PDB Chemical Component US5
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 US5
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| P |
O5' |
1.596 |
1.610 |
| P |
O2P |
1.478 |
1.611 |
| N1 |
C2 |
1.385 |
1.346 |
| C2 |
O2 |
1.218 |
1.219 |
| C2 |
N3 |
1.380 |
1.335 |
| C4 |
N3 |
1.390 |
1.318 |
| C4 |
SE4 |
1.232 |
1.961 |
| SE4 |
HSE4 |
1.460 |
1.560 |
| C5 |
C4 |
1.448 |
1.398 |
| C5 |
H5 |
1.081 |
1.080 |
| C6 |
N1 |
1.388 |
1.359 |
| C6 |
C5 |
1.343 |
1.360 |
| C6 |
H6 |
1.080 |
1.080 |
| C1' |
N1 |
1.513 |
1.465 |
| C1' |
H1' |
1.100 |
1.090 |
| OP3 |
P |
1.478 |
1.611 |
| OP3 |
HOP3 |
0.950 |
0.967 |
| C2' |
C1' |
1.527 |
1.550 |
| C2' |
H2' |
1.100 |
1.090 |
| O2' |
C2' |
1.415 |
1.429 |
| O2' |
HO2' |
0.950 |
0.967 |
| O2P |
HO2P |
0.950 |
0.967 |
| C3' |
C2' |
1.523 |
1.548 |
| C3' |
C4' |
1.520 |
1.541 |
| C3' |
H3' |
1.100 |
1.091 |
| O3' |
C3' |
1.419 |
1.428 |
| O3' |
HO3' |
0.950 |
0.967 |
| C4' |
O4' |
1.454 |
1.439 |
| C4' |
H4' |
1.100 |
1.090 |
| O4' |
C1' |
1.418 |
1.444 |
| C5' |
C4' |
1.516 |
1.530 |
| C5' |
O5' |
1.424 |
1.429 |
| C5' |
H5' |
1.100 |
1.090 |
| C5' |
H5'A |
1.100 |
1.090 |
| P |
OP1 |
1.470 |
1.479 |
Bond Angles for US5
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O2P |
P |
O5' |
106.7 |
109.4 |
| OP3 |
P |
O5' |
109.2 |
109.5 |
| P |
O5' |
C5' |
121.7 |
123.0 |
| O5' |
P |
OP1 |
63.7 |
109.5 |
| OP3 |
P |
O2P |
119.6 |
109.4 |
| P |
O2P |
HO2P |
109.5 |
114.0 |
| O2P |
P |
OP1 |
43.6 |
109.5 |
| N1 |
C2 |
O2 |
123.0 |
119.5 |
| N1 |
C2 |
N3 |
115.1 |
120.9 |
| O2 |
C2 |
N3 |
121.8 |
119.5 |
| C4 |
SE4 |
HSE4 |
109.5 |
101.0 |
| C6 |
C5 |
H5 |
120.4 |
120.5 |
| C2' |
C1' |
H1' |
111.0 |
110.6 |
| O4' |
C1' |
H1' |
111.3 |
110.6 |
| OP3 |
P |
OP1 |
127.8 |
109.5 |
| O2' |
C2' |
H2' |
103.3 |
110.8 |
| C3' |
C2' |
H2' |
113.8 |
110.9 |
| C4' |
C3' |
H3' |
115.0 |
110.5 |
| O3' |
C3' |
C4' |
112.1 |
110.5 |
| C3' |
C4' |
O4' |
103.3 |
107.4 |
| C3' |
C4' |
H4' |
110.0 |
109.9 |
| O3' |
C3' |
H3' |
102.9 |
110.6 |
| O4' |
C4' |
H4' |
115.4 |
109.7 |
| C5' |
C4' |
H4' |
103.5 |
110.0 |
| O5' |
C5' |
H5' |
109.3 |
109.4 |
| O5' |
C5' |
H5'A |
109.3 |
109.4 |
| H5' |
C5' |
H5'A |
109.7 |
109.4 |
Torsion Angles for US5
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP3 |
P |
O5' |
O2P |
229.4 |
240.1 |
| O5' |
P |
O2P |
HO2P |
350.7 |
180.0 |
| O2P |
P |
O5' |
OP1 |
7.1 |
240.0 |
| OP3 |
P |
O5' |
OP1 |
236.6 |
120.1 |
| P |
O5' |
C5' |
H5' |
42.9 |
59.9 |
| P |
O5' |
C5' |
H5'A |
282.9 |
300.0 |
| OP3 |
P |
O2P |
O5' |
124.5 |
120.0 |
