PDB Chemical Component 5UD
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 5UD
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| F5 |
C5 |
1.351 |
1.351 |
| C5 |
C4 |
1.483 |
1.415 |
| C5 |
C6 |
1.417 |
1.351 |
| C4 |
O4 |
1.251 |
1.219 |
| C4 |
N3 |
1.325 |
1.348 |
| N3 |
C2 |
1.347 |
1.346 |
| N3 |
HN3 |
1.020 |
0.970 |
| C2 |
O2 |
1.240 |
1.216 |
| C2 |
N1 |
1.407 |
1.344 |
| C6 |
N1 |
1.359 |
1.370 |
| C6 |
H6 |
1.103 |
1.080 |
| N1 |
C1' |
1.500 |
1.465 |
| C1' |
C2' |
1.545 |
1.550 |
| C1' |
O4' |
1.430 |
1.443 |
| C1' |
H1' |
1.115 |
1.090 |
| C2' |
O2' |
1.423 |
1.429 |
| C2' |
C3' |
1.521 |
1.551 |
| C2' |
H2' |
1.116 |
1.090 |
| O2' |
HO2' |
0.950 |
0.967 |
| C3' |
O3' |
1.418 |
1.428 |
| C3' |
C4' |
1.513 |
1.539 |
| C3' |
H3' |
1.115 |
1.090 |
| O3' |
HO3' |
0.950 |
0.967 |
| C4' |
O4' |
1.423 |
1.438 |
| C4' |
C5' |
1.522 |
1.530 |
| C4' |
H4' |
1.114 |
1.090 |
| C5' |
O5' |
1.413 |
1.429 |
| C5' |
H5'1 |
1.115 |
1.090 |
| C5' |
H5'2 |
1.115 |
1.089 |
| O5' |
HO5' |
0.950 |
0.967 |
Bond Angles for 5UD
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| F5 |
C5 |
C4 |
113.5 |
120.5 |
| F5 |
C5 |
C6 |
126.7 |
120.4 |
| C4 |
C5 |
C6 |
119.7 |
119.1 |
| C5 |
C4 |
O4 |
122.9 |
120.3 |
| C5 |
C4 |
N3 |
115.7 |
119.4 |
| C5 |
C6 |
N1 |
121.5 |
119.6 |
| C5 |
C6 |
H6 |
121.5 |
120.2 |
| O4 |
C4 |
N3 |
121.4 |
120.3 |
| C4 |
N3 |
C2 |
122.9 |
120.3 |
| C4 |
N3 |
HN3 |
117.7 |
119.8 |
| C2 |
N3 |
HN3 |
119.4 |
119.9 |
| N3 |
C2 |
O2 |
114.7 |
119.5 |
| N3 |
C2 |
N1 |
124.6 |
120.9 |
| O2 |
C2 |
N1 |
120.7 |
119.5 |
| C2 |
N1 |
C6 |
115.6 |
120.6 |
| C2 |
N1 |
C1' |
124.1 |
119.7 |
| N1 |
C6 |
H6 |
117.0 |
120.2 |
| C6 |
N1 |
C1' |
120.3 |
119.7 |
| N1 |
C1' |
C2' |
130.4 |
110.8 |
| N1 |
C1' |
O4' |
120.2 |
110.6 |
| N1 |
C1' |
H1' |
76.9 |
110.5 |
| C2' |
C1' |
O4' |
97.4 |
103.5 |
| C2' |
C1' |
H1' |
109.7 |
110.6 |
| C1' |
C2' |
O2' |
121.0 |
110.9 |
| C1' |
C2' |
C3' |
105.6 |
102.1 |
| C1' |
C2' |
H2' |
109.2 |
110.8 |
| O4' |
C1' |
H1' |
123.7 |
110.6 |
| C1' |
O4' |
C4' |
114.2 |
106.9 |
| O2' |
C2' |
C3' |
120.0 |
110.9 |
| O2' |
C2' |
H2' |
88.7 |
110.8 |
| C2' |
O2' |
HO2' |
