PDB Chemical Component XUG
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 XUG
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O6 |
C6 |
1.250 |
|
| C6 |
C5 |
1.393 |
|
| C6 |
N1 |
1.353 |
|
| C5 |
N7 |
1.348 |
|
| C5 |
C4 |
1.384 |
|
| N7 |
C8 |
1.353 |
|
| C8 |
N9 |
1.340 |
|
| C8 |
H8 |
1.080 |
|
| N1 |
C2 |
1.354 |
|
| N1 |
HN1 |
1.000 |
|
| C2 |
N2 |
1.351 |
|
| C2 |
N3 |
1.349 |
|
| N2 |
HN21 |
1.000 |
|
| N2 |
HN22 |
1.000 |
|
| N3 |
C4 |
1.352 |
|
| C4 |
N9 |
1.332 |
|
| N9 |
C1' |
1.483 |
|
| C1' |
O4' |
1.431 |
|
| C1' |
C2' |
1.515 |
|
| C1' |
H1' |
1.100 |
|
| O4' |
C4' |
1.428 |
|
| C2' |
SE2' |
1.964 |
|
| C2' |
C3' |
1.506 |
|
| C2' |
H2' |
1.100 |
|
| SE2' |
CA' |
1.972 |
|
| CA' |
HA'1 |
1.100 |
|
| CA' |
HA'2 |
1.100 |
|
| CA' |
HA'3 |
1.100 |
|
| C3' |
O3' |
1.424 |
|
| C3' |
C4' |
1.504 |
|
| C3' |
H3' |
1.100 |
|
| O3' |
HO3' |
0.950 |
|
| C4' |
C5' |
1.509 |
|
| C4' |
H4' |
1.100 |
|
| C5' |
O5' |
1.410 |
|
| C5' |
H5' |
1.100 |
|
| C5' |
H5'' |
1.100 |
|
| O5' |
P |
1.592 |
|
| P |
OP1 |
1.509 |
|
| P |
OP2 |
1.513 |
|
| P |
OP3 |
1.420 |
|
| OP2 |
HOP2 |
0.950 |
|
| OP3 |
HOP3 |
0.950 |
|
Bond Angles for XUG
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O6 |
C6 |
C5 |
120.7 |
|
| O6 |
C6 |
N1 |
119.9 |
|
| C5 |
C6 |
N1 |
119.4 |
|
| C6 |
C5 |
N7 |
133.9 |
|
| C6 |
C5 |
C4 |
119.0 |
|
| C6 |
N1 |
C2 |
120.6 |
|
| C6 |
N1 |
HN1 |
119.7 |
|
| N7 |
C5 |
C4 |
107.1 |
|
| C5 |
N7 |
C8 |
107.6 |
|
| C5 |
C4 |
N3 |
119.8 |
|
| C5 |
C4 |
N9 |
108.0 |
|
| N7 |
C8 |
N9 |
109.1 |
|
| N7 |
C8 |
H8 |
125.5 |
|
| N9 |
C8 |
H8 |
125.5 |
|
| C8 |
N9 |
C4 |
108.2 |
|
| C8 |
N9 |
C1' |
126.8 |
|
| C2 |
N1 |
HN1 |
119.7 |
|
| N1 |
C2 |
N2 |
120.5 |
|
| N1 |
C2 |
N3 |
120.8 |
|
| N2 |
C2 |
N3 |
118.7 |
|
| C2 |
N2 |
HN21 |
110.1 |
|
| C2 |
N2 |
HN22 |
124.9 |
|
| C2 |
N3 |
C4 |
120.5 |
|
| HN21 |
N2 |
HN22 |
125.0 |
|
| N3 |
C4 |
N9 |
132.2 |
|
| C4 |
N9 |
C1' |
125.0 |
|
| N9 |
C1' |
O4' |
110.1 |
|
| N9 |
C1' |
C2' |
108.6 |
|
| N9 |
C1' |
H1' |