| O2P |
P |
O5' |
C5' |
178.5 |
185.0 |
| O5' |
P |
O2P |
OP1 |
350.7 |
120.1 |
| OP3 |
P |
O2P |
OP1 |
115.2 |
240.0 |
| O2 |
C2 |
N1 |
N3 |
180.6 |
180.0 |
| N1 |
C2 |
O2 |
N3 |
179.4 |
180.0 |
| N1 |
C2 |
N3 |
O2 |
180.5 |
180.0 |
| C5 |
C4 |
SE4 |
HSE4 |
180.1 |
180.0 |
| H6 |
C6 |
C5 |
H5 |
0.0 |
0.0 |
| O2P |
P |
OP3 |
O5' |
236.7 |
240.1 |
| OP3 |
P |
O5' |
C5' |
47.9 |
65.1 |
| O5' |
P |
OP3 |
OP1 |
71.1 |
239.9 |
| OP3 |
P |
O2P |
HO2P |
115.2 |
300.0 |
| O2P |
P |
OP3 |
OP1 |
307.8 |
120.0 |
| HOP3 |
OP3 |
P |
O5' |
71.1 |
60.0 |
| HOP3 |
OP3 |
P |
O2P |
307.8 |
300.0 |
| HOP3 |
OP3 |
P |
OP1 |
360.0 |
180.0 |
| O4' |
C1' |
C2' |
H1' |
120.9 |
118.6 |
| H2' |
C2' |
C1' |
H1' |
84.0 |
160.1 |
| O2' |
C2' |
C1' |
H1' |
326.7 |
36.6 |
| C3' |
C2' |
O2' |
H2' |
236.6 |
236.4 |
| HO2' |
O2' |
C2' |
H2' |
55.5 |
56.4 |
| HO2P |
O2P |
P |
O5' |
350.7 |
180.0 |
| HO2P |
O2P |
P |
OP1 |
360.0 |
60.0 |
| C3' |
C2' |
C1' |
H1' |
206.7 |
278.4 |
| O2' |
C2' |
C3' |
H2' |
117.4 |
123.5 |
| C4' |
C3' |
C2' |
H2' |
167.4 |
97.4 |
| O3' |
C3' |
C4' |
H3' |
117.1 |
122.7 |
| O4' |
C4' |
C3' |
H4' |
236.3 |
240.7 |
| C5' |
C4' |
C3' |
H4' |
116.5 |
121.1 |
| H3' |
C3' |
C2' |
H2' |
43.9 |
338.7 |
| O3' |
C3' |
H3' |
C4' |
237.9 |
237.4 |
| H3' |
C3' |
C4' |
O4' |
82.8 |
116.8 |
| H3' |
C3' |
C4' |
H4' |
206.6 |
236.1 |
| O3' |
C3' |
C2' |
H2' |
286.8 |
216.0 |
| C4' |
C3' |
O3' |
H3' |
235.9 |
237.4 |
| O3' |
C3' |
C4' |
O4' |
199.9 |
239.4 |
| O3' |
C3' |
C4' |
H4' |
323.6 |
358.7 |
| HO3' |
O3' |
C3' |
C4' |
292.3 |
176.2 |
| HO3' |
O3' |
C3' |
H3' |
56.4 |
298.8 |
| C4' |
O4' |
C1' |
H1' |
128.1 |
78.8 |
| O4' |
C4' |
C3' |
H3' |
82.8 |
116.8 |
| C3' |
C4' |
O4' |
H4' |
120.1 |
119.4 |
| C5' |
C4' |
O4' |
H4' |
243.5 |
238.9 |
| H4' |
C4' |
C3' |
H3' |
206.6 |
236.1 |
| C3' |
C4' |
H4' |
O4' |
243.6 |
242.1 |
| C2' |
C1' |
O4' |
H1' |
239.3 |
241.4 |
| P |
O5' |
C5' |
C4' |
162.9 |
180.0 |
| C5' |
C4' |
C3' |
H3' |
323.1 |
357.2 |
| C3' |
C4' |
C5' |
H4' |
239.9 |
238.9 |
| O4' |
C4' |
C5' |
H4' |
123.8 |
120.9 |
| C5' |
O5' |
P |
OP1 |
171.3 |
305.0 |
| O5' |
C5' |
C4' |
H4' |
175.2 |
306.1 |
| H5' |
C5' |
O5' |
H5'A |
120.0 |
119.9 |
| H5' |
C5' |
C4' |
H4' |
295.2 |
66.1 |
| O5' |
C5' |
H5' |
H5'A |
240.2 |
240.1 |
| H5'A |
C5' |
C4' |
H4' |
55.3 |
186.1 |
| O5' |
C5' |
H5'A |
H5' |
119.8 |
119.9 |
| O2P |
P |
OP1 |
O5' |
189.9 |
120.0 |
| OP3 |
P |
OP1 |
O5' |
94.7 |
240.0 |
| OP1 |
P |
O5' |
C5' |
171.3 |
305.0 |
| OP3 |
P |
OP1 |
O2P |
264.8 |
119.9 |
| OP1 |
P |
O2P |
HO2P |
360.0 |
60.0 |