PDB Chemical Component UD5
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 UD5
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| P |
OP1 |
1.490 |
1.610 |
| P |
OP2 |
1.483 |
1.610 |
| P |
O5' |
1.603 |
1.610 |
| OP1 |
H1P |
0.950 |
0.968 |
| OP2 |
H2P |
0.951 |
0.967 |
| O5' |
C5' |
1.433 |
1.429 |
| C5' |
C4' |
1.517 |
1.530 |
| C5' |
H5' |
1.114 |
1.090 |
| C5' |
H5'' |
1.115 |
1.090 |
| C4' |
O4' |
1.457 |
1.447 |
| C4' |
C3' |
1.538 |
1.545 |
| C4' |
H4' |
1.115 |
1.090 |
| O4' |
C1' |
1.403 |
1.444 |
| C3' |
O3' |
1.427 |
1.429 |
| C3' |
C2' |
1.527 |
1.546 |
| C3' |
H3' |
1.115 |
1.090 |
| O3' |
H2 |
0.950 |
0.967 |
| C2' |
O2' |
1.410 |
1.429 |
| C2' |
C1' |
1.513 |
1.545 |
| C2' |
H2' |
1.115 |
1.090 |
| O2' |
H1 |
0.950 |
0.967 |
| C1' |
N1 |
1.459 |
1.465 |
| C1' |
H1' |
1.115 |
1.090 |
| N1 |
C2 |
1.383 |
1.345 |
| N1 |
C6 |
1.357 |
1.371 |
| C2 |
O2 |
1.216 |
1.216 |
| C2 |
N3 |
1.365 |
1.346 |
| N3 |
C4 |
1.366 |
1.349 |
| N3 |
HN3 |
1.020 |
0.970 |
| C4 |
O4 |
1.228 |
1.218 |
| C4 |
C5 |
1.435 |
1.417 |
| C5 |
C6 |
1.325 |
1.350 |
| C5 |
F |
1.362 |
1.351 |
| C6 |
H6 |
1.103 |
1.081 |
Bond Angles for UD5
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP1 |
P |
OP2 |
119.4 |
95.0 |
| OP1 |
P |
O5' |
110.1 |
95.0 |
| P |
OP1 |
H1P |
119.4 |
106.8 |
| OP2 |
P |
O5' |
108.5 |
95.0 |
| P |
OP2 |
H2P |
119.4 |
106.8 |
| P |
O5' |
C5' |
122.3 |
106.8 |
| O5' |
C5' |
C4' |
109.8 |
109.5 |
| O5' |
C5' |
H5' |
112.1 |
109.5 |
| O5' |
C5' |
H5'' |
112.0 |
109.5 |
| C4' |
C5' |
H5' |
112.1 |
109.4 |
| C4' |
C5' |
H5'' |
112.1 |
109.4 |
| C5' |
C4' |
O4' |
110.5 |
110.4 |
| C5' |
C4' |
C3' |
110.3 |
110.7 |
| C5' |
C4' |
H4' |
106.9 |
110.4 |
| H5' |
C5' |
H5'' |
98.3 |
109.5 |
| O4' |
C4' |
C3' |
105.2 |
104.7 |
| O4' |
C4' |
H4' |
111.9 |
110.3 |
| C4' |
O4' |
C1' |
108.7 |
105.4 |
| C3' |
C4' |
H4' |
112.0 |
110.3 |
| C4' |
C3' |
O3' |
108.9 |
110.5 |
| C4' |
C3' |
C2' |
105.9 |
104.2 |
| C4' |
C3' |
H3' |
113.2 |
110.5 |
| O4' |
C1' |
C2' |
110.9 |
104.8 |
| O4' |
C1' |
N1 |
113.3 |
110.5 |
| O4' |
C1' |
H1' |
111.7 |
110.4 |
| O3' |
C3' |
C2' |
112.5 |
110.5 |
| O3' |
C3' |
H3' |
106.8 |
110.4 |
| C3' |
O3' |
H2 |
108.9 |
106.8 |
| C2' |
C3' |
H3' |
109.7 |
110.5 |
| C3' |
C2' |
O2' |
116.4 |
110.5 |
| C3' |
C2' |
C1' |
