PDB Chemical Component US3
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 US3
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| P |
OP2 |
1.514 |
1.611 |
| N1 |
C1' |
1.449 |
1.465 |
| N1 |
C6 |
1.356 |
1.362 |
| C2 |
N1 |
1.440 |
1.346 |
| C2 |
N3 |
1.393 |
1.305 |
| SE2 |
C2 |
1.463 |
1.960 |
| SE2 |
HSE2 |
1.461 |
1.560 |
| N3 |
C4 |
1.419 |
1.344 |
| C4 |
O4 |
1.290 |
1.221 |
| C4 |
C5 |
1.426 |
1.417 |
| C5 |
C5A |
1.498 |
1.507 |
| C6 |
C5 |
1.372 |
1.353 |
| C6 |
H6 |
1.080 |
1.081 |
| C1' |
O4' |
1.439 |
1.445 |
| C1' |
H1' |
1.100 |
1.091 |
| OP3 |
P |
1.522 |
1.610 |
| OP3 |
HOP3 |
0.950 |
0.967 |
| C2' |
C1' |
1.481 |
1.544 |
| C2' |
C3' |
1.559 |
1.545 |
| C2' |
H2' |
1.100 |
1.091 |
| C2' |
H2'A |
1.100 |
1.090 |
| OP2 |
HOP2 |
0.950 |
0.967 |
| C3' |
C4' |
1.511 |
1.545 |
| C3' |
H3' |
1.100 |
1.090 |
| O3' |
C3' |
1.432 |
1.429 |
| O3' |
HO3' |
0.950 |
0.967 |
| C4' |
O4' |
1.409 |
1.444 |
| C4' |
C5' |
1.522 |
1.530 |
| C4' |
H4' |
1.101 |
1.089 |
| C5' |
O5' |
1.428 |
1.428 |
| C5' |
H5' |
1.100 |
1.090 |
| C5' |
H5'A |
1.100 |
1.091 |
| O5' |
P |
1.604 |
1.611 |
| C5A |
H5A |
1.100 |
1.090 |
| C5A |
H5AA |
1.100 |
1.090 |
| C5A |
H5AB |
1.100 |
1.090 |
| P |
OP1 |
1.830 |
1.480 |
Bond Angles for US3
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP3 |
P |
OP2 |
118.7 |
109.5 |
| P |
OP2 |
HOP2 |
109.5 |
114.0 |
| OP2 |
P |
OP1 |
69.2 |
109.5 |
| C6 |
N1 |
C1' |
112.2 |
119.7 |
| C2 |
N1 |
C1' |
116.4 |
119.7 |
| N1 |
C1' |
O4' |
110.1 |
110.4 |
| N1 |
C1' |
H1' |
111.6 |
110.3 |
| C2 |
N1 |
C6 |
131.4 |
120.6 |
| N1 |
C6 |
C5 |
124.6 |
119.2 |
| N1 |
C6 |
H6 |
117.7 |
120.5 |
| SE2 |
C2 |
N3 |
130.0 |
119.3 |
| C2 |
N3 |
C4 |
134.6 |
120.8 |
| N3 |
C4 |
O4 |
128.1 |
120.3 |
| N3 |
C4 |
C5 |
118.3 |
119.3 |
| O4 |
C4 |
C5 |
113.5 |
120.4 |
| C4 |
C5 |
C5A |
122.9 |
120.7 |
| C6 |
C5 |
C5A |
126.0 |
120.7 |
| C5 |
C5A |
H5A |
109.5 |
109.5 |
| C5 |
C5A |
H5AA |
109.5 |
109.5 |
| C5 |
C5A |
H5AB |
109.5 |
109.5 |
| O4' |
C1' |
H1' |
107.1 |
110.3 |
| C2' |
C1' |
O4' |
110.9 |
104.8 |
| C1' |
O4' |
C4' |
108.1 |
105.3 |
| C2' |
C1' |
H1' |
110.8 |
110.5 |
| OP3 |
P |
OP1 |
50.5 |
109.5 |
| C3' |
C2' |
H2' |
113.0 |
110.5 |
| C3' |
C2' |
H2'A |
113.0 |
110.5 |
| C2' |
C3' |
C4' |
103.7 |
104.0 |
| C2' |
C3' |
H3' |
110.2 |
110.5 |
| H2' |
C2' |
H2'A |
105.7 |
110.5 |
| C4' |
C3' |
H3' |
113.6 |
110.5 |
| O3' |
C3' |
C4' |
113.3 |
110.5 |
| C3' |
C4' |
O4' |
103.1 |
