PDB Chemical Component C25
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 C25
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| OP3 |
P |
|
1.617 |
| OP3 |
HOP3 |
|
0.980 |
| P |
OP1 |
1.480 |
1.501 |
| P |
OP2 |
1.482 |
1.618 |
| P |
O5' |
1.612 |
1.619 |
| OP2 |
HOP2 |
0.950 |
0.980 |
| O5' |
C5' |
1.436 |
1.416 |
| C5' |
C4' |
1.528 |
1.523 |
| C5' |
H5' |
1.100 |
1.092 |
| C5' |
H5'' |
1.100 |
1.091 |
| C4' |
O4' |
1.442 |
1.444 |
| C4' |
C3' |
1.526 |
1.523 |
| C4' |
H4' |
1.100 |
1.095 |
| O4' |
C1' |
1.442 |
1.437 |
| C3' |
O3' |
1.433 |
1.427 |
| C3' |
C2' |
1.502 |
1.514 |
| C3' |
H3' |
1.100 |
1.093 |
| O3' |
HO'3 |
0.950 |
0.969 |
| C2' |
O2' |
1.443 |
1.413 |
| C2' |
C1' |
1.517 |
1.519 |
| C2' |
H2' |
1.100 |
1.097 |
| O2' |
HO2' |
0.950 |
0.973 |
| C1' |
N1 |
1.473 |
1.435 |
| C1' |
H1' |
1.100 |
1.094 |
| N1 |
C2 |
1.389 |
1.418 |
| N1 |
C6 |
1.363 |
1.387 |
| C2 |
O2 |
1.230 |
1.232 |
| C2 |
N3 |
1.362 |
1.384 |
| N3 |
C4 |
1.338 |
1.307 |
| C4 |
N4 |
1.329 |
1.376 |
| C4 |
C5 |
1.431 |
1.486 |
| N4 |
H41 |
1.000 |
0.991 |
| N4 |
H42 |
1.000 |
0.992 |
| C5 |
C6 |
1.342 |
1.332 |
| C5 |
H5 |
1.080 |
1.082 |
| C6 |
H6 |
1.080 |
1.085 |
Bond Angles for C25
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| P |
OP3 |
HOP3 |
|
119.0 |
| OP3 |
P |
OP1 |
|
115.3 |
| OP3 |
P |
OP2 |
|
103.3 |
| OP3 |
P |
O5' |
|
103.8 |
| OP1 |
P |
OP2 |
119.7 |
114.9 |
| OP1 |
P |
O5' |
108.2 |
115.0 |
| OP2 |
P |
O5' |
108.1 |
102.9 |
| P |
OP2 |
HOP2 |
109.5 |
119.0 |
| P |
O5' |
C5' |
120.0 |
118.5 |
| O5' |
C5' |
C4' |
111.8 |
108.6 |
| O5' |
C5' |
H5' |
108.2 |
109.2 |
| O5' |
C5' |
H5'' |
108.7 |
109.3 |
| C4' |
C5' |
H5' |
108.2 |
110.1 |
| C4' |
C5' |
H5'' |
108.7 |
110.1 |
| C5' |
C4' |
O4' |
110.1 |
108.2 |
| C5' |
C4' |
C3' |
112.1 |
113.3 |
| C5' |
C4' |
H4' |
106.8 |
109.3 |
| H5' |
C5' |
H5'' |
111.3 |
109.6 |
| O4' |
C4' |
C3' |
107.7 |
105.9 |
| O4' |
C4' |
H4' |
111.1 |
107.7 |
| C4' |
O4' |
C1' |
109.7 |
109.2 |
| C3' |
C4' |
H4' |
109.1 |
112.2 |
| C4' |
C3' |
