PDB Chemical Component XUA
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 XUA
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| OP1 |
P |
1.462 |
1.480 |
| O5' |
P |
1.603 |
1.609 |
| P |
OP2 |
1.484 |
1.610 |
| P |
OP3 |
1.582 |
1.610 |
| C2 |
N1 |
1.346 |
1.321 |
| C6 |
N1 |
1.359 |
1.329 |
| N3 |
C2 |
1.330 |
1.316 |
| C2 |
H2 |
1.080 |
1.080 |
| N3 |
C4 |
1.355 |
1.328 |
| N9 |
C4 |
1.368 |
1.372 |
| C4 |
C5 |
1.377 |
1.406 |
| N7 |
C5 |
1.390 |
1.355 |
| C5 |
C6 |
1.420 |
1.405 |
| C6 |
N6 |
1.340 |
1.383 |
| N6 |
HN6 |
1.000 |
0.971 |
| N6 |
HN6A |
1.000 |
0.970 |
| C8 |
N7 |
1.305 |
1.301 |
| N9 |
C8 |
1.363 |
1.363 |
| C8 |
H8 |
1.080 |
1.079 |
| C1' |
N9 |
1.470 |
1.465 |
| C2' |
C1' |
1.509 |
1.540 |
| O4' |
C1' |
1.427 |
1.437 |
| C1' |
H1' |
1.100 |
1.090 |
| SE2' |
C2' |
1.974 |
1.959 |
| C3' |
C2' |
1.530 |
1.548 |
| C2' |
H2' |
1.100 |
1.091 |
| SE2' |
CA' |
1.953 |
1.960 |
| OP2 |
HOP2 |
0.950 |
0.967 |
| O3' |
C3' |
1.424 |
1.429 |
| C3' |
C4' |
1.520 |
1.550 |
| C3' |
H3' |
1.100 |
1.091 |
| O3' |
HO3' |
0.950 |
0.967 |
| OP3 |
HOP3 |
0.950 |
0.967 |
| C4' |
C5' |
1.514 |
1.531 |
| C4' |
O4' |
1.440 |
1.446 |
| C4' |
H4' |
1.100 |
1.090 |
| C5' |
O5' |
1.414 |
1.429 |
| C5' |
H5' |
1.100 |
1.090 |
| C5' |
H5'' |
1.100 |
1.091 |
| CA' |
HA1 |
1.099 |
1.090 |
| CA' |
HA2 |
1.100 |
1.090 |
| CA' |
HA3 |
1.101 |
1.090 |
Bond Angles for XUA
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP1 |
P |
OP2 |
122.0 |
109.4 |
| OP1 |
P |
OP3 |
103.6 |
109.5 |
| OP2 |
P |
OP3 |
107.6 |
109.5 |
| P |
OP2 |
HOP2 |
109.5 |
114.0 |
| P |
OP3 |
HOP3 |
109.5 |
114.0 |
| N3 |
C2 |
H2 |
116.7 |
118.8 |
| N3 |
C4 |
C5 |
127.3 |
119.1 |
| C4 |
C5 |
C6 |
115.4 |
118.2 |
| C5 |
C6 |
N6 |
123.9 |
120.8 |
| C6 |
N6 |
HN6 |
109.5 |
120.0 |
| C6 |
N6 |
HN6A |
109.5 |
120.0 |
| HN6 |
N6 |
HN6A |
109.5 |
120.0 |
| N9 |
C8 |
H8 |
123.1 |
125.1 |
| C2' |
C1' |
H1' |
106.0 |
109.9 |
| O4' |
C1' |
H1' |
113.7 |
109.9 |
| SE2' |
C2' |
H2' |
103.5 |
110.4 |
| C3' |
C2' |
H2' |
115.6 |
110.5 |
| SE2' |
CA' |
HA1 |
109.5 |
109.5 |
| SE2' |
CA' |
HA2 |
109.5 |
109.5 |
| SE2' |
CA' |
HA3 |
109.5 |
109.4 |
| O3' |
C3' |
C4' |
115.2 |
110.9 |
| O3' |
C3' |
H3' |
101.8 |
110.8 |
| C4' |
C3' |
H3' |
111.5 |
110.9 |
