PDB Chemical Component USM
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 USM
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| P |
OP2 |
1.594 |
1.610 |
| OP2 |
HOP2 |
0.950 |
0.967 |
| OP1 |
P |
1.477 |
1.481 |
| O5' |
P |
1.608 |
1.609 |
| P |
OP3 |
1.484 |
1.610 |
| OP3 |
HOP3 |
0.950 |
0.968 |
| C5' |
O5' |
1.435 |
1.429 |
| C6 |
N1 |
1.365 |
1.368 |
| N1 |
C2 |
1.359 |
1.346 |
| N1 |
C1' |
1.549 |
1.465 |
| C5 |
C6 |
1.343 |
1.350 |
| C6 |
H6 |
1.080 |
1.080 |
| N3 |
C2 |
1.390 |
1.346 |
| C2 |
O2 |
1.216 |
1.216 |
| C4 |
N3 |
1.382 |
1.348 |
| C5 |
C4 |
1.448 |
1.415 |
| O4 |
C4 |
1.229 |
1.218 |
| C5 |
H5 |
1.080 |
1.080 |
| C3' |
C2' |
1.505 |
1.545 |
| C2' |
C1' |
1.526 |
1.545 |
| C2' |
S2' |
1.811 |
1.814 |
| C2' |
H2' |
1.100 |
1.090 |
| S2' |
C2A |
1.793 |
1.813 |
| C2A |
H2A |
1.100 |
1.090 |
| C2A |
H2AA |
1.100 |
1.090 |
| C2A |
H2AB |
1.100 |
1.090 |
| C5' |
C4' |
1.505 |
1.530 |
| C5' |
H5' |
1.100 |
1.090 |
| C5' |
H5'A |
1.100 |
1.090 |
| C3' |
C4' |
1.529 |
1.545 |
| C4' |
O4' |
1.444 |
1.444 |
| C4' |
H4' |
1.100 |
1.090 |
| O4' |
C1' |
1.429 |
1.445 |
| C1' |
H1' |
1.100 |
1.090 |
| O3' |
C3' |
1.462 |
1.429 |
| C3' |
H3' |
1.100 |
1.089 |
| O3' |
HO3' |
0.950 |
0.967 |
| N3 |
HN3 |
1.000 |
0.969 |
Bond Angles for USM
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| P |
OP2 |
HOP2 |
109.5 |
114.0 |
| OP1 |
P |
OP3 |
119.3 |
109.5 |
| P |
OP3 |
HOP3 |
109.5 |
114.0 |
| C6 |
N1 |
C2 |
125.5 |
120.6 |
| C6 |
N1 |
C1' |
126.3 |
119.7 |
| C2 |
N1 |
C1' |
108.2 |
119.7 |
| N1 |
C2 |
O2 |
126.6 |
119.5 |
| N1 |
C1' |
C2' |
125.2 |
110.4 |
| N1 |
C1' |
O4' |
97.2 |
110.3 |
| N1 |
C1' |
H1' |
107.5 |
110.4 |
| C5 |
C6 |
H6 |
119.3 |
120.2 |
| C4 |
N3 |
HN3 |
117.4 |
119.9 |
| C3' |
C2' |
H2' |
108.9 |
110.6 |
| S2' |
C2' |
C1' |
101.7 |
110.5 |
| C1' |
C2' |
H2' |
121.5 |
110.5 |
| C2' |
C1' |
O4' |
107.6 |
104.8 |
| C2' |
C1' |
H1' |
97.0 |
110.4 |
| S2' |
C2' |
H2' |
108.3 |
110.5 |
| C2' |
S2' |
C2A |
102.2 |
103.0 |
| S2' |
C2A |
H2A |
109.5 |
109.5 |
| S2' |
C2A |
H2AA |
109.5 |
109.5 |
| S2' |
C2A |
H2AB |
109.5 |
109.5 |
| H2A |
C2A |
H2AA |
109.4 |
109.4 |
| H2A |
C2A |
H2AB |
109.5 |
109.4 |
| H2AA |
C2A |
H2AB |
109.5 |
109.5 |
| C4' |
C5' |
H5' |
108.7 |
109.5 |
| C4' |
C5' |
H5'A |
108.1 |
109.5 |
| C5' |
C4' |
O4' |
111.5 |
110.4 |
| C5' |
C4' |
H4' |
103.2 |