O3' |
110.9 |
107.9 |
| C4' |
C3' |
C2' |
105.8 |
102.1 |
| C4' |
C3' |
H3' |
111.5 |
114.5 |
| O4' |
C1' |
C2' |
107.3 |
106.5 |
| O4' |
C1' |
N1 |
109.2 |
109.0 |
| O4' |
C1' |
H1' |
111.3 |
108.9 |
| O3' |
C3' |
C2' |
111.2 |
110.3 |
| O3' |
C3' |
H3' |
106.2 |
107.8 |
| C3' |
O3' |
HO'3 |
109.5 |
106.4 |
| C2' |
C3' |
H3' |
111.3 |
114.0 |
| C3' |
C2' |
O2' |
110.8 |
112.3 |
| C3' |
C2' |
C1' |
105.2 |
102.0 |
| C3' |
C2' |
H2' |
111.5 |
110.1 |
| O2' |
C2' |
C1' |
109.8 |
112.6 |
| O2' |
C2' |
H2' |
107.1 |
108.6 |
| C2' |
O2' |
HO2' |
109.5 |
107.1 |
| C1' |
C2' |
H2' |
112.5 |
111.1 |
| C2' |
C1' |
N1 |
109.9 |
112.5 |
| C2' |
C1' |
H1' |
110.5 |
112.6 |
| N1 |
C1' |
H1' |
108.7 |
107.3 |
| C1' |
N1 |
C2 |
118.6 |
122.0 |
| C1' |
N1 |
C6 |
119.7 |
118.7 |
| C2 |
N1 |
C6 |
121.6 |
119.3 |
| N1 |
C2 |
O2 |
120.4 |
120.9 |
| N1 |
C2 |
N3 |
118.0 |
118.9 |
| N1 |
C6 |
C5 |
120.8 |
122.7 |
| N1 |
C6 |
H6 |
119.6 |
116.1 |
| O2 |
C2 |
N3 |
121.6 |
120.2 |
| C2 |
N3 |
C4 |
120.9 |
121.1 |
| N3 |
C4 |
N4 |
119.2 |
120.2 |
| N3 |
C4 |
C5 |
121.2 |
121.6 |
| N4 |
C4 |
C5 |
119.6 |
118.2 |
| C4 |
N4 |
H41 |
124.8 |
118.0 |
| C4 |
N4 |
H42 |
110.4 |
118.1 |
| C4 |
C5 |
C6 |
117.5 |
116.4 |
| C4 |
C5 |
H5 |
121.2 |
120.5 |
| H41 |
N4 |
H42 |
124.8 |
123.9 |
| C6 |
C5 |
H5 |
121.2 |
123.1 |
| C5 |
C6 |
H6 |
119.6 |
121.2 |
Torsion Angles for C25
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP1 |
P |
OP3 |
OP2 |
|
126.2 |
| OP1 |
P |
OP3 |
O5' |
|
233.4 |
| OP2 |
P |
OP3 |
O5' |
|
107.1 |
| OP3 |
P |
OP2 |
HOP2 |
|
78.5 |
| OP3 |
P |
O5' |
C5' |
|
53.2 |
| HOP3 |
OP3 |
P |
OP1 |
|
48.7 |
| HOP3 |
OP3 |
P |
OP2 |
|
282.5 |
| HOP3 |
OP3 |
P |
O5' |
|
175.4 |
| OP1 |
P |
OP3 |
HOP3 |
|
48.7 |
| OP3 |
P |
OP1 |
OP2 |
|
240.0 |
| OP3 |
P |
OP1 |
O5' |
|
120.7 |
| OP2 |
P |
OP1 |
O5' |
235.6 |
240.7 |
| OP1 |
P |
OP2 |
HOP2 |
204.1 |
312.0 |
| OP1 |
P |
O5' |
C5' |
303.1 |
180.1 |
| OP2 |
P |
OP3 |
HOP3 |
|
282.5 |
| OP3 |
P |
OP2 |
OP1 |
|
126.5 |
| OP3 |
P |
OP2 |
O5' |
|
252.3 |
| OP1 |
