PDB Chemical Component NBO
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 NBO
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C1 |
C2 |
1.500 |
1.507 |
| O1 |
C2 |
1.197 |
1.207 |
| C2 |
C3 |
1.505 |
1.507 |
| C3 |
C4 |
1.531 |
1.530 |
| C4 |
C1' |
1.496 |
1.507 |
| C10' |
C1' |
1.364 |
1.393 |
| C10' |
C9' |
1.377 |
1.361 |
| C1' |
C2' |
1.355 |
1.361 |
| C11' |
O2' |
1.374 |
1.430 |
| C2' |
C3' |
1.371 |
1.405 |
| O2' |
C6' |
1.348 |
1.359 |
| C3' |
C4' |
1.375 |
1.407 |
| C3' |
C8' |
1.365 |
1.418 |
| C4' |
C5' |
1.350 |
1.360 |
| C5' |
C6' |
1.352 |
1.398 |
| C6' |
C7' |
1.370 |
1.365 |
| C7' |
C8' |
1.366 |
1.405 |
| C8' |
C9' |
1.381 |
1.406 |
| C1 |
H1 |
1.100 |
1.091 |
| C1 |
H1A |
1.100 |
1.090 |
| C1 |
H1B |
1.100 |
1.090 |
| C3 |
H3 |
1.100 |
1.090 |
| C3 |
H3A |
1.100 |
1.090 |
| C4 |
H4 |
1.100 |
1.090 |
| C4 |
H4A |
1.100 |
1.090 |
| C10' |
H10' |
1.080 |
1.080 |
| C11' |
H11' |
1.100 |
1.090 |
| C11' |
H11A |
1.100 |
1.090 |
| C11' |
H11B |
1.100 |
1.090 |
| C2' |
H2' |
1.080 |
1.079 |
| C4' |
H4' |
1.080 |
1.080 |
| C5' |
H5' |
1.080 |
1.080 |
| C7' |
H7' |
1.080 |
1.080 |
| C9' |
H9' |
1.080 |
1.080 |
Bond Angles for NBO
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C1 |
C2 |
O1 |
126.8 |
120.0 |
| C1 |
C2 |
C3 |
119.6 |
120.0 |
| C2 |
C1 |
H1 |
109.5 |
109.4 |
| C2 |
C1 |
H1A |
109.4 |
109.5 |
| C2 |
C1 |
H1B |
109.5 |
109.5 |
| O1 |
C2 |
C3 |
113.6 |
120.0 |
| C2 |
C3 |
C4 |
99.5 |
109.5 |
| C2 |
C3 |
H3 |
113.0 |
109.5 |
| C2 |
C3 |
H3A |
113.0 |
109.5 |
| C3 |
C4 |
C1' |
113.5 |
109.5 |
| C4 |
C3 |
H3 |
112.9 |
109.5 |
| C4 |
C3 |
H3A |
113.0 |
109.5 |
| C3 |
C4 |
H4 |
108.2 |
109.4 |
| C3 |
C4 |
H4A |
108.1 |
109.4 |
| C4 |
C1' |
C10' |
122.0 |
119.5 |
| C4 |
C1' |
C2' |
116.7 |
119.5 |
| C1' |
C4 |
H4 |
108.2 |
109.5 |
| C1' |
C4 |
H4A |
108.2 |
109.5 |
| C1' |
C10' |
C9' |
119.3 |
121.0 |
| C10' |
C1' |
C2' |
121.4 |
121.0 |
| C1' |
C10' |
H10' |
120.4 |
119.6 |
| C10' |
C9' |
C8' |
119.1 |
119.7 |
| C9' |
C10' |
H10' |
120.4 |
119.5 |
| C10' |
C9' |
H9' |
120.4 |
120.2 |
| C1' |
C2' |
C3' |
120.2 |
119.6 |
| C1' |
C2' |
H2' |
119.9 |
120.2 |
| C11' |
O2' |
C6' |
116.0 |
117.0 |
| O2' |
C11' |
H11' |
109.5 |
109.5 |
| O2' |
C11' |
H11A |
109.5 |
109.5 |