99.4 |
104.1 |
| C3' |
C2' |
H2' |
110.4 |
110.5 |
| O2' |
C2' |
C1' |
105.0 |
110.7 |
| O2' |
C2' |
H2' |
105.3 |
110.4 |
| C2' |
O2' |
H1 |
116.4 |
106.8 |
| C1' |
C2' |
H2' |
120.9 |
110.6 |
| C2' |
C1' |
N1 |
121.5 |
110.3 |
| C2' |
C1' |
H1' |
100.4 |
110.4 |
| N1 |
C1' |
H1' |
97.1 |
110.3 |
| C1' |
N1 |
C2 |
115.8 |
119.7 |
| C1' |
N1 |
C6 |
122.7 |
119.7 |
| C2 |
N1 |
C6 |
121.5 |
120.6 |
| N1 |
C2 |
O2 |
122.7 |
119.6 |
| N1 |
C2 |
N3 |
115.1 |
121.0 |
| N1 |
C6 |
C5 |
122.2 |
119.7 |
| N1 |
C6 |
H6 |
120.1 |
120.1 |
| O2 |
C2 |
N3 |
122.1 |
119.5 |
| C2 |
N3 |
C4 |
126.5 |
120.3 |
| C2 |
N3 |
HN3 |
116.7 |
119.9 |
| C4 |
N3 |
HN3 |
116.9 |
119.9 |
| N3 |
C4 |
O4 |
119.1 |
120.3 |
| N3 |
C4 |
C5 |
114.7 |
119.4 |
| O4 |
C4 |
C5 |
126.2 |
120.3 |
| C4 |
C5 |
C6 |
120.0 |
119.1 |
| C4 |
C5 |
F |
120.4 |
120.4 |
| C6 |
C5 |
F |
119.6 |
120.5 |
| C5 |
C6 |
H6 |
117.8 |
120.2 |
Torsion Angles for UD5
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP2 |
P |
OP1 |
O5' |
126.5 |
95.5 |
| OP1 |
P |
OP2 |
H2P |
180.0 |
84.5 |
| OP1 |
P |
O5' |
C5' |
184.5 |
260.4 |
| OP1 |
P |
OP2 |
O5' |
232.7 |
264.6 |
| OP2 |
P |
OP1 |
H1P |
180.1 |
275.5 |
| OP2 |
P |
O5' |
C5' |
52.1 |
165.0 |
| OP1 |
P |
O5' |
OP2 |
132.4 |
95.5 |
| O5' |
P |
OP1 |
H1P |
53.6 |
180.1 |
| O5' |
P |
OP2 |
H2P |
307.2 |
180.0 |
| P |
O5' |
C5' |
C4' |
156.4 |
180.0 |
| P |
O5' |
C5' |
H5' |
281.7 |
60.1 |
| P |
O5' |
C5' |
H5'' |
31.2 |
300.0 |
| H1P |
OP1 |
P |
OP2 |
180.1 |
275.5 |
| H1P |
OP1 |
P |
O5' |
53.6 |
180.1 |
| H2P |
OP2 |
P |
O5' |
307.2 |
180.0 |
| C4' |
C5' |
O5' |
H5' |
234.7 |
120.0 |
| C4' |
C5' |
O5' |
H5'' |
125.2 |
240.0 |
| O5' |
C5' |
C4' |
O4' |
80.1 |
66.5 |
| O5' |
C5' |
C4' |
C3' |
196.1 |
181.9 |
| O5' |
C5' |
C4' |
H4' |
318.1 |
304.3 |
| H5' |
C5' |
O5' |
H5'' |
250.5 |
120.0 |
| O5' |
C5' |
C4' |
H5' |
125.3 |
240.0 |
| O5' |
C5' |
C4' |
H5'' |
234.8 |
120.1 |
| H5' |
C5' |
C4' |
H5'' |
109.5 |
240.0 |
| O4' |
C4' |
C5' |
C3' |
244.1 |
244.6 |
| O4' |
C4' |
C5' |
H4' |
122.0 |
122.2 |
| C5' |
C4' |
O4' |
C1' |
116.1 |
159.5 |
| C3' |
C4' |
C5' |
H4' |
238.0 |
237.6 |
| C5' |
C4' |
C3' |
O3' |
141.2 |
98.6 |
| C5' |
C4' |
C3' |
C2' |
262.4 |
217.3 |
| C5' |
C4' |
C3' |
H3' |
22.6 |
336.0 |
| O5' |
C5' |
H5' |
C4' |
235.9 |
120.0 |
| O5' |
C5' |
