PDB Chemical Component D09
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 D09
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C'6 |
C'1 |
1.413 |
1.397 |
| C'1 |
C11 |
1.403 |
1.473 |
| C'1 |
C'2 |
1.424 |
1.403 |
| C'2 |
C'3 |
1.403 |
1.385 |
| C'2 |
O13 |
1.390 |
1.359 |
| C'4 |
C'3 |
1.410 |
1.383 |
| C'3 |
H'3 |
1.080 |
1.080 |
| C'5 |
C'4 |
1.413 |
1.384 |
| C'4 |
H'4 |
1.080 |
1.080 |
| C'6 |
C'5 |
1.415 |
1.379 |
| C'5 |
H'5 |
1.080 |
1.080 |
| C'6 |
H'6 |
1.080 |
1.079 |
| C8' |
N1' |
1.362 |
1.330 |
| N1' |
C2' |
1.345 |
1.324 |
| C10 |
C11 |
1.541 |
1.506 |
| C10 |
H10 |
1.100 |
1.090 |
| C10 |
H10A |
1.100 |
1.090 |
| C10 |
H10B |
1.100 |
1.090 |
| C11 |
C9' |
1.520 |
1.344 |
| O13 |
C13 |
1.480 |
1.429 |
| C13 |
H13 |
1.100 |
1.090 |
| C13 |
H13A |
1.100 |
1.090 |
| C13 |
H13B |
1.100 |
1.090 |
| C2' |
N2' |
1.300 |
1.385 |
| C2' |
N3' |
1.347 |
1.326 |
| N2' |
HN2' |
1.000 |
0.971 |
| N2' |
HN2A |
1.001 |
0.970 |
| C4' |
N3' |
1.357 |
1.330 |
| C5' |
C4' |
1.414 |
1.399 |
| C4' |
N4' |
1.339 |
1.383 |
| N4' |
HN4' |
1.000 |
0.970 |
| N4' |
HN4A |
1.000 |
0.971 |
| C8' |
C5' |
1.406 |
1.403 |
| C6' |
C5' |
1.400 |
1.473 |
| C7' |
C6' |
1.346 |
1.359 |
| C6' |
C9' |
1.533 |
1.472 |
| O8' |
C7' |
1.394 |
1.345 |
| C7' |
H7' |
1.080 |
1.080 |
| O8' |
C8' |
1.401 |
1.344 |
| C9' |
H9' |
1.080 |
1.080 |
Bond Angles for D09
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C'6 |
C'1 |
C11 |
121.6 |
120.2 |
| C'2 |
C'1 |
C11 |
117.9 |
120.2 |
| C'1 |
C11 |
C10 |
118.7 |
120.0 |
| C'1 |
C11 |
C9' |
117.9 |
120.0 |
| C'1 |
C'2 |
C'3 |
119.4 |
119.7 |
| C'1 |
C'2 |
O13 |
119.0 |
120.1 |
| C'3 |
C'2 |
O13 |
121.6 |
120.1 |
| C'2 |
C'3 |
H'3 |
120.1 |
119.9 |
| C'2 |
O13 |
C13 |
126.5 |
117.0 |
| C'4 |
C'3 |
H'3 |
120.1 |
120.0 |
| C'5 |
C'4 |
H'4 |
119.2 |
119.8 |
| C'6 |
C'5 |
H'5 |
120.7 |
119.9 |
| N1' |
C2' |
N2' |
120.4 |
118.7 |
| N1' |
C2' |
N3' |
121.0 |
122.5 |
| C11 |
C10 |
H10 |
109.5 |
109.5 |
| C11 |
C10 |
H10A |
109.5 |
109.5 |
| C11 |
C10 |
H10B |
109.5 |
109.5 |
| C10 |
C11 |
C9' |
123.3 |
120.0 |
| H10 |
C10 |
H10A |
109.4 |
109.4 |
| H10 |
C10 |
H10B |
109.4 |
109.5 |
| H10A |
C10 |
H10B |
109.5 |
109.4 |
| C11 |
C9' |
C6' |
121.6 |
120.0 |
| C11 |
C9' |
H9' |
119.2 |
120.0 |
| O13 |
C13 |
H13 |
109.5 |
109.5 |
| O13 |
C13 |
H13A |
109.4 |
109.5 |
| O13 |
C13 |
H13B |
109.5 |
109.5 |
| H13 |
