PDB Chemical Component U25
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 U25
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
OP3 |
P |
|
1.610 |
OP3 |
HOP3 |
|
0.967 |
P |
OP1 |
1.510 |
1.480 |
P |
OP2 |
1.511 |
1.610 |
P |
O5' |
1.614 |
1.610 |
OP2 |
HOP2 |
0.950 |
0.968 |
O5' |
C5' |
1.428 |
1.429 |
C5' |
C4' |
1.524 |
1.530 |
C5' |
H5' |
1.100 |
1.090 |
C5' |
H5'' |
1.100 |
1.089 |
C4' |
O4' |
1.431 |
1.444 |
C4' |
C3' |
1.524 |
1.551 |
C4' |
H4' |
1.100 |
1.089 |
O4' |
C1' |
1.429 |
1.437 |
C3' |
O3' |
1.429 |
1.429 |
C3' |
C2' |
1.516 |
1.548 |
C3' |
H3' |
1.100 |
1.089 |
O3' |
HO'3 |
0.950 |
0.967 |
C2' |
O2' |
1.432 |
1.429 |
C2' |
C1' |
1.521 |
1.541 |
C2' |
H2' |
1.100 |
1.089 |
O2' |
HO2' |
0.950 |
0.967 |
C1' |
N1 |
1.470 |
1.466 |
C1' |
H1' |
1.100 |
1.089 |
N1 |
C2 |
1.355 |
1.346 |
N1 |
C6 |
1.343 |
1.368 |
C2 |
O2 |
1.253 |
1.215 |
C2 |
N3 |
1.357 |
1.346 |
N3 |
C4 |
1.355 |
1.349 |
N3 |
H3 |
1.000 |
0.970 |
C4 |
O4 |
1.248 |
1.218 |
C4 |
C5 |
1.388 |
1.415 |
C5 |
C6 |
1.389 |
1.351 |
C5 |
H5 |
1.080 |
1.080 |
C6 |
H6 |
1.080 |
1.080 |
Bond Angles for U25
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
P |
OP3 |
HOP3 |
|
106.8 |
OP3 |
P |
OP1 |
|
109.5 |
OP3 |
P |
OP2 |
|
109.5 |
OP3 |
P |
O5' |
|
109.5 |
OP1 |
P |
OP2 |
119.3 |
109.5 |
OP1 |
P |
O5' |
108.4 |
109.4 |
OP2 |
P |
O5' |
108.1 |
109.5 |
P |
OP2 |
HOP2 |
109.5 |
106.7 |
P |
O5' |
C5' |
121.1 |
106.8 |
O5' |
C5' |
C4' |
110.2 |
109.5 |
O5' |
C5' |
H5' |
109.2 |
109.4 |
O5' |
C5' |
H5'' |
109.0 |
109.5 |
C4' |
C5' |
H5' |
109.2 |
109.5 |
C4' |
C5' |
H5'' |
109.1 |
109.5 |
C5' |
C4' |
O4' |
110.8 |
110.6 |
C5' |
C4' |
C3' |
111.7 |
110.6 |
C5' |
C4' |
H4' |
106.3 |
110.7 |
H5' |
C5' |
H5'' |
110.1 |
109.5 |
O4' |
C4' |
C3' |
107.1 |
103.5 |
O4' |
C4' |
H4' |
111.0 |
110.6 |
C4' |
O4' |
C1' |
108.5 |
107.0 |
C3' |
C4' |
H4' |
110.0 |
110.6 |
C4' |
C3' |
O3' |
