PDB Chemical Component U
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 U
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| OP3 |
P |
1.590 |
1.610 |
| OP3 |
HOP3 |
0.949 |
0.967 |
| P |
OP1 |
1.472 |
1.480 |
| P |
OP2 |
1.460 |
1.610 |
| P |
O5' |
1.582 |
1.610 |
| OP2 |
HOP2 |
0.950 |
0.966 |
| O5' |
C5' |
1.452 |
1.427 |
| C5' |
C4' |
1.496 |
1.529 |
| C5' |
H5' |
1.115 |
1.090 |
| C5' |
H5'' |
1.116 |
1.089 |
| C4' |
O4' |
1.446 |
1.446 |
| C4' |
C3' |
1.527 |
1.544 |
| C4' |
H4' |
1.115 |
1.090 |
| O4' |
C1' |
1.459 |
1.444 |
| C3' |
O3' |
1.426 |
1.429 |
| C3' |
C2' |
1.515 |
1.544 |
| C3' |
H3' |
1.114 |
1.090 |
| O3' |
HO3' |
0.950 |
0.968 |
| C2' |
O2' |
1.400 |
1.429 |
| C2' |
C1' |
1.468 |
1.544 |
| C2' |
H2' |
1.114 |
1.090 |
| O2' |
HO2' |
0.950 |
0.966 |
| C1' |
N1 |
1.469 |
1.466 |
| C1' |
H1' |
1.114 |
1.089 |
| N1 |
C2 |
1.410 |
1.343 |
| N1 |
C6 |
1.380 |
1.368 |
| C2 |
O2 |
1.197 |
1.215 |
| C2 |
N3 |
1.353 |
1.347 |
| N3 |
C4 |
1.404 |
1.348 |
| N3 |
H3 |
1.020 |
0.970 |
| C4 |
O4 |
1.248 |
1.218 |
| C4 |
C5 |
1.417 |
1.415 |
| C5 |
C6 |
1.308 |
1.350 |
| C5 |
H5 |
1.103 |
1.080 |
| C6 |
H6 |
1.103 |
1.079 |
Bond Angles for U
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| P |
OP3 |
HOP3 |
106.2 |
106.8 |
| OP3 |
P |
OP1 |
106.2 |
109.5 |
| OP3 |
P |
OP2 |
110.7 |
109.4 |
| OP3 |
P |
O5' |
104.6 |
109.5 |
| OP1 |
P |
OP2 |
117.8 |
109.5 |
| OP1 |
P |
O5' |
110.9 |
109.5 |
| OP2 |
P |
O5' |
105.9 |
109.5 |
| P |
OP2 |
HOP2 |
117.8 |
106.8 |
| P |
O5' |
C5' |
119.3 |
106.8 |
| O5' |
C5' |
C4' |
106.7 |
109.5 |
| O5' |
C5' |
H5' |
113.3 |
109.4 |
| O5' |
C5' |
H5'' |
113.2 |
109.5 |
| C4' |
C5' |
H5' |
113.3 |
109.5 |
| C4' |
C5' |
H5'' |
113.2 |
109.5 |
| C5' |
C4' |
O4' |
111.1 |
110.4 |
| C5' |
C4' |
C3' |
117.5 |
110.7 |
| C5' |
C4' |
H4' |
100.3 |
110.4 |
| H5' |
C5' |
H5'' |
97.2 |
109.5 |
| O4' |
C4' |
C3' |
100.2 |
104.7 |
| O4' |
C4' |
H4' |
117.5 |
110.4 |
| C4' |
O4' |
C1' |
109.6 |
105.3 |
| C3' |
C4' |
H4' |
111.2 |
110.2 |