| O2' |
C11' |
H11B |
109.4 |
109.5 |
| C2' |
C3' |
C4' |
119.0 |
121.2 |
| C2' |
C3' |
C8' |
119.0 |
119.4 |
| C3' |
C2' |
H2' |
119.9 |
120.2 |
| O2' |
C6' |
C5' |
119.8 |
119.6 |
| O2' |
C6' |
C7' |
119.4 |
119.5 |
| C4' |
C3' |
C8' |
122.0 |
119.4 |
| C3' |
C4' |
C5' |
118.7 |
119.8 |
| C3' |
C4' |
H4' |
120.6 |
120.1 |
| C3' |
C8' |
C7' |
117.9 |
119.4 |
| C3' |
C8' |
C9' |
121.1 |
119.3 |
| C4' |
C5' |
C6' |
120.3 |
120.9 |
| C5' |
C4' |
H4' |
120.6 |
120.1 |
| C4' |
C5' |
H5' |
119.9 |
119.6 |
| C5' |
C6' |
C7' |
120.6 |
120.9 |
| C6' |
C5' |
H5' |
119.8 |
119.5 |
| C6' |
C7' |
C8' |
120.3 |
119.6 |
| C6' |
C7' |
H7' |
119.9 |
120.2 |
| C7' |
C8' |
C9' |
121.1 |
121.3 |
| C8' |
C7' |
H7' |
119.9 |
120.2 |
| C8' |
C9' |
H9' |
120.5 |
120.1 |
| H1 |
C1 |
H1A |
109.5 |
109.5 |
| H1 |
C1 |
H1B |
109.5 |
109.4 |
| H1A |
C1 |
H1B |
109.5 |
109.5 |
| H3 |
C3 |
H3A |
105.8 |
109.4 |
| H4 |
C4 |
H4A |
110.7 |
109.5 |
| H11' |
C11' |
H11A |
109.5 |
109.5 |
| H11' |
C11' |
H11B |
109.4 |
109.5 |
| H11A |
C11' |
H11B |
109.5 |
109.5 |
Torsion Angles for NBO
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O1 |
C2 |
C1 |
C3 |
179.6 |
180.0 |
| C1 |
C2 |
C3 |
C4 |
193.0 |
180.0 |
| C1 |
C2 |
C3 |
H3 |
313.0 |
300.0 |
| C1 |
C2 |
C3 |
H3A |
73.0 |
60.0 |
| H1 |
C1 |
C2 |
H1A |
240.0 |
240.0 |
| H1 |
C1 |
C2 |
H1B |
120.0 |
120.0 |
| H1A |
C1 |
C2 |
H1B |
240.0 |
239.9 |
| C1 |
C2 |
O1 |
C3 |
180.3 |
180.0 |
| O1 |
C2 |
C1 |
H1 |
360.0 |
360.0 |
| O1 |
C2 |
C1 |
H1A |
120.0 |
120.0 |
| O1 |
C2 |
C1 |
H1B |
240.0 |
240.0 |
| O1 |
C2 |
C3 |
C4 |
13.3 |
0.0 |
| O1 |
C2 |
C3 |
H3 |
133.3 |
120.0 |
| O1 |
C2 |
C3 |
H3A |
253.3 |
240.0 |
| C1 |
C2 |
C3 |
O1 |
179.7 |
180.0 |
| C3 |
C2 |
C1 |
H1 |
180.4 |
180.0 |
| C3 |
C2 |
C1 |
H1A |
300.4 |
300.0 |
| C3 |
C2 |
C1 |
H1B |
60.4 |
60.1 |
| C2 |
C3 |
C4 |
C1' |
129.5 |
180.0 |
| C4 |
C3 |
C2 |
H3 |
240.0 |
240.0 |
| C4 |
C3 |
C2 |
H3A |
120.0 |
120.0 |
| C2 |
C3 |
C4 |
H4 |
249.5 |
300.0 |
| C2 |
C3 |
C4 |
H4A |
9.5 |
60.0 |
| H3 |
C3 |
C2 |
H3A |
240.0 |
240.0 |
| C2 |
C3 |
C4 |
H3 |
120.0 |
120.0 |
| C2 |
C3 |
C4 |
H3A |
240.0 |
240.0 |
| C3 |
C4 |
C1' |
C10' |
358.9 |
90.0 |
| C3 |
C4 |
C1' |
C2' |
177.9 |
269.9 |
| C1' |
C4 |
C3 |
H4 |
240.0 |
240.0 |
