PDB Chemical Component US1
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 US1
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O3P |
P |
1.620 |
1.611 |
| O3P |
HO3P |
0.950 |
0.966 |
| P |
O1P |
1.477 |
1.611 |
| P |
O2P |
1.475 |
1.480 |
| P |
O5' |
1.641 |
1.610 |
| O1P |
HO1P |
0.949 |
0.967 |
| O5' |
C5' |
1.459 |
1.429 |
| C5' |
C4' |
1.579 |
1.530 |
| C5' |
H5'1 |
1.100 |
1.090 |
| C5' |
H5'2 |
1.100 |
1.090 |
| C4' |
O4' |
1.440 |
1.444 |
| C4' |
C3' |
1.537 |
1.550 |
| C4' |
H4' |
1.100 |
1.090 |
| O4' |
C1' |
1.436 |
1.437 |
| C3' |
C2' |
1.516 |
1.550 |
| C3' |
S |
1.698 |
1.814 |
| C3' |
H3' |
1.100 |
1.089 |
| C2' |
C1' |
1.481 |
1.541 |
| C2' |
H2'1 |
1.101 |
1.090 |
| C2' |
H2'2 |
1.100 |
1.090 |
| C1' |
N1 |
1.456 |
1.465 |
| C1' |
H1' |
1.100 |
1.091 |
| N1 |
C2 |
1.398 |
1.346 |
| N1 |
C6 |
1.387 |
1.368 |
| C2 |
O2 |
1.246 |
1.216 |
| C2 |
N3 |
1.408 |
1.346 |
| N3 |
C4 |
1.425 |
1.348 |
| N3 |
HN3 |
1.000 |
0.970 |
| C4 |
O4 |
1.223 |
1.218 |
| C4 |
C5 |
1.433 |
1.416 |
| C5 |
C6 |
1.342 |
1.350 |
| C5 |
H5 |
1.080 |
1.080 |
| C6 |
H6 |
1.080 |
1.080 |
| S |
HS |
1.300 |
1.345 |
Bond Angles for US1
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| P |
O3P |
HO3P |
109.5 |
106.8 |
| O3P |
P |
O1P |
109.2 |
109.4 |
| O3P |
P |
O2P |
110.2 |
109.5 |
| O3P |
P |
O5' |
104.9 |
109.4 |
| O1P |
P |
O2P |
118.4 |
109.5 |
| O1P |
P |
O5' |
105.3 |
109.5 |
| P |
O1P |
HO1P |
109.5 |
106.8 |
| O2P |
P |
O5' |
107.9 |
109.5 |
| P |
O5' |
C5' |
128.4 |
106.8 |
| O5' |
C5' |
C4' |
115.9 |
109.5 |
| O5' |
C5' |
H5'1 |
107.4 |
109.5 |
| O5' |
C5' |
H5'2 |
105.9 |
109.5 |
| C4' |
C5' |
H5'1 |
107.4 |
109.5 |
| C4' |
C5' |
H5'2 |
105.9 |
109.5 |
| C5' |
C4' |
O4' |
118.0 |
110.6 |
| C5' |
C4' |
C3' |
105.6 |
110.6 |
| C5' |
C4' |
H4' |
105.0 |
110.6 |
| H5'1 |
C5' |
H5'2 |
114.7 |
109.5 |
| O4' |
C4' |
C3' |
104.8 |
103.6 |
| O4' |
C4' |
H4' |
105.9 |
110.6 |
| C4' |
O4' |
C1' |
102.0 |
106.9 |
| C3' |
C4' |
H4' |
118.2 |
110.6 |
| C4' |
C3' |
C2' |
101.6 |
