PDB Chemical Component GDO
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 GDO
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| OP1 |
P |
1.487 |
1.480 |
| C5' |
C4' |
1.514 |
1.530 |
| C5' |
O5' |
1.446 |
1.429 |
| O2' |
C2' |
1.413 |
1.429 |
| C3' |
C4' |
1.519 |
1.551 |
| C3' |
C2' |
1.524 |
1.548 |
| C4' |
O4' |
1.453 |
1.443 |
| O5' |
P |
1.597 |
1.610 |
| C2' |
C1' |
1.531 |
1.541 |
| P |
OP2 |
1.482 |
1.610 |
| O4' |
C1' |
1.417 |
1.438 |
| C1' |
N9 |
1.459 |
1.465 |
| N9 |
C8 |
1.376 |
1.366 |
| N9 |
C4 |
1.374 |
1.369 |
| C8 |
N7 |
1.305 |
1.301 |
| N3 |
C4 |
1.351 |
1.338 |
| N3 |
C2 |
1.324 |
1.314 |
| C4 |
C5 |
1.379 |
1.399 |
| N7 |
C5 |
1.389 |
1.355 |
| C5 |
C6 |
1.423 |
1.415 |
| C2 |
N2 |
1.342 |
1.372 |
| C2 |
N1 |
1.375 |
1.363 |
| N1 |
C6 |
1.393 |
1.352 |
| C6 |
O6 |
1.238 |
1.219 |
| P |
OP3 |
1.626 |
1.610 |
| N1 |
H1 |
1.000 |
0.970 |
| C8 |
H2 |
1.080 |
1.080 |
| N2 |
H3 |
1.000 |
0.970 |
| N2 |
H4 |
1.000 |
0.970 |
| OP2 |
H5 |
0.950 |
0.967 |
| C5' |
H6 |
1.100 |
1.091 |
| C5' |
H7 |
1.099 |
1.090 |
| C4' |
H8 |
1.100 |
1.090 |
| C3' |
H9 |
1.100 |
1.090 |
| C3' |
H10 |
1.100 |
1.090 |
| C2' |
H11 |
1.100 |
1.090 |
| O2' |
H12 |
0.950 |
0.967 |
| C1' |
H13 |
1.101 |
1.090 |
| OP3 |
H14 |
0.950 |
0.967 |
Bond Angles for GDO
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP1 |
P |
OP2 |
118.8 |
109.4 |
| OP1 |
P |
OP3 |
106.7 |
109.5 |
| C5' |
C4' |
O4' |
110.1 |
110.6 |
| C4' |
C5' |
H6 |
109.2 |
109.5 |
| C4' |
C5' |
H7 |
109.2 |
109.5 |
| C5' |
C4' |
H8 |
108.6 |
110.6 |
| O2' |
C2' |
C1' |
111.8 |
110.5 |
| O2' |
C2' |
H11 |
110.7 |
110.6 |
| C3' |
C4' |
H8 |
108.5 |
110.7 |
| C3' |
C2' |
C1' |
101.8 |
104.2 |
| C2' |
C3' |
H9 |
111.3 |
110.9 |
| C2' |
C3' |
H10 |
111.3 |
110.9 |
| C3' |
C2' |
H11 |
109.1 |
110.5 |
| C4' |
O4' |
C1' |
109.5 |
107.0 |
| O4' |
C4' |
H8 |
109.3 |
110.6 |
| O5' |
P |
OP3 |
108.8 |
109.5 |
| O4' |
C1' |
C2' |
107.6 |
107.3 |
| C2' |
C1' |
N9 |
111.9 |
109.9 |
| C1' |
C2' |
H11 |
109.0 |
110.5 |
| C2' |
C1' |
H13 |
108.7 |
109.9 |
| OP2 |
P |
OP3 |
110.8 |
109.5 |
| P |
OP2 |
H5 |
109.5 |
114.0 |
| O4' |
C1' |
N9 |
108.8 |
109.9 |
| O4' |
C1' |
H13 |
110.2 |
109.9 |
| N9 |
C1' |
H13 |
109.6 |
110.0 |
| N9 |
C8 |
N7 |
113.1 |
109.8 |
| N9 |
C8 |
H2 |
123.4 |
125.1 |
| N7 |
C8 |
H2 |
123.5 |
125.2 |
| C4 |
C5 |
C6 |
118.8 |
118.6 |
| C5 |
C6 |
O6 |
128.6 |
120.8 |
| C2 |
N2 |
H3 |