P |
OP2 |
O5' |
124.4 |
125.8 |
| OP2 |
P |
O5' |
C5' |
74.1 |
305.8 |
| O5' |
P |
OP3 |
HOP3 |
|
175.4 |
| OP3 |
P |
O5' |
OP1 |
|
233.1 |
| OP3 |
P |
O5' |
OP2 |
|
107.4 |
| OP1 |
P |
O5' |
OP2 |
229.0 |
234.2 |
| O5' |
P |
OP2 |
HOP2 |
79.7 |
186.2 |
| P |
O5' |
C5' |
C4' |
138.2 |
180.0 |
| P |
O5' |
C5' |
H5' |
19.2 |
300.1 |
| P |
O5' |
C5' |
H5'' |
258.2 |
59.9 |
| HOP2 |
OP2 |
P |
O5' |
79.7 |
186.2 |
| C4' |
C5' |
O5' |
H5' |
119.0 |
239.9 |
| C4' |
C5' |
O5' |
H5'' |
240.0 |
120.1 |
| O5' |
C5' |
C4' |
O4' |
312.3 |
62.4 |
| O5' |
C5' |
C4' |
C3' |
72.1 |
179.5 |
| O5' |
C5' |
C4' |
H4' |
191.6 |
305.4 |
| H5' |
C5' |
O5' |
H5'' |
121.0 |
240.2 |
| O5' |
C5' |
C4' |
H5' |
241.0 |
119.5 |
| O5' |
C5' |
C4' |
H5'' |
120.0 |
240.4 |
| H5' |
C5' |
C4' |
H5'' |
239.0 |
120.9 |
| O4' |
C4' |
C5' |
C3' |
240.1 |
242.9 |
| O4' |
C4' |
C5' |
H4' |
120.7 |
117.0 |
| C5' |
C4' |
O4' |
C1' |
127.5 |
109.0 |
| C3' |
C4' |
C5' |
H4' |
240.6 |
234.1 |
| C5' |
C4' |
C3' |
O3' |
126.4 |
156.8 |
| C5' |
C4' |
C3' |
C2' |
247.0 |
273.1 |
| C5' |
C4' |
C3' |
H3' |
8.2 |
36.8 |
| O5' |
C5' |
H5' |
C4' |
121.3 |
240.8 |
| O5' |
C5' |
H5' |
H5'' |
240.6 |
119.6 |
| C4' |
C5' |
H5' |
H5'' |
119.4 |
238.8 |
| H5' |
C5' |
C4' |
O4' |
71.3 |
302.9 |
| H5' |
C5' |
C4' |
C3' |
191.2 |
60.0 |
| H5' |
C5' |
C4' |
H4' |
310.6 |
185.9 |
| O5' |
C5' |
H5'' |
C4' |
238.1 |
119.2 |
| O5' |
C5' |
H5'' |
H5' |
119.1 |
240.4 |
| C4' |
C5' |
H5'' |
H5' |
241.0 |
121.2 |
| H5'' |
C5' |
C4' |
O4' |
192.3 |
182.0 |
| H5'' |
C5' |
C4' |
C3' |
312.2 |
299.1 |
| H5'' |
C5' |
C4' |
H4' |
71.6 |
65.0 |
| O4' |
C4' |
C5' |
H5' |
71.3 |
302.9 |
| O4' |
C4' |
C5' |
H5'' |
192.3 |
182.0 |
| C5' |
C4' |
O4' |
C3' |
122.4 |
121.7 |
| C5' |
C4' |
O4' |
H4' |
242.0 |
241.9 |
| C3' |
C4' |
O4' |
H4' |
119.5 |
120.2 |
| O4' |
C4' |
C3' |
O3' |
247.6 |
275.3 |
| O4' |
C4' |
C3' |
C2' |
8.2 |
31.5 |
| O4' |
C4' |
C3' |
H3' |
129.4 |
155.2 |
| C4' |
O4' |
C1' |
C2' |
343.7 |
348.7 |
| C4' |
O4' |
C1' |
N1 |
224.5 |
227.1 |
| C4' |
O4' |