121.0 |
106.8 |
| C3' |
C2' |
H2' |
110.6 |
111.0 |
| C2' |
C3' |
O3' |
124.5 |
110.5 |
| C2' |
C3' |
C4' |
107.2 |
104.1 |
| C2' |
C3' |
H3' |
98.2 |
110.4 |
| O3' |
C3' |
C4' |
100.0 |
110.8 |
| O3' |
C3' |
H3' |
105.6 |
110.4 |
| C3' |
O3' |
HO3' |
124.5 |
106.8 |
| C4' |
C3' |
H3' |
123.4 |
110.5 |
| C3' |
C4' |
O4' |
99.8 |
107.5 |
| C3' |
C4' |
C5' |
113.2 |
109.9 |
| C3' |
C4' |
H4' |
112.6 |
110.0 |
| O4' |
C4' |
C5' |
106.9 |
109.9 |
| O4' |
C4' |
H4' |
118.3 |
109.8 |
| C5' |
C4' |
H4' |
106.1 |
109.8 |
| C4' |
C5' |
O5' |
120.2 |
109.5 |
| C4' |
C5' |
H5'1 |
108.3 |
109.4 |
| C4' |
C5' |
H5'2 |
108.3 |
109.5 |
| O5' |
C5' |
H5'1 |
108.4 |
109.4 |
| O5' |
C5' |
H5'2 |
108.4 |
109.5 |
| C5' |
O5' |
HO5' |
120.2 |
106.8 |
| H5'1 |
C5' |
H5'2 |
101.6 |
109.5 |
Torsion Angles for 5UD
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C4 |
C5 |
F5 |
C6 |
180.5 |
180.0 |
| F5 |
C5 |
C4 |
O4 |
359.9 |
0.0 |
| F5 |
C5 |
C4 |
N3 |
179.9 |
180.0 |
| F5 |
C5 |
C6 |
N1 |
180.7 |
180.0 |
| F5 |
C5 |
C6 |
H6 |
0.7 |
0.1 |
| F5 |
C5 |
C4 |
C6 |
179.5 |
180.0 |
| C4 |
C5 |
C6 |
N1 |
0.2 |
360.0 |
| C4 |
C5 |
C6 |
H6 |
180.2 |
180.1 |
| O4 |
C4 |
C5 |
N3 |
180.0 |
180.1 |
| C5 |
C4 |
N3 |
C2 |
359.8 |
359.8 |
| C5 |
C4 |
N3 |
HN3 |
179.8 |
180.0 |
| F5 |
C5 |
C6 |
C4 |
180.5 |
180.0 |
| C6 |
C5 |
C4 |
O4 |
180.3 |
180.0 |
| C6 |
C5 |
C4 |
N3 |
0.4 |
360.0 |
| C2 |
N1 |
C6 |
C5 |
359.2 |
0.3 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
179.9 |
| C5 |
C6 |
N1 |
C1' |
181.5 |
180.0 |
| O4 |
C4 |
C5 |
C6 |
180.3 |
180.0 |
| C5 |
C4 |
O4 |
N3 |
180.1 |
179.9 |
| O4 |
C4 |
N3 |
C2 |
179.8 |
179.7 |
| O4 |
C4 |
N3 |
HN3 |
359.8 |
359.9 |
| N3 |
C4 |
C5 |
C6 |
0.4 |
360.0 |
| C5 |
C4 |
N3 |
O4 |
180.0 |
180.1 |
| C2 |
N3 |
C4 |
HN3 |
180.0 |
179.8 |
| C4 |
N3 |
C2 |
O2 |
180.3 |
180.0 |
| C4 |
N3 |
C2 |
N1 |
359.5 |
0.5 |
| C4 |
N3 |
C2 |
HN3 |
180.0 |
180.2 |
| O2 |
C2 |
N3 |
N1 |
180.8 |
179.5 |
| N3 |
C2 |
N1 |
C6 |
1.0 |
359.5 |
| N3 |
C2 |
N1 |
C1' |
178.6 |
179.7 |
| C4 |
N3 |
HN3 |
C2 |
180.0 |
179.8 |
| HN3 |
N3 |
C2 |
O2 |
0.3 |
359.8 |
| HN3 |
N3 |
C2 |
N1 |
179.5 |
180.3 |
| O2 |
C2 |
N3 |
HN3 |