102.0 |
| C4' |
C3' |
S |
105.3 |
111.2 |
| C4' |
C3' |
H3' |
120.4 |
110.8 |
| O4' |
C1' |
C2' |
108.2 |
107.3 |
| O4' |
C1' |
N1 |
127.7 |
109.9 |
| O4' |
C1' |
H1' |
101.8 |
109.9 |
| C2' |
C3' |
S |
118.5 |
110.9 |
| C2' |
C3' |
H3' |
107.7 |
110.9 |
| C3' |
C2' |
C1' |
90.7 |
104.3 |
| C3' |
C2' |
H2'1 |
116.3 |
110.4 |
| C3' |
C2' |
H2'2 |
119.8 |
110.6 |
| S |
C3' |
H3' |
104.2 |
110.8 |
| C3' |
S |
HS |
109.5 |
100.0 |
| C1' |
C2' |
H2'1 |
116.3 |
110.5 |
| C1' |
C2' |
H2'2 |
119.8 |
110.5 |
| C2' |
C1' |
N1 |
120.4 |
110.0 |
| C2' |
C1' |
H1' |
118.9 |
109.8 |
| H2'1 |
C2' |
H2'2 |
96.0 |
110.5 |
| N1 |
C1' |
H1' |
71.9 |
109.9 |
| C1' |
N1 |
C2 |
120.3 |
119.7 |
| C1' |
N1 |
C6 |
116.5 |
119.7 |
| C2 |
N1 |
C6 |
123.2 |
120.6 |
| N1 |
C2 |
O2 |
123.3 |
119.5 |
| N1 |
C2 |
N3 |
112.7 |
120.9 |
| N1 |
C6 |
C5 |
122.9 |
119.7 |
| N1 |
C6 |
H6 |
118.6 |
120.1 |
| O2 |
C2 |
N3 |
124.0 |
119.6 |
| C2 |
N3 |
C4 |
126.4 |
120.3 |
| C2 |
N3 |
HN3 |
116.8 |
119.8 |
| C4 |
N3 |
HN3 |
116.8 |
119.9 |
| N3 |
C4 |
O4 |
123.0 |
120.3 |
| N3 |
C4 |
C5 |
115.6 |
119.4 |
| O4 |
C4 |
C5 |
121.4 |
120.3 |
| C4 |
C5 |
C6 |
119.3 |
119.1 |
| C4 |
C5 |
H5 |
120.4 |
120.5 |
| C6 |
C5 |
H5 |
120.4 |
120.4 |
| C5 |
C6 |
H6 |
118.5 |
120.2 |
Torsion Angles for US1
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O1P |
P |
O3P |
O2P |
228.3 |
240.0 |
| O1P |
P |
O3P |
O5' |
112.4 |
120.0 |
| O3P |
P |
O1P |
HO1P |
117.6 |
60.0 |
| O2P |
P |
O3P |
O5' |
244.1 |
240.0 |
| O3P |
P |
O5' |
C5' |
307.8 |
295.0 |
| HO3P |
O3P |
P |
O1P |
226.3 |
60.0 |
| HO3P |
O3P |
P |
O2P |
358.0 |
180.0 |
| HO3P |
O3P |
P |
O5' |
113.8 |
300.0 |
| O1P |
P |
O3P |
HO3P |
226.3 |
60.0 |
| O3P |
P |
O1P |
O2P |
127.1 |
120.0 |
| O3P |
P |
O1P |
O5' |
247.8 |
240.1 |
| O2P |
P |
O1P |
O5' |
120.6 |
120.1 |
| O1P |
P |
O5' |
C5' |
192.6 |
175.0 |
| O2P |
P |
O3P |
HO3P |
358.0 |
180.0 |
| O3P |
P |
O2P |
O1P |
233.3 |
240.0 |
| O3P |
P |
O2P |
O5' |
114.0 |
120.0 |
| O1P |
P |
O2P |
O5' |
240.7 |
240.0 |
