PDB Chemical Component T5O
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 T5O
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| P |
OP3 |
1.480 |
1.610 |
| N1 |
C6 |
1.391 |
1.372 |
| N1 |
C1' |
1.511 |
1.465 |
| C2 |
N1 |
1.379 |
1.345 |
| O2 |
C2 |
1.207 |
1.217 |
| N3 |
C2 |
1.364 |
1.346 |
| N3 |
C4 |
1.377 |
1.347 |
| N3 |
HN3 |
1.000 |
0.971 |
| C4 |
C5 |
1.444 |
1.420 |
| O4 |
C4 |
1.223 |
1.218 |
| C5 |
O5 |
1.427 |
1.363 |
| C5 |
C6 |
1.341 |
1.352 |
| O5 |
C7 |
1.428 |
1.429 |
| C6 |
H6 |
1.080 |
1.079 |
| C1' |
O4' |
1.413 |
1.444 |
| C1' |
C2' |
1.530 |
1.545 |
| C1' |
H1' |
1.100 |
1.090 |
| OP3 |
HOP3 |
0.950 |
0.967 |
| C2' |
C3' |
1.526 |
1.545 |
| C2' |
H2' |
1.100 |
1.089 |
| C2' |
H2'A |
1.100 |
1.089 |
| OP2 |
P |
1.466 |
1.610 |
| OP2 |
HOP2 |
0.951 |
0.967 |
| C3' |
O3' |
1.421 |
1.430 |
| C3' |
H3' |
1.100 |
1.090 |
| O3' |
HO3' |
0.950 |
0.966 |
| C4' |
C3' |
1.521 |
1.545 |
| C4' |
C5' |
1.513 |
1.530 |
| C4' |
H4' |
1.100 |
1.090 |
| O4' |
C4' |
1.448 |
1.445 |
| C5' |
H5' |
1.100 |
1.091 |
| C5' |
H5'A |
1.100 |
1.090 |
| O5' |
P |
1.596 |
1.611 |
| O5' |
C5' |
1.420 |
1.429 |
| C7 |
HC7 |
1.100 |
1.090 |
| C7 |
HC7A |
1.100 |
1.090 |
| C7 |
HC7B |
1.100 |
1.090 |
| P |
OP1 |
1.830 |
1.480 |
Bond Angles for T5O
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| P |
OP3 |
HOP3 |
109.5 |
113.9 |
| OP3 |
P |
OP1 |
80.9 |
109.5 |
| C6 |
N1 |
C1' |
121.3 |
119.7 |
| C2 |
N1 |
C6 |
121.1 |
120.6 |
| N1 |
C6 |
C5 |
122.6 |
119.6 |
| N1 |
C6 |
H6 |
118.7 |
120.2 |
| C2 |
N1 |
C1' |
117.5 |
119.7 |
| N1 |
C1' |
O4' |
110.4 |
110.4 |
| N1 |
C1' |
C2' |
112.3 |
110.4 |
| N1 |
C1' |
H1' |
106.0 |
110.3 |
| C4 |
N3 |
HN3 |
117.0 |
119.8 |
| N3 |
C4 |
C5 |
116.4 |
119.4 |
| O4 |
C4 |
C5 |
121.4 |
120.3 |
| C4 |
C5 |
O5 |
116.0 |
120.5 |
| C4 |
C5 |
C6 |
118.2 |
119.1 |
| O5 |
C5 |
C6 |
125.8 |
120.5 |
| C5 |
O5 |
C7 |
113.0 |
117.0 |
| C5 |
C6 |
H6 |
118.7 |
120.2 |
| O5 |
C7 |
HC7 |
109.5 |
109.5 |
| O5 |
C7 |
HC7A |
109.4 |
109.4 |
| O5 |
C7 |
HC7B |
109.5 |
109.4 |
| C2' |
C1' |
O4' |
106.7 |
104.8 |
| O4' |
C1' |
H1' |
111.7 |
110.4 |
| C1' |
O4' |
C4' |
108.2 |
105.3 |
| C2' |
C1' |
H1' |
109.8 |
110.5 |
| C1' |
C2' |
C3' |
101.7 |
104.0 |
| C1' |
C2' |
H2' |
112.1 |
110.5 |
| C1' |
C2' |
H2'A |
112.1 |
110.5 |
| C3' |
C2' |
H2' |
112.1 |
110.5 |
| C3' |
C2' |
H2'A |
112.1 |
110.5 |
| C2' |
C3' |
O3' |
114.3 |
110.5 |
| C2' |
C3' |
H3' |
113.6 |
110.5 |
| H2' |