| C1' |
C4 |
C3 |
H4A |
120.0 |
120.0 |
| H3 |
C3 |
C4 |
H3A |
120.0 |
120.0 |
| H4 |
C4 |
C3 |
H4A |
240.0 |
240.0 |
| C1' |
C4 |
C3 |
H3 |
9.5 |
60.0 |
| C1' |
C4 |
C3 |
H3A |
249.5 |
300.0 |
| C3 |
C4 |
C1' |
H4 |
120.0 |
120.0 |
| C3 |
C4 |
C1' |
H4A |
240.0 |
240.0 |
| C4 |
C1' |
C10' |
C9' |
179.6 |
180.0 |
| C10' |
C1' |
C4 |
C2' |
181.1 |
180.1 |
| C4 |
C1' |
C10' |
H10' |
359.6 |
359.7 |
| C4 |
C1' |
C2' |
C3' |
180.8 |
180.0 |
| C4 |
C1' |
C2' |
H2' |
0.8 |
0.1 |
| H4 |
C4 |
C1' |
H4A |
120.0 |
120.1 |
| C4 |
C1' |
C10' |
C2' |
178.9 |
179.9 |
| C10' |
C1' |
C4 |
H4 |
238.9 |
330.1 |
| C10' |
C1' |
C4 |
H4A |
118.9 |
210.0 |
| C1' |
C10' |
C9' |
C8' |
358.9 |
360.0 |
| C9' |
C10' |
C1' |
H10' |
180.0 |
180.3 |
| C1' |
C10' |
C9' |
H9' |
178.9 |
180.0 |
| C10' |
C1' |
C2' |
C3' |
359.7 |
359.9 |
| C10' |
C1' |
C2' |
H2' |
179.7 |
180.0 |
| C9' |
C10' |
C1' |
C2' |
0.7 |
0.1 |
| C1' |
C10' |
C9' |
H10' |
180.0 |
179.7 |
| C3' |
C8' |
C9' |
C10' |
1.2 |
360.0 |
| C7' |
C8' |
C9' |
C10' |
180.3 |
180.0 |
| C8' |
C9' |
C10' |
H9' |
180.0 |
180.0 |
| C4 |
C1' |
C2' |
C10' |
181.1 |
180.1 |
| C2' |
C1' |
C4 |
H4 |
57.9 |
150.0 |
| C2' |
C1' |
C4 |
H4A |
297.9 |
29.9 |
| C2' |
C1' |
C10' |
C9' |
0.7 |
0.1 |
| C2' |
C1' |
C10' |
H10' |
180.7 |
179.8 |
| C1' |
C2' |
C3' |
C4' |
180.7 |
180.1 |
| C1' |
C2' |
C3' |
C8' |
0.3 |
0.0 |
| C3' |
C2' |
C1' |
H2' |
180.0 |
179.9 |
| C11' |
O2' |
C6' |
C5' |
272.8 |
360.0 |
| C11' |
O2' |
C6' |
C7' |
89.2 |
180.0 |
| H11' |
C11' |
O2' |
H11A |
240.0 |
240.0 |
| H11' |
C11' |
O2' |
H11B |
120.0 |
120.0 |
| H11A |
C11' |
O2' |
H11B |
240.0 |
240.0 |
| C1' |
C2' |
C3' |
H2' |
180.0 |
180.1 |
| C4' |
C3' |
C2' |
C8' |
180.3 |
180.0 |
| C2' |
C3' |
C4' |
C5' |
180.8 |
180.0 |
| C2' |
C3' |
C4' |
H4' |
0.8 |
359.9 |
| C2' |
C3' |
C8' |
C7' |
180.1 |
180.0 |
| C2' |
C3' |
C8' |
C9' |
359.2 |
0.0 |
| C6' |
O2' |
C11' |
H11' |
180.0 |
180.0 |
| C6' |
O2' |
C11' |
H11A |
300.0 |
300.0 |
| C6' |
O2' |
C11' |
H11B |
60.0 |
60.0 |
| C4' |
C5' |
C6' |
O2' |
180.2 |
180.0 |
| C5' |
C6' |
O2' |
C7' |
183.6 |
180.0 |
| O2' |
C6' |
C5' |
H5' |
0.2 |
0.0 |
| O2' |
C6' |
C7' |
C8' |
180.7 |
180.0 |
| O2' |
C6' |
C7' |
H7' |
0.7 |
0.0 |
| C2' |
C3' |
C4' |
C8' |
179.6 |