| C4' |
C3' |
O3' |
109.6 |
110.5 |
| C4' |
C3' |
C2' |
101.3 |
104.2 |
| C4' |
C3' |
H3' |
117.0 |
110.5 |
| O4' |
C1' |
C2' |
106.0 |
104.8 |
| O4' |
C1' |
N1 |
108.8 |
110.4 |
| O4' |
C1' |
H1' |
113.3 |
110.4 |
| O3' |
C3' |
C2' |
115.8 |
110.5 |
| O3' |
C3' |
H3' |
102.9 |
110.4 |
| C3' |
O3' |
HO3' |
109.6 |
106.8 |
| C2' |
C3' |
H3' |
111.0 |
110.5 |
| C3' |
C2' |
O2' |
108.3 |
110.5 |
| C3' |
C2' |
C1' |
100.4 |
104.1 |
| C3' |
C2' |
H2' |
116.8 |
110.6 |
| O2' |
C2' |
C1' |
112.2 |
110.6 |
| O2' |
C2' |
H2' |
105.9 |
110.4 |
| C2' |
O2' |
HO2' |
108.3 |
106.8 |
| C1' |
C2' |
H2' |
113.2 |
110.5 |
| C2' |
C1' |
N1 |
112.7 |
110.4 |
| C2' |
C1' |
H1' |
109.4 |
110.4 |
| N1 |
C1' |
H1' |
106.7 |
110.4 |
| C1' |
N1 |
C2 |
115.7 |
119.7 |
| C1' |
N1 |
C6 |
126.4 |
119.6 |
| C2 |
N1 |
C6 |
117.9 |
120.7 |
| N1 |
C2 |
O2 |
119.6 |
119.6 |
| N1 |
C2 |
N3 |
115.4 |
120.9 |
| N1 |
C6 |
C5 |
125.8 |
119.6 |
| N1 |
C6 |
H6 |
120.1 |
120.2 |
| O2 |
C2 |
N3 |
125.1 |
119.5 |
| C2 |
N3 |
C4 |
127.5 |
120.3 |
| C2 |
N3 |
H3 |
114.1 |
119.8 |
| C4 |
N3 |
H3 |
118.4 |
119.9 |
| N3 |
C4 |
O4 |
118.6 |
120.3 |
| N3 |
C4 |
C5 |
113.9 |
119.4 |
| O4 |
C4 |
C5 |
127.4 |
120.4 |
| C4 |
C5 |
C6 |
119.5 |
119.2 |
| C4 |
C5 |
H5 |
124.2 |
120.4 |
| C6 |
C5 |
H5 |
116.3 |
120.5 |
| C5 |
C6 |
H6 |
114.1 |
120.2 |
Torsion Angles for U
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP1 |
P |
OP3 |
OP2 |
129.0 |
240.0 |
| OP1 |
P |
OP3 |
O5' |
242.6 |
120.0 |
| OP2 |
P |
OP3 |
O5' |
113.6 |
240.0 |
| OP3 |
P |
OP2 |
HOP2 |
302.5 |
60.0 |
| OP3 |
P |
O5' |
C5' |
292.3 |
180.0 |
| HOP3 |
OP3 |
P |
OP1 |
180.0 |
300.1 |
| HOP3 |
OP3 |
P |
OP2 |
51.0 |
60.1 |
| HOP3 |
OP3 |
P |
O5' |
297.4 |
180.0 |
| OP1 |
P |
OP3 |
HOP3 |
180.0 |
300.1 |
| OP3 |
P |
OP1 |
OP2 |
235.3 |
119.9 |
| OP3 |
P |
OP1 |
O5' |
113.1 |
239.9 |
| OP2 |
P |
OP1 |
O5' |
237.8 |
120.0 |
| OP1 |
P |
OP2 |
HOP2 |
180.1 |
180.0 |
| OP1 |
P |
O5' |
C5' |
46.4 |
60.0 |
| OP2 |
P |
OP3 |
HOP3 |
51.0 |
60.1 |
| OP3 |
P |
OP2 |
