PDB Chemical Component T5S
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 T5S
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| P |
OP3 |
1.604 |
1.610 |
| OP3 |
HOP3 |
0.950 |
0.966 |
| OP1 |
P |
1.494 |
1.480 |
| P |
OP2 |
1.469 |
1.610 |
| P |
O5' |
1.588 |
1.610 |
| OP2 |
HOP2 |
0.950 |
0.967 |
| C5' |
O5' |
1.418 |
1.429 |
| C1' |
N1 |
1.502 |
1.465 |
| C6 |
N1 |
1.387 |
1.369 |
| N1 |
C2 |
1.391 |
1.345 |
| C6 |
C5 |
1.390 |
1.350 |
| C6 |
H6 |
1.080 |
1.080 |
| C2 |
O2 |
1.213 |
1.216 |
| C2 |
N3 |
1.389 |
1.346 |
| C4 |
N3 |
1.395 |
1.349 |
| N3 |
HN3 |
1.000 |
0.969 |
| C5 |
C4 |
1.472 |
1.417 |
| C4 |
O4 |
1.234 |
1.218 |
| SE |
C5 |
1.923 |
1.960 |
| CH3 |
SE |
1.467 |
1.961 |
| CH3 |
HH3 |
1.100 |
1.090 |
| CH3 |
HH3A |
1.100 |
1.090 |
| CH3 |
HH3B |
1.100 |
1.090 |
| C3' |
C2' |
1.517 |
1.545 |
| C2' |
C1' |
1.517 |
1.544 |
| C2' |
H2' |
1.100 |
1.090 |
| C2' |
H2'A |
1.100 |
1.090 |
| C5' |
C4' |
1.509 |
1.529 |
| C5' |
H5' |
1.100 |
1.091 |
| C5' |
H5'A |
1.100 |
1.090 |
| C3' |
C4' |
1.528 |
1.544 |
| C4' |
O4' |
1.451 |
1.444 |
| C4' |
H4' |
1.100 |
1.090 |
| O4' |
C1' |
1.429 |
1.445 |
| C1' |
H1' |
1.100 |
1.089 |
| O3' |
C3' |
1.411 |
1.429 |
| C3' |
H3' |
1.100 |
1.090 |
| O3' |
HO3' |
0.950 |
0.968 |
Bond Angles for T5S
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| P |
OP3 |
HOP3 |
109.5 |
114.0 |
| OP1 |
P |
OP2 |
119.6 |
109.5 |
| OP1 |
P |
O5' |
110.0 |
109.5 |
| OP2 |
P |
O5' |
106.8 |
109.4 |
| P |
OP2 |
HOP2 |
109.5 |
114.1 |
| C6 |
N1 |
C2 |
121.1 |
120.6 |
| N1 |
C2 |
O2 |
122.7 |
119.5 |
| N1 |
C2 |
N3 |
115.5 |
121.0 |
| C5 |
C6 |
H6 |
118.4 |
120.2 |
| C6 |
C5 |
C4 |
117.7 |
119.1 |
| O2 |
C2 |
N3 |
121.7 |
119.5 |
| C2 |
N3 |
HN3 |
116.3 |
119.9 |
| C4 |
N3 |
HN3 |
116.3 |
119.8 |
| HH3 |
CH3 |
HH3A |
109.5 |
109.5 |
| HH3 |
CH3 |
HH3B |
109.4 |
109.5 |
| HH3A |
CH3 |
HH3B |
109.5 |
109.4 |
| C3' |
C2' |
H2' |
110.5 |
110.5 |
| C3' |
C2' |
H2'A |
111.1 |
110.6 |
| C1' |
C2' |
H2' |
110.5 |
110.5 |
| C1' |
C2' |
H2'A |
111.2 |
110.5 |
| C2' |
C1' |
O4' |