| O2P |
P |
O1P |
HO1P |
350.4 |
300.0 |
| O2P |
P |
O5' |
C5' |
65.3 |
55.0 |
| O5' |
P |
O3P |
HO3P |
113.8 |
300.0 |
| O3P |
P |
O5' |
O1P |
115.2 |
119.9 |
| O3P |
P |
O5' |
O2P |
242.6 |
240.0 |
| O1P |
P |
O5' |
O2P |
127.3 |
120.1 |
| O5' |
P |
O1P |
HO1P |
229.8 |
180.0 |
| P |
O5' |
C5' |
C4' |
157.5 |
180.0 |
| P |
O5' |
C5' |
H5'1 |
277.5 |
300.0 |
| P |
O5' |
C5' |
H5'2 |
40.5 |
60.0 |
| HO1P |
O1P |
P |
O2P |
350.4 |
300.0 |
| HO1P |
O1P |
P |
O5' |
229.8 |
180.0 |
| C4' |
C5' |
O5' |
H5'1 |
240.0 |
240.0 |
| C4' |
C5' |
O5' |
H5'2 |
117.0 |
120.0 |
| O5' |
C5' |
C4' |
O4' |
284.0 |
68.6 |
| O5' |
C5' |
C4' |
C3' |
40.6 |
182.8 |
| O5' |
C5' |
C4' |
H4' |
166.3 |
305.7 |
| H5'1 |
C5' |
O5' |
H5'2 |
237.0 |
240.0 |
| O5' |
C5' |
C4' |
H5'1 |
120.0 |
120.0 |
| O5' |
C5' |
C4' |
H5'2 |
243.0 |
240.0 |
| H5'1 |
C5' |
C4' |
H5'2 |
123.0 |
120.0 |
| O4' |
C4' |
C5' |
C3' |
243.4 |
245.8 |
| O4' |
C4' |
C5' |
H4' |
117.7 |
122.9 |
| C5' |
C4' |
O4' |
C1' |
116.9 |
158.5 |
| C3' |
C4' |
C5' |
H4' |
234.3 |
237.1 |
| C5' |
C4' |
C3' |
C2' |
201.1 |
204.6 |
| C5' |
C4' |
C3' |
S |
76.9 |
86.3 |
| C5' |
C4' |
C3' |
H3' |
319.8 |
322.7 |
| O5' |
C5' |
H5'1 |
C4' |
234.7 |
240.0 |
| O5' |
C5' |
H5'1 |
H5'2 |
117.4 |
120.0 |
| C4' |
C5' |
H5'1 |
H5'2 |
242.7 |
240.0 |
| H5'1 |
C5' |
C4' |
O4' |
164.0 |
308.6 |
| H5'1 |
C5' |
C4' |
C3' |
280.6 |
62.8 |
| H5'1 |
C5' |
C4' |
H4' |
46.3 |
185.7 |
| O5' |
C5' |
H5'2 |
C4' |
123.6 |
120.0 |
| O5' |
C5' |
H5'2 |
H5'1 |
241.8 |
240.0 |
| C4' |
C5' |
H5'2 |
H5'1 |
118.2 |
120.0 |
| H5'2 |
C5' |
C4' |
O4' |
41.0 |
188.6 |
| H5'2 |
C5' |
C4' |
C3' |
157.6 |
302.8 |
| H5'2 |
C5' |
C4' |
H4' |
283.3 |
65.7 |
| O4' |
C4' |
C5' |
H5'1 |
164.0 |
308.6 |
| O4' |
C4' |
C5' |
H5'2 |
41.0 |
188.6 |
| C5' |
C4' |
O4' |
C3' |
117.1 |
118.6 |
| C5' |
C4' |
O4' |
H4' |
242.8 |
237.2 |
| C3' |
C4' |
O4' |
H4' |
125.7 |
118.6 |
| O4' |
C4' |
C3' |
C2' |
326.3 |
323.1 |
| O4' |
C4' |
C3' |
S |
202.2 |
204.9 |
| O4' |
C4' |
C3' |
H3' |
85.1 |
81.2 |
| C4' |