H5' |
H5'' |
117.9 |
239.9 |
| C4' |
C5' |
H5' |
H5'' |
242.0 |
119.9 |
| H5' |
C5' |
C4' |
O4' |
314.8 |
186.4 |
| H5' |
C5' |
C4' |
C3' |
70.8 |
301.8 |
| H5' |
C5' |
C4' |
H4' |
192.8 |
64.2 |
| O5' |
C5' |
H5'' |
C4' |
124.0 |
240.0 |
| O5' |
C5' |
H5'' |
H5' |
242.0 |
120.0 |
| C4' |
C5' |
H5'' |
H5' |
118.0 |
240.1 |
| H5'' |
C5' |
C4' |
O4' |
205.4 |
306.4 |
| H5'' |
C5' |
C4' |
C3' |
321.3 |
61.8 |
| H5'' |
C5' |
C4' |
H4' |
83.4 |
184.2 |
| O4' |
C4' |
C5' |
H5' |
314.8 |
186.4 |
| O4' |
C4' |
C5' |
H5'' |
205.4 |
306.4 |
| C5' |
C4' |
O4' |
C3' |
119.1 |
119.1 |
| C5' |
C4' |
O4' |
H4' |
241.0 |
237.8 |
| C3' |
C4' |
O4' |
H4' |
121.9 |
118.6 |
| O4' |
C4' |
C3' |
O3' |
260.3 |
217.5 |
| O4' |
C4' |
C3' |
C2' |
21.5 |
336.2 |
| O4' |
C4' |
C3' |
H3' |
141.8 |
94.9 |
| C4' |
O4' |
C1' |
C2' |
342.6 |
319.6 |
| C4' |
O4' |
C1' |
N1 |
202.1 |
200.8 |
| C4' |
O4' |
C1' |
H1' |
93.6 |
78.4 |
| C3' |
C4' |
C5' |
H5' |
70.8 |
301.8 |
| C3' |
C4' |
C5' |
H5'' |
321.3 |
61.8 |
| C5' |
C4' |
C3' |
O4' |
240.8 |
241.1 |
| C5' |
C4' |
C3' |
H4' |
119.0 |
122.4 |
| O4' |
C4' |
C3' |
H4' |
238.2 |
241.3 |
| C3' |
C4' |
O4' |
C1' |
357.1 |
40.3 |
| O3' |
C3' |
C4' |
C2' |
238.8 |
241.3 |
| O3' |
C3' |
C4' |
H3' |
118.6 |
122.6 |
| C4' |
C3' |
O3' |
H2 |
180.0 |
178.1 |
| C2' |
C3' |
C4' |
H3' |
239.8 |
241.3 |
| C4' |
C3' |
C2' |
O2' |
218.2 |
241.1 |
| C4' |
C3' |
C2' |
C1' |
330.3 |
359.9 |
| C4' |
C3' |
C2' |
H2' |
98.3 |
118.6 |
| H4' |
C4' |
C5' |
H5' |
192.8 |
64.2 |
| H4' |
C4' |
C5' |
H5'' |
83.4 |
184.2 |
| C5' |
C4' |
H4' |
O4' |
121.1 |
122.2 |
| C5' |
C4' |
H4' |
C3' |
239.0 |
237.4 |
| O4' |
C4' |
H4' |
C3' |
117.9 |
115.2 |
| H4' |
C4' |
O4' |
C1' |
235.2 |
281.7 |
| H4' |
C4' |
C3' |
O3' |
22.2 |
336.2 |
| H4' |
C4' |
C3' |
C2' |
143.4 |
94.9 |
| H4' |
C4' |
C3' |
H3' |
263.6 |
213.6 |
| C1' |
O4' |
C4' |
C3' |
357.1 |
40.3 |
| C1' |
O4' |
C4' |
H4' |
235.2 |
281.7 |
| C3' |
C2' |
C1' |
O4' |
29.5 |
24.0 |
| O2' |
C2' |
C1' |
O4' |
150.2 |
142.7 |
| O4' |
C1' |
C2' |
H2' |
268.8 |
265.4 |
| C2' |
C1' |
O4' |
N1 |
140.5 |
118.8 |
| C2' |
C1' |
O4' |
H1' |
249.0 |
241.2 |
| N1 |
C1' |
O4' |
H1' |
108.5 |
122.3 |
| O4' |
C1' |
N1 |
C2 |
208.4 |
50.1 |
| O4' |
C1' |
N1 |
C6 |
27.0 |
230.5 |
| O3' |
C3' |
C4' |
H4' |
22.2 |
336.2 |
| C4' |