104.8 |
| C3' |
C4' |
C5' |
114.3 |
110.4 |
| C3' |
C4' |
H4' |
111.5 |
110.4 |
| O3' |
C3' |
H3' |
99.9 |
110.6 |
| O4' |
C4' |
C5' |
112.0 |
110.3 |
| O4' |
C4' |
H4' |
113.8 |
110.4 |
| C5' |
C4' |
H4' |
102.5 |
110.4 |
| C4' |
C5' |
O5' |
107.0 |
109.5 |
| C4' |
C5' |
H5' |
110.3 |
109.5 |
| C4' |
C5' |
H5'A |
110.3 |
109.5 |
| O5' |
C5' |
H5' |
110.3 |
109.5 |
| O5' |
C5' |
H5'A |
110.3 |
109.5 |
| H5' |
C5' |
H5'A |
108.6 |
109.4 |
| O5' |
P |
OP1 |
136.0 |
109.5 |
| H5A |
C5A |
H5AA |
109.5 |
109.5 |
| H5A |
C5A |
H5AB |
109.5 |
109.5 |
| H5AA |
C5A |
H5AB |
109.5 |
109.5 |
Torsion Angles for US3
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP3 |
P |
OP2 |
OP1 |
9.9 |
240.0 |
| O5' |
P |
OP2 |
OP1 |
133.3 |
120.0 |
| C2 |
N1 |
C1' |
C6 |
179.9 |
180.3 |
| C1' |
N1 |
C6 |
C5 |
179.2 |
179.8 |
| C1' |
N1 |
C6 |
H6 |
359.2 |
0.0 |
| O4' |
C1' |
N1 |
H1' |
241.2 |
237.8 |
| C2' |
C1' |
N1 |
O4' |
239.8 |
244.6 |
| N1 |
C1' |
O4' |
C4' |
233.6 |
200.6 |
| C2' |
C1' |
N1 |
H1' |
121.0 |
122.4 |
| C2 |
N1 |
C6 |
C1' |
180.2 |
179.7 |
| C6 |
N1 |
C1' |
O4' |
24.5 |
233.5 |
| C6 |
N1 |
C1' |
H1' |
143.4 |
355.7 |
| N1 |
C6 |
C5 |
C5A |
183.1 |
180.3 |
| C6 |
N1 |
C2 |
C1' |
179.8 |
180.3 |
| C2 |
N1 |
C1' |
O4' |
204.4 |
53.8 |
| C2 |
N1 |
C1' |
H1' |
323.2 |
176.0 |
| C2 |
N1 |
C6 |
C5 |
359.4 |
359.5 |
| C2 |
N1 |
C6 |
H6 |
179.4 |
179.7 |
| N3 |
C2 |
N1 |
C1' |
180.2 |
179.9 |
| N3 |
C2 |
N1 |
C6 |
0.0 |
0.2 |
| C2 |
N3 |
C4 |
O4 |
184.0 |
180.0 |
| C2 |
N3 |
C4 |
C5 |
5.7 |
359.9 |
| SE2 |
C2 |
N1 |
C1' |
357.1 |
360.0 |
| SE2 |
C2 |
N1 |
C6 |
177.0 |
180.3 |
| SE2 |
C2 |
N3 |
C4 |
180.3 |
180.0 |
| HSE2 |
SE2 |
C2 |
N3 |
360.0 |
0.0 |
| O4 |
C4 |
N3 |
C5 |
178.3 |
180.1 |
| N3 |
C4 |
C5 |
C5A |
175.0 |
180.0 |
| N3 |
C4 |
O4 |
C5 |
181.6 |
179.9 |
| O4 |
C4 |
C5 |
C5A |
356.4 |
359.9 |
| N1 |
C6 |
C5 |
C4 |
3.1 |
0.5 |
| N3 |
C4 |
C5 |
O4 |
178.6 |
180.1 |
| C6 |
C5 |
C4 |
C5A |
180.0 |
179.7 |
| C4 |
C5 |
C5A |
H5A |
180.0 |
0.0 |
| C4 |
C5 |
C5A |
H5AA |
300.0 |
120.0 |
| C4 |
C5 |
C5A |
H5AB |
60.0 |
240.0 |
| H5A |
C5A |
C5 |
H5AA |
240.0 |
240.0 |
| H5A |
C5A |
C5 |
H5AB |
120.0 |
120.0 |
| H5AA |
C5A |
C5 |
H5AB |
240.0 |
240.0 |
| C5 |
C6 |
N1 |
C1' |
179.2 |
179.8 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.3 |
| C4 |
C5 |
C6 |
C5A |
180.0 |
180.3 |
| C6 |
C5 |
C5A |
H5A |
0.0 |
180.3 |
| C6 |
C5 |
C5A |
H5AA |
120.0 |
300.3 |
| C6 |
C5 |
C5A |
H5AB |
240.0 |
60.3 |
| H6 |