C1' |
H1' |
104.6 |
110.3 |
| C3' |
C4' |
C5' |
H5' |
191.2 |
60.0 |
| C3' |
C4' |
C5' |
H5'' |
312.2 |
299.1 |
| C5' |
C4' |
C3' |
O4' |
238.8 |
241.6 |
| C5' |
C4' |
C3' |
H4' |
118.0 |
124.4 |
| O4' |
C4' |
C3' |
H4' |
239.2 |
242.8 |
| C3' |
C4' |
O4' |
C1' |
5.1 |
347.2 |
| O3' |
C3' |
C4' |
C2' |
239.3 |
243.7 |
| O3' |
C3' |
C4' |
H3' |
118.2 |
120.1 |
| C4' |
C3' |
O3' |
HO'3 |
1.2 |
15.2 |
| C2' |
C3' |
C4' |
H3' |
238.8 |
236.3 |
| C4' |
C3' |
C2' |
O2' |
223.9 |
202.0 |
| C4' |
C3' |
C2' |
C1' |
342.5 |
322.9 |
| C4' |
C3' |
C2' |
H2' |
104.7 |
80.9 |
| H4' |
C4' |
C5' |
H5' |
310.6 |
185.9 |
| H4' |
C4' |
C5' |
H5'' |
71.6 |
65.0 |
| C5' |
C4' |
H4' |
O4' |
120.0 |
117.3 |
| C5' |
C4' |
H4' |
C3' |
238.7 |
233.5 |
| O4' |
C4' |
H4' |
C3' |
118.7 |
116.2 |
| H4' |
C4' |
O4' |
C1' |
245.5 |
227.0 |
| H4' |
C4' |
C3' |
O3' |
8.3 |
32.5 |
| H4' |
C4' |
C3' |
C2' |
129.0 |
148.7 |
| H4' |
C4' |
C3' |
H3' |
250.2 |
272.4 |
| C1' |
O4' |
C4' |
C3' |
5.1 |
347.2 |
| C1' |
O4' |
C4' |
H4' |
245.5 |
227.0 |
| C3' |
C2' |
C1' |
O4' |
21.0 |
30.7 |
| O2' |
C2' |
C1' |
O4' |
140.2 |
151.3 |
| O4' |
C1' |
C2' |
H2' |
259.4 |
273.4 |
| C2' |
C1' |
O4' |
N1 |
119.1 |
121.6 |
| C2' |
C1' |
O4' |
H1' |
239.1 |
238.4 |
| N1 |
C1' |
O4' |
H1' |
119.9 |
116.8 |
| O4' |
C1' |
N1 |
C2 |
235.5 |
212.2 |
| O4' |
C1' |
N1 |
C6 |
55.0 |
32.3 |
| O3' |
C3' |
C4' |
H4' |
8.3 |
32.5 |
| C4' |
C3' |
O3' |
C2' |
117.4 |
110.7 |
| C4' |
C3' |
O3' |
H3' |
238.6 |
235.8 |
| C2' |
C3' |
O3' |
H3' |
121.2 |
125.1 |
| O3' |
C3' |
C2' |
O2' |
344.4 |
316.5 |
| O3' |
C3' |
C2' |
C1' |
103.0 |
77.4 |
| O3' |
C3' |
C2' |
H2' |
225.2 |
195.4 |
| C2' |
C3' |
C4' |
H4' |
129.0 |
148.7 |
| C4' |
C3' |
C2' |
O3' |
239.5 |
245.5 |
| C4' |
C3' |
C2' |
H3' |
121.3 |
124.0 |
| O4' |
C1' |
C2' |
C3' |
21.0 |
30.7 |
| O3' |
C3' |
C2' |
H3' |
241.8 |
238.5 |
| C2' |
C3' |
O3' |
HO'3 |
243.8 |
264.4 |
| O2' |
C2' |
C3' |
C1' |
241.5 |
239.2 |
| O2' |
C2' |
C3' |
H2' |
119.2 |
121.1 |
| C3' |
C2' |
O2' |
HO2' |
69.5 |
168.8 |