108.9 |
|
| O4' |
C1' |
C2' |
107.1 |
|
| O4' |
C1' |
H1' |
110.4 |
|
| C1' |
O4' |
C4' |
110.1 |
|
| C2' |
C1' |
H1' |
111.7 |
|
| C1' |
C2' |
SE2' |
109.2 |
|
| C1' |
C2' |
C3' |
103.1 |
|
| C1' |
C2' |
H2' |
113.8 |
|
| O4' |
C4' |
C3' |
105.9 |
|
| O4' |
C4' |
C5' |
111.7 |
|
| O4' |
C4' |
H4' |
109.9 |
|
| SE2' |
C2' |
C3' |
109.5 |
|
| SE2' |
C2' |
H2' |
107.8 |
|
| C2' |
SE2' |
CA' |
98.6 |
|
| C3' |
C2' |
H2' |
113.4 |
|
| C2' |
C3' |
O3' |
114.8 |
|
| C2' |
C3' |
C4' |
104.1 |
|
| C2' |
C3' |
H3' |
110.0 |
|
| SE2' |
CA' |
HA'1 |
109.5 |
|
| SE2' |
CA' |
HA'2 |
109.5 |
|
| SE2' |
CA' |
HA'3 |
109.5 |
|
| HA'1 |
CA' |
HA'2 |
109.5 |
|
| HA'1 |
CA' |
HA'3 |
109.5 |
|
| HA'2 |
CA' |
HA'3 |
109.5 |
|
| O3' |
C3' |
C4' |
110.4 |
|
| O3' |
C3' |
H3' |
103.5 |
|
| C3' |
O3' |
HO3' |
109.5 |
|
| C4' |
C3' |
H3' |
114.4 |
|
| C3' |
C4' |
C5' |
107.8 |
|
| C3' |
C4' |
H4' |
113.6 |
|
| C5' |
C4' |
H4' |
108.0 |
|
| C4' |
C5' |
O5' |
106.9 |
|
| C4' |
C5' |
H5' |
110.3 |
|
| C4' |
C5' |
H5'' |
110.9 |
|
| O5' |
C5' |
H5' |
110.4 |
|
| O5' |
C5' |
H5'' |
110.9 |
|
| C5' |
O5' |
P |
117.4 |
|
| H5' |
C5' |
H5'' |
107.5 |
|
| O5' |
P |
OP1 |
106.7 |
|
| O5' |
P |
OP2 |
108.3 |
|
| O5' |
P |
OP3 |
116.7 |
|
| OP1 |
P |
OP2 |
120.2 |
|
| OP1 |
P |
OP3 |
103.6 |
|
| OP2 |
P |
OP3 |
101.9 |
|
| P |
OP2 |
HOP2 |
108.3 |
|
| P |
OP3 |
HOP3 |
109.5 |
|
Torsion Angles for XUG
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C5 |
C6 |
O6 |
N1 |
179.7 |
|
| O6 |
C6 |
C5 |
N7 |
0.3 |
|
| O6 |
C6 |
C5 |
C4 |
180.1 |
|
| O6 |
C6 |
N1 |
C2 |
179.8 |
|
| O6 |
C6 |
N1 |
HN1 |
359.8 |
|
| O6 |
C6 |
C5 |
N1 |
180.3 |
|
| C5 |
C6 |
N1 |
C2 |
0.1 |
|
| C5 |
C6 |
N1 |
HN1 |
180.2 |
|
| N7 |
C5 |
C6 |
C4 |
180.2 |
|
| C6 |
C5 |
N7 |
C8 |
179.8 |
|
| C6 |
C5 |
C4 |
N3 |
0.2 |
|
| C6 |
C5 |
C4 |
N9 |
180.2 |
|
| O6 |
C6 |
N1 |
C5 |
179.7 |
|
| N1 |
C6 |
C5 |
N7 |
180.0 |
|
| N1 |
C6 |
C5 |
C4 |
359.8 |
|
| C2 |
N1 |
C6 |
HN1 |
180.0 |
|
| C6 |
N1 |
C2 |
N2 |
179.9 |
|
| C6 |
N1 |
C2 |
N3 |
0.0 |
|