C6 |
N1 |
C1' |
359.2 |
0.0 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
179.7 |
| H6 |
C6 |
C5 |
C5A |
3.1 |
360.0 |
| N1 |
C1' |
O4' |
H1' |
121.6 |
122.2 |
| C2' |
C1' |
O4' |
H1' |
239.0 |
241.1 |
| C3' |
C4' |
O4' |
C1' |
29.9 |
40.5 |
| C1' |
O4' |
C4' |
C5' |
153.2 |
159.3 |
| C1' |
O4' |
C4' |
H4' |
268.9 |
281.7 |
| N1 |
C1' |
H1' |
O4' |
239.4 |
237.8 |
| C2' |
C1' |
H1' |
O4' |
121.1 |
115.4 |
| H1' |
C1' |
O4' |
C4' |
112.0 |
78.4 |
| OP3 |
P |
OP2 |
HOP2 |
9.9 |
60.0 |
| OP2 |
P |
OP3 |
OP1 |
348.0 |
120.0 |
| O5' |
P |
OP3 |
OP1 |
224.9 |
240.0 |
| HOP3 |
OP3 |
P |
OP2 |
348.0 |
60.0 |
| HOP3 |
OP3 |
P |
OP1 |
0.0 |
300.0 |
| N1 |
C1' |
C2' |
O4' |
119.7 |
118.8 |
| N1 |
C1' |
C2' |
H1' |
238.5 |
237.7 |
| O4' |
C1' |
C2' |
H1' |
118.8 |
118.8 |
| C2' |
C1' |
O4' |
C4' |
351.0 |
319.5 |
| C3' |
C2' |
C1' |
O4' |
344.9 |
23.9 |
| C3' |
C2' |
C1' |
H1' |
226.1 |
265.1 |
| H2' |
C2' |
C3' |
H2'A |
120.0 |
122.6 |
| C4' |
C3' |
C2' |
H3' |
121.9 |
118.7 |
| O3' |
C3' |
C2' |
C4' |
125.2 |
118.6 |
| C2' |
C3' |
C4' |
O4' |
320.9 |
336.0 |
| C2' |
C3' |
C4' |
C5' |
199.1 |
217.2 |
| C2' |
C3' |
C4' |
H4' |
83.4 |
94.9 |
| O3' |
C3' |
C2' |
H3' |
247.2 |
237.3 |
| H2' |
C2' |
C1' |
O4' |
104.9 |
142.6 |
| H2' |
C2' |
C1' |
H1' |
346.1 |
23.8 |
| C3' |
C2' |
H2' |
H2'A |
235.9 |
237.4 |
| H2' |
C2' |
C3' |
C4' |
272.2 |
241.3 |
| H2' |
C2' |
C3' |
H3' |
150.3 |
122.6 |
| H2'A |
C2' |
C1' |
O4' |
224.9 |
265.3 |
| H2'A |
C2' |
C1' |
H1' |
106.1 |
146.4 |
| C3' |
C2' |
H2'A |
H2' |
124.1 |
122.6 |
| H2'A |
C2' |
C3' |
C4' |
152.2 |
118.7 |
| H2'A |
C2' |
C3' |
H3' |
30.3 |
0.0 |
| HOP2 |
OP2 |
P |
OP1 |
360.0 |
180.0 |
| C1' |
O4' |
C4' |
C3' |
29.9 |
40.5 |
| C4' |
C3' |
C2' |
H2' |
272.2 |
241.3 |
| C4' |
C3' |
C2' |
H2'A |
152.2 |
118.7 |
| C2' |
C3' |
C4' |
H3' |
240.4 |
241.3 |
| O3' |
C3' |
C4' |
H3' |
113.1 |
122.7 |
| O4' |
C4' |
C3' |
C5' |
121.8 |
118.8 |
| O4' |
C4' |
C3' |
H4' |
237.5 |
241.1 |
| C5' |
C4' |
C3' |
H4' |
115.7 |
122.3 |
| C3' |
C4' |
C5' |
O5' |
55.9 |
185.0 |
| C3' |
C4' |
C5' |
H5' |
175.9 |
305.0 |
| C3' |
C4' |
C5' |
H5'A |
295.9 |
64.9 |
| H3' |
C3' |
C2' |
H2' |
150.3 |
122.6 |
| H3' |
C3' |
C2' |
H2'A |
30.3 |
0.0 |
| C2' |
C3' |
H3' |
C4' |
115.8 |
114.6 |
| O3' |
C3' |
H3' |
C4' |
239.0 |
237.3 |
| H3' |
C3' |
C4' |
O4' |
80.5 |
94.6 |
| H3' |
C3' |
C4' |
C5' |
318.7 |
335.9 |
| H3' |
C3' |
C4' |
H4' |
203.0 |
213.5 |
| O3' |
C3' |
C2' |
H2' |
37.5 |