C2' |
H2'A |
106.7 |
110.6 |
| OP2 |
P |
OP1 |
63.8 |
109.5 |
| O3' |
C3' |
H3' |
103.4 |
110.4 |
| C3' |
O3' |
HO3' |
109.5 |
114.0 |
| C4' |
C3' |
H3' |
118.2 |
110.6 |
| C5' |
C4' |
H4' |
103.6 |
110.4 |
| O4' |
C4' |
C5' |
110.0 |
110.4 |
| C4' |
C5' |
H5' |
109.3 |
109.4 |
| C4' |
C5' |
H5'A |
109.3 |
109.5 |
| O4' |
C4' |
H4' |
114.9 |
110.4 |
| H5' |
C5' |
H5'A |
109.6 |
109.4 |
| O5' |
C5' |
H5' |
109.3 |
109.5 |
| O5' |
C5' |
H5'A |
109.3 |
109.5 |
| O5' |
P |
OP1 |
170.0 |
109.5 |
| HC7 |
C7 |
HC7A |
109.5 |
109.5 |
| HC7 |
C7 |
HC7B |
109.5 |
109.5 |
| HC7A |
C7 |
HC7B |
109.5 |
109.5 |
Torsion Angles for T5O
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP2 |
P |
OP3 |
OP1 |
53.0 |
120.1 |
| O5' |
P |
OP3 |
OP1 |
175.5 |
240.0 |
| C2 |
N1 |
C6 |
C1' |
181.0 |
179.8 |
| C6 |
N1 |
C1' |
O4' |
21.8 |
233.6 |
| C6 |
N1 |
C1' |
C2' |
262.9 |
118.2 |
| C6 |
N1 |
C1' |
H1' |
143.0 |
355.8 |
| C4 |
C5 |
C6 |
N1 |
0.4 |
0.0 |
| O5 |
C5 |
C6 |
N1 |
179.8 |
180.0 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
180.2 |
| C2 |
N1 |
C1' |
C6 |
179.0 |
180.2 |
| C1' |
N1 |
C6 |
C5 |
179.1 |
180.2 |
| C1' |
N1 |
C6 |
H6 |
359.1 |
0.0 |
| C2' |
C1' |
N1 |
O4' |
241.1 |
244.6 |
| O4' |
C1' |
N1 |
H1' |
238.8 |
237.7 |
| N1 |
C1' |
O4' |
C4' |
235.5 |
200.7 |
| C2' |
C1' |
N1 |
H1' |
119.9 |
122.4 |
| N1 |
C1' |
C2' |
C3' |
95.3 |
142.8 |
| N1 |
C1' |
C2' |
H2' |
215.3 |
261.5 |
| N1 |
C1' |
C2' |
H2'A |
335.3 |
24.2 |
| C6 |
N1 |
C2 |
C1' |
179.0 |
180.2 |
| C2 |
N1 |
C6 |
C5 |
0.1 |
0.0 |
| C2 |
N1 |
C6 |
H6 |
180.1 |
179.8 |
| C2 |
N1 |
C1' |
O4' |
200.9 |
53.8 |
| C2 |
N1 |
C1' |
C2' |
81.9 |
298.4 |
| C2 |
N1 |
C1' |
H1' |
322.0 |
176.0 |
| O2 |
C2 |
N1 |
C6 |
179.3 |
180.0 |
| O2 |
C2 |
N1 |
C1' |
0.2 |
359.8 |
| N3 |
C2 |
N1 |
C6 |
359.0 |
360.0 |
| N3 |
C2 |
N1 |
C1' |
180.0 |
179.7 |
| O4 |
C4 |
N3 |
C5 |
180.2 |
180.0 |
| N3 |
C4 |
C5 |
O5 |
180.6 |
180.0 |
| N3 |
C4 |
C5 |
C6 |
0.1 |
360.0 |
| HN3 |
N3 |
C4 |
C5 |
179.0 |
180.0 |
| N1 |
C6 |
C5 |
C4 |
0.4 |
0.0 |
| C5 |
C4 |
N3 |
HN3 |
179.0 |
180.0 |
| O5 |
C5 |
C4 |
C6 |
180.5 |
180.1 |
| C4 |
C5 |
O5 |
C7 |
179.1 |
180.0 |
| C4 |
C5 |
C6 |
H6 |
180.4 |
180.3 |
| O4 |
C4 |
N3 |
HN3 |
359.2 |
0.1 |
| N3 |
C4 |
O4 |
C5 |
179.8 |
180.0 |
| O4 |
C4 |
C5 |
O5 |
0.3 |
360.0 |
| O4 |
C4 |
C5 |
C6 |
179.8 |
179.9 |
| N1 |
C6 |
C5 |
O5 |
179.8 |
180.0 |
| C4 |
C5 |
O5 |
C6 |
179.5 |
179.9 |
| O5 |
C5 |
C6 |
H6 |
359.8 |
0.2 |
| C5 |
O5 |