| N7 |
C5 |
C6 |
N1 |
180.0 |
|
| C6 |
C5 |
N7 |
C4 |
179.8 |
|
| N7 |
C5 |
C4 |
N3 |
180.0 |
|
| N7 |
C5 |
C4 |
N9 |
0.0 |
|
| C5 |
N7 |
C8 |
N9 |
359.9 |
|
| C5 |
N7 |
C8 |
H8 |
179.9 |
|
| C4 |
C5 |
C6 |
N1 |
359.8 |
|
| C6 |
C5 |
C4 |
N7 |
180.2 |
|
| C4 |
C5 |
N7 |
C8 |
0.0 |
|
| C8 |
N9 |
C4 |
C5 |
359.9 |
|
| C2 |
N3 |
C4 |
C5 |
0.0 |
|
| N3 |
C4 |
C5 |
N9 |
180.0 |
|
| C5 |
C4 |
N9 |
C1' |
180.2 |
|
| C8 |
N7 |
C5 |
C4 |
0.0 |
|
| N9 |
C8 |
N7 |
H8 |
180.0 |
|
| N7 |
C8 |
N9 |
C4 |
0.1 |
|
| N7 |
C8 |
N9 |
C1' |
179.8 |
|
| C5 |
C4 |
N9 |
C8 |
359.9 |
|
| N7 |
C8 |
N9 |
H8 |
180.0 |
|
| N3 |
C4 |
N9 |
C8 |
180.0 |
|
| C4 |
N9 |
C8 |
C1' |
180.3 |
|
| C8 |
N9 |
C1' |
O4' |
4.4 |
|
| C8 |
N9 |
C1' |
C2' |
247.4 |
|
| C8 |
N9 |
C1' |
H1' |
125.5 |
|
| N7 |
C8 |
H8 |
N9 |
180.0 |
|
| H8 |
C8 |
N9 |
C4 |
180.1 |
|
| H8 |
C8 |
N9 |
C1' |
359.9 |
|
| C6 |
N1 |
C2 |
HN1 |
180.0 |
|
| N2 |
C2 |
N1 |
N3 |
179.9 |
|
| N1 |
C2 |
N2 |
HN21 |
360.0 |
|
| N1 |
C2 |
N2 |
HN22 |
180.0 |
|
| N1 |
C2 |
N3 |
C4 |
359.9 |
|
| C6 |
N1 |
HN1 |
C2 |
180.0 |
|
| HN1 |
N1 |
C2 |
N2 |
359.9 |
|
| HN1 |
N1 |
C2 |
N3 |
180.0 |
|
| N2 |
C2 |
N1 |
HN1 |
359.9 |
|
| N1 |
C2 |
N2 |
N3 |
180.1 |
|
| N2 |
C2 |
N3 |
C4 |
180.0 |
|
| HN21 |
N2 |
C2 |
HN22 |
180.0 |
|
| C5 |
C4 |
N3 |
C2 |
0.0 |
|
| N3 |
C2 |
N1 |
HN1 |
180.0 |
|
| N1 |
C2 |
N3 |
N2 |
179.9 |
|
| N3 |
C2 |
N2 |
HN21 |
179.9 |
|
| N3 |
C2 |
N2 |
HN22 |
359.9 |
|
| C2 |
N3 |
C4 |
N9 |
180.0 |
|
| HN21 |
N2 |
C2 |
N3 |
179.9 |
|
| C2 |
N2 |
HN21 |
HN22 |
180.0 |
|
| HN22 |
N2 |
C2 |
N3 |
359.9 |
|
| C2 |
N2 |
HN22 |
HN21 |
180.0 |
|
| C5 |
C4 |
N3 |
N9 |
180.0 |
|
| C8 |
N9 |
C4 |
N3 |
180.0 |
|
| N3 |
C4 |
N9 |
C1' |
0.2 |
|
| C5 |
C4 |
N9 |
N3 |
180.0 |
|
| C4 |
N9 |
C8 |
H8 |
180.1 |
|
| C8 |
N9 |
C4 |
C1' |
179.7 |
|
| C4 |
N9 |
C1' |
O4' |
184.1 |
|
| C4 |
N9 |
C1' |
C2' |
67.1 |
|
| C4 |
N9 |
C1' |
H1' |
305.2 |
|
| C1' |
N9 |
C8 |
H8 |
359.9 |
|
| C8 |
N9 |
C1' |
C4 |
180.3 |
|
| O4' |
C1' |
N9 |
C2' |
117.0 |
|
| O4' |
C1' |
N9 |