109.7 |
110.9 |
C4' |
C3' |
C2' |
105.8 |
102.1 |
C4' |
C3' |
H3' |
111.8 |
110.9 |
O4' |
C1' |
C2' |
106.2 |
107.3 |
O4' |
C1' |
N1 |
113.1 |
109.9 |
O4' |
C1' |
H1' |
110.6 |
109.9 |
O3' |
C3' |
C2' |
109.8 |
110.9 |
O3' |
C3' |
H3' |
108.0 |
110.8 |
C3' |
O3' |
HO'3 |
109.5 |
106.8 |
C2' |
C3' |
H3' |
111.7 |
111.0 |
C3' |
C2' |
O2' |
111.9 |
110.5 |
C3' |
C2' |
C1' |
103.4 |
104.2 |
C3' |
C2' |
H2' |
112.4 |
110.4 |
O2' |
C2' |
C1' |
110.9 |
110.5 |
O2' |
C2' |
H2' |
105.1 |
110.4 |
C2' |
O2' |
HO2' |
109.5 |
106.8 |
C1' |
C2' |
H2' |
113.3 |
110.6 |
C2' |
C1' |
N1 |
113.0 |
109.8 |
C2' |
C1' |
H1' |
110.7 |
109.9 |
N1 |
C1' |
H1' |
103.4 |
110.0 |
C1' |
N1 |
C2 |
123.7 |
119.7 |
C1' |
N1 |
C6 |
115.9 |
119.7 |
C2 |
N1 |
C6 |
120.4 |
120.7 |
N1 |
C2 |
O2 |
121.8 |
119.5 |
N1 |
C2 |
N3 |
120.1 |
120.9 |
N1 |
C6 |
C5 |
120.8 |
119.6 |
N1 |
C6 |
H6 |
119.6 |
120.2 |
O2 |
C2 |
N3 |
118.1 |
119.6 |
C2 |
N3 |
C4 |
120.9 |
120.3 |
C2 |
N3 |
H3 |
119.6 |
119.9 |
C4 |
N3 |
H3 |
119.5 |
119.9 |
N3 |
C4 |
O4 |
120.5 |
120.3 |
N3 |
C4 |
C5 |
119.7 |
119.4 |
O4 |
C4 |
C5 |
119.8 |
120.3 |
C4 |
C5 |
C6 |
118.2 |
119.1 |
C4 |
C5 |
H5 |
120.9 |
120.5 |
C6 |
C5 |
H5 |
120.9 |
120.4 |
C5 |
C6 |
H6 |
119.6 |
120.2 |
Torsion Angles for U25
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
OP1 |
P |
OP3 |
OP2 |
|
240.0 |
OP1 |
P |
OP3 |
O5' |
|
120.0 |
OP2 |
P |
OP3 |
O5' |
|
240.0 |
OP3 |
P |
OP2 |
HOP2 |
|
299.9 |
OP3 |
P |
O5' |
C5' |
|
65.0 |
HOP3 |
OP3 |
P |
OP1 |
|
180.0 |
HOP3 |
OP3 |
P |
OP2 |
|
300.0 |
HOP3 |
OP3 |
P |
O5' |
|
60.0 |
OP1 |
P |
OP3 |
HOP3 |
|
180.0 |
OP3 |
P |
OP1 |
OP2 |
|
120.1 |
OP3 |
P |
OP1 |
O5' |
|
240.0 |
OP2 |
P |
OP1 |
O5' |
235.7 |
120.0 |
OP1 |
P |
OP2 |
HOP2 |
49.8 |
60.0 |
OP1 |
P |
O5' |
C5' |
1.3 |
305.0 |
OP2 |
P |
OP3 |
HOP3 |
|
300.0 |
OP3 |
P |
OP2 |
OP1 |
|
239.9 |
OP3 |
P |
OP2 |
O5' |
|
120.0 |
OP1 |
P |
OP2 |
O5' |
124.5 |