O4' |
C1' |
C2' |
36.2 |
333.5 |
| C4' |
O4' |
C1' |
N1 |
238.4 |
213.9 |
| C4' |
O4' |
C1' |
H1' |
162.2 |
92.9 |
| C3' |
C4' |
C5' |
H5'1 |
280.6 |
62.8 |
| C3' |
C4' |
C5' |
H5'2 |
157.6 |
302.8 |
| C5' |
C4' |
C3' |
O4' |
234.7 |
241.4 |
| C5' |
C4' |
C3' |
H4' |
117.1 |
122.9 |
| O4' |
C4' |
C3' |
H4' |
242.4 |
241.4 |
| C3' |
C4' |
O4' |
C1' |
359.8 |
40.0 |
| C2' |
C3' |
C4' |
S |
124.1 |
118.3 |
| C2' |
C3' |
C4' |
H3' |
241.2 |
241.9 |
| C4' |
C3' |
C2' |
C1' |
50.1 |
20.7 |
| C4' |
C3' |
C2' |
H2'1 |
170.0 |
262.0 |
| C4' |
C3' |
C2' |
H2'2 |
284.7 |
139.5 |
| S |
C3' |
C4' |
H3' |
117.1 |
123.7 |
| C4' |
C3' |
S |
HS |
143.5 |
174.2 |
| H4' |
C4' |
C5' |
H5'1 |
46.3 |
185.7 |
| H4' |
C4' |
C5' |
H5'2 |
283.3 |
65.7 |
| C5' |
C4' |
H4' |
O4' |
125.6 |
122.8 |
| C5' |
C4' |
H4' |
C3' |
242.6 |
237.1 |
| O4' |
C4' |
H4' |
C3' |
117.0 |
114.3 |
| H4' |
C4' |
O4' |
C1' |
234.1 |
281.4 |
| H4' |
C4' |
C3' |
C2' |
84.0 |
81.7 |
| H4' |
C4' |
C3' |
S |
319.8 |
323.5 |
| H4' |
C4' |
C3' |
H3' |
202.7 |
199.8 |
| C1' |
O4' |
C4' |
C3' |
359.8 |
40.0 |
| C1' |
O4' |
C4' |
H4' |
234.1 |
281.4 |
| C3' |
C2' |
C1' |
O4' |
305.3 |
2.1 |
| O4' |
C1' |
C2' |
H2'1 |
185.3 |
120.7 |
| O4' |
C1' |
C2' |
H2'2 |
70.7 |
243.3 |
| C2' |
C1' |
O4' |
N1 |
157.9 |
119.6 |
| C2' |
C1' |
O4' |
H1' |
234.0 |
240.6 |
| N1 |
C1' |
O4' |
H1' |
76.2 |
121.0 |
| O4' |
C1' |
N1 |
C2 |
284.8 |
53.3 |
| O4' |
C1' |
N1 |
C6 |
103.3 |
233.6 |
| C2' |
C3' |
C4' |
H4' |
84.0 |
81.7 |
| C4' |
C3' |
C2' |
S |
245.3 |
241.6 |
| C4' |
C3' |
C2' |
H3' |
127.5 |
118.0 |
| O4' |
C1' |
C2' |
C3' |
305.3 |
2.1 |
| S |
C3' |
C2' |
H3' |
242.2 |
236.5 |
| C2' |
C3' |
S |
HS |
30.8 |
61.4 |
| C1' |
C2' |
C3' |
H2'1 |
240.0 |
118.7 |
| C1' |
C2' |
C3' |
H2'2 |
125.4 |
241.2 |
| C3' |
C2' |
C1' |
N1 |
105.1 |
121.7 |
| C3' |
C2' |
C1' |
H1' |
190.1 |
242.7 |
| H2'1 |
C2' |
C3' |
H2'2 |
245.4 |
122.5 |
| S |
C3' |
C4' |
H4' |
319.8 |
323.5 |
| C4' |
C3' |
S |
C2' |
112.7 |
112.7 |
| C4' |
C3' |
S |
H3' |
232.4 |