H1' |
238.9 |
|
| N9 |
C1' |
O4' |
C4' |
245.7 |
|
| C2' |
C1' |
N9 |
H1' |
121.9 |
|
| N9 |
C1' |
C2' |
SE2' |
213.7 |
|
| N9 |
C1' |
C2' |
C3' |
97.4 |
|
| N9 |
C1' |
C2' |
H2' |
334.2 |
|
| N9 |
C1' |
O4' |
C2' |
242.1 |
|
| N9 |
C1' |
O4' |
H1' |
120.2 |
|
| C2' |
C1' |
O4' |
H1' |
238.2 |
|
| O4' |
C1' |
C2' |
SE2' |
94.8 |
|
| O4' |
C1' |
C2' |
C3' |
338.5 |
|
| O4' |
C1' |
C2' |
H2' |
215.3 |
|
| C1' |
O4' |
C4' |
C3' |
16.0 |
|
| C1' |
O4' |
C4' |
C5' |
133.1 |
|
| C1' |
O4' |
C4' |
H4' |
252.9 |
|
| N9 |
C1' |
C2' |
O4' |
118.9 |
|
| N9 |
C1' |
C2' |
H1' |
239.9 |
|
| O4' |
C1' |
C2' |
H1' |
121.0 |
|
| C2' |
C1' |
O4' |
C4' |
3.6 |
|
| SE2' |
C2' |
C1' |
C3' |
116.3 |
|
| SE2' |
C2' |
C1' |
H2' |
239.5 |
|
| C1' |
C2' |
SE2' |
CA' |
82.8 |
|
| C3' |
C2' |
C1' |
H2' |
123.3 |
|
| C1' |
C2' |
C3' |
O3' |
151.2 |
|
| C1' |
C2' |
C3' |
C4' |
30.4 |
|
| C1' |
C2' |
C3' |
H3' |
267.5 |
|
| N9 |
C1' |
H1' |
O4' |
239.1 |
|
| N9 |
C1' |
H1' |
C2' |
120.0 |
|
| O4' |
C1' |
H1' |
C2' |
240.9 |
|
| H1' |
C1' |
O4' |
C4' |
125.4 |
|
| H1' |
C1' |
C2' |
SE2' |
333.8 |
|
| H1' |
C1' |
C2' |
C3' |
217.5 |
|
| H1' |
C1' |
C2' |
H2' |
94.3 |
|
| C4' |
O4' |
C1' |
C2' |
3.6 |
|
| C4' |
O4' |
C1' |
H1' |
125.4 |
|
| C2' |
C3' |
C4' |
O4' |
330.9 |
|
| O3' |
C3' |
C4' |
O4' |
207.1 |
|
| O4' |
C4' |
C3' |
H3' |
90.9 |
|
| C3' |
C4' |
O4' |
C5' |
242.9 |
|
| C3' |
C4' |
O4' |
H4' |
123.1 |
|
| C5' |
C4' |
O4' |
H4' |
240.2 |
|
| O4' |
C4' |
C5' |
O5' |
61.7 |
|
| O4' |
C4' |
C5' |
H5' |
181.7 |
|
| O4' |
C4' |
C5' |
H5'' |
300.7 |
|
| SE2' |
C2' |
C1' |
H1' |
333.8 |
|
| C1' |
C2' |
SE2' |
C3' |
247.9 |
|
| C1' |
C2' |
SE2' |
H2' |
124.0 |
|
| C3' |
C2' |
SE2' |
H2' |
236.2 |
|
| SE2' |
C2' |
C3' |
O3' |
35.2 |
|
| SE2' |
C2' |
C3' |
C4' |
274.3 |
|
| SE2' |
C2' |
C3' |
H3' |
151.4 |
|
| C2' |
SE2' |
CA' |
HA'1 |
240.7 |
|
| C2' |
SE2' |
CA' |
HA'2 |
0.6 |
|
| C2' |
SE2' |
CA' |
HA'3 |
120.6 |
|
| C3' |
C2' |
C1' |
H1' |
217.5 |
|
| C1' |
C2' |
C3' |
SE2' |
116.1 |
|
| C1' |
C2' |
C3' |