C3' |
O3' |
C2' |
117.1 |
114.8 |
| C4' |
C3' |
O3' |
H3' |
237.4 |
237.4 |
| C2' |
C3' |
O3' |
H3' |
120.3 |
122.6 |
| O3' |
C3' |
C2' |
O2' |
337.1 |
359.8 |
| O3' |
C3' |
C2' |
C1' |
89.1 |
118.6 |
| O3' |
C3' |
C2' |
H2' |
217.2 |
237.3 |
| C2' |
C3' |
C4' |
H4' |
143.4 |
94.9 |
| C4' |
C3' |
C2' |
O3' |
241.1 |
241.3 |
| C4' |
C3' |
C2' |
H3' |
122.5 |
118.7 |
| O4' |
C1' |
C2' |
C3' |
29.5 |
24.0 |
| O3' |
C3' |
C2' |
H3' |
241.4 |
237.4 |
| C2' |
C3' |
O3' |
H2 |
62.9 |
63.3 |
| O2' |
C2' |
C3' |
C1' |
248.0 |
241.2 |
| O2' |
C2' |
C3' |
H2' |
119.9 |
122.5 |
| C3' |
C2' |
O2' |
H1 |
180.0 |
298.6 |
| C1' |
C2' |
C3' |
H2' |
231.9 |
241.3 |
| C3' |
C2' |
C1' |
N1 |
166.3 |
142.9 |
| C3' |
C2' |
C1' |
H1' |
271.4 |
265.1 |
| H3' |
C3' |
C4' |
H4' |
263.6 |
213.6 |
| C4' |
C3' |
H3' |
O3' |
119.8 |
122.6 |
| C4' |
C3' |
H3' |
C2' |
241.9 |
245.2 |
| O3' |
C3' |
H3' |
C2' |
122.1 |
122.6 |
| H3' |
C3' |
O3' |
H2 |
302.6 |
300.7 |
| H3' |
C3' |
C2' |
O2' |
95.7 |
122.4 |
| H3' |
C3' |
C2' |
C1' |
207.8 |
241.2 |
| H3' |
C3' |
C2' |
H2' |
335.8 |
359.9 |
| H2 |
O3' |
C3' |
C2' |
62.9 |
63.3 |
| H2 |
O3' |
C3' |
H3' |
302.6 |
300.7 |
| O4' |
C1' |
C2' |
O2' |
150.2 |
142.7 |
| O2' |
C2' |
C3' |
H3' |
95.7 |
122.4 |
| C3' |
C2' |
O2' |
C1' |
108.8 |
114.7 |
| C3' |
C2' |
O2' |
H2' |
237.4 |
237.5 |
| C1' |
C2' |
O2' |
H2' |
128.6 |
122.8 |
| O2' |
C2' |
C1' |
N1 |
287.0 |
261.6 |
| O2' |
C2' |
C1' |
H1' |
32.1 |
23.8 |
| O4' |
C1' |
C2' |
N1 |
223.2 |
241.1 |
| O4' |
C1' |
C2' |
H1' |
118.1 |
118.9 |
| C1' |
C2' |
C3' |
H3' |
207.8 |
241.2 |
| C3' |
C2' |
C1' |
O2' |
239.3 |
241.3 |
| C3' |
C2' |
C1' |
H2' |
120.7 |
118.6 |
| O2' |
C2' |
C1' |
H2' |
241.4 |
237.3 |
| C1' |
C2' |
O2' |
H1 |
71.3 |
183.9 |
| N1 |
C1' |
C2' |
H1' |
254.9 |
237.8 |
| C2' |
C1' |
N1 |
C2 |
72.5 |
294.7 |
| C2' |
C1' |
N1 |
C6 |
251.2 |
115.0 |
| H2' |
C2' |
C3' |
H3' |
335.8 |
359.9 |
| C3' |
C2' |
H2' |
O2' |
126.4 |
122.5 |
| C3' |
C2' |
H2' |
C1' |
244.8 |
245.4 |
| O2' |
C2' |
H2' |
C1' |
118.4 |
122.8 |
| H2' |
C2' |
O2' |
H1 |
302.6 |
61.1 |
| H2' |
C2' |
C1' |
N1 |
45.6 |
24.3 |
| H2' |
C2' |
C1' |
H1' |
150.7 |
146.5 |
| H1 |
O2' |
C2' |
C1' |
71.3 |
183.9 |
| H1 |
O2' |
C2' |
H2' |
302.6 |
61.1 |
| O4' |
C1' |
N1 |
C2' |
135.8 |
115.4 |
| O4' |
C1' |
N1 |
H1' |