236.3 |
| C2' |
C3' |
S |
H3' |
119.7 |
123.6 |
| S |
C3' |
C2' |
C1' |
164.7 |
139.1 |
| S |
C3' |
C2' |
H2'1 |
284.7 |
20.4 |
| S |
C3' |
C2' |
H2'2 |
39.3 |
257.9 |
| H3' |
C3' |
C4' |
H4' |
202.7 |
199.8 |
| C4' |
C3' |
H3' |
C2' |
244.3 |
247.5 |
| C4' |
C3' |
H3' |
S |
117.6 |
123.9 |
| C2' |
C3' |
H3' |
S |
233.3 |
236.4 |
| H3' |
C3' |
C2' |
C1' |
282.6 |
262.7 |
| H3' |
C3' |
C2' |
H2'1 |
42.5 |
144.0 |
| H3' |
C3' |
C2' |
H2'2 |
157.2 |
21.4 |
| H3' |
C3' |
S |
HS |
271.1 |
297.8 |
| O4' |
C1' |
C2' |
N1 |
200.2 |
240.5 |
| O4' |
C1' |
C2' |
H1' |
115.2 |
119.4 |
| C1' |
C2' |
C3' |
S |
164.7 |
139.1 |
| C1' |
C2' |
C3' |
H3' |
282.6 |
262.7 |
| C3' |
C2' |
C1' |
H2'1 |
120.0 |
241.4 |
| C3' |
C2' |
C1' |
H2'2 |
234.6 |
118.8 |
| H2'1 |
C2' |
C1' |
H2'2 |
114.6 |
237.4 |
| N1 |
C1' |
C2' |
H1' |
275.0 |
239.0 |
| C2' |
C1' |
N1 |
C2 |
129.4 |
295.4 |
| C2' |
C1' |
N1 |
C6 |
307.8 |
115.6 |
| H2'1 |
C2' |
C3' |
S |
284.7 |
20.4 |
| H2'1 |
C2' |
C3' |
H3' |
42.5 |
144.0 |
| C3' |
C2' |
H2'1 |
C1' |
255.0 |
114.8 |
| C3' |
C2' |
H2'1 |
H2'2 |
127.5 |
237.4 |
| C1' |
C2' |
H2'1 |
H2'2 |
232.5 |
122.6 |
| H2'1 |
C2' |
C1' |
N1 |
345.1 |
240.3 |
| H2'1 |
C2' |
C1' |
H1' |
70.1 |
1.3 |
| H2'2 |
C2' |
C3' |
S |
39.3 |
257.9 |
| H2'2 |
C2' |
C3' |
H3' |
157.2 |
21.4 |
| C3' |
C2' |
H2'2 |
C1' |
110.1 |
245.1 |
| C3' |
C2' |
H2'2 |
H2'1 |
235.1 |
122.5 |
| C1' |
C2' |
H2'2 |
H2'1 |
124.9 |
237.4 |
| H2'2 |
C2' |
C1' |
N1 |
230.5 |
2.9 |
| H2'2 |
C2' |
C1' |
H1' |
315.5 |
123.9 |
| O4' |
C1' |
N1 |
C2' |
155.5 |
117.9 |
| O4' |
C1' |
N1 |
H1' |
268.9 |
239.0 |
| N1 |
C1' |
C2' |
H2'1 |
345.1 |
240.3 |
| N1 |
C1' |
C2' |
H2'2 |
230.5 |
2.9 |
| C2' |
C1' |
N1 |
H1' |
113.4 |
121.0 |
| C2 |
N1 |
C1' |
C6 |
181.6 |
179.7 |
| C1' |
N1 |
C2 |
O2 |
357.5 |
0.3 |
| C1' |
N1 |
C2 |
N3 |
178.4 |
179.8 |
| C1' |
N1 |
C6 |
C5 |
181.5 |
180.0 |
| C1' |
N1 |
C6 |
H6 |
1.5 |
359.9 |
| O4' |
C1' |
H1' |
C2' |
241.4 |
242.2 |
| O4' |
C1' |
H1' |
N1 |
126.0 |
121.0 |
| H1' |
C1' |
C2' |
H2'1 |