OP1 |
122.4 |
240.0 |
| OP3 |
P |
OP2 |
O5' |
247.2 |
120.0 |
| OP1 |
P |
OP2 |
O5' |
124.8 |
240.0 |
| OP2 |
P |
O5' |
C5' |
175.4 |
300.0 |
| O5' |
P |
OP3 |
HOP3 |
297.4 |
180.0 |
| OP3 |
P |
O5' |
OP1 |
245.9 |
120.1 |
| OP3 |
P |
O5' |
OP2 |
117.0 |
240.1 |
| OP1 |
P |
O5' |
OP2 |
231.1 |
120.0 |
| O5' |
P |
OP2 |
HOP2 |
55.3 |
300.0 |
| P |
O5' |
C5' |
C4' |
167.3 |
180.0 |
| P |
O5' |
C5' |
H5' |
292.6 |
60.0 |
| P |
O5' |
C5' |
H5'' |
42.0 |
300.0 |
| HOP2 |
OP2 |
P |
O5' |
55.3 |
300.0 |
| C4' |
C5' |
O5' |
H5' |
234.7 |
120.0 |
| C4' |
C5' |
O5' |
H5'' |
125.3 |
240.0 |
| O5' |
C5' |
C4' |
O4' |
293.8 |
61.5 |
| O5' |
C5' |
C4' |
C3' |
48.2 |
176.9 |
| O5' |
C5' |
C4' |
H4' |
168.8 |
299.2 |
| H5' |
C5' |
O5' |
H5'' |
250.6 |
120.0 |
| O5' |
C5' |
C4' |
H5' |
125.3 |
240.0 |
| O5' |
C5' |
C4' |
H5'' |
234.7 |
120.0 |
| H5' |
C5' |
C4' |
H5'' |
109.4 |
240.0 |
| O4' |
C4' |
C5' |
C3' |
245.5 |
244.6 |
| O4' |
C4' |
C5' |
H4' |
125.0 |
122.3 |
| C5' |
C4' |
O4' |
C1' |
149.5 |
159.5 |
| C3' |
C4' |
C5' |
H4' |
239.4 |
237.7 |
| C5' |
C4' |
C3' |
O3' |
73.7 |
98.6 |
| C5' |
C4' |
C3' |
C2' |
196.5 |
217.3 |
| C5' |
C4' |
C3' |
H3' |
317.2 |
336.0 |
| O5' |
C5' |
H5' |
C4' |
238.3 |
120.0 |
| O5' |
C5' |
H5' |
H5'' |
119.1 |
240.0 |
| C4' |
C5' |
H5' |
H5'' |
240.9 |
120.0 |
| H5' |
C5' |
C4' |
O4' |
168.4 |
181.4 |
| H5' |
C5' |
C4' |
C3' |
282.9 |
296.9 |
| H5' |
C5' |
C4' |
H4' |
43.5 |
59.2 |
| O5' |
C5' |
H5'' |
C4' |
121.7 |
240.0 |
| O5' |
C5' |
H5'' |
H5' |
240.8 |
120.0 |
| C4' |
C5' |
H5'' |
H5' |
119.1 |
240.0 |
| H5'' |
C5' |
C4' |
O4' |
59.1 |
301.4 |
| H5'' |
C5' |
C4' |
C3' |
173.5 |
56.9 |
| H5'' |
C5' |
C4' |
H4' |
294.1 |
179.1 |
| O4' |
C4' |
C5' |
H5' |
168.4 |
181.4 |
| O4' |
C4' |
C5' |
H5'' |
59.1 |
301.4 |
| C5' |
C4' |
O4' |
C3' |
124.9 |
119.1 |
| C5' |
C4' |
O4' |
H4' |
245.4 |
237.7 |
| C3' |
C4' |
O4' |
H4' |
120.5 |
118.6 |
| O4' |
C4' |
C3' |
O3' |
194.1 |
217.5 |
| O4' |
C4' |
C3' |
C2' |
316.9 |
336.2 |
| O4' |
C4' |
C3' |
H3' |