C13 |
H13A |
109.5 |
109.5 |
| H13 |
C13 |
H13B |
109.5 |
109.5 |
| H13A |
C13 |
H13B |
109.5 |
109.4 |
| N2' |
C2' |
N3' |
118.6 |
118.8 |
| C2' |
N2' |
HN2' |
109.5 |
120.0 |
| C2' |
N2' |
HN2A |
109.4 |
120.0 |
| HN2' |
N2' |
HN2A |
109.5 |
120.0 |
| C4' |
N4' |
HN4' |
109.5 |
120.0 |
| C4' |
N4' |
HN4A |
109.4 |
120.0 |
| HN4' |
N4' |
HN4A |
109.5 |
120.0 |
| C7' |
C6' |
C9' |
131.0 |
127.1 |
| C6' |
C9' |
H9' |
119.2 |
120.0 |
| O8' |
C7' |
H7' |
124.6 |
125.2 |
Torsion Angles for D09
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C'2 |
C'1 |
C'6 |
C11 |
181.6 |
179.7 |
| C'6 |
C'1 |
C11 |
C10 |
267.6 |
254.8 |
| C'6 |
C'1 |
C11 |
C9' |
91.9 |
74.7 |
| C'6 |
C'1 |
C'2 |
O13 |
180.8 |
180.2 |
| C11 |
C'1 |
C'2 |
C'3 |
179.5 |
180.0 |
| C11 |
C'1 |
C'2 |
O13 |
2.4 |
359.9 |
| C'1 |
C11 |
C10 |
H10 |
180.0 |
94.2 |
| C'1 |
C11 |
C10 |
H10A |
300.0 |
214.2 |
| C'1 |
C11 |
C10 |
H10B |
60.0 |
334.2 |
| C10 |
C11 |
C'1 |
C9' |
175.7 |
180.1 |
| C'1 |
C11 |
C9' |
C6' |
187.7 |
186.6 |
| C'1 |
C11 |
C9' |
H9' |
7.7 |
6.7 |
| C'6 |
C'1 |
C'2 |
C11 |
178.4 |
180.3 |
| C'2 |
C'1 |
C11 |
C10 |
86.0 |
75.1 |
| C'2 |
C'1 |
C11 |
C9' |
270.3 |
255.0 |
| C'3 |
C'2 |
C'1 |
O13 |
177.1 |
180.1 |
| C'1 |
C'2 |
C'3 |
H'3 |
181.6 |
179.9 |
| C'1 |
C'2 |
O13 |
C13 |
242.6 |
180.0 |
| C'3 |
C'2 |
C'1 |
C11 |
179.5 |
180.0 |
| C'1 |
C'2 |
C'3 |
O13 |
183.0 |
179.9 |
| C'3 |
C'2 |
O13 |
C13 |
65.5 |
359.9 |
| C'4 |
C'3 |
C'2 |
H'3 |
180.0 |
180.0 |
| O13 |
C'2 |
C'1 |
C11 |
2.4 |
359.9 |
| C'1 |
C'2 |
O13 |
C'3 |
177.1 |
180.1 |
| O13 |
C'2 |
C'3 |
H'3 |
358.7 |
0.0 |
| C'2 |
O13 |
C13 |
H13 |
180.0 |
60.0 |
| C'2 |
O13 |
C13 |
H13A |
300.0 |
180.1 |
| C'2 |
O13 |
C13 |
H13B |
60.0 |
300.0 |
| C'4 |
C'3 |
C'2 |
O13 |
178.7 |
180.1 |
| C'2 |
C'3 |
C'4 |
H'3 |
180.0 |
180.0 |
| H'3 |
C'3 |
C'2 |
O13 |
358.7 |
0.0 |
| C'5 |
C'4 |
C'3 |
H'3 |
179.5 |
180.0 |
| H'4 |
C'4 |
C'3 |
H'3 |
359.5 |
0.0 |
| C'5 |
C'6 |
C'1 |
C11 |
179.8 |
179.7 |
| C'6 |
C'5 |
C'4 |
H'4 |
179.9 |
179.7 |
| H'5 |
C'5 |
C'4 |
H'4 |
359.9 |
360.0 |
| H'6 |
C'6 |
C'1 |
C11 |
359.8 |
0.1 |
| H'6 |
C'6 |
C'5 |
H'5 |
359.7 |
359.9 |
| N2' |
C2' |
N1' |
N3' |
182.1 |
180.1 |
| N1' |
C2' |
N2' |
HN2' |
360.0 |
359.9 |
| N1' |
C2' |
N2' |
HN2A |
120.0 |
180.0 |
| C'1 |
C11 |
C10 |
C9' |
184.5 |
179.9 |
| H10 |
C10 |
C11 |
H10A |
240.0 |
240.0 |
| H10 |
C10 |
C11 |
H10B |