70.1 |
1.3 |
| H1' |
C1' |
C2' |
H2'2 |
315.5 |
123.9 |
| C2' |
C1' |
H1' |
N1 |
244.7 |
238.9 |
| H1' |
C1' |
N1 |
C2 |
16.0 |
174.3 |
| H1' |
C1' |
N1 |
C6 |
194.4 |
354.6 |
| C2 |
N1 |
C1' |
H1' |
16.0 |
174.3 |
| C1' |
N1 |
C2 |
C6 |
178.3 |
180.3 |
| C2 |
N1 |
C6 |
C5 |
359.9 |
0.3 |
| C2 |
N1 |
C6 |
H6 |
179.9 |
180.2 |
| O2 |
C2 |
N1 |
N3 |
179.2 |
180.6 |
| N1 |
C2 |
N3 |
C4 |
0.1 |
0.5 |
| N1 |
C2 |
N3 |
HN3 |
180.1 |
180.3 |
| C6 |
N1 |
C1' |
H1' |
194.4 |
354.6 |
| C1' |
N1 |
C6 |
C2 |
181.6 |
179.7 |
| C6 |
N1 |
C2 |
O2 |
179.2 |
180.0 |
| C6 |
N1 |
C2 |
N3 |
0.0 |
359.5 |
| C4 |
C5 |
C6 |
N1 |
0.1 |
0.0 |
| N1 |
C6 |
C5 |
H5 |
180.1 |
180.0 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
180.0 |
| O2 |
C2 |
N1 |
C6 |
179.2 |
180.0 |
| N1 |
C2 |
O2 |
N3 |
180.9 |
179.4 |
| O2 |
C2 |
N3 |
C4 |
180.9 |
180.0 |
| O2 |
C2 |
N3 |
HN3 |
0.9 |
359.7 |
| N3 |
C2 |
N1 |
C6 |
0.0 |
359.5 |
| N1 |
C2 |
N3 |
O2 |
179.2 |
180.6 |
| C4 |
N3 |
C2 |
HN3 |
180.0 |
180.3 |
| C2 |
N3 |
C4 |
O4 |
179.1 |
179.7 |
| C2 |
N3 |
C4 |
C5 |
359.9 |
359.7 |
| C2 |
N3 |
C4 |
HN3 |
180.0 |
179.7 |
| O4 |
C4 |
N3 |
C5 |
179.2 |
180.0 |
| N3 |
C4 |
C5 |
C6 |
0.0 |
360.0 |
| N3 |
C4 |
C5 |
H5 |
180.0 |
180.0 |
| C2 |
N3 |
HN3 |
C4 |
180.0 |
180.3 |
| HN3 |
N3 |
C4 |
O4 |
359.1 |
360.0 |
| HN3 |
N3 |
C4 |
C5 |
179.9 |
180.0 |
| O4 |
C4 |
N3 |
HN3 |
359.1 |
360.0 |
| N3 |
C4 |
O4 |
C5 |
180.9 |
180.0 |
| O4 |
C4 |
C5 |
C6 |
180.8 |
180.0 |
| O4 |
C4 |
C5 |
H5 |
0.9 |
0.1 |
| N1 |
C6 |
C5 |
C4 |
0.1 |
0.0 |
| C5 |
C4 |
N3 |
HN3 |
179.9 |
180.0 |
| N3 |
C4 |
C5 |
O4 |
179.2 |
180.0 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
180.0 |
| C4 |
C5 |
C6 |
H6 |
180.1 |
180.0 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.0 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
180.0 |
| C4 |
C5 |
H5 |
C6 |
180.0 |
180.0 |
| H5 |
C5 |
C6 |
H6 |
0.0 |
0.0 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
180.0 |
| H6 |
C6 |
C5 |
H5 |
0.0 |
0.0 |
| HS |
S |
C3' |
H3' |
271.1 |
297.8 |