0.3 |
359.8 |
| N3 |
C2 |
O2 |
N1 |
179.2 |
180.5 |
| O2 |
C2 |
N1 |
C6 |
180.2 |
180.0 |
| O2 |
C2 |
N1 |
C1' |
357.7 |
0.3 |
| C5 |
C6 |
N1 |
C2 |
359.2 |
0.3 |
| N1 |
C2 |
N3 |
HN3 |
179.5 |
180.3 |
| N3 |
C2 |
N1 |
O2 |
180.9 |
179.5 |
| C2 |
N1 |
C6 |
H6 |
179.1 |
180.2 |
| C6 |
N1 |
C2 |
C1' |
182.5 |
179.7 |
| C2 |
N1 |
C1' |
C2' |
6.7 |
304.1 |
| C2 |
N1 |
C1' |
O4' |
140.4 |
58.3 |
| C2 |
N1 |
C1' |
H1' |
261.9 |
181.2 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
180.1 |
| C2 |
N1 |
C6 |
C1' |
177.6 |
180.3 |
| C6 |
N1 |
C1' |
C2' |
184.1 |
124.4 |
| C6 |
N1 |
C1' |
O4' |
317.8 |
238.6 |
| C6 |
N1 |
C1' |
H1' |
79.3 |
1.5 |
| C5 |
C6 |
H6 |
N1 |
180.0 |
179.9 |
| H6 |
C6 |
N1 |
C1' |
1.5 |
359.9 |
| C2 |
N1 |
C1' |
C6 |
182.6 |
179.7 |
| C1' |
N1 |
C6 |
H6 |
1.5 |
359.9 |
| C2' |
C1' |
N1 |
O4' |
226.3 |
245.8 |
| C2' |
C1' |
N1 |
H1' |
104.8 |
122.9 |
| N1 |
C1' |
C2' |
O2' |
253.9 |
273.8 |
| N1 |
C1' |
C2' |
C3' |
113.2 |
155.7 |
| N1 |
C1' |
C2' |
H2' |
354.3 |
37.4 |
| O4' |
C1' |
N1 |
H1' |
238.5 |
237.1 |
| N1 |
C1' |
O4' |
C4' |
255.8 |
201.3 |
| N1 |
C1' |
C2' |
O4' |
141.0 |
118.6 |
| N1 |
C1' |
C2' |
H1' |
270.8 |
237.1 |
| O4' |
C1' |
C2' |
H1' |
129.8 |
118.5 |
| C2' |
C1' |
O4' |
C4' |
42.0 |
320.0 |
| O2' |
C2' |
C1' |
C3' |
140.6 |
118.2 |
| O2' |
C2' |
C1' |
H2' |
259.6 |
236.4 |
| C1' |
C2' |
O2' |
HO2' |
180.0 |
180.0 |
| C3' |
C2' |
C1' |
H2' |
118.9 |
118.3 |
| C1' |
C2' |
C3' |
O3' |
124.4 |
98.0 |
| C1' |
C2' |
C3' |
C4' |
8.7 |
339.0 |
| C1' |
C2' |
C3' |
H3' |
239.8 |
220.5 |
| N1 |
C1' |
O4' |
C2' |
213.8 |
241.3 |
| N1 |
C1' |
O4' |
H1' |
94.1 |
122.9 |
| C2' |
C1' |
O4' |
H1' |
240.4 |
241.5 |
| O4' |
C1' |
C2' |
O2' |
112.9 |
155.3 |
| O4' |
C1' |
C2' |
C3' |
332.3 |
37.1 |
| O4' |
C1' |
C2' |
H2' |
213.3 |
278.8 |
| C3' |
C4' |
O4' |
C1' |
322.8 |
26.4 |
| C1' |
O4' |
C4' |
C5' |
80.8 |
146.0 |
| C1' |
O4' |
C4' |
H4' |
200.4 |
266.8 |
| N1 |
C1' |
H1' |
C2' |
128.5 |
123.0 |
| N1 |
C1' |
H1' |
O4' |
242.2 |
237.1 |
| C2' |
C1' |
H1' |
O4' |
113.7 |
114.1 |
| H1' |
C1' |
C2' |
O2' |
343.1 |
36.7 |
| H1' |
C1' |
C2' |
C3' |
202.5 |
278.6 |
| H1' |
C1' |