240.1 |
OP2 |
P |
O5' |
C5' |
132.1 |
185.0 |
O5' |
P |
OP3 |
HOP3 |
|
60.0 |
OP3 |
P |
O5' |
OP1 |
|
120.0 |
OP3 |
P |
O5' |
OP2 |
|
240.0 |
OP1 |
P |
O5' |
OP2 |
229.3 |
120.0 |
O5' |
P |
OP2 |
HOP2 |
285.3 |
180.0 |
P |
O5' |
C5' |
C4' |
220.9 |
180.0 |
P |
O5' |
C5' |
H5' |
340.9 |
60.0 |
P |
O5' |
C5' |
H5'' |
101.2 |
300.0 |
HOP2 |
OP2 |
P |
O5' |
285.3 |
180.0 |
C4' |
C5' |
O5' |
H5' |
240.0 |
120.0 |
C4' |
C5' |
O5' |
H5'' |
119.7 |
240.0 |
O5' |
C5' |
C4' |
O4' |
56.8 |
293.5 |
O5' |
C5' |
C4' |
C3' |
176.1 |
179.5 |
O5' |
C5' |
C4' |
H4' |
296.1 |
56.5 |
H5' |
C5' |
O5' |
H5'' |
239.7 |
120.0 |
O5' |
C5' |
C4' |
H5' |
120.0 |
240.0 |
O5' |
C5' |
C4' |
H5'' |
240.3 |
120.0 |
H5' |
C5' |
C4' |
H5'' |
120.3 |
240.0 |
O4' |
C4' |
C5' |
C3' |
240.7 |
114.0 |
O4' |
C4' |
C5' |
H4' |
120.7 |
237.0 |
C5' |
C4' |
O4' |
C1' |
141.9 |
201.5 |
C3' |
C4' |
C5' |
H4' |
240.0 |
123.0 |
C5' |
C4' |
C3' |
O3' |
118.7 |
37.3 |
C5' |
C4' |
C3' |
C2' |
237.1 |
155.5 |
C5' |
C4' |
C3' |
H3' |
359.0 |
273.8 |
O5' |
C5' |
H5' |
C4' |
239.4 |
120.0 |
O5' |
C5' |
H5' |
H5'' |
119.7 |
240.0 |
C4' |
C5' |
H5' |
H5'' |
240.3 |
120.0 |
H5' |
C5' |
C4' |
O4' |
296.8 |
53.5 |
H5' |
C5' |
C4' |
C3' |
56.1 |
299.5 |
H5' |
C5' |
C4' |
H4' |
176.1 |
176.5 |
O5' |
C5' |
H5'' |
C4' |
120.4 |
240.0 |
O5' |
C5' |
H5'' |
H5' |
240.2 |
119.9 |
C4' |
C5' |
H5'' |
H5' |
119.8 |
240.0 |
H5'' |
C5' |
C4' |
O4' |
176.4 |
173.5 |
H5'' |
C5' |
C4' |
C3' |
295.8 |
59.5 |
H5'' |
C5' |
C4' |
H4' |
55.8 |
296.5 |
O4' |
C4' |
C5' |
H5' |
296.8 |
53.5 |
O4' |
C4' |
C5' |
H5'' |
176.4 |
173.5 |
C5' |
C4' |
O4' |
C3' |
122.1 |
241.5 |
C5' |
C4' |
O4' |
H4' |
242.2 |
123.0 |
C3' |
C4' |
O4' |
H4' |
120.1 |
241.5 |
O4' |
C4' |
C3' |
O3' |
240.2 |
278.8 |
O4' |
C4' |
C3' |
C2' |
358.6 |
37.0 |
O4' |
C4' |
C3' |
H3' |
120.4 |
155.3 |
C4' |
O4' |
C1' |
C2' |
329.5 |
26.5 |
C4' |
O4' |
C1' |
N1 |
205.0 |