180.0 |
| C4' |
C3' |
C2' |
H2' |
0.7 |
0.0 |
| C4' |
C3' |
C8' |
C7' |
359.7 |
360.0 |
| C4' |
C3' |
C8' |
C9' |
178.8 |
180.0 |
| C3' |
C4' |
C5' |
C6' |
357.1 |
360.0 |
| C5' |
C4' |
C3' |
H4' |
180.0 |
180.1 |
| C3' |
C4' |
C5' |
H5' |
177.1 |
179.9 |
| C10' |
C9' |
C8' |
C3' |
1.2 |
360.0 |
| C2' |
C3' |
C8' |
C4' |
180.4 |
180.0 |
| C8' |
C3' |
C2' |
H2' |
180.4 |
180.0 |
| C8' |
C3' |
C4' |
C5' |
1.2 |
0.0 |
| C8' |
C3' |
C4' |
H4' |
181.2 |
180.0 |
| C6' |
C7' |
C8' |
C3' |
1.1 |
0.0 |
| C7' |
C8' |
C3' |
C9' |
180.9 |
180.0 |
| C3' |
C8' |
C7' |
H7' |
181.1 |
180.0 |
| C3' |
C8' |
C9' |
H9' |
181.2 |
180.0 |
| O2' |
C6' |
C5' |
C4' |
180.2 |
180.0 |
| C5' |
C4' |
C3' |
C8' |
1.2 |
0.0 |
| C3' |
C4' |
C5' |
H4' |
180.0 |
179.9 |
| C4' |
C5' |
C6' |
C7' |
3.8 |
0.0 |
| C6' |
C5' |
C4' |
H5' |
180.0 |
180.1 |
| O2' |
C6' |
C5' |
C7' |
176.4 |
180.0 |
| C6' |
C5' |
C4' |
H4' |
177.1 |
180.0 |
| C4' |
C5' |
C6' |
H5' |
180.0 |
179.9 |
| C5' |
C6' |
C7' |
C8' |
357.1 |
360.0 |
| C5' |
C6' |
C7' |
H7' |
177.1 |
180.0 |
| O2' |
C6' |
C7' |
C5' |
183.6 |
180.0 |
| C3' |
C8' |
C7' |
C6' |
1.1 |
0.0 |
| C7' |
C6' |
C5' |
H5' |
183.8 |
180.1 |
| C6' |
C7' |
C8' |
C9' |
182.0 |
180.0 |
| C8' |
C7' |
C6' |
H7' |
180.0 |
180.0 |
| C10' |
C9' |
C8' |
C7' |
180.3 |
180.0 |
| C3' |
C8' |
C7' |
C9' |
179.1 |
180.0 |
| C6' |
C7' |
C8' |
H7' |
180.0 |
180.0 |
| C7' |
C8' |
C9' |
H9' |
0.3 |
360.0 |
| C8' |
C9' |
C10' |
H10' |
178.9 |
180.3 |
| C10' |
C9' |
C8' |
H9' |
180.0 |
180.0 |
| C3' |
C8' |
C9' |
C7' |
180.9 |
180.0 |
| C9' |
C8' |
C7' |
H7' |
2.0 |
0.0 |
| H1 |
C1 |
C2 |
O1 |
360.0 |
360.0 |
| H1 |
C1 |
C2 |
C3 |
180.4 |
180.0 |
| C2 |
C1 |
H1 |
H1A |
120.0 |
120.0 |
| C2 |
C1 |
H1 |
H1B |
240.0 |
240.0 |
| H1A |
C1 |
H1 |
H1B |
120.0 |
120.0 |
| H1A |
C1 |
C2 |
O1 |
120.0 |
120.0 |
| H1A |
C1 |
C2 |
C3 |
300.4 |
300.0 |
| C2 |
C1 |
H1A |
H1 |
240.0 |
240.0 |
| C2 |
C1 |
H1A |
H1B |
120.0 |
120.1 |
| H1 |
C1 |
H1A |
H1B |
240.0 |
240.0 |
| H1B |
C1 |
C2 |
O1 |
240.0 |
240.0 |
| H1B |
C1 |
C2 |
C3 |
60.4 |
60.1 |
| C2 |
C1 |
H1B |
H1 |
120.0 |
120.0 |
| C2 |
C1 |
H1B |
H1A |
240.0 |
240.0 |
| H1 |
C1 |
H1B |
H1A |
120.0 |
120.0 |
| C2 |
C3 |
H3 |
C4 |
248.1 |
240.0 |
| C2 |
C3 |
H3 |
H3A |
124.1 |
