PDB Chemical Component D8X
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 D8X
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C2' |
C1' |
1.524 |
1.531 |
| C1' |
C1 |
1.537 |
1.530 |
| C1' |
C22 |
1.554 |
1.530 |
| O3P |
P |
1.482 |
1.480 |
| C1 |
C2 |
1.491 |
1.507 |
| O4 |
C4 |
1.406 |
1.429 |
| C2 |
O2 |
1.237 |
1.207 |
| C2 |
C3 |
1.544 |
1.507 |
| P |
O2P |
1.578 |
1.610 |
| P |
O1P |
1.489 |
1.610 |
| P |
O5 |
1.638 |
1.609 |
| O3 |
C3 |
1.385 |
1.429 |
| C4 |
C3 |
1.539 |
1.530 |
| C4 |
C5 |
1.503 |
1.529 |
| C3 |
O3' |
1.418 |
1.429 |
| O5 |
C5 |
1.404 |
1.429 |
| O1P |
H1 |
0.950 |
0.967 |
| O2P |
H2 |
0.950 |
0.967 |
| C5 |
H3 |
1.100 |
1.090 |
| C5 |
H4 |
1.100 |
1.090 |
| C4 |
H5 |
1.100 |
1.090 |
| O4 |
H6 |
0.950 |
0.967 |
| O3 |
H7 |
0.950 |
0.967 |
| O3' |
H8 |
0.950 |
0.967 |
| C1 |
H9 |
1.100 |
1.091 |
| C1 |
H10 |
1.100 |
1.090 |
| C1' |
H11 |
1.100 |
1.090 |
| C2' |
H12 |
1.100 |
1.091 |
| C2' |
H13 |
1.100 |
1.090 |
| C2' |
H14 |
1.100 |
1.090 |
| C22 |
H15 |
1.100 |
1.090 |
| C22 |
H16 |
1.100 |
1.090 |
| C22 |
H17 |
1.099 |
1.090 |
Bond Angles for D8X
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2' |
C1' |
C22 |
108.8 |
109.5 |
| C2' |
C1' |
H11 |
109.1 |
109.5 |
| C1' |
C1 |
H9 |
110.2 |
109.5 |
| C1' |
C1 |
H10 |
110.2 |
109.5 |
| C22 |
C1' |
H11 |
108.7 |
109.5 |
| C1' |
C22 |
H15 |
109.5 |
109.4 |
| C1' |
C22 |
H16 |
109.5 |
109.4 |
| C1' |
C22 |
H17 |
109.5 |
109.4 |
| O3P |
P |
O2P |
108.9 |
109.5 |
| O3P |
P |
O1P |
110.2 |
109.4 |
| O3P |
P |
O5 |
108.0 |
109.5 |
| O4 |
C4 |
C3 |
108.7 |
109.5 |
| O4 |
C4 |
H5 |
110.3 |
109.4 |
| O1P |
P |
O2P |
111.0 |
109.5 |
| O2P |
P |
O5 |
110.3 |
109.5 |
| P |
O2P |
H2 |
109.5 |
114.0 |
| O1P |
P |
O5 |
108.4 |
109.5 |
| P |
O1P |
H1 |
109.5 |
114.0 |
| P |
O5 |
C5 |
120.9 |
123.0 |
| O3 |
C3 |
O3' |
107.6 |
109.5 |
| C4 |
C3 |
O3' |
107.2 |
109.5 |
| C3 |
C4 |
H5 |
108.5 |
109.5 |
| C4 |
C5 |
H3 |
109.9 |
109.5 |
| C4 |
C5 |
H4 |
109.9 |
109.5 |
| C3 |
O3' |
H8 |
109.5 |
114.0 |
| O5 |
C5 |
H3 |
109.9 |
109.5 |
| O5 |
C5 |
H4 |
109.9 |
109.4 |
| H3 |
C5 |
H4 |
109.5 |
109.4 |
| H9 |
C1 |
H10 |