267.1 |
C4' |
O4' |
C1' |
H1' |
89.6 |
145.9 |
C3' |
C4' |
C5' |
H5' |
56.1 |
299.5 |
C3' |
C4' |
C5' |
H5'' |
295.8 |
59.5 |
C5' |
C4' |
C3' |
O4' |
238.5 |
118.5 |
C5' |
C4' |
C3' |
H4' |
117.8 |
237.0 |
O4' |
C4' |
C3' |
H4' |
239.3 |
118.5 |
C3' |
C4' |
O4' |
C1' |
19.8 |
320.0 |
O3' |
C3' |
C4' |
C2' |
241.6 |
241.8 |
O3' |
C3' |
C4' |
H3' |
119.8 |
123.5 |
C4' |
C3' |
O3' |
HO'3 |
327.2 |
174.2 |
C2' |
C3' |
C4' |
H3' |
238.2 |
241.7 |
C4' |
C3' |
C2' |
O2' |
224.6 |
220.4 |
C4' |
C3' |
C2' |
C1' |
344.0 |
339.1 |
C4' |
C3' |
C2' |
H2' |
106.6 |
98.0 |
H4' |
C4' |
C5' |
H5' |
176.1 |
176.5 |
H4' |
C4' |
C5' |
H5'' |
55.8 |
296.5 |
C5' |
C4' |
H4' |
O4' |
120.5 |
237.0 |
C5' |
C4' |
H4' |
C3' |
238.9 |
123.0 |
O4' |
C4' |
H4' |
C3' |
118.3 |
246.0 |
H4' |
C4' |
O4' |
C1' |
259.7 |
78.4 |
H4' |
C4' |
C3' |
O3' |
0.9 |
160.3 |
H4' |
C4' |
C3' |
C2' |
119.3 |
278.5 |
H4' |
C4' |
C3' |
H3' |
241.2 |
36.8 |
C1' |
O4' |
C4' |
C3' |
19.8 |
320.0 |
C1' |
O4' |
C4' |
H4' |
259.7 |
78.4 |
C3' |
C2' |
C1' |
O4' |
28.2 |
358.0 |
O2' |
C2' |
C1' |
O4' |
148.4 |
116.7 |
O4' |
C1' |
C2' |
H2' |
266.3 |
239.3 |
C2' |
C1' |
O4' |
N1 |
124.5 |
119.4 |
C2' |
C1' |
O4' |
H1' |
239.9 |
240.6 |
N1 |
C1' |
O4' |
H1' |
115.4 |
121.2 |
O4' |
C1' |
N1 |
C2 |
56.4 |
194.6 |
O4' |
C1' |
N1 |
C6 |
236.5 |
14.7 |
O3' |
C3' |
C4' |
H4' |
0.9 |
160.3 |
C4' |
C3' |
O3' |
C2' |
115.9 |
112.7 |
C4' |
C3' |
O3' |
H3' |
237.9 |
236.4 |
C2' |
C3' |
O3' |
H3' |
122.0 |
123.7 |
O3' |
C3' |
C2' |
O2' |
342.8 |
338.6 |
O3' |
C3' |
C2' |
C1' |
102.3 |
97.3 |
O3' |
C3' |
C2' |
H2' |
224.9 |
216.1 |
C2' |
C3' |
C4' |
H4' |
119.3 |
278.5 |
C4' |
C3' |
C2' |
O3' |
241.7 |
241.8 |
C4' |
C3' |
C2' |
H3' |
121.9 |
118.2 |
O4' |
C1' |
C2' |
C3' |
28.2 |
358.0 |
O3' |
C3' |
C2' |
H3' |
240.2 |
236.4 |
C2' |
C3' |
O3' |
HO'3 |
211.3 |
61.5 |
O2' |
C2' |
C3' |
C1' |
240.5 |
241.3 |
O2' |
C2' |
C3' |
H2' |