120.0 |
| H3 |
C3 |
C4 |
C1' |
9.5 |
60.0 |
| C4 |
C3 |
H3 |
H3A |
236.0 |
240.0 |
| H3 |
C3 |
C4 |
H4 |
129.5 |
180.0 |
| H3 |
C3 |
C4 |
H4A |
249.4 |
300.0 |
| C2 |
C3 |
H3A |
C4 |
111.9 |
120.0 |
| C2 |
C3 |
H3A |
H3 |
235.9 |
240.0 |
| H3A |
C3 |
C4 |
C1' |
249.5 |
300.0 |
| C4 |
C3 |
H3A |
H3 |
124.0 |
120.0 |
| H3A |
C3 |
C4 |
H4 |
9.5 |
60.0 |
| H3A |
C3 |
C4 |
H4A |
129.5 |
180.0 |
| C3 |
C4 |
H4 |
C1' |
236.7 |
240.0 |
| H4 |
C4 |
C3 |
H3 |
129.5 |
180.0 |
| H4 |
C4 |
C3 |
H3A |
9.5 |
60.0 |
| C3 |
C4 |
H4 |
H4A |
118.3 |
120.0 |
| H4 |
C4 |
C1' |
C10' |
238.9 |
330.1 |
| H4 |
C4 |
C1' |
C2' |
57.9 |
150.0 |
| C1' |
C4 |
H4 |
H4A |
241.6 |
239.9 |
| C3 |
C4 |
H4A |
C1' |
123.3 |
120.0 |
| H4A |
C4 |
C3 |
H3 |
249.4 |
300.0 |
| H4A |
C4 |
C3 |
H3A |
129.5 |
180.0 |
| C3 |
C4 |
H4A |
H4 |
241.7 |
240.1 |
| H4A |
C4 |
C1' |
C10' |
118.9 |
210.0 |
| H4A |
C4 |
C1' |
C2' |
297.9 |
29.9 |
| C1' |
C4 |
H4A |
H4 |
118.4 |
120.1 |
| C1' |
C10' |
H10' |
C9' |
180.0 |
180.3 |
| H10' |
C10' |
C1' |
C2' |
180.7 |
179.8 |
| H10' |
C10' |
C9' |
C8' |
178.9 |
180.3 |
| H10' |
C10' |
C9' |
H9' |
358.9 |
0.3 |
| H11' |
C11' |
O2' |
C6' |
180.0 |
180.0 |
| O2' |
C11' |
H11' |
H11A |
120.0 |
120.0 |
| O2' |
C11' |
H11' |
H11B |
240.0 |
240.0 |
| H11A |
C11' |
H11' |
H11B |
120.0 |
120.0 |
| H11A |
C11' |
O2' |
C6' |
300.0 |
300.0 |
| O2' |
C11' |
H11A |
H11' |
240.0 |
240.0 |
| O2' |
C11' |
H11A |
H11B |
120.0 |
120.0 |
| H11' |
C11' |
H11A |
H11B |
240.0 |
240.0 |
| H11B |
C11' |
O2' |
C6' |
60.0 |
60.0 |
| O2' |
C11' |
H11B |
H11' |
120.0 |
120.0 |
| O2' |
C11' |
H11B |
H11A |
240.0 |
240.0 |
| H11' |
C11' |
H11B |
H11A |
120.0 |
120.0 |
| C1' |
C2' |
H2' |
C3' |
180.0 |
179.9 |
| H2' |
C2' |
C3' |
C4' |
0.7 |
0.0 |
| H2' |
C2' |
C3' |
C8' |
180.4 |
180.0 |
| H4' |
C4' |
C3' |
C8' |
181.2 |
180.0 |
| C3' |
C4' |
H4' |
C5' |
180.0 |
180.1 |
| H4' |
C4' |
C5' |
C6' |
177.1 |
180.0 |
| H4' |
C4' |
C5' |
H5' |
357.1 |
360.0 |
| C4' |
C5' |
H5' |
C6' |
180.0 |
180.1 |
| H5' |
C5' |
C4' |
H4' |
357.1 |
360.0 |
| H5' |
C5' |
C6' |
C7' |
183.8 |
180.1 |
| C6' |
C7' |
H7' |
C8' |
180.0 |
180.0 |
| H7' |
C7' |
C8' |
C9' |
2.0 |
0.0 |
| C10' |
C9' |
H9' |
C8' |
180.0 |
180.0 |
| H9' |
C9' |
C10' |
H10' |
358.9 |
0.3 |