109.5 |
109.4 |
| H12 |
C2' |
H13 |
109.5 |
109.5 |
| H12 |
C2' |
H14 |
109.5 |
109.5 |
| H13 |
C2' |
H14 |
109.5 |
109.5 |
| H15 |
C22 |
H16 |
109.4 |
109.5 |
| H15 |
C22 |
H17 |
109.5 |
109.6 |
| H16 |
C22 |
H17 |
109.5 |
109.5 |
Torsion Angles for D8X
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2' |
C1' |
C1 |
H9 |
304.3 |
55.0 |
| C2' |
C1' |
C1 |
H10 |
65.2 |
295.0 |
| C22 |
C1' |
C2' |
H11 |
241.6 |
120.0 |
| C2' |
C1' |
C22 |
H15 |
180.0 |
60.0 |
| C2' |
C1' |
C22 |
H16 |
300.0 |
180.0 |
| C2' |
C1' |
C22 |
H17 |
60.0 |
300.0 |
| H9 |
C1 |
C1' |
H10 |
239.1 |
120.0 |
| C2' |
C1' |
C22 |
H11 |
118.7 |
240.0 |
| C22 |
C1' |
C1 |
H9 |
183.7 |
175.0 |
| C22 |
C1' |
C1 |
H10 |
304.6 |
55.0 |
| H15 |
C22 |
C1' |
H16 |
240.0 |
240.1 |
| H15 |
C22 |
C1' |
H17 |
120.0 |
120.1 |
| H16 |
C22 |
C1' |
H17 |
240.0 |
240.0 |
| O1P |
P |
O3P |
O2P |
238.0 |
240.0 |
| O2P |
P |
O3P |
O5 |
240.2 |
240.0 |
| O3P |
P |
O2P |
H2 |
360.0 |
180.1 |
| O1P |
P |
O3P |
O5 |
118.3 |
120.0 |
| O3P |
P |
O1P |
H1 |
0.0 |
60.0 |
| O3P |
P |
O5 |
C5 |
290.4 |
305.0 |
| O4 |
C4 |
C3 |
O3' |
181.7 |
295.0 |
| C3 |
C4 |
O4 |
H5 |
241.1 |
240.0 |
| O4 |
C4 |
C5 |
H3 |
42.3 |
175.0 |
| O4 |
C4 |
C5 |
H4 |
162.8 |
55.0 |
| C2 |
C3 |
C4 |
H5 |
306.4 |
295.0 |
| C2 |
C3 |
O3' |
H8 |
18.1 |
300.0 |
| O3P |
P |
O2P |
O1P |
238.5 |
240.1 |
| O3P |
P |
O2P |
O5 |
118.4 |
120.1 |
| O1P |
P |
O2P |
O5 |
239.9 |
240.0 |
| O2P |
P |
O1P |
H1 |
239.3 |
300.0 |
| O2P |
P |
O5 |
C5 |
49.4 |
65.0 |
| O3P |
P |
O1P |
O2P |
120.7 |
120.0 |
| O3P |
P |
O1P |
O5 |
241.9 |
240.0 |
| O2P |
P |
O1P |
O5 |
121.2 |
120.0 |
| O1P |
P |
O2P |
H2 |
121.5 |
300.0 |
| O1P |
P |
O5 |
C5 |
171.0 |
185.0 |
| O3P |
P |
O5 |
O2P |
241.1 |
240.0 |
| O3P |
P |
O5 |
O1P |
119.4 |
120.0 |
| O1P |
P |
O5 |
O2P |
121.6 |
120.0 |
| O5 |
P |
O2P |
H2 |
241.6 |
60.0 |
| O5 |
P |
O1P |
H1 |
118.1 |
180.0 |
| P |
O5 |
C5 |
H3 |
345.1 |
300.0 |
| P |
O5 |
C5 |
H4 |
224.6 |
60.0 |
| C4 |
C3 |
O3 |
O3' |
241.6 |
120.0 |
| O3 |
C3 |
C4 |
H5 |
180.3 |
55.0 |
| O3 |
C3 |
O3' |
H8 |
136.5 |
180.0 |
| O4 |
C4 |
C3 |
H5 |
120.0 |
120.0 |
| O3 |
C3 |
C4 |
O3' |