77.6 |
94.9 |
| C4' |
O4' |
C1' |
C2' |
3.8 |
319.5 |
| C4' |
O4' |
C1' |
N1 |
242.4 |
200.7 |
| C4' |
O4' |
C1' |
H1' |
123.8 |
78.4 |
| C3' |
C4' |
C5' |
H5' |
282.9 |
296.9 |
| C3' |
C4' |
C5' |
H5'' |
173.5 |
56.9 |
| C5' |
C4' |
C3' |
O4' |
239.6 |
241.1 |
| C5' |
C4' |
C3' |
H4' |
114.7 |
122.4 |
| O4' |
C4' |
C3' |
H4' |
235.0 |
241.3 |
| C3' |
C4' |
O4' |
C1' |
24.7 |
40.3 |
| O3' |
C3' |
C4' |
C2' |
237.2 |
241.3 |
| O3' |
C3' |
C4' |
H3' |
116.5 |
122.6 |
| C4' |
C3' |
O3' |
HO3' |
180.0 |
178.1 |
| C2' |
C3' |
C4' |
H3' |
239.3 |
241.3 |
| C4' |
C3' |
C2' |
O2' |
288.0 |
241.1 |
| C4' |
C3' |
C2' |
C1' |
45.8 |
359.9 |
| C4' |
C3' |
C2' |
H2' |
168.6 |
118.6 |
| H4' |
C4' |
C5' |
H5' |
43.5 |
59.2 |
| H4' |
C4' |
C5' |
H5'' |
294.1 |
179.1 |
| C5' |
C4' |
H4' |
O4' |
120.4 |
122.3 |
| C5' |
C4' |
H4' |
C3' |
235.0 |
237.4 |
| O4' |
C4' |
H4' |
C3' |
114.6 |
115.2 |
| H4' |
C4' |
O4' |
C1' |
264.1 |
281.8 |
| H4' |
C4' |
C3' |
O3' |
319.1 |
336.2 |
| H4' |
C4' |
C3' |
C2' |
81.9 |
94.9 |
| H4' |
C4' |
C3' |
H3' |
202.6 |
213.6 |
| C1' |
O4' |
C4' |
C3' |
24.7 |
40.3 |
| C1' |
O4' |
C4' |
H4' |
264.1 |
281.8 |
| C3' |
C2' |
C1' |
O4' |
329.1 |
24.0 |
| O2' |
C2' |
C1' |
O4' |
84.0 |
142.8 |
| O4' |
C1' |
C2' |
H2' |
203.8 |
265.3 |
| C2' |
C1' |
O4' |
N1 |
121.5 |
118.8 |
| C2' |
C1' |
O4' |
H1' |
240.0 |
241.1 |
| N1 |
C1' |
O4' |
H1' |
118.5 |
122.3 |
| O4' |
C1' |
N1 |
C2 |
200.3 |
55.1 |
| O4' |
C1' |
N1 |
C6 |
21.2 |
235.4 |
| O3' |
C3' |
C4' |
H4' |
319.1 |
336.2 |
| C4' |
C3' |
O3' |
C2' |
113.7 |
114.8 |
| C4' |
C3' |
O3' |
H3' |
234.9 |
237.4 |
| C2' |
C3' |
O3' |
H3' |
121.2 |
122.6 |
| O3' |
C3' |
C2' |
O2' |
46.4 |
359.8 |
| O3' |
C3' |
C2' |
C1' |
164.2 |
118.6 |
| O3' |
C3' |
C2' |
H2' |
287.0 |
237.3 |
| C2' |
C3' |
C4' |
H4' |
81.9 |
94.9 |
| C4' |
C3' |
C2' |
O3' |
241.6 |
241.3 |
| C4' |
C3' |
C2' |
H3' |
124.9 |
118.7 |
| O4' |
C1' |
C2' |
C3' |
329.1 |
24.0 |
| O3' |
C3' |
C2' |
H3' |
243.3 |
237.4 |
| C2' |
C3' |
O3' |
HO3' |
66.3 |
63.3 |