117.9 |
122.5 |
C3' |
C2' |
O2' |
HO2' |
93.3 |
298.5 |
C1' |
C2' |
C3' |
H2' |
237.4 |
241.2 |
C3' |
C2' |
C1' |
N1 |
152.8 |
117.4 |
C3' |
C2' |
C1' |
H1' |
268.2 |
238.5 |
H3' |
C3' |
C4' |
H4' |
241.2 |
36.8 |
C4' |
C3' |
H3' |
O3' |
120.8 |
123.6 |
C4' |
C3' |
H3' |
C2' |
241.6 |
247.3 |
O3' |
C3' |
H3' |
C2' |
120.8 |
123.7 |
H3' |
C3' |
O3' |
HO'3 |
89.3 |
297.8 |
H3' |
C3' |
C2' |
O2' |
102.6 |
102.2 |
H3' |
C3' |
C2' |
C1' |
222.1 |
220.9 |
H3' |
C3' |
C2' |
H2' |
344.7 |
339.7 |
HO'3 |
O3' |
C3' |
C2' |
211.3 |
61.5 |
HO'3 |
O3' |
C3' |
H3' |
89.3 |
297.8 |
O4' |
C1' |
C2' |
O2' |
148.4 |
116.7 |
O2' |
C2' |
C3' |
H3' |
102.6 |
102.2 |
C3' |
C2' |
O2' |
C1' |
114.9 |
114.8 |
C3' |
C2' |
O2' |
H2' |
237.8 |
237.5 |
C1' |
C2' |
O2' |
H2' |
122.8 |
122.8 |
O2' |
C2' |
C1' |
N1 |
272.9 |
236.0 |
O2' |
C2' |
C1' |
H1' |
28.3 |
357.2 |
O4' |
C1' |
C2' |
N1 |
235.5 |
240.6 |
O4' |
C1' |
C2' |
H1' |
120.0 |
119.5 |
C1' |
C2' |
C3' |
H3' |
222.1 |
220.9 |
C3' |
C2' |
C1' |
O2' |
239.9 |
241.3 |
C3' |
C2' |
C1' |
H2' |
122.0 |
118.7 |
O2' |
C2' |
C1' |
H2' |
242.1 |
237.4 |
C1' |
C2' |
O2' |
HO2' |
338.4 |
183.8 |
N1 |
C1' |
C2' |
H1' |
244.6 |
238.9 |
C2' |
C1' |
N1 |
C2 |
295.7 |
76.7 |
C2' |
C1' |
N1 |
C6 |
115.8 |
256.9 |
H2' |
C2' |
C3' |
H3' |
344.7 |
339.7 |
C3' |
C2' |
H2' |
O2' |
121.9 |
122.5 |
C3' |
C2' |
H2' |
C1' |
243.2 |
245.2 |
O2' |
C2' |
H2' |
C1' |
121.3 |
122.7 |
H2' |
C2' |
O2' |
HO2' |
215.6 |
61.0 |
H2' |
C2' |
C1' |
N1 |
30.8 |
358.7 |
H2' |
C2' |
C1' |
H1' |
146.2 |
119.8 |
HO2' |
O2' |
C2' |
C1' |
338.4 |
183.8 |
HO2' |
O2' |
C2' |
H2' |
215.6 |
61.0 |
O4' |
C1' |
N1 |
C2' |
120.7 |
117.8 |
O4' |
C1' |
N1 |
H1' |
240.4 |
238.9 |
N1 |
C1' |
C2' |
H2' |
30.8 |
358.7 |
C2' |
C1' |
N1 |
H1' |
119.7 |
121.1 |
C2 |
N1 |
C1' |
C6 |
180.0 |
179.8 |
C1' |
N1 |
C2 |
O2 |
360.0 |
0.2 |
C1' |
N1 |
C2 |
N3 |
179.9 |
179.7 |
C1' |
N1 |
C6 |
C5 |