118.6 |
240.0 |
| C3 |
C4 |
C5 |
H3 |
282.5 |
55.0 |
| C3 |
C4 |
C5 |
H4 |
43.0 |
295.0 |
| C4 |
C3 |
O3' |
H8 |
258.8 |
60.0 |
| O5 |
C5 |
C4 |
H3 |
240.3 |
120.0 |
| O5 |
C5 |
C4 |
H4 |
119.7 |
240.0 |
| H3 |
C5 |
C4 |
H4 |
239.4 |
120.0 |
| O3' |
C3 |
C4 |
H5 |
61.7 |
175.0 |
| C4 |
C5 |
O5 |
H3 |
119.8 |
240.0 |
| C4 |
C5 |
O5 |
H4 |
240.3 |
120.0 |
| H3 |
C5 |
O5 |
H4 |
120.5 |
240.0 |
| H1 |
O1P |
P |
O2P |
239.3 |
300.0 |
| H1 |
O1P |
P |
O5 |
118.1 |
180.0 |
| H2 |
O2P |
P |
O5 |
241.6 |
60.0 |
| C4 |
C5 |
H3 |
H4 |
120.8 |
240.0 |
| O5 |
C5 |
H3 |
H4 |
239.2 |
120.0 |
| C4 |
C5 |
H4 |
H3 |
239.2 |
120.0 |
| O5 |
C5 |
H4 |
H3 |
120.8 |
240.0 |
| O4 |
C4 |
H5 |
C3 |
241.0 |
240.0 |
| H5 |
C4 |
C3 |
O3' |
61.7 |
175.0 |
| H5 |
C4 |
C5 |
H3 |
161.3 |
294.9 |
| H5 |
C4 |
C5 |
H4 |
281.9 |
175.0 |
| H6 |
O4 |
C4 |
C3 |
160.3 |
60.0 |
| H6 |
O4 |
C4 |
H5 |
279.2 |
180.0 |
| H7 |
O3 |
C3 |
O3' |
65.1 |
179.9 |
| C1' |
C1 |
H9 |
H10 |
121.3 |
240.0 |
| C1' |
C1 |
H10 |
H9 |
238.7 |
120.0 |
| C2' |
C1' |
H11 |
C22 |
241.5 |
120.0 |
| H11 |
C1' |
C1 |
H9 |
63.1 |
295.0 |
| H11 |
C1' |
C1 |
H10 |
184.0 |
175.0 |
| H11 |
C1' |
C22 |
H15 |
61.3 |
180.0 |
| H11 |
C1' |
C22 |
H16 |
181.3 |
300.0 |
| H11 |
C1' |
C22 |
H17 |
301.3 |
60.0 |
| H12 |
C2' |
C1' |
C22 |
303.0 |
300.0 |
| H12 |
C2' |
C1' |
H11 |
61.4 |
180.0 |
| H13 |
C2' |
H12 |
H14 |
120.1 |
120.1 |
| H13 |
C2' |
C1' |
C22 |
63.0 |
60.0 |
| H13 |
C2' |
C1' |
H11 |
181.4 |
300.0 |
| H12 |
C2' |
H13 |
H14 |
239.9 |
239.9 |
| H14 |
C2' |
C1' |
C22 |
183.0 |
180.0 |
| H14 |
C2' |
C1' |
H11 |
301.4 |
60.0 |
| H12 |
C2' |
H14 |
H13 |
120.0 |
120.1 |
| H15 |
C22 |
C1' |
H11 |
61.3 |
180.0 |
| C1' |
C22 |
H15 |
H16 |
120.0 |
119.9 |
| C1' |
C22 |
H15 |
H17 |
240.0 |
240.0 |
| H16 |
C22 |
H15 |
H17 |
120.0 |
120.1 |
| H16 |
C22 |
C1' |
H11 |
181.3 |
300.0 |
| C1' |
C22 |
H16 |
H15 |
240.0 |
240.1 |
| C1' |
C22 |
H16 |
H17 |
120.0 |
120.0 |
| H15 |
C22 |
H16 |
H17 |
240.0 |
239.9 |
| H17 |
C22 |
C1' |
H11 |
301.3 |
60.0 |
| C1' |
C22 |
H17 |
H15 |
120.1 |
120.0 |
| C1' |
C22 |
H17 |
H16 |
240.0 |
240.0 |
| H15 |
C22 |
H17 |
H16 |
119.9 |
120.1 |