H2' |
236.5 |
|
| O4' |
C4' |
C3' |
C2' |
330.9 |
|
| SE2' |
C2' |
C3' |
H2' |
120.5 |
|
| C3' |
C2' |
SE2' |
CA' |
194.9 |
|
| O3' |
C3' |
C2' |
C4' |
120.8 |
|
| O3' |
C3' |
C2' |
H3' |
243.8 |
|
| C2' |
C3' |
O3' |
HO3' |
164.1 |
|
| C4' |
C3' |
C2' |
H3' |
122.9 |
|
| C2' |
C3' |
C4' |
C5' |
211.2 |
|
| C2' |
C3' |
C4' |
H4' |
91.6 |
|
| H2' |
C2' |
C1' |
H1' |
94.3 |
|
| C1' |
C2' |
H2' |
SE2' |
238.8 |
|
| C1' |
C2' |
H2' |
C3' |
117.4 |
|
| SE2' |
C2' |
H2' |
C3' |
238.6 |
|
| H2' |
C2' |
SE2' |
CA' |
318.7 |
|
| H2' |
C2' |
C3' |
O3' |
274.7 |
|
| H2' |
C2' |
C3' |
C4' |
153.9 |
|
| H2' |
C2' |
C3' |
H3' |
30.9 |
|
| CA' |
SE2' |
C2' |
C3' |
194.9 |
|
| CA' |
SE2' |
C2' |
H2' |
318.7 |
|
| HA'1 |
CA' |
SE2' |
HA'2 |
240.0 |
|
| HA'1 |
CA' |
SE2' |
HA'3 |
120.0 |
|
| HA'2 |
CA' |
SE2' |
HA'3 |
240.0 |
|
| SE2' |
CA' |
HA'1 |
HA'2 |
120.0 |
|
| SE2' |
CA' |
HA'1 |
HA'3 |
240.0 |
|
| HA'2 |
CA' |
HA'1 |
HA'3 |
120.0 |
|
| SE2' |
CA' |
HA'2 |
HA'1 |
240.0 |
|
| SE2' |
CA' |
HA'2 |
HA'3 |
120.0 |
|
| HA'1 |
CA' |
HA'2 |
HA'3 |
240.0 |
|
| SE2' |
CA' |
HA'3 |
HA'1 |
120.0 |
|
| SE2' |
CA' |
HA'3 |
HA'2 |
240.0 |
|
| HA'1 |
CA' |
HA'3 |
HA'2 |
120.0 |
|
| O4' |
C4' |
C3' |
O3' |
207.1 |
|
| O3' |
C3' |
C2' |
H2' |
274.7 |
|
| C2' |
C3' |
O3' |
C4' |
242.7 |
|
| C2' |
C3' |
O3' |
H3' |
119.9 |
|
| C4' |
C3' |
O3' |
H3' |
237.2 |
|
| O3' |
C3' |
C4' |
C5' |
87.4 |
|
| O3' |
C3' |
C4' |
H4' |
327.8 |
|
| O4' |
C4' |
C3' |
C5' |
119.7 |
|
| O4' |
C4' |
C3' |
H4' |
239.3 |
|
| C4' |
C3' |
C2' |
H2' |
153.9 |
|
| C2' |
C3' |
C4' |
O3' |
123.8 |
|
| C2' |
C3' |
C4' |
H3' |
240.0 |
|
| O3' |
C3' |
C4' |
H3' |
116.2 |
|
| C4' |
C3' |
O3' |
HO3' |
281.4 |
|
| C5' |
C4' |
C3' |
H4' |
119.6 |
|
| C3' |
C4' |
C5' |
O5' |
177.6 |
|
| C3' |
C4' |
C5' |
H5' |
297.6 |
|
| C3' |
C4' |
C5' |
H5'' |
56.6 |
|
| H3' |
C3' |
C2' |
H2' |
30.9 |
|
| C2' |
C3' |
H3' |
O3' |
236.8 |
|
| C2' |
C3' |
H3' |
C4' |
116.6 |
|
| O3' |
C3' |
H3' |
C4' |
239.8 |
|
| H3' |
C3' |
O3' |
HO3' |
44.3 |
|
| H3' |