180.0 |
180.0 |
C1' |
N1 |
C6 |
H6 |
0.0 |
0.0 |
O4' |
C1' |
H1' |
C2' |
242.6 |
242.1 |
O4' |
C1' |
H1' |
N1 |
121.3 |
121.1 |
H1' |
C1' |
C2' |
H2' |
146.2 |
119.8 |
C2' |
C1' |
H1' |
N1 |
238.7 |
239.0 |
H1' |
C1' |
N1 |
C2 |
176.0 |
315.7 |
H1' |
C1' |
N1 |
C6 |
356.1 |
135.9 |
C2 |
N1 |
C1' |
H1' |
176.0 |
315.7 |
C1' |
N1 |
C2 |
C6 |
180.0 |
180.2 |
C2 |
N1 |
C6 |
C5 |
0.1 |
0.2 |
C2 |
N1 |
C6 |
H6 |
180.1 |
180.2 |
O2 |
C2 |
N1 |
N3 |
180.1 |
180.5 |
N1 |
C2 |
N3 |
C4 |
0.1 |
0.5 |
N1 |
C2 |
N3 |
H3 |
180.1 |
180.2 |
C6 |
N1 |
C1' |
H1' |
356.1 |
135.9 |
C1' |
N1 |
C6 |
C2 |
180.0 |
179.8 |
C6 |
N1 |
C2 |
O2 |
179.9 |
180.1 |
C6 |
N1 |
C2 |
N3 |
359.9 |
359.6 |
C4 |
C5 |
C6 |
N1 |
360.0 |
0.0 |
N1 |
C6 |
C5 |
H5 |
179.9 |
180.0 |
C5 |
C6 |
N1 |
H6 |
180.0 |
180.0 |
O2 |
C2 |
N1 |
C6 |
179.9 |
180.1 |
N1 |
C2 |
O2 |
N3 |
179.9 |
179.5 |
O2 |
C2 |
N3 |
C4 |
180.0 |
180.0 |
O2 |
C2 |
N3 |
H3 |
0.0 |
359.7 |
N3 |
C2 |
N1 |
C6 |
359.9 |
359.6 |
N1 |
C2 |
N3 |
O2 |
180.1 |
180.5 |
C4 |
N3 |
C2 |
H3 |
180.0 |
180.3 |
C2 |
N3 |
C4 |
O4 |
180.1 |
179.7 |
C2 |
N3 |
C4 |
C5 |
360.0 |
359.8 |
C2 |
N3 |
C4 |
H3 |
180.0 |
179.7 |
O4 |
C4 |
N3 |
C5 |
180.1 |
179.9 |
N3 |
C4 |
C5 |
C6 |
0.0 |
360.0 |
N3 |
C4 |
C5 |
H5 |
180.0 |
180.0 |
C2 |
N3 |
H3 |
C4 |
180.0 |
180.3 |
H3 |
N3 |
C4 |
O4 |
0.1 |
359.9 |
H3 |
N3 |
C4 |
C5 |
180.0 |
180.0 |
O4 |
C4 |
N3 |
H3 |
0.1 |
359.9 |
N3 |
C4 |
O4 |
C5 |
179.9 |
180.1 |
O4 |
C4 |
C5 |
C6 |
179.9 |
180.1 |
O4 |
C4 |
C5 |
H5 |
359.9 |
0.1 |
N1 |
C6 |
C5 |
C4 |
360.0 |
0.0 |
C5 |
C4 |
N3 |
H3 |
180.0 |
180.0 |
N3 |
C4 |
C5 |
O4 |
180.1 |
179.9 |
C6 |
C5 |
C4 |
H5 |
180.0 |
180.0 |
C4 |
C5 |
C6 |
H6 |
180.0 |
180.0 |
N1 |
C6 |
C5 |
H6 |
180.0 |
180.0 |
C4 |
C5 |
C6 |
H5 |
180.0 |
180.0 |
C4 |
C5 |
H5 |
C6 |
180.0 |
180.0 |
H5 |
C5 |
C6 |
H6 |
360.0 |
360.0 |
N1 |
C6 |
H6 |
C5 |
180.0 |
180.0 |
H6 |
C6 |
C5 |
H5 |
360.0 |
360.0 |