C7 |
HC7 |
180.0 |
300.0 |
| C5 |
O5 |
C7 |
HC7A |
300.0 |
60.0 |
| C5 |
O5 |
C7 |
HC7B |
60.0 |
180.0 |
| C5 |
C6 |
N1 |
C1' |
179.1 |
180.2 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
179.8 |
| C4 |
C5 |
C6 |
O5 |
180.5 |
180.1 |
| C6 |
C5 |
O5 |
C7 |
359.6 |
0.1 |
| C7 |
O5 |
C5 |
C6 |
359.6 |
0.1 |
| HC7 |
C7 |
O5 |
HC7A |
240.0 |
240.0 |
| HC7 |
C7 |
O5 |
HC7B |
120.0 |
120.0 |
| HC7A |
C7 |
O5 |
HC7B |
240.0 |
240.0 |
| H6 |
C6 |
N1 |
C1' |
359.1 |
0.0 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
180.2 |
| N1 |
C1' |
O4' |
C2' |
237.7 |
241.2 |
| N1 |
C1' |
O4' |
H1' |
117.7 |
122.2 |
| C2' |
C1' |
O4' |
H1' |
240.0 |
241.1 |
| O4' |
C1' |
C2' |
C3' |
334.2 |
24.0 |
| O4' |
C1' |
C2' |
H2' |
94.2 |
142.6 |
| O4' |
C1' |
C2' |
H2'A |
214.2 |
265.4 |
| C1' |
O4' |
C4' |
C5' |
153.5 |
159.3 |
| C1' |
O4' |
C4' |
H4' |
269.9 |
281.7 |
| N1 |
C1' |
C2' |
O4' |
121.1 |
118.8 |
| N1 |
C1' |
C2' |
H1' |
242.3 |
237.7 |
| O4' |
C1' |
C2' |
H1' |
121.2 |
118.9 |
| C2' |
C1' |
O4' |
C4' |
357.8 |
319.5 |
| C3' |
C2' |
C1' |
H2' |
240.0 |
241.4 |
| C3' |
C2' |
C1' |
H2'A |
120.0 |
118.6 |
| C1' |
C2' |
C3' |
O3' |
157.3 |
118.7 |
| C1' |
C2' |
C3' |
H3' |
275.7 |
241.2 |
| H2' |
C2' |
C1' |
H2'A |
240.0 |
237.3 |
| N1 |
C1' |
H1' |
O4' |
239.7 |
237.7 |
| N1 |
C1' |
H1' |
C2' |
121.5 |
122.3 |
| C2' |
C1' |
H1' |
O4' |
118.1 |
115.4 |
| H1' |
C1' |
O4' |
C4' |
117.8 |
78.4 |
| H1' |
C1' |
C2' |
C3' |
213.0 |
265.1 |
| H1' |
C1' |
C2' |
H2' |
333.0 |
23.7 |
| H1' |
C1' |
C2' |
H2'A |
93.0 |
146.5 |
| HOP3 |
OP3 |
P |
OP1 |
0.0 |
300.0 |
| C3' |
C2' |
C1' |
O4' |
334.2 |
24.0 |
| C3' |
C2' |
C1' |
H1' |
213.0 |
265.1 |
| C1' |
C2' |
C3' |
H2' |
120.0 |
118.6 |
| C1' |
C2' |
C3' |
H2'A |
240.0 |
241.4 |
| H2' |
C2' |
C3' |
H2'A |
120.0 |
122.8 |
| O3' |
C3' |
C2' |
H3' |
241.7 |
237.5 |
| C2' |
C3' |
O3' |
HO3' |
180.0 |
61.4 |
| C4' |
C3' |
C2' |
H3' |
125.8 |
118.8 |
| H2' |
C2' |
C1' |
O4' |
94.2 |
142.6 |
| H2' |
C2' |
C1' |
H1' |
333.0 |
23.7 |
| C1' |
C2' |
H2' |
C3' |
246.3 |
245.4 |
| C1' |
C2' |
H2' |
H2'A |
123.1 |
122.7 |
| C3' |
C2' |
H2' |
H2'A |
236.9 |
237.3 |
| H2' |
C2' |
C3' |
O3' |
37.3 |
0.1 |
| H2' |
C2' |
C3' |
H3' |
155.7 |
122.6 |
| H2'A |
C2' |
C1' |
O4' |
214.2 |
265.4 |
| H2'A |
C2' |
C1' |
H1' |
93.0 |
146.5 |
| C1' |
C2' |
H2'A |
C3' |
113.7 |
114.6 |
| C1' |
C2' |
H2'A |
H2' |
236.8 |
237.3 |
| C3' |
C2' |
H2'A |
H2' |
123.1 |
122.8 |
| H2'A |
C2' |
C3' |