| C1' |
C2' |
C3' |
H2' |
237.7 |
242.0 |
| C3' |
C2' |
C1' |
N1 |
139.6 |
150.0 |
| C3' |
C2' |
C1' |
H1' |
259.6 |
271.5 |
| H3' |
C3' |
C4' |
H4' |
250.2 |
272.4 |
| C4' |
C3' |
H3' |
O3' |
121.0 |
120.1 |
| C4' |
C3' |
H3' |
C2' |
242.1 |
243.0 |
| O3' |
C3' |
H3' |
C2' |
121.1 |
122.8 |
| H3' |
C3' |
O3' |
HO'3 |
122.6 |
139.4 |
| H3' |
C3' |
C2' |
O2' |
102.6 |
78.0 |
| H3' |
C3' |
C2' |
C1' |
221.2 |
198.9 |
| H3' |
C3' |
C2' |
H2' |
343.4 |
316.9 |
| HO'3 |
O3' |
C3' |
C2' |
243.8 |
264.4 |
| HO'3 |
O3' |
C3' |
H3' |
122.6 |
139.4 |
| O4' |
C1' |
C2' |
O2' |
140.2 |
151.3 |
| O2' |
C2' |
C3' |
H3' |
102.6 |
78.0 |
| C3' |
C2' |
O2' |
C1' |
115.8 |
114.5 |
| C3' |
C2' |
O2' |
H2' |
238.2 |
238.0 |
| C1' |
C2' |
O2' |
H2' |
122.4 |
123.5 |
| O2' |
C2' |
C1' |
N1 |
258.8 |
270.6 |
| O2' |
C2' |
C1' |
H1' |
18.8 |
32.1 |
| O4' |
C1' |
C2' |
N1 |
241.4 |
240.7 |
| O4' |
C1' |
C2' |
H1' |
121.4 |
119.3 |
| C1' |
C2' |
C3' |
H3' |
221.2 |
198.9 |
| C3' |
C2' |
C1' |
O2' |
240.8 |
239.4 |
| C3' |
C2' |
C1' |
H2' |
121.6 |
117.3 |
| O2' |
C2' |
C1' |
H2' |
240.8 |
237.9 |
| C1' |
C2' |
O2' |
HO2' |
313.8 |
54.3 |
| N1 |
C1' |
C2' |
H1' |
240.1 |
238.6 |
| C2' |
C1' |
N1 |
C2 |
118.0 |
94.4 |
| C2' |
C1' |
N1 |
C6 |
297.5 |
274.4 |
| H2' |
C2' |
C3' |
H3' |
343.4 |
316.9 |
| C3' |
C2' |
H2' |
O2' |
121.3 |
123.3 |
| C3' |
C2' |
H2' |
C1' |
242.0 |
247.7 |
| O2' |
C2' |
H2' |
C1' |
120.7 |
124.4 |
| H2' |
C2' |
O2' |
HO2' |
191.3 |
290.8 |
| H2' |
C2' |
C1' |
N1 |
18.0 |
32.7 |
| H2' |
C2' |
C1' |
H1' |
137.9 |
154.2 |
| HO2' |
O2' |
C2' |
C1' |
313.8 |
54.3 |
| HO2' |
O2' |
C2' |
H2' |
191.3 |
290.8 |
| O4' |
C1' |
N1 |
C2' |
117.5 |
117.9 |
| O4' |
C1' |
N1 |
H1' |
238.5 |
242.3 |
| N1 |
C1' |
C2' |
H2' |
18.0 |
32.7 |
| C2' |
C1' |
N1 |
H1' |
121.0 |
124.4 |
| C2 |
N1 |
C1' |
C6 |
180.5 |
180.0 |
| C1' |
N1 |
C2 |
O2 |
359.5 |
360.0 |
| C1' |
N1 |
C2 |
N3 |
179.4 |
180.0 |
| C1' |
N1 |
C6 |
C5 |
180.7 |
180.0 |
| C1' |
N1 |
C6 |
H6 |
0.7 |
359.9 |
| O4' |
C1' |
H1' |
C2' |
240.9 |
242.1 |
