
120.0 |
| C4' |
C5' |
O5' |
P |
93.0 |
180.0 |
| H5'1 |
C5' |
C4' |
H5'2 |
238.4 |
240.0 |
| H4' |
C4' |
C3' |
O3' |
36.6 |
336.2 |
| H4' |
C4' |
C3' |
H3' |
280.9 |
213.7 |
| C3' |
C4' |
H4' |
O4' |
243.0 |
244.8 |
| C3' |
C4' |
H4' |
C5' |
125.7 |
122.5 |
| O4' |
C4' |
H4' |
C5' |
242.7 |
237.7 |
| H4' |
C4' |
C5' |
O5' |
301.9 |
304.2 |
| H4' |
C4' |
C5' |
H5'1 |
61.9 |
64.2 |
| H4' |
C4' |
C5' |
H5'2 |
183.5 |
184.2 |
| HO3' |
O3' |
C3' |
H3' |
107.9 |
300.7 |
| O5' |
C5' |
C4' |
H4' |
301.9 |
304.2 |
| C4' |
C5' |
O5' |
H5'1 |
120.0 |
120.0 |
| C4' |
C5' |
O5' |
H5'2 |
241.6 |
240.0 |
| H5'1 |
C5' |
O5' |
H5'2 |
121.6 |
120.0 |
| C5' |
O5' |
P |
O1P |
59.6 |
305.0 |
| C5' |
O5' |
P |
O2P |
299.3 |
65.0 |
| C5' |
O5' |
P |
O3P |
185.7 |
185.0 |
| H5'1 |
C5' |
C4' |
H4' |
61.9 |
64.2 |
| C4' |
C5' |
H5'1 |
O5' |
237.0 |
240.0 |
| C4' |
C5' |
H5'1 |
H5'2 |
118.5 |
120.0 |
| O5' |
C5' |
H5'1 |
H5'2 |
241.5 |
240.0 |
| H5'1 |
C5' |
O5' |
P |
333.0 |
60.0 |
| H5'2 |
C5' |
C4' |
H4' |
183.5 |
184.2 |
| C4' |
C5' |
H5'2 |
O5' |
122.0 |
120.0 |
| C4' |
C5' |
H5'2 |
H5'1 |
241.0 |
240.0 |
| O5' |
C5' |
H5'2 |
H5'1 |
119.0 |
120.0 |
| H5'2 |
C5' |
O5' |
P |
211.5 |
300.0 |
| P |
O5' |
C5' |
H5'1 |
333.0 |
60.0 |
| P |
O5' |
C5' |
H5'2 |
211.5 |
300.0 |
| O1P |
P |
O5' |
O2P |
120.3 |
240.0 |
| O1P |
P |
O5' |
O3P |
233.9 |
120.0 |
| O2P |
P |
O5' |
O3P |
113.6 |
240.0 |
| O5' |
P |
O2P |
HOP2 |
225.4 |
60.0 |
| O5' |
P |
O3P |
HOP3 |
334.2 |
180.0 |
| O5' |
P |
O1P |
O2P |
236.9 |
120.0 |
| O5' |
P |
O1P |
O3P |
118.1 |
240.0 |
| O2P |
P |
O1P |
O3P |
241.2 |
120.0 |
| O1P |
P |
O2P |
HOP2 |
98.1 |
180.0 |
| O1P |
P |
O3P |
HOP3 |
101.2 |
60.0 |
| O5' |
P |
O2P |
O1P |
127.3 |
240.0 |
| O5' |
P |
O2P |
O3P |
251.2 |
120.0 |
| O1P |
P |
O2P |
O3P |
123.9 |
240.0 |
| O2P |
P |
O3P |
HOP3 |
218.5 |
300.0 |
| O5' |
P |
O3P |
O1P |
232.9 |
120.0 |
| O5' |
P |
O3P |
O2P |
115.6 |
240.0 |
| O1P |
P |
O3P |
O2P |
242.7 |
120.0 |
| O3P |
P |
O2P |
HOP2 |
334.2 |
300.0 |
| HOP2 |
O2P |
P |
O3P |
334.2 |
300.0 |