O3' |
277.3 |
237.3 |
| H2'A |
C2' |
C3' |
H3' |
35.6 |
359.8 |
| OP2 |
P |
OP3 |
HOP3 |
53.0 |
60.0 |
| OP3 |
P |
OP2 |
OP1 |
298.6 |
239.9 |
| O5' |
P |
OP2 |
OP1 |
175.6 |
120.0 |
| HOP2 |
OP2 |
P |
OP1 |
0.0 |
180.0 |
| O3' |
C3' |
C2' |
H2' |
37.3 |
0.1 |
| O3' |
C3' |
C2' |
H2'A |
277.3 |
237.3 |
| C2' |
C3' |
O3' |
H3' |
124.0 |
122.6 |
| C4' |
C3' |
O3' |
H3' |
233.2 |
237.3 |
| H3' |
C3' |
C2' |
H2' |
155.7 |
122.6 |
| H3' |
C3' |
C2' |
H2'A |
35.6 |
359.8 |
| C2' |
C3' |
H3' |
O3' |
235.5 |
237.4 |
| H3' |
C3' |
O3' |
HO3' |
56.0 |
298.8 |
| HO3' |
O3' |
C3' |
H3' |
56.0 |
298.8 |
| C1' |
O4' |
C4' |
C3' |
29.8 |
40.5 |
| C4' |
C3' |
C2' |
H2' |
281.5 |
241.4 |
| C4' |
C3' |
C2' |
H2'A |
161.5 |
118.6 |
| C2' |
C3' |
C4' |
H3' |
237.4 |
241.3 |
| O3' |
C3' |
C4' |
H3' |
117.9 |
122.6 |
| C4' |
C3' |
O3' |
HO3' |
289.2 |
176.1 |
| C5' |
C4' |
C3' |
H3' |
318.1 |
336.0 |
| O4' |
C4' |
C5' |
H4' |
123.3 |
122.4 |
| H5' |
C5' |
C4' |
H5'A |
240.0 |
240.1 |
| O5' |
C5' |
C4' |
H5' |
240.0 |
240.0 |
| O5' |
C5' |
C4' |
H5'A |
120.0 |
120.1 |
| H4' |
C4' |
C3' |
H3' |
201.7 |
213.7 |
| O4' |
C4' |
H4' |
C5' |
240.0 |
237.7 |
| H4' |
C4' |
C5' |
H5' |
293.1 |
67.3 |
| H4' |
C4' |
C5' |
H5'A |
53.0 |
187.2 |
| C4' |
O4' |
C1' |
H1' |
117.8 |
78.4 |
| O4' |
C4' |
C3' |
H3' |
78.4 |
94.8 |
| C5' |
C4' |
O4' |
H4' |
243.6 |
237.7 |
| O4' |
C4' |
C5' |
H5' |
56.3 |
189.7 |
| O4' |
C4' |
C5' |
H5'A |
176.3 |
309.6 |
| H5' |
C5' |
C4' |
H4' |
293.1 |
67.3 |
| C4' |
C5' |
H5' |
H5'A |
119.8 |
120.0 |
| O5' |
C5' |
H5' |
H5'A |
240.2 |
240.0 |
| H5'A |
C5' |
C4' |
H4' |
53.0 |
187.2 |
| C4' |
C5' |
H5'A |
H5' |
240.2 |
240.1 |
| O5' |
C5' |
H5'A |
H5' |
119.8 |
120.0 |
| O5' |
P |
OP3 |
HOP3 |
175.5 |
180.0 |
| OP3 |
P |
O5' |
OP1 |
206.8 |
120.0 |
| OP2 |
P |
O5' |
OP1 |
336.5 |
240.0 |
| O5' |
C5' |
C4' |
H4' |
173.0 |
307.3 |
| C4' |
C5' |
O5' |
H5' |
120.0 |
119.9 |
| C4' |
C5' |
O5' |
H5'A |
240.0 |
239.9 |
| H5' |
C5' |
O5' |
H5'A |
120.0 |
120.0 |
| C5' |
O5' |
P |
OP1 |
196.5 |
55.0 |
| O5 |
C7 |
HC7 |
HC7A |
120.0 |
120.0 |
| O5 |
C7 |
HC7 |
HC7B |
240.0 |
240.1 |
| HC7A |
C7 |
HC7 |
HC7B |
120.0 |
120.1 |
| O5 |
C7 |
HC7A |
HC7 |
240.0 |
240.0 |
| O5 |
C7 |
HC7A |
HC7B |
120.0 |
120.0 |
| HC7 |
C7 |
HC7A |
HC7B |
240.0 |
240.0 |
| O5 |
C7 |
HC7B |
HC7 |
120.0 |
120.0 |
| O5 |
C7 |
HC7B |
HC7A |
240.0 |
240.0 |
| HC7 |
C7 |
HC7B |
HC7A |
120.0 |
120.1 |
| OP1 |
P |
OP3 |
HOP3 |
0.0 |
300.0 |