110.3 |
| H5' |
C5' |
H5'A |
111.3 |
109.5 |
| C3' |
C4' |
H4' |
110.8 |
110.5 |
| O4' |
C4' |
H4' |
113.6 |
110.4 |
| C4' |
O4' |
C1' |
110.0 |
105.3 |
| O4' |
C1' |
H1' |
125.0 |
110.5 |
| O3' |
C3' |
H3' |
103.4 |
110.6 |
Torsion Angles for USM
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP1 |
P |
OP2 |
HOP2 |
236.1 |
300.0 |
| OP1 |
P |
OP3 |
HOP3 |
324.4 |
180.0 |
| O5' |
P |
OP2 |
HOP2 |
121.2 |
180.0 |
| O5' |
P |
OP3 |
HOP3 |
90.9 |
300.0 |
| OP3 |
P |
OP2 |
HOP2 |
7.3 |
59.9 |
| C2 |
N1 |
C6 |
C1' |
179.8 |
180.3 |
| C6 |
N1 |
C2 |
O2 |
180.5 |
179.8 |
| C6 |
N1 |
C1' |
C2' |
258.6 |
295.3 |
| C6 |
N1 |
C1' |
O4' |
16.2 |
50.6 |
| C6 |
N1 |
C1' |
H1' |
146.4 |
173.0 |
| C6 |
N1 |
C2 |
C1' |
180.1 |
179.7 |
| C2 |
N1 |
C1' |
C2' |
78.8 |
115.0 |
| C2 |
N1 |
C1' |
O4' |
196.3 |
230.3 |
| C2 |
N1 |
C1' |
H1' |
326.6 |
352.7 |
| C6 |
N1 |
C1' |
C2 |
179.9 |
180.3 |
| C1' |
N1 |
C2 |
O2 |
0.3 |
0.1 |
| S2' |
C2' |
C1' |
N1 |
205.4 |
261.4 |
| N1 |
C1' |
C2' |
H2' |
325.6 |
24.0 |
| C2' |
C1' |
N1 |
O4' |
242.4 |
244.7 |
| C2' |
C1' |
N1 |
H1' |
112.2 |
122.3 |
| C4' |
O4' |
C1' |
N1 |
236.1 |
200.7 |
| O4' |
C1' |
N1 |
H1' |
229.7 |
237.6 |
| C5 |
C6 |
N1 |
C1' |
180.3 |
179.7 |
| H6 |
C6 |
N1 |
C2 |
180.2 |
180.0 |
| H6 |
C6 |
N1 |
C1' |
0.3 |
359.7 |
| N3 |
C2 |
N1 |
C1' |
179.5 |
180.0 |
| O2 |
C2 |
N1 |
C1' |
0.3 |
0.1 |
| C4 |
C5 |
C6 |
H6 |
180.1 |
180.5 |
| C5 |
C4 |
N3 |
HN3 |
179.9 |
180.5 |
| O4 |
C4 |
N3 |
HN3 |
359.5 |
0.1 |
| H5 |
C5 |
C6 |
H6 |
0.2 |
360.0 |
| C1' |
C2' |
C3' |
H2' |
231.0 |
241.3 |
| C3' |
C2' |
C1' |
H1' |
203.2 |
265.1 |
| S2' |
C2' |
C3' |
H2' |
122.2 |
122.7 |
| N1 |
C1' |
C2' |
O4' |
112.7 |
118.8 |
| N1 |
C1' |
C2' |
H1' |
242.9 |
237.7 |
| C3' |
C2' |
C1' |
H2' |
120.5 |
118.8 |
| S2' |
C2' |
C1' |
H2' |
239.8 |
237.5 |
| C1' |
C2' |
S2' |
C2A |
66.0 |
175.0 |
| C4' |
O4' |
C1' |
C2' |
6.6 |
319.5 |
| O4' |
C1' |
C2' |
H1' |
130.2 |
118.9 |
| N1 |
C1' |
C2' |
S2' |
205.4 |
261.4 |
| C3' |
C2' |
S2' |
H2' |
237.5 |
237.2 |
| C1' |
C2' |
S2' |
H2' |
129.1 |
122.5 |
| S2' |
C2' |
C1' |
O4' |
92.8 |
142.7 |
| S2' |
C2' |
C1' |
H1' |
322.6 |
23.7 |
| C2' |
S2' |
C2A |
H2A |
231.9 |
60.0 |
| C2' |
S2' |
C2A |
H2AA |
351.9 |
180.0 |
| C2' |
S2' |
C2A |
H2AB |
111.9 |
300.0 |
| S2' |
C2' |
H2' |
C1' |
117.0 |
122.6 |
| H2' |
C2' |
C1' |
O4' |
213.0 |
265.2 |
| H2' |