120.0 |
120.0 |
| C2 |
N2 |
H4 |
120.0 |
120.0 |
| C2 |
N1 |
H1 |
117.5 |
119.8 |
| N1 |
C6 |
O6 |
119.9 |
120.9 |
| P |
OP3 |
H14 |
109.5 |
114.0 |
| H3 |
N2 |
H4 |
120.0 |
120.0 |
| H6 |
C5' |
H7 |
109.5 |
109.4 |
| H9 |
C3' |
H10 |
109.5 |
110.9 |
Torsion Angles for GDO
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O5' |
P |
OP1 |
OP3 |
243.0 |
240.0 |
| OP2 |
P |
OP1 |
OP3 |
126.1 |
120.0 |
| OP1 |
P |
OP2 |
H5 |
0.0 |
300.0 |
| OP1 |
P |
OP3 |
H14 |
0.0 |
180.0 |
| C3' |
C4' |
C5' |
H8 |
237.5 |
237.0 |
| C5' |
C4' |
O4' |
C1' |
148.2 |
158.6 |
| O4' |
C4' |
C5' |
H8 |
119.7 |
122.9 |
| H6 |
C5' |
C4' |
H7 |
240.4 |
120.0 |
| C5' |
O5' |
P |
OP3 |
318.4 |
295.0 |
| C3' |
C2' |
O2' |
C1' |
114.8 |
114.8 |
| O2' |
C2' |
C3' |
H9 |
156.8 |
144.0 |
| O2' |
C2' |
C3' |
H10 |
34.4 |
20.4 |
| C3' |
C2' |
O2' |
H11 |
236.5 |
237.4 |
| O4' |
C1' |
C2' |
O2' |
98.9 |
120.7 |
| O2' |
C2' |
C1' |
N9 |
218.3 |
240.1 |
| C1' |
C2' |
O2' |
H11 |
121.7 |
122.6 |
| O2' |
C2' |
C1' |
H13 |
339.5 |
1.3 |
| C3' |
C4' |
C5' |
H6 |
169.5 |
60.6 |
| C3' |
C4' |
C5' |
H7 |
289.1 |
300.6 |
| C5' |
C4' |
C3' |
H8 |
122.5 |
122.9 |
| C3' |
C4' |
O4' |
C1' |
23.2 |
40.1 |
| O4' |
C4' |
C3' |
H8 |
243.6 |
241.4 |
| O2' |
C2' |
C3' |
C1' |
239.5 |
241.3 |
| O2' |
C2' |
C3' |
H11 |
124.4 |
122.7 |
| C2' |
C3' |
C4' |
H8 |
79.5 |
81.5 |
| O4' |
C1' |
C2' |
C3' |
336.7 |
2.0 |
| C3' |
C2' |
C1' |
N9 |
96.2 |
121.5 |
| C1' |
C2' |
C3' |
H11 |
244.9 |
241.3 |
| C3' |
C2' |
C1' |
H13 |
217.4 |
242.6 |
| H9 |
C3' |
C2' |
H10 |
122.4 |
123.6 |
| O4' |
C4' |
C5' |
H6 |
51.6 |
306.5 |
| O4' |
C4' |
C5' |
H7 |
171.2 |
186.5 |
| C5' |
C4' |
O4' |
H8 |
240.8 |
237.1 |
| C3' |
C4' |
O4' |
H8 |
115.8 |
118.6 |
| C4' |
O4' |
C1' |
C2' |
0.3 |
333.5 |
| C4' |
O4' |
C1' |
N9 |
238.9 |
214.0 |
| C4' |
O4' |
C1' |
H13 |
118.6 |
92.9 |
| OP1 |
P |
O5' |
OP3 |
115.6 |
120.0 |
| OP2 |
P |
O5' |
OP3 |
242.4 |
240.0 |
| O5' |
P |
OP2 |
H5 |
240.4 |
180.0 |
| O5' |
P |
OP3 |
H14 |
116.6 |
300.0 |
| O2' |
C2' |
C1' |
H11 |
237.3 |
237.3 |
| C1' |
C2' |
C3' |
H9 |
277.3 |
262.7 |
| C1' |
C2' |
C3' |
H10 |
154.9 |
139.1 |
| C3' |
C2' |
C1' |
H11 |
115.2 |
118.7 |
| O4' |
C1' |
C2' |
N9 |
240.5 |
240.5 |
| O4' |
C1' |
C2' |
H13 |
119.3 |
119.4 |
| N9 |
C1' |
C2' |
H13 |
238.8 |
238.9 |
| OP1 |
P |
OP2 |
OP3 |
235.9 |
240.0 |
| O5' |
P |
OP2 |
OP3 |
116.2 |
120.0 |
| OP2 |
P |
OP3 |
H14 |
229.2 |