359.9 |
| O3' |
C3' |
C2' |
H2'A |
277.4 |
237.3 |
| C2' |
C3' |
O3' |
C4' |
239.8 |
245.4 |
| C2' |
C3' |
O3' |
H3' |
118.6 |
122.7 |
| C4' |
C3' |
O3' |
H3' |
238.8 |
237.3 |
| O3' |
C3' |
C4' |
O4' |
193.6 |
217.4 |
| O3' |
C3' |
C4' |
C5' |
71.8 |
98.6 |
| O3' |
C3' |
C4' |
H4' |
316.1 |
336.3 |
| HO3' |
O3' |
C3' |
C4' |
300.2 |
176.1 |
| HO3' |
O3' |
C3' |
H3' |
61.4 |
298.8 |
| C4' |
O4' |
C1' |
H1' |
112.0 |
78.4 |
| O4' |
C4' |
C3' |
H3' |
80.5 |
94.6 |
| C3' |
C4' |
O4' |
C5' |
236.7 |
241.2 |
| C3' |
C4' |
O4' |
H4' |
121.0 |
118.9 |
| C5' |
C4' |
O4' |
H4' |
244.3 |
237.7 |
| O4' |
C4' |
C5' |
O5' |
299.1 |
69.7 |
| O4' |
C4' |
C5' |
H5' |
59.1 |
189.7 |
| O4' |
C4' |
C5' |
H5'A |
179.1 |
309.6 |
| C5' |
C4' |
C3' |
H3' |
318.7 |
335.9 |
| C3' |
C4' |
C5' |
O4' |
116.8 |
115.3 |
| C3' |
C4' |
C5' |
H4' |
239.2 |
237.7 |
| O4' |
C4' |
C5' |
H4' |
122.4 |
122.3 |
| O5' |
C5' |
C4' |
H5' |
240.0 |
240.0 |
| O5' |
C5' |
C4' |
H5'A |
120.0 |
120.1 |
| H5' |
C5' |
C4' |
H5'A |
240.0 |
240.1 |
| H4' |
C4' |
C3' |
H3' |
203.0 |
213.5 |
| C3' |
C4' |
H4' |
O4' |
243.9 |
244.6 |
| C3' |
C4' |
H4' |
C5' |
122.7 |
122.3 |
| O4' |
C4' |
H4' |
C5' |
238.8 |
237.7 |
| H4' |
C4' |
C5' |
O5' |
176.7 |
307.3 |
| H4' |
C4' |
C5' |
H5' |
296.7 |
67.3 |
| H4' |
C4' |
C5' |
H5'A |
56.7 |
187.3 |
| O5' |
C5' |
C4' |
H4' |
176.7 |
307.3 |
| C4' |
C5' |
O5' |
H5' |
120.0 |
120.0 |
| C4' |
C5' |
O5' |
H5'A |
240.0 |
239.9 |
| H5' |
C5' |
O5' |
H5'A |
120.0 |
119.9 |
| C5' |
O5' |
P |
OP1 |
115.1 |
54.9 |
| H5' |
C5' |
C4' |
H4' |
296.7 |
67.3 |
| C4' |
C5' |
H5' |
O5' |
242.0 |
240.0 |
| C4' |
C5' |
H5' |
H5'A |
121.0 |
120.0 |
| O5' |
C5' |
H5' |
H5'A |
239.0 |
240.0 |
| H5'A |
C5' |
C4' |
H4' |
56.7 |
187.3 |
| C4' |
C5' |
H5'A |
O5' |
118.0 |
120.0 |
| C4' |
C5' |
H5'A |
H5' |
239.0 |
240.0 |
| O5' |
C5' |
H5'A |
H5' |
121.0 |
120.0 |
| O5' |
P |
OP2 |
HOP2 |
133.3 |
300.0 |
| OP2 |
P |
O5' |
OP1 |
282.0 |
240.1 |
| OP3 |
P |
O5' |
OP1 |
51.6 |
120.1 |
| C5 |
C5A |
H5A |
H5AA |
120.0 |
120.0 |
| C5 |
C5A |
H5A |
H5AB |
240.0 |
240.0 |
| H5AA |
C5A |
H5A |
H5AB |
120.0 |
120.0 |
| C5 |
C5A |
H5AA |
H5A |
240.0 |
240.0 |
| C5 |
C5A |
H5AA |
H5AB |
120.0 |
120.0 |
| H5A |
C5A |
H5AA |
H5AB |
240.0 |
240.0 |
| C5 |
C5A |
H5AB |
H5A |
120.1 |
120.0 |
| C5 |
C5A |
H5AB |
H5AA |
240.0 |
240.0 |
| H5A |
C5A |
H5AB |
H5AA |
120.0 |
120.0 |
| OP3 |
P |
OP1 |
OP2 |
191.3 |
120.0 |
| OP1 |
P |
OP2 |
HOP2 |
360.0 |
180.0 |