106.5 |
104.8 |
| C2' |
C1' |
H1' |
112.6 |
110.4 |
| H2' |
C2' |
H2'A |
107.1 |
110.4 |
| C4' |
C5' |
H5' |
109.4 |
109.4 |
| C4' |
C5' |
H5'A |
109.3 |
109.5 |
| C5' |
C4' |
O4' |
107.9 |
110.4 |
| C5' |
C4' |
H4' |
107.8 |
110.3 |
| H5' |
C5' |
H5'A |
109.7 |
109.4 |
| C3' |
C4' |
H4' |
110.4 |
110.5 |
| O4' |
C4' |
H4' |
114.0 |
110.3 |
| C4' |
O4' |
C1' |
109.6 |
105.3 |
| O4' |
C1' |
H1' |
115.0 |
110.4 |
| O3' |
C3' |
H3' |
107.0 |
110.6 |
Torsion Angles for T5S
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP1 |
P |
OP3 |
HOP3 |
206.1 |
300.0 |
| OP2 |
P |
OP1 |
O5' |
235.9 |
120.0 |
| OP1 |
P |
OP2 |
HOP2 |
180.1 |
180.0 |
| OP2 |
P |
OP3 |
HOP3 |
75.0 |
60.0 |
| OP1 |
P |
OP2 |
O5' |
125.7 |
240.0 |
| O5' |
P |
OP3 |
HOP3 |
321.3 |
180.0 |
| OP1 |
P |
O5' |
OP2 |
228.7 |
120.0 |
| O5' |
P |
OP2 |
HOP2 |
54.4 |
300.0 |
| HOP2 |
OP2 |
P |
O5' |
54.4 |
300.0 |
| C6 |
N1 |
C2 |
O2 |
183.0 |
180.0 |
| C6 |
N1 |
C2 |
N3 |
3.0 |
360.0 |
| O2 |
C2 |
N1 |
N3 |
180.0 |
180.1 |
| N1 |
C2 |
N3 |
HN3 |
179.4 |
180.0 |
| C5 |
C6 |
N1 |
C2 |
356.2 |
0.1 |
| H6 |
C6 |
N1 |
C2 |
176.2 |
180.0 |
| H6 |
C6 |
C5 |
C4 |
181.8 |
180.0 |
| N1 |
C2 |
O2 |
N3 |
180.0 |
179.9 |
| O2 |
C2 |
N3 |
HN3 |
359.5 |
359.9 |
| N1 |
C2 |
N3 |
O2 |
180.0 |
180.1 |
| C4 |
N3 |
C2 |
HN3 |
180.0 |
180.0 |
| C6 |
C5 |
C4 |
N3 |
0.6 |
0.1 |
| C2 |
N3 |
C4 |
HN3 |
180.0 |
180.0 |
| C4 |
C5 |
C6 |
H6 |
181.8 |
180.0 |
| C5 |
C4 |
N3 |
HN3 |
178.8 |
180.0 |
| C6 |
C5 |
C4 |
O4 |
180.9 |
180.1 |
| O4 |
C4 |
N3 |
HN3 |
358.5 |
360.0 |
| SE |
C5 |
C6 |
H6 |
2.9 |
0.1 |
| HH3A |
CH3 |
HH3 |
HH3B |
120.0 |
120.0 |
| HH3 |
CH3 |
HH3A |
HH3B |
240.1 |
239.9 |
| HH3 |
CH3 |
HH3B |
HH3A |
120.0 |
120.1 |
| C1' |
C2' |
C3' |
H2' |
240.0 |
118.6 |
| C1' |
C2' |
C3' |
H2'A |
121.2 |
241.3 |
| C3' |
C2' |
C1' |
H1' |
243.3 |
265.2 |
| H2' |
C2' |
C3' |
H2'A |
241.2 |
122.6 |
| C3' |
C2' |
C1' |
H2' |
120.0 |
241.3 |
| C3' |
C2' |
C1' |
H2'A |
238.8 |
118.8 |
| H2' |
C2' |
C1' |
H2'A |
118.8 |
237.5 |
| C4' |
O4' |
C1' |
C2' |
336.0 |
319.5 |
| O4' |