C2' |
C1' |
H1' |
82.8 |
146.3 |
| H2' |
C2' |
S2' |
C2A |
296.9 |
52.4 |
| C2A |
S2' |
C2' |
C1' |
66.0 |
175.0 |
| C2A |
S2' |
C2' |
H2' |
296.9 |
52.4 |
| H2A |
C2A |
S2' |
H2AA |
240.0 |
240.0 |
| H2A |
C2A |
S2' |
H2AB |
120.0 |
120.0 |
| H2AA |
C2A |
S2' |
H2AB |
240.0 |
239.9 |
| S2' |
C2A |
H2A |
H2AA |
120.0 |
120.0 |
| S2' |
C2A |
H2A |
H2AB |
240.0 |
240.0 |
| H2AA |
C2A |
H2A |
H2AB |
120.0 |
120.0 |
| S2' |
C2A |
H2AA |
H2A |
240.0 |
240.0 |
| S2' |
C2A |
H2AA |
H2AB |
120.0 |
120.0 |
| H2A |
C2A |
H2AA |
H2AB |
240.0 |
240.0 |
| S2' |
C2A |
H2AB |
H2A |
120.0 |
120.0 |
| S2' |
C2A |
H2AB |
H2AA |
240.0 |
240.0 |
| H2A |
C2A |
H2AB |
H2AA |
120.0 |
119.9 |
| H5' |
C5' |
C4' |
H5'A |
121.0 |
120.0 |
| C3' |
C4' |
C5' |
H4' |
239.6 |
237.6 |
| O4' |
C4' |
C5' |
H4' |
122.2 |
122.2 |
| C5' |
C4' |
O4' |
C1' |
139.6 |
159.4 |
| C4' |
C5' |
H5' |
H5'A |
241.0 |
240.0 |
| H5' |
C5' |
C4' |
O4' |
328.7 |
306.5 |
| H5' |
C5' |
C4' |
H4' |
206.5 |
184.3 |
| C4' |
C5' |
H5'A |
H5' |
119.3 |
120.0 |
| H5'A |
C5' |
C4' |
O4' |
207.7 |
186.4 |
| H5'A |
C5' |
C4' |
H4' |
85.4 |
64.2 |
| C4' |
C3' |
C2' |
H2' |
164.6 |
118.7 |
| C3' |
C4' |
C5' |
H5' |
86.1 |
61.9 |
| C3' |
C4' |
C5' |
H5'A |
325.1 |
301.8 |
| C5' |
C4' |
C3' |
H4' |
116.0 |
122.3 |
| O4' |
C4' |
C3' |
H4' |
237.7 |
241.1 |
| N1 |
C1' |
O4' |
C4' |
236.1 |
200.7 |
| C2' |
C1' |
O4' |
C4' |
6.6 |
319.5 |
| O4' |
C4' |
C5' |
H5' |
328.7 |
306.5 |
| O4' |
C4' |
C5' |
H5'A |
207.7 |
186.4 |
| C5' |
C4' |
O4' |
H4' |
244.0 |
237.8 |
| C3' |
C4' |
O4' |
H4' |
120.5 |
119.0 |
| C4' |
O4' |
C1' |
H1' |
118.8 |
78.3 |
| H4' |
C4' |
C5' |
H5' |
206.5 |
184.3 |
| H4' |
C4' |
C5' |
H5'A |
85.4 |
64.2 |
| C5' |
C4' |
H4' |
O4' |
120.8 |
122.2 |
| H4' |
C4' |
O4' |
C1' |
255.7 |
281.6 |
| N1 |
C1' |
O4' |
C2' |
229.5 |
241.2 |
| N1 |
C1' |
O4' |
H1' |
117.3 |
122.3 |
| O4' |
C1' |
C2' |
H2' |
213.0 |
265.2 |
| C2' |
C1' |
O4' |
H1' |
247.8 |
241.2 |
| C1' |
O4' |
C4' |
H4' |
255.7 |
281.6 |
| N1 |
C1' |
H1' |
C2' |
130.3 |
122.3 |
| N1 |
C1' |
H1' |
O4' |
247.6 |
237.7 |
| H1' |
C1' |
C2' |
H2' |
82.8 |
146.3 |
| C2' |
C1' |
H1' |
O4' |
117.3 |
115.4 |
| O3' |
C3' |
C2' |
H2' |
286.4 |
237.3 |
| O3' |
C3' |
C4' |
H4' |
326.2 |
336.2 |
| H3' |
C3' |
C2' |
H2' |
42.5 |
0.1 |
| H3' |
C3' |
C4' |
H4' |
210.1 |
213.5 |
| HO3' |
O3' |
C3' |
H3' |
11.1 |
57.3 |