| O4' |
C1' |
H1' |
N1 |
120.2 |
117.8 |
| H1' |
C1' |
C2' |
H2' |
137.9 |
154.2 |
| C2' |
C1' |
H1' |
N1 |
239.3 |
235.7 |
| H1' |
C1' |
N1 |
C2 |
357.0 |
330.0 |
| H1' |
C1' |
N1 |
C6 |
176.5 |
150.0 |
| C2 |
N1 |
C1' |
H1' |
357.0 |
330.0 |
| C1' |
N1 |
C2 |
C6 |
179.5 |
180.0 |
| C2 |
N1 |
C6 |
C5 |
0.2 |
0.0 |
| C2 |
N1 |
C6 |
H6 |
180.2 |
180.0 |
| O2 |
C2 |
N1 |
N3 |
180.1 |
180.0 |
| N1 |
C2 |
N3 |
C4 |
360.0 |
360.0 |
| C6 |
N1 |
C1' |
H1' |
176.5 |
150.0 |
| C1' |
N1 |
C6 |
C2 |
180.5 |
180.0 |
| C6 |
N1 |
C2 |
O2 |
180.0 |
180.0 |
| C6 |
N1 |
C2 |
N3 |
359.9 |
360.0 |
| C4 |
C5 |
C6 |
N1 |
359.9 |
360.0 |
| N1 |
C6 |
C5 |
H5 |
179.9 |
179.9 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
180.1 |
| O2 |
C2 |
N1 |
C6 |
180.0 |
180.0 |
| N1 |
C2 |
O2 |
N3 |
179.9 |
180.0 |
| O2 |
C2 |
N3 |
C4 |
179.9 |
180.0 |
| N3 |
C2 |
N1 |
C6 |
359.9 |
360.0 |
| N1 |
C2 |
N3 |
O2 |
180.1 |
180.0 |
| C2 |
N3 |
C4 |
N4 |
180.2 |
180.0 |
| C2 |
N3 |
C4 |
C5 |
0.0 |
0.0 |
| N4 |
C4 |
N3 |
C5 |
180.2 |
180.0 |
| N3 |
C4 |
N4 |
H41 |
0.0 |
265.0 |
| N3 |
C4 |
N4 |
H42 |
180.0 |
84.9 |
| N3 |
C4 |
C5 |
C6 |
0.1 |
0.0 |
| N3 |
C4 |
C5 |
H5 |
180.0 |
180.1 |
| N3 |
C4 |
N4 |
C5 |
179.8 |
180.0 |
| N4 |
C4 |
C5 |
C6 |
179.9 |
180.0 |
| N4 |
C4 |
C5 |
H5 |
359.8 |
0.0 |
| H41 |
N4 |
C4 |
H42 |
180.0 |
180.1 |
| N1 |
C6 |
C5 |
C4 |
359.9 |
360.0 |
| N3 |
C4 |
C5 |
N4 |
180.2 |
180.0 |
| C5 |
C4 |
N4 |
H41 |
180.2 |
85.0 |
| C5 |
C4 |
N4 |
H42 |
0.2 |
264.9 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
179.9 |
| C4 |
C5 |
C6 |
H6 |
179.8 |
180.0 |
| H41 |
N4 |
C4 |
C5 |
180.2 |
85.0 |
| C4 |
N4 |
H41 |
H42 |
180.0 |
179.9 |
| H42 |
N4 |
C4 |
C5 |
0.2 |
264.9 |
| C4 |
N4 |
H42 |
H41 |
180.0 |
180.1 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
179.9 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
180.1 |
| C4 |
C5 |
H5 |
C6 |
180.0 |
179.9 |
| H5 |
C5 |
C6 |
H6 |
359.9 |
360.0 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
180.1 |
| H6 |
C6 |
C5 |
H5 |
359.9 |
360.0 |