C3' |
C4' |
C5' |
331.2 |
|
| H3' |
C3' |
C4' |
H4' |
211.6 |
|
| HO3' |
O3' |
C3' |
C4' |
281.4 |
|
| HO3' |
O3' |
C3' |
H3' |
44.3 |
|
| O4' |
C4' |
C5' |
C3' |
244.1 |
|
| O4' |
C4' |
C5' |
H4' |
120.9 |
|
| C5' |
C4' |
C3' |
H3' |
331.2 |
|
| C3' |
C4' |
C5' |
H4' |
236.8 |
|
| O5' |
C5' |
C4' |
H5' |
240.0 |
|
| O5' |
C5' |
C4' |
H5'' |
121.0 |
|
| C4' |
C5' |
O5' |
P |
220.2 |
|
| H5' |
C5' |
C4' |
H5'' |
241.0 |
|
| O4' |
C4' |
H4' |
C3' |
118.4 |
|
| O4' |
C4' |
H4' |
C5' |
237.9 |
|
| H4' |
C4' |
C3' |
H3' |
211.6 |
|
| C3' |
C4' |
H4' |
C5' |
119.6 |
|
| H4' |
C4' |
C5' |
O5' |
300.8 |
|
| H4' |
C4' |
C5' |
H5' |
60.8 |
|
| H4' |
C4' |
C5' |
H5'' |
179.8 |
|
| O5' |
C5' |
C4' |
H4' |
300.8 |
|
| C4' |
C5' |
O5' |
H5' |
120.0 |
|
| C4' |
C5' |
O5' |
H5'' |
239.0 |
|
| H5' |
C5' |
O5' |
H5'' |
119.0 |
|
| C5' |
O5' |
P |
OP1 |
262.4 |
|
| C5' |
O5' |
P |
OP2 |
33.1 |
|
| C5' |
O5' |
P |
OP3 |
147.3 |
|
| H5' |
C5' |
C4' |
H4' |
60.8 |
|
| C4' |
C5' |
H5' |
O5' |
242.1 |
|
| C4' |
C5' |
H5' |
H5'' |
121.1 |
|
| O5' |
C5' |
H5' |
H5'' |
239.0 |
|
| H5' |
C5' |
O5' |
P |
100.2 |
|
| H5'' |
C5' |
C4' |
H4' |
179.8 |
|
| C4' |
C5' |
H5'' |
O5' |
118.6 |
|
| C4' |
C5' |
H5'' |
H5' |
239.3 |
|
| O5' |
C5' |
H5'' |
H5' |
120.7 |
|
| H5'' |
C5' |
O5' |
P |
341.2 |
|
| P |
O5' |
C5' |
H5' |
100.2 |
|
| P |
O5' |
C5' |
H5'' |
341.2 |
|
| OP1 |
P |
O5' |
OP2 |
229.3 |
|
| OP1 |
P |
O5' |
OP3 |
115.2 |
|
| OP2 |
P |
O5' |
OP3 |
245.9 |
|
| O5' |
P |
OP2 |
HOP2 |
180.0 |
|
| O5' |
P |
OP3 |
HOP3 |
335.5 |
|
| O5' |
P |
OP1 |
OP2 |
123.6 |
|
| O5' |
P |
OP1 |
OP3 |
236.3 |
|
| OP2 |
P |
OP1 |
OP3 |
112.7 |
|
| OP1 |
P |
OP2 |
HOP2 |
302.8 |
|
| OP1 |
P |
OP3 |
HOP3 |
218.7 |
|
| O5' |
P |
OP2 |
OP1 |
237.2 |
|
| O5' |
P |
OP2 |
OP3 |
123.6 |
|
| OP1 |
P |
OP2 |
OP3 |
246.4 |
|
| OP2 |
P |
OP3 |
HOP3 |
93.2 |
|
| O5' |
P |
OP3 |
OP1 |
116.9 |
|
| O5' |
P |
OP3 |
OP2 |
242.3 |
|
| OP1 |
P |
OP3 |
OP2 |
125.5 |
|
| OP3 |
P |
OP2 |
HOP2 |
56.4 |
|
| HOP2 |
OP2 |
P |
OP3 |
56.4 |
|