| O2' |
C2' |
C3' |
C1' |
242.2 |
241.2 |
| O2' |
C2' |
C3' |
H2' |
119.4 |
122.5 |
| C3' |
C2' |
O2' |
HO2' |
180.0 |
298.6 |
| C1' |
C2' |
C3' |
H2' |
237.2 |
241.3 |
| C3' |
C2' |
C1' |
N1 |
88.0 |
142.9 |
| C3' |
C2' |
C1' |
H1' |
206.6 |
265.2 |
| H3' |
C3' |
C4' |
H4' |
202.6 |
213.6 |
| C4' |
C3' |
H3' |
O3' |
120.2 |
122.6 |
| C4' |
C3' |
H3' |
C2' |
244.6 |
245.2 |
| O3' |
C3' |
H3' |
C2' |
124.4 |
122.6 |
| H3' |
C3' |
O3' |
HO3' |
305.1 |
300.7 |
| H3' |
C3' |
C2' |
O2' |
163.1 |
122.4 |
| H3' |
C3' |
C2' |
C1' |
280.9 |
241.2 |
| H3' |
C3' |
C2' |
H2' |
43.7 |
359.9 |
| HO3' |
O3' |
C3' |
C2' |
66.3 |
63.3 |
| HO3' |
O3' |
C3' |
H3' |
305.1 |
300.7 |
| O4' |
C1' |
C2' |
O2' |
84.0 |
142.8 |
| O2' |
C2' |
C3' |
H3' |
163.1 |
122.4 |
| C3' |
C2' |
O2' |
C1' |
110.0 |
114.7 |
| C3' |
C2' |
O2' |
H2' |
233.9 |
237.4 |
| C1' |
C2' |
O2' |
H2' |
124.0 |
122.7 |
| O2' |
C2' |
C1' |
N1 |
202.9 |
261.6 |
| O2' |
C2' |
C1' |
H1' |
321.5 |
23.9 |
| O4' |
C1' |
C2' |
N1 |
241.1 |
241.1 |
| O4' |
C1' |
C2' |
H1' |
122.5 |
118.9 |
| C1' |
C2' |
C3' |
H3' |
280.9 |
241.2 |
| C3' |
C2' |
C1' |
O2' |
245.1 |
241.3 |
| C3' |
C2' |
C1' |
H2' |
125.3 |
118.7 |
| O2' |
C2' |
C1' |
H2' |
240.2 |
237.4 |
| C1' |
C2' |
O2' |
HO2' |
70.0 |
183.9 |
| N1 |
C1' |
C2' |
H1' |
241.4 |
237.7 |
| C2' |
C1' |
N1 |
C2 |
83.0 |
299.8 |
| C2' |
C1' |
N1 |
C6 |
263.8 |
120.0 |
| H2' |
C2' |
C3' |
H3' |
43.7 |
359.9 |
| C3' |
C2' |
H2' |
O2' |
120.7 |
122.6 |
| C3' |
C2' |
H2' |
C1' |
244.1 |
245.3 |
| O2' |
C2' |
H2' |
C1' |
123.4 |
122.7 |
| H2' |
C2' |
O2' |
HO2' |
306.0 |
61.2 |
| H2' |
C2' |
C1' |
N1 |
322.7 |
24.2 |
| H2' |
C2' |
C1' |
H1' |
81.3 |
146.5 |
| HO2' |
O2' |
C2' |
C1' |
70.0 |
183.9 |
| HO2' |
O2' |
C2' |
H2' |
306.0 |
61.2 |
| O4' |
C1' |
N1 |
C2' |
117.3 |
115.4 |
| O4' |
C1' |
N1 |
H1' |
237.4 |
237.7 |
| N1 |
C1' |
C2' |
H2' |
322.7 |
24.2 |
| C2' |
C1' |
N1 |
H1' |
120.1 |
122.3 |
| C2 |
N1 |
C1' |
C6 |
179.1 |
179.8 |
| C1' |
N1 |
C2 |
O2 |
0.4 |
0.3 |
| C1' |
N1 |
C2 |