| C3' |
C4' |
C5' |
116.3 |
110.6 |
| C3' |
C4' |
O4' |
103.6 |
103.6 |
| C3' |
C4' |
H4' |
108.4 |
110.6 |
| O4' |
C4' |
C5' |
107.2 |
110.6 |
| C5' |
C4' |
H4' |
104.7 |
110.6 |
| C4' |
C5' |
O5' |
107.9 |
109.5 |
| C4' |
C5' |
H5' |
110.0 |
109.5 |
| C4' |
C5' |
H5'' |
110.0 |
109.4 |
| O4' |
C4' |
H4' |
117.2 |
110.6 |
| O5' |
C5' |
H5' |
110.0 |
109.5 |
| O5' |
C5' |
H5'' |
110.0 |
109.5 |
| H5' |
C5' |
H5'' |
108.9 |
109.4 |
| HA1 |
CA' |
HA2 |
109.5 |
109.5 |
| HA1 |
CA' |
HA3 |
109.4 |
109.4 |
| HA2 |
CA' |
HA3 |
109.5 |
109.5 |
Torsion Angles for XUA
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP2 |
P |
OP1 |
OP3 |
121.2 |
240.0 |
| OP1 |
P |
OP2 |
HOP2 |
0.0 |
180.0 |
| OP1 |
P |
OP3 |
HOP3 |
360.0 |
300.0 |
| O5' |
P |
OP2 |
HOP2 |
233.2 |
300.0 |
| O5' |
P |
OP3 |
HOP3 |
115.0 |
180.0 |
| OP1 |
P |
OP2 |
OP3 |
240.7 |
120.0 |
| OP2 |
P |
OP3 |
HOP3 |
229.5 |
60.0 |
| OP1 |
P |
OP3 |
OP2 |
130.5 |
240.0 |
| OP3 |
P |
OP2 |
HOP2 |
119.3 |
60.0 |
| C4 |
N3 |
C2 |
H2 |
180.1 |
180.0 |
| N3 |
C4 |
C5 |
C6 |
0.8 |
0.0 |
| C4 |
C5 |
C6 |
N6 |
180.1 |
180.0 |
| C5 |
C6 |
N6 |
HN6 |
179.6 |
360.0 |
| C5 |
C6 |
N6 |
HN6A |
299.6 |
180.0 |
| HN6 |
N6 |
C6 |
HN6A |
240.0 |
180.0 |
| C6 |
N6 |
HN6 |
HN6A |
120.0 |
180.0 |
| C6 |
N6 |
HN6A |
HN6 |
240.0 |
180.0 |
| C1' |
N9 |
C8 |
H8 |
2.0 |
0.1 |
| O4' |
C1' |
C2' |
H1' |
122.1 |
119.5 |
| C2' |
C1' |
O4' |
H1' |
242.7 |
240.5 |
| SE2' |
C2' |
C1' |
H1' |
328.9 |
1.3 |
| C3' |
C2' |
SE2' |
H2' |
235.3 |
237.4 |
| C3' |
C2' |
C1' |
H1' |
210.6 |
242.4 |
| SE2' |
C2' |
C3' |
H2' |
117.5 |
122.6 |
| H2' |
C2' |
C1' |
H1' |
86.5 |
123.8 |
| CA' |
SE2' |
C2' |
H2' |
291.6 |
57.5 |
| HA1 |
CA' |
SE2' |
HA2 |
240.0 |
239.9 |
| HA1 |
CA' |
SE2' |
HA3 |
120.0 |
119.9 |
| HA2 |
CA' |
SE2' |
HA3 |
240.0 |
240.0 |
| HOP2 |
OP2 |
P |
OP3 |
119.3 |
60.0 |
| O3' |
C3' |
C2' |
H2' |
285.2 |
257.8 |
| C4' |
C3' |
O3' |
H3' |
239.1 |
236.4 |
| O3' |
C3' |
C4' |
C5' |
83.7 |
86.3 |
| O3' |
C3' |
C4' |
O4' |
201.0 |
204.8 |
| O3' |
C3' |
C4' |
H4' |
326.1 |
323.4 |
| C4' |
C3' |
C2' |
H2' |
161.6 |
139.6 |
| O3' |
C3' |
C4' |
H3' |
115.4 |
123.6 |
| O4' |
C4' |
C3' |
C5' |
117.3 |
118.5 |
| C5' |
C4' |
C3' |
H4' |
117.6 |
122.9 |
| C3' |
C4' |
C5' |
O5' |
53.9 |