C1' |
C2' |
H1' |
126.9 |
118.8 |
| C3' |
C2' |
H2' |
H2'A |
121.2 |
237.3 |
| C1' |
C2' |
H2' |
H2'A |
238.8 |
122.6 |
| H2' |
C2' |
C1' |
O4' |
250.2 |
142.7 |
| H2' |
C2' |
C1' |
H1' |
123.3 |
23.8 |
| C3' |
C2' |
H2'A |
H2' |
239.2 |
122.7 |
| C1' |
C2' |
H2'A |
H2' |
120.8 |
237.4 |
| H2'A |
C2' |
C1' |
O4' |
131.4 |
265.2 |
| H2'A |
C2' |
C1' |
H1' |
4.5 |
146.4 |
| H5' |
C5' |
C4' |
H5'A |
120.1 |
119.9 |
| C3' |
C4' |
C5' |
H4' |
238.6 |
237.6 |
| O4' |
C4' |
C5' |
H4' |
123.5 |
122.2 |
| C5' |
C4' |
O4' |
C1' |
147.2 |
159.4 |
| C4' |
C5' |
H5' |
H5'A |
240.1 |
240.0 |
| H5' |
C5' |
C4' |
O4' |
160.7 |
306.4 |
| H5' |
C5' |
C4' |
H4' |
37.2 |
184.2 |
| C4' |
C5' |
H5'A |
H5' |
119.9 |
120.0 |
| H5'A |
C5' |
C4' |
O4' |
40.6 |
186.5 |
| H5'A |
C5' |
C4' |
H4' |
277.1 |
64.2 |
| C4' |
C3' |
C2' |
H2' |
126.2 |
241.3 |
| C4' |
C3' |
C2' |
H2'A |
245.0 |
118.7 |
| C3' |
C4' |
C5' |
H5' |
275.9 |
61.8 |
| C3' |
C4' |
C5' |
H5'A |
155.8 |
301.9 |
| C5' |
C4' |
C3' |
H4' |
119.8 |
122.3 |
| O4' |
C4' |
C3' |
H4' |
236.7 |
241.2 |
| C2' |
C1' |
O4' |
C4' |
336.0 |
319.5 |
| O4' |
C4' |
C5' |
H5' |
160.7 |
306.4 |
| O4' |
C4' |
C5' |
H5'A |
40.6 |
186.5 |
| C5' |
C4' |
O4' |
H4' |
240.4 |
237.8 |
| C3' |
C4' |
O4' |
H4' |
121.0 |
118.9 |
| C4' |
O4' |
C1' |
H1' |
101.4 |
78.4 |
| H4' |
C4' |
C5' |
H5' |
37.2 |
184.2 |
| H4' |
C4' |
C5' |
H5'A |
277.1 |
64.2 |
| C5' |
C4' |
H4' |
O4' |
119.8 |
122.2 |
| H4' |
C4' |
O4' |
C1' |
266.9 |
281.6 |
| O4' |
C1' |
C2' |
H2' |
250.2 |
142.7 |
| O4' |
C1' |
C2' |
H2'A |
131.4 |
265.2 |
| C2' |
C1' |
O4' |
H1' |
234.6 |
241.1 |
| C1' |
O4' |
C4' |
H4' |
266.9 |
281.6 |
| H1' |
C1' |
C2' |
H2' |
123.3 |
23.8 |
| H1' |
C1' |
C2' |
H2'A |
4.5 |
146.4 |
| C2' |
C1' |
H1' |
O4' |
122.2 |
115.4 |
| O3' |
C3' |
C2' |
H2' |
248.6 |
360.0 |
| O3' |
C3' |
C2' |
H2'A |
7.4 |
237.4 |
| O3' |
C3' |
C4' |
H4' |
347.5 |
336.2 |
| H3' |
C3' |
C2' |
H2' |
7.4 |
122.7 |
| H3' |
C3' |
C2' |
H2'A |
126.2 |
0.0 |
| H3' |
C3' |
C4' |
H4' |
228.4 |
213.5 |
| HO3' |
O3' |
C3' |
H3' |
54.8 |
298.8 |