N3 |
180.2 |
179.7 |
| C1' |
N1 |
C6 |
C5 |
179.5 |
180.0 |
| C1' |
N1 |
C6 |
H6 |
359.5 |
0.0 |
| O4' |
C1' |
H1' |
C2' |
241.9 |
244.6 |
| O4' |
C1' |
H1' |
N1 |
119.7 |
122.3 |
| H1' |
C1' |
C2' |
H2' |
81.3 |
146.5 |
| C2' |
C1' |
H1' |
N1 |
237.8 |
237.7 |
| H1' |
C1' |
N1 |
C2 |
322.9 |
177.4 |
| H1' |
C1' |
N1 |
C6 |
143.7 |
357.7 |
| C2 |
N1 |
C1' |
H1' |
322.9 |
177.4 |
| C1' |
N1 |
C2 |
C6 |
180.8 |
180.2 |
| C2 |
N1 |
C6 |
C5 |
0.4 |
0.2 |
| C2 |
N1 |
C6 |
H6 |
180.4 |
180.3 |
| O2 |
C2 |
N1 |
N3 |
180.2 |
180.5 |
| N1 |
C2 |
N3 |
C4 |
0.7 |
0.5 |
| N1 |
C2 |
N3 |
H3 |
180.7 |
180.2 |
| C6 |
N1 |
C1' |
H1' |
143.7 |
357.7 |
| C1' |
N1 |
C6 |
C2 |
179.1 |
179.8 |
| C6 |
N1 |
C2 |
O2 |
179.6 |
180.0 |
| C6 |
N1 |
C2 |
N3 |
359.4 |
359.5 |
| C4 |
C5 |
C6 |
N1 |
359.7 |
0.0 |
| N1 |
C6 |
C5 |
H5 |
179.7 |
180.0 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
180.0 |
| O2 |
C2 |
N1 |
C6 |
179.6 |
180.0 |
| N1 |
C2 |
O2 |
N3 |
179.8 |
179.5 |
| O2 |
C2 |
N3 |
C4 |
180.5 |
180.0 |
| O2 |
C2 |
N3 |
H3 |
0.4 |
359.7 |
| N3 |
C2 |
N1 |
C6 |
359.4 |
359.5 |
| N1 |
C2 |
N3 |
O2 |
180.2 |
180.5 |
| C4 |
N3 |
C2 |
H3 |
180.0 |
180.3 |
| C2 |
N3 |
C4 |
O4 |
180.1 |
179.7 |
| C2 |
N3 |
C4 |
C5 |
359.5 |
359.7 |
| C2 |
N3 |
C4 |
H3 |
180.0 |
179.7 |
| O4 |
C4 |
N3 |
C5 |
180.7 |
180.0 |
| N3 |
C4 |
C5 |
C6 |
0.3 |
0.0 |
| N3 |
C4 |
C5 |
H5 |
180.3 |
180.0 |
| C2 |
N3 |
H3 |
C4 |
180.0 |
180.3 |
| H3 |
N3 |
C4 |
O4 |
0.2 |
0.0 |
| H3 |
N3 |
C4 |
C5 |
179.5 |
180.0 |
| O4 |
C4 |
N3 |
H3 |
0.2 |
0.0 |
| N3 |
C4 |
O4 |
C5 |
179.2 |
180.0 |
| O4 |
C4 |
C5 |
C6 |
179.5 |
180.0 |
| O4 |
C4 |
C5 |
H5 |
359.5 |
0.0 |
| N1 |
C6 |
C5 |
C4 |
359.7 |
0.0 |
| C5 |
C4 |
N3 |
H3 |
179.5 |
180.0 |
| N3 |
C4 |
C5 |
O4 |
180.8 |
180.0 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
180.0 |
| C4 |
C5 |
C6 |
H6 |
179.7 |
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 |
359.7 |
360.0 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
180.0 |
| H6 |
C6 |
C5 |
H5 |
359.7 |
360.0 |