C2' |
H2' |
83.5 |
160.3 |
| H1' |
C1' |
O4' |
C4' |
161.6 |
78.4 |
| O2' |
C2' |
C1' |
O4' |
112.9 |
155.3 |
| O2' |
C2' |
C1' |
H1' |
343.1 |
36.7 |
| C1' |
C2' |
O2' |
C3' |
224.9 |
247.3 |
| C1' |
C2' |
O2' |
H2' |
111.7 |
123.6 |
| C3' |
C2' |
O2' |
H2' |
246.9 |
236.2 |
| O2' |
C2' |
C3' |
O3' |
343.3 |
339.8 |
| O2' |
C2' |
C3' |
C4' |
227.6 |
220.8 |
| O2' |
C2' |
C3' |
H3' |
98.7 |
102.3 |
| C3' |
C2' |
C1' |
O4' |
332.3 |
37.1 |
| C3' |
C2' |
C1' |
H1' |
202.5 |
278.6 |
| C1' |
C2' |
C3' |
O2' |
141.1 |
118.2 |
| C1' |
C2' |
C3' |
H2' |
242.0 |
241.8 |
| O2' |
C2' |
C3' |
H2' |
100.9 |
123.6 |
| C3' |
C2' |
O2' |
HO2' |
315.1 |
292.7 |
| O3' |
C3' |
C2' |
C4' |
115.8 |
119.0 |
| O3' |
C3' |
C2' |
H3' |
244.6 |
237.6 |
| C2' |
C3' |
O3' |
HO3' |
180.0 |
180.0 |
| C4' |
C3' |
C2' |
H3' |
128.9 |
118.6 |
| C2' |
C3' |
C4' |
O4' |
14.5 |
358.1 |
| C2' |
C3' |
C4' |
C5' |
261.2 |
238.6 |
| C2' |
C3' |
C4' |
H4' |
140.9 |
117.6 |
| H2' |
C2' |
C1' |
O4' |
213.3 |
278.8 |
| H2' |
C2' |
C1' |
H1' |
83.5 |
160.3 |
| C1' |
C2' |
H2' |
O2' |
237.5 |
236.4 |
| C1' |
C2' |
H2' |
C3' |
115.8 |
112.7 |
| O2' |
C2' |
H2' |
C3' |
238.3 |
236.3 |
| H2' |
C2' |
O2' |
HO2' |
68.3 |
56.4 |
| H2' |
C2' |
C3' |
O3' |
242.4 |
216.2 |
| H2' |
C2' |
C3' |
C4' |
126.7 |
97.2 |
| H2' |
C2' |
C3' |
H3' |
357.8 |
338.6 |
| HO2' |
O2' |
C2' |
C3' |
315.1 |
292.7 |
| HO2' |
O2' |
C2' |
H2' |
68.3 |
56.4 |
| O3' |
C3' |
C2' |
H2' |
242.4 |
216.2 |
| C2' |
C3' |
O3' |
C4' |
240.9 |
245.2 |
| C2' |
C3' |
O3' |
H3' |
111.8 |
122.5 |
| C4' |
C3' |
O3' |
H3' |
230.9 |
237.3 |
| O3' |
C3' |
C4' |
O4' |
243.4 |
239.3 |
| O3' |
C3' |
C4' |
C5' |
130.1 |
119.8 |
| O3' |
C3' |
C4' |
H4' |
9.8 |
358.8 |
| C1' |
O4' |
C4' |
C3' |
322.8 |
26.4 |
| C4' |
C3' |
C2' |
H2' |
126.7 |
97.2 |
| C2' |
C3' |
C4' |
O3' |
131.1 |
118.8 |
| C2' |
C3' |
C4' |
H3' |
247.5 |
241.5 |
| O3' |
C3' |
C4' |
H3' |
116.3 |
122.7 |
| C4' |
C3' |
O3' |
HO3' |
299.1 |
294.8 |
| O4' |
C4' |
C3' |
C5' |
113.3 |
119.5 |
| O4' |
C4' |
C3' |
H4' |
233.6 |
240.5 |
| C5' |
C4' |
C3' |
H4' |
120.3 |
121.0 |
| C3' |
C4' |
C5' |
O5' |
153.9 |
179.7 |
| C3' |
C4' |
C5' |