120.0 |
120.1 |
| H10A |
C10 |
C11 |
H10B |
240.0 |
240.0 |
| C10 |
C11 |
C9' |
C6' |
12.2 |
6.6 |
| C10 |
C11 |
C9' |
H9' |
192.2 |
186.6 |
| C11 |
C10 |
H10 |
H10A |
120.0 |
120.0 |
| C11 |
C10 |
H10 |
H10B |
240.0 |
239.9 |
| H10 |
C10 |
C11 |
C9' |
355.5 |
274.3 |
| H10A |
C10 |
H10 |
H10B |
120.0 |
119.9 |
| C11 |
C10 |
H10A |
H10 |
239.9 |
240.0 |
| C11 |
C10 |
H10A |
H10B |
120.0 |
120.0 |
| H10A |
C10 |
C11 |
C9' |
115.5 |
34.3 |
| H10 |
C10 |
H10A |
H10B |
240.1 |
240.0 |
| C11 |
C10 |
H10B |
H10 |
120.0 |
120.1 |
| C11 |
C10 |
H10B |
H10A |
240.0 |
240.0 |
| H10B |
C10 |
C11 |
C9' |
235.5 |
154.3 |
| H10 |
C10 |
H10B |
H10A |
120.0 |
119.9 |
| C'1 |
C11 |
C9' |
C10 |
175.5 |
180.1 |
| C9' |
C11 |
C10 |
H10 |
355.5 |
274.3 |
| C9' |
C11 |
C10 |
H10A |
115.5 |
34.3 |
| C9' |
C11 |
C10 |
H10B |
235.5 |
154.3 |
| C7' |
C6' |
C9' |
C11 |
350.9 |
18.2 |
| C6' |
C9' |
C11 |
H9' |
180.0 |
180.0 |
| H13 |
C13 |
O13 |
H13A |
240.0 |
239.9 |
| H13 |
C13 |
O13 |
H13B |
120.0 |
120.0 |
| H13A |
C13 |
O13 |
H13B |
240.0 |
240.1 |
| O13 |
C13 |
H13 |
H13A |
120.0 |
120.1 |
| O13 |
C13 |
H13 |
H13B |
240.0 |
240.0 |
| H13A |
C13 |
H13 |
H13B |
120.0 |
120.0 |
| O13 |
C13 |
H13A |
H13 |
240.0 |
240.0 |
| O13 |
C13 |
H13A |
H13B |
120.0 |
120.0 |
| H13 |
C13 |
H13A |
H13B |
240.0 |
240.0 |
| O13 |
C13 |
H13B |
H13 |
120.0 |
120.0 |
| O13 |
C13 |
H13B |
H13A |
240.0 |
240.0 |
| H13 |
C13 |
H13B |
H13A |
120.0 |
120.0 |
| N1' |
C2' |
N2' |
N3' |
177.9 |
179.9 |
| HN2' |
N2' |
C2' |
HN2A |
240.0 |
179.9 |
| N1' |
C2' |
N3' |
N2' |
182.1 |
180.1 |
| N3' |
C2' |
N2' |
HN2' |
182.0 |
180.0 |
| N3' |
C2' |
N2' |
HN2A |
302.1 |
0.1 |
| HN2' |
N2' |
C2' |
N3' |
182.0 |
180.0 |
| C2' |
N2' |
HN2' |
HN2A |
120.0 |
180.1 |
| HN2A |
N2' |
C2' |
N3' |
302.1 |
0.1 |
| C2' |
N2' |
HN2A |
HN2' |
240.0 |
179.9 |
| C5' |
C4' |
N4' |
HN4' |
179.5 |
180.0 |
| C5' |
C4' |
N4' |
HN4A |
299.5 |
0.1 |
| HN4' |
N4' |
C4' |
HN4A |
240.0 |
180.0 |
| C4' |
N4' |
HN4' |
HN4A |
120.0 |
180.0 |
| C4' |
N4' |
HN4A |
HN4' |
240.0 |
180.0 |
| C11 |
C9' |
C6' |
C5' |
168.2 |
198.3 |
| C11 |
C9' |
C6' |
C7' |
350.9 |
18.2 |
| C7' |
C6' |
C9' |
H9' |
170.9 |
198.2 |
| C11 |
C9' |
C6' |
H9' |
180.0 |
180.0 |
| O8' |
C7' |
C6' |
C9' |
179.1 |
180.1 |
| H7' |
C7' |
C6' |
C9' |
359.1 |
0.1 |
| C8' |
O8' |
C7' |
H7' |
178.8 |
179.9 |
| C11 |
C9' |
H9' |
C6' |
180.0 |
180.0 |