PDB Chemical Component DBJ
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 DBJ
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C7 |
C5 |
1.470 |
1.535 |
| C7 |
O8 |
1.398 |
1.432 |
| C5 |
O5 |
1.395 |
1.432 |
| O8 |
C9 |
1.398 |
1.361 |
| O5 |
C4 |
1.405 |
1.361 |
| C9 |
C4 |
1.387 |
1.390 |
| C9 |
C10 |
1.437 |
1.386 |
| C4 |
C3 |
1.415 |
1.386 |
| C10 |
C11 |
1.413 |
1.383 |
| C3 |
C2 |
1.485 |
1.507 |
| C3 |
C12 |
1.436 |
1.382 |
| C2 |
O1 |
1.347 |
1.428 |
| C11 |
C12 |
1.435 |
1.382 |
| O1 |
H1 |
0.950 |
0.967 |
| C2 |
H2 |
1.100 |
1.090 |
| C2 |
H3 |
1.100 |
1.090 |
| C5 |
H4 |
1.100 |
1.091 |
| C5 |
H5 |
1.100 |
1.090 |
| C7 |
H6 |
1.100 |
1.090 |
| C7 |
H7 |
1.100 |
1.090 |
| C10 |
H8 |
1.080 |
1.080 |
| C11 |
H9 |
1.080 |
1.079 |
| C12 |
H10 |
1.080 |
1.080 |
Bond Angles for DBJ
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C7 |
C5 |
H4 |
108.2 |
109.7 |
| C7 |
C5 |
H5 |
108.2 |
109.7 |
| C7 |
O8 |
C9 |
118.8 |
116.7 |
| O8 |
C7 |
H6 |
106.8 |
109.7 |
| O8 |
C7 |
H7 |
106.8 |
109.7 |
| O8 |
C9 |
C10 |
123.6 |
119.4 |
| C9 |
C10 |
C11 |
122.2 |
120.1 |
| C9 |
C10 |
H8 |
118.9 |
120.0 |
| C4 |
C3 |
C12 |
121.7 |
120.1 |
| C10 |
C11 |
C12 |
117.4 |
120.1 |
| C11 |
C10 |
H8 |
118.9 |
119.9 |
| C10 |
C11 |
H9 |
121.3 |
119.9 |
| C3 |
C2 |
H2 |
107.7 |
109.4 |
| C3 |
C2 |
H3 |
107.8 |
109.4 |
| C3 |
C12 |
C11 |
119.6 |
120.1 |
| C3 |
C12 |
H10 |
120.2 |
119.9 |
| C2 |
O1 |
H1 |
109.5 |
114.0 |
| C12 |
C11 |
H9 |
121.3 |
120.0 |
| C11 |
C12 |
H10 |
120.2 |
119.9 |
| H2 |
C2 |
H3 |
109.5 |
109.4 |
| H4 |
C5 |
H5 |
109.4 |
109.7 |
| H6 |
C7 |
H7 |
109.5 |
109.8 |
Torsion Angles for DBJ
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| H4 |
C5 |
C7 |
H5 |
241.6 |
120.5 |
| O8 |
C7 |
C5 |
H4 |
113.9 |
180.5 |
| O8 |
C7 |
C5 |
H5 |
232.3 |
60.0 |
| C7 |
O8 |
C9 |
C10 |
155.0 |
162.8 |
| H6 |
C7 |
O8 |
H7 |
117.1 |
120.7 |
| C9 |
O8 |
C7 |
H6 |
267.0 |
286.5 |
| C9 |
O8 |
C7 |
H7 |
149.9 |
165.9 |
| O8 |
C9 |
C10 |
C11 |
179.0 |
179.9 |
| O8 |
C9 |
C10 |
H8 |
359.0 |
359.8 |
| O5 |
C4 |
C3 |
C12 |
179.1 |
180.0 |
| C9 |
C4 |
C3 |
C12 |
357.5 |
0.2 |
| C9 |
C10 |
C11 |
C12 |
0.7 |
359.7 |
| C11 |
C10 |
C9 |
H8 |
180.0 |
180.1 |
| C9 |
C10 |
C11 |
H9 |
180.7 |
179.9 |
| C4 |
C3 |
C2 |
H2 |
282.7 |
60.3 |
| C4 |
C3 |
C2 |
H3 |
40.8 |
300.4 |
| C4 |
C3 |
C12 |
C11 |
1.8 |
359.4 |
| C4 |
C3 |
C12 |
H10 |
181.8 |
179.6 |
| C9 |
C10 |
C11 |
H8 |
180.0 |
179.9 |
| C3 |
C12 |
C11 |
C10 |
359.1 |
0.7 |
| C12 |
C11 |
C10 |
H9 |
180.0 |
179.8 |
| C10 |
C11 |
C12 |
H10 |
179.1 |
180.4 |
| C3 |
C2 |
O1 |
H1 |
180.0 |
180.0 |
| H2 |
C2 |
C3 |
H3 |
242.0 |
119.9 |
| C10 |
C11 |
C12 |
C3 |
359.1 |
0.7 |
| C12 |
C3 |
C2 |
H2 |
104.6 |
240.0 |
| C12 |
C3 |
C2 |
H3 |
222.7 |
120.0 |
| C3 |
C12 |
C11 |
H9 |
179.2 |
180.4 |
| C11 |
C12 |
C3 |
H10 |
180.0 |
179.8 |
| C12 |
C11 |
C10 |
H8 |
180.7 |
179.8 |
| C10 |
C11 |
C12 |
H9 |
180.0 |
180.2 |
| C3 |
C12 |
C11 |
H10 |
180.0 |
180.2 |
| C3 |
C2 |
H2 |
H3 |
116.9 |
240.1 |
| H2 |
C2 |
O1 |
H1 |
59.0 |
299.9 |
| C3 |
C2 |
H3 |
H2 |
243.1 |
119.9 |
| H3 |
C2 |
O1 |
H1 |
301.0 |
59.9 |
| C7 |
C5 |
H4 |
H5 |
117.7 |
239.4 |
| C7 |
C5 |
H5 |
H4 |
242.3 |
120.5 |
| H6 |
C7 |
C5 |
H4 |
235.3 |
300.2 |
| H6 |
C7 |
C5 |
H5 |
353.8 |
179.7 |
| H6 |
C7 |
O8 |
C9 |
267.0 |
286.5 |
| O8 |
C7 |
H6 |
H7 |
244.7 |
239.4 |
| H7 |
C7 |
C5 |
H4 |
352.4 |
60.9 |
| H7 |
C7 |
C5 |
H5 |
110.8 |
300.4 |
| H7 |
C7 |
O8 |
C9 |
149.9 |
165.9 |
| O8 |
C7 |
H7 |
H6 |
115.2 |
120.6 |
| C9 |
C10 |
H8 |
C11 |
180.0 |
180.1 |
| H8 |
C10 |
C11 |
C12 |
180.7 |
179.8 |
| H8 |
C10 |
C11 |
H9 |
0.7 |
0.0 |
| C10 |
C11 |
H9 |
C12 |
180.0 |
179.8 |
| H9 |
C11 |
C10 |
H8 |
0.7 |
0.0 |
| H9 |
C11 |
C12 |
H10 |
359.1 |
0.2 |
| C3 |
C12 |
H10 |
C11 |
180.0 |
179.8 |
| H10 |
C12 |
C11 |
H9 |
359.1 |
0.2 |