H5'1 |
279.2 |
59.7 |
| C3' |
C4' |
C5' |
H5'2 |
28.6 |
299.7 |
| H3' |
C3' |
C2' |
H2' |
357.8 |
338.6 |
| C2' |
C3' |
H3' |
O3' |
230.6 |
237.5 |
| C2' |
C3' |
H3' |
C4' |
117.0 |
114.6 |
| O3' |
C3' |
H3' |
C4' |
246.4 |
237.1 |
| H3' |
C3' |
O3' |
HO3' |
68.1 |
57.5 |
| H3' |
C3' |
C4' |
O4' |
127.0 |
116.6 |
| H3' |
C3' |
C4' |
C5' |
13.7 |
357.1 |
| H3' |
C3' |
C4' |
H4' |
253.4 |
236.1 |
| HO3' |
O3' |
C3' |
C4' |
299.1 |
294.8 |
| HO3' |
O3' |
C3' |
H3' |
68.1 |
57.5 |
| C4' |
O4' |
C1' |
H1' |
161.6 |
78.4 |
| O4' |
C4' |
C3' |
H3' |
127.0 |
116.6 |
| C3' |
C4' |
O4' |
C5' |
242.0 |
240.5 |
| C3' |
C4' |
O4' |
H4' |
122.4 |
119.6 |
| C5' |
C4' |
O4' |
H4' |
240.4 |
239.1 |
| O4' |
C4' |
C5' |
O5' |
45.0 |
61.6 |
| O4' |
C4' |
C5' |
H5'1 |
170.3 |
301.7 |
| O4' |
C4' |
C5' |
H5'2 |
279.8 |
181.7 |
| C5' |
C4' |
C3' |
H3' |
13.7 |
357.1 |
| C3' |
C4' |
C5' |
O4' |
108.9 |
118.0 |
| C3' |
C4' |
C5' |
H4' |
236.1 |
238.9 |
| O4' |
C4' |
C5' |
H4' |
127.2 |
120.9 |
| O5' |
C5' |
C4' |
H5'1 |
234.7 |
119.9 |
| O5' |
C5' |
C4' |
H5'2 |
125.3 |
240.0 |
| C4' |
C5' |
O5' |
HO5' |
180.0 |
180.0 |
| H5'1 |
C5' |
C4' |
H5'2 |
250.6 |
120.1 |
| H4' |
C4' |
C3' |
H3' |
253.4 |
236.1 |
| C3' |
C4' |
H4' |
O4' |
244.3 |
242.0 |
| C3' |
C4' |
H4' |
C5' |
124.3 |
121.0 |
| O4' |
C4' |
H4' |
C5' |
240.0 |
239.1 |
| H4' |
C4' |
C5' |
O5' |
277.8 |
300.8 |
| H4' |
C4' |
C5' |
H5'1 |
43.1 |
180.8 |
| H4' |
C4' |
C5' |
H5'2 |
152.6 |
60.8 |
| O5' |
C5' |
C4' |
H4' |
277.8 |
300.8 |
| C4' |
C5' |
O5' |
H5'1 |
125.3 |
240.1 |
| C4' |
C5' |
O5' |
H5'2 |
234.8 |
120.0 |
| H5'1 |
C5' |
O5' |
H5'2 |
109.5 |
239.9 |
| H5'1 |
C5' |
C4' |
H4' |
43.1 |
180.8 |
| C4' |
C5' |
H5'1 |
O5' |
228.0 |
120.0 |
| C4' |
C5' |
H5'1 |
H5'2 |
114.0 |
240.0 |
| O5' |
C5' |
H5'1 |
H5'2 |
246.0 |
120.0 |
| H5'1 |
C5' |
O5' |
HO5' |
54.8 |
299.9 |
| H5'2 |
C5' |
C4' |
H4' |
152.6 |
60.8 |
| C4' |
C5' |
H5'2 |
O5' |
132.0 |
240.0 |
| C4' |
C5' |
H5'2 |
H5'1 |
246.0 |
120.0 |
| O5' |
C5' |
H5'2 |
H5'1 |
114.0 |
240.0 |
| H5'2 |
C5' |
O5' |
HO5' |
305.3 |
60.0 |
| HO5' |
O5' |
C5' |
H5'1 |
54.8 |
299.9 |
| HO5' |
O5' |
C5' |
H5'2 |
305.3 |
60.0 |