242.7 |
237.6 |
| N1 |
C1' |
C2' |
H2' |
45.6 |
24.3 |
| C2' |
C1' |
N1 |
H1' |
106.8 |
122.2 |
| C2 |
N1 |
C1' |
C6 |
181.3 |
179.6 |
| C1' |
N1 |
C2 |
O2 |
357.5 |
0.3 |
| C1' |
N1 |
C2 |
N3 |
177.2 |
179.8 |
| C1' |
N1 |
C6 |
C5 |
182.9 |
179.9 |
| C1' |
N1 |
C6 |
H6 |
2.9 |
359.9 |
| O4' |
C1' |
H1' |
C2' |
242.5 |
244.6 |
| O4' |
C1' |
H1' |
N1 |
118.6 |
122.4 |
| H1' |
C1' |
C2' |
H2' |
150.7 |
146.5 |
| C2' |
C1' |
H1' |
N1 |
236.1 |
237.8 |
| H1' |
C1' |
N1 |
C2 |
325.7 |
172.5 |
| H1' |
C1' |
N1 |
C6 |
144.4 |
352.8 |
| C2 |
N1 |
C1' |
H1' |
325.7 |
172.5 |
| C1' |
N1 |
C2 |
C6 |
178.7 |
180.4 |
| C2 |
N1 |
C6 |
C5 |
1.5 |
0.3 |
| C2 |
N1 |
C6 |
H6 |
181.5 |
180.3 |
| O2 |
C2 |
N1 |
N3 |
180.3 |
180.5 |
| N1 |
C2 |
N3 |
C4 |
0.4 |
0.6 |
| N1 |
C2 |
N3 |
HN3 |
180.5 |
180.3 |
| C6 |
N1 |
C1' |
H1' |
144.4 |
352.8 |
| C1' |
N1 |
C6 |
C2 |
181.4 |
179.6 |
| C6 |
N1 |
C2 |
O2 |
178.8 |
179.9 |
| C6 |
N1 |
C2 |
N3 |
358.5 |
359.4 |
| C4 |
C5 |
C6 |
N1 |
359.7 |
0.0 |
| N1 |
C6 |
C5 |
F |
180.4 |
180.0 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
180.0 |
| O2 |
C2 |
N1 |
C6 |
178.8 |
179.9 |
| N1 |
C2 |
O2 |
N3 |
179.7 |
179.5 |
| O2 |
C2 |
N3 |
C4 |
180.2 |
180.1 |
| O2 |
C2 |
N3 |
HN3 |
0.2 |
359.8 |
| N3 |
C2 |
N1 |
C6 |
358.5 |
359.4 |
| N1 |
C2 |
N3 |
O2 |
180.3 |
180.5 |
| C4 |
N3 |
C2 |
HN3 |
180.0 |
180.3 |
| C2 |
N3 |
C4 |
O4 |
181.0 |
179.7 |
| C2 |
N3 |
C4 |
C5 |
0.6 |
359.7 |
| C2 |
N3 |
C4 |
HN3 |
180.0 |
179.7 |
| O4 |
C4 |
N3 |
C5 |
180.3 |
180.0 |
| N3 |
C4 |
C5 |
C6 |
359.3 |
360.0 |
| N3 |
C4 |
C5 |
F |
178.6 |
180.0 |
| C2 |
N3 |
HN3 |
C4 |
180.0 |
180.3 |
| HN3 |
N3 |
C4 |
O4 |
0.9 |
360.0 |
| HN3 |
N3 |
C4 |
C5 |
180.6 |
180.0 |
| O4 |
C4 |
N3 |
HN3 |
0.9 |
360.0 |
| N3 |
C4 |
O4 |
C5 |
179.6 |
180.0 |
| O4 |
C4 |
C5 |
C6 |
179.0 |
180.0 |
| O4 |
C4 |
C5 |
F |
358.2 |
0.1 |
| N1 |
C6 |
C5 |
C4 |
359.7 |
0.0 |
| C5 |
C4 |
N3 |
HN3 |
180.6 |
180.0 |
| N3 |
C4 |
C5 |
O4 |
180.4 |
180.0 |
| C6 |
C5 |
C4 |
F |
180.7 |
179.9 |
| C4 |
C5 |
C6 |
H6 |
179.7 |
180.0 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.0 |
| C4 |
C5 |
C6 |
F |
179.3 |
180.1 |
| C4 |
C5 |
F |
C6 |
180.7 |
179.9 |
| F |
C5 |
C6 |
H6 |
0.4 |
360.0 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
180.0 |
| H6 |
C6 |
C5 |
F |
0.4 |
360.0 |