60.0 |
| O2' |
C2' |
C1' |
O4' |
98.9 |
120.7 |
| C3' |
C2' |
C1' |
O4' |
336.7 |
2.0 |
| C1' |
O4' |
C4' |
H8 |
267.4 |
281.4 |
| C2' |
C1' |
O4' |
N9 |
121.4 |
119.4 |
| O4' |
C1' |
C2' |
H11 |
221.5 |
243.3 |
| C2' |
C1' |
O4' |
H13 |
241.7 |
240.6 |
| N9 |
C1' |
O4' |
H13 |
120.2 |
121.2 |
| O4' |
C1' |
N9 |
C2' |
118.7 |
117.8 |
| N9 |
C1' |
C2' |
H11 |
341.0 |
2.8 |
| C2' |
C1' |
N9 |
H13 |
120.6 |
121.1 |
| O4' |
C1' |
N9 |
H13 |
239.4 |
238.9 |
| C1' |
N9 |
C8 |
N7 |
178.0 |
179.8 |
| C1' |
N9 |
C8 |
H2 |
358.0 |
0.2 |
| N7 |
C8 |
N9 |
H2 |
180.0 |
179.6 |
| N9 |
C8 |
N7 |
H2 |
180.0 |
180.4 |
| N3 |
C2 |
N2 |
H3 |
360.0 |
360.0 |
| N3 |
C2 |
N2 |
H4 |
180.0 |
180.0 |
| N3 |
C2 |
N1 |
H1 |
179.7 |
180.1 |
| C4 |
C5 |
C6 |
O6 |
179.8 |
180.0 |
| N1 |
C6 |
C5 |
O6 |
180.2 |
180.0 |
| N2 |
C2 |
N1 |
H1 |
359.9 |
0.1 |
| H3 |
N2 |
C2 |
H4 |
180.0 |
180.0 |
| C5 |
C6 |
N1 |
O6 |
179.8 |
180.0 |
| OP1 |
P |
OP3 |
OP2 |
130.8 |
120.0 |
| OP3 |
P |
OP2 |
H5 |
124.2 |
60.0 |
| H1 |
N1 |
C6 |
O6 |
0.3 |
360.0 |
| N9 |
C8 |
H2 |
N7 |
180.0 |
179.6 |
| C2 |
N2 |
H3 |
H4 |
180.0 |
180.0 |
| C2 |
N2 |
H4 |
H3 |
180.0 |
180.0 |
| H5 |
OP2 |
P |
OP3 |
124.2 |
60.0 |
| H6 |
C5' |
C4' |
O4' |
51.6 |
306.5 |
| C4' |
C5' |
H6 |
H7 |
119.4 |
240.0 |
| H6 |
C5' |
C4' |
H8 |
291.9 |
183.6 |
| H7 |
C5' |
C4' |
O4' |
171.2 |
186.5 |
| C4' |
C5' |
H7 |
H6 |
240.6 |
120.0 |
| H7 |
C5' |
C4' |
H8 |
51.6 |
63.6 |
| C5' |
C4' |
H8 |
O4' |
120.1 |
122.9 |
| H8 |
C4' |
C5' |
H6 |
291.9 |
183.6 |
| H8 |
C4' |
C5' |
H7 |
51.6 |
63.6 |
| H8 |
C4' |
O4' |
C1' |
267.4 |
281.4 |
| H9 |
C3' |
C4' |
H8 |
198.2 |
199.7 |
| H9 |
C3' |
C2' |
C1' |
277.3 |
262.7 |
| C2' |
C3' |
H9 |
H10 |
236.6 |
236.4 |
| H9 |
C3' |
C2' |
H11 |
32.4 |
21.4 |
| H10 |
C3' |
C4' |
H8 |
320.7 |
323.4 |
| H10 |
C3' |
C2' |
C1' |
154.9 |
139.1 |
| C2' |
C3' |
H10 |
H9 |
123.4 |
123.6 |
| H10 |
C3' |
C2' |
H11 |
270.0 |
257.7 |
| O2' |
C2' |
H11 |
C1' |
123.3 |
122.6 |
| C3' |
C2' |
H11 |
C1' |
249.7 |
245.2 |
| H11 |
C2' |
C3' |
H9 |
32.4 |
21.4 |
| H11 |
C2' |
C3' |
H10 |
270.0 |
257.7 |
| H11 |
C2' |
C1' |
N9 |
341.0 |
2.8 |
| H11 |
C2' |
C1' |
H13 |
102.2 |
123.9 |
| H12 |
O2' |
C2' |
C1' |
65.3 |
183.7 |
| H12 |
O2' |
C2' |
H11 |
303.5 |
61.1 |
| O4' |
C1' |
H13 |
C2' |
242.4 |
242.2 |
| C2' |
C1' |
H13 |
N9 |
237.4 |
238.9 |
| H13 |
C1' |
C2' |
H11 |
102.2 |
123.9 |
| O4' |
C1' |
H13 |
N9 |
119.8 |
121.1 |