185.0 |
| C3' |
C4' |
C5' |
H5' |
173.9 |
305.0 |
| C3' |
C4' |
C5' |
H5'' |
293.9 |
65.0 |
| O4' |
C4' |
C3' |
H4' |
234.9 |
241.4 |
| H3' |
C3' |
C2' |
H2' |
40.6 |
21.4 |
| O3' |
C3' |
H3' |
C4' |
236.7 |
236.3 |
| H3' |
C3' |
C4' |
C5' |
328.3 |
322.7 |
| H3' |
C3' |
C4' |
O4' |
85.6 |
81.2 |
| H3' |
C3' |
C4' |
H4' |
210.7 |
199.8 |
| HO3' |
O3' |
C3' |
C4' |
296.0 |
292.7 |
| HO3' |
O3' |
C3' |
H3' |
56.8 |
56.4 |
| C5' |
C4' |
C3' |
H3' |
328.3 |
322.7 |
| C3' |
C4' |
C5' |
O4' |
115.3 |
114.2 |
| C3' |
C4' |
C5' |
H4' |
240.5 |
237.1 |
| O4' |
C4' |
C5' |
H4' |
125.2 |
122.9 |
| O5' |
C5' |
C4' |
H5' |
240.0 |
240.0 |
| O5' |
C5' |
C4' |
H5'' |
120.0 |
120.0 |
| H5' |
C5' |
C4' |
H5'' |
240.0 |
240.1 |
| C4' |
O4' |
C1' |
H1' |
121.5 |
93.2 |
| O4' |
C4' |
C3' |
H3' |
85.6 |
81.2 |
| C3' |
C4' |
O4' |
C5' |
236.5 |
241.4 |
| C3' |
C4' |
O4' |
H4' |
119.2 |
118.6 |
| C5' |
C4' |
O4' |
H4' |
242.7 |
237.2 |
| O4' |
C4' |
C5' |
O5' |
298.6 |
70.8 |
| O4' |
C4' |
C5' |
H5' |
58.6 |
190.8 |
| O4' |
C4' |
C5' |
H5'' |
178.6 |
310.8 |
| H4' |
C4' |
C3' |
H3' |
210.7 |
199.8 |
| C3' |
C4' |
H4' |
C5' |
124.7 |
122.9 |
| C3' |
C4' |
H4' |
O4' |
243.4 |
245.8 |
| O4' |
C4' |
H4' |
C5' |
241.3 |
237.1 |
| H4' |
C4' |
C5' |
O5' |
173.5 |
307.9 |
| H4' |
C4' |
C5' |
H5' |
293.5 |
67.9 |
| H4' |
C4' |
C5' |
H5'' |
53.5 |
187.9 |
| O5' |
C5' |
C4' |
H4' |
173.5 |
307.9 |
| C4' |
C5' |
O5' |
H5' |
120.0 |
120.0 |
| C4' |
C5' |
O5' |
H5'' |
240.0 |
240.0 |
| H5' |
C5' |
O5' |
H5'' |
120.0 |
120.0 |
| H5' |
C5' |
C4' |
H4' |
293.5 |
67.9 |
| C4' |
C5' |
H5' |
O5' |
241.3 |
240.0 |
| C4' |
C5' |
H5' |
H5'' |
120.6 |
119.9 |
| O5' |
C5' |
H5' |
H5'' |
239.4 |
240.0 |
| H5'' |
C5' |
C4' |
H4' |
53.5 |
187.9 |
| C4' |
C5' |
H5'' |
O5' |
118.7 |
120.0 |
| C4' |
C5' |
H5'' |
H5' |
239.3 |
240.0 |
| O5' |
C5' |
H5'' |
H5' |
120.6 |
120.0 |
| SE2' |
CA' |
HA1 |
HA2 |
120.0 |
120.1 |
| SE2' |
CA' |
HA1 |
HA3 |
240.0 |
240.1 |
| HA2 |
CA' |
HA1 |
HA3 |
120.0 |
120.0 |
| SE2' |
CA' |
HA2 |
HA1 |
239.9 |
239.9 |
| SE2' |
CA' |
HA2 |
HA3 |
120.0 |
120.0 |
| HA1 |
CA' |
HA2 |
HA3 |
240.0 |
240.0 |
| SE2' |
CA' |
HA3 |
HA1 |
120.0 |
120.0 |
| SE2' |
CA' |
HA3 |
HA2 |
240.0 |
240.0 |
| HA1 |
CA' |
HA3 |
HA2 |
120.0 |
120.0 |