PDB Chemical Component SD5
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 SD5
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N01 |
C02 |
1.349 |
1.387 |
| N01 |
HN01 |
1.000 |
0.971 |
| N01 |
HN0A |
1.001 |
0.970 |
| C03 |
C02 |
1.390 |
1.393 |
| C02 |
N07 |
1.345 |
1.325 |
| C03 |
C04 |
1.391 |
1.380 |
| C03 |
H03 |
1.079 |
1.080 |
| C26 |
C04 |
1.505 |
1.507 |
| C04 |
C05 |
1.404 |
1.401 |
| C05 |
C08 |
1.492 |
1.482 |
| C05 |
C06 |
1.382 |
1.392 |
| N07 |
C06 |
1.337 |
1.318 |
| C06 |
H06 |
1.080 |
1.080 |
| C09 |
C08 |
1.385 |
1.393 |
| C08 |
N13 |
1.350 |
1.333 |
| C09 |
C10 |
1.397 |
1.394 |
| C09 |
H09 |
1.080 |
1.080 |
| N20 |
C10 |
1.369 |
1.386 |
| C10 |
N11 |
1.332 |
1.330 |
| N11 |
C12 |
1.341 |
1.324 |
| N13 |
C12 |
1.347 |
1.324 |
| C12 |
N14 |
1.353 |
1.384 |
| N14 |
C19 |
1.469 |
1.470 |
| N14 |
C15 |
1.459 |
1.470 |
| C15 |
C16 |
1.506 |
1.531 |
| C15 |
H15 |
1.100 |
1.090 |
| C15 |
H15A |
1.100 |
1.090 |
| C16 |
O17 |
1.425 |
1.430 |
| C16 |
H16 |
1.100 |
1.090 |
| C16 |
H16A |
1.100 |
1.090 |
| C18 |
O17 |
1.422 |
1.430 |
| C19 |
C18 |
1.502 |
1.530 |
| C18 |
H18 |
1.100 |
1.091 |
| C18 |
H18A |
1.099 |
1.090 |
| C19 |
H19 |
1.100 |
1.090 |
| C19 |
H19A |
1.100 |
1.090 |
| C25 |
N20 |
1.461 |
1.470 |
| N20 |
C21 |
1.468 |
1.470 |
| C21 |
C22 |
1.500 |
1.531 |
| C21 |
H21 |
1.100 |
1.090 |
| C21 |
H21A |
1.100 |
1.090 |
| O23 |
C22 |
1.421 |
1.429 |
| C22 |
H22 |
1.100 |
1.090 |
| C22 |
H22A |
1.100 |
1.090 |
| C24 |
O23 |
1.421 |
1.430 |
| C25 |
C24 |
1.505 |
1.530 |
| C24 |
H24 |
1.100 |
1.090 |
| C24 |
H24A |
1.100 |
1.090 |
| C25 |
H25 |
1.100 |
1.090 |
| C25 |
H25A |
1.100 |
1.090 |
| F27 |
C26 |
1.322 |
1.399 |
| F29 |
C26 |
1.333 |
1.400 |
| C26 |
F28 |
1.329 |
1.399 |
Bond Angles for SD5
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C02 |
N01 |
HN01 |
109.5 |
120.0 |
| C02 |
N01 |
HN0A |
109.5 |
120.0 |
| N01 |
C02 |
N07 |
117.5 |
119.6 |
| HN01 |
N01 |
HN0A |
109.4 |
120.0 |
| C03 |
C02 |
N07 |
120.8 |
120.9 |
| C02 |
N07 |
C06 |
118.3 |
121.7 |
| C04 |
C03 |
H03 |
119.9 |
120.4 |
| C03 |
C04 |
C05 |
119.4 |
118.4 |
| C04 |
C05 |
C08 |
122.7 |
120.4 |
| C04 |
C05 |
C06 |
115.8 |
119.1 |
| C06 |
C05 |
C08 |
121.5 |
120.5 |
| C05 |
C08 |
N13 |
115.5 |
120.5 |
| C05 |
C06 |
H06 |
117.2 |
119.7 |
| N07 |
C06 |
H06 |
117.2 |
119.6 |
| C09 |
C08 |
N13 |
122.7 |
119.1 |
| C08 |
N13 |
C12 |
115.5 |
120.8 |
| C10 |
C09 |
H09 |
121.5 |
120.8 |
| C09 |
C10 |
N11 |
121.4 |
119.1 |
| C10 |
N11 |
C12 |
117.4 |
120.9 |
| N11 |
C12 |
N14 |
117.0 |
119.2 |
| N13 |
C12 |
N14 |
116.9 |
119.1 |
| C12 |
N14 |
C19 |
122.1 |
111.0 |
| C12 |
N14 |
C15 |
123.3 |
111.0 |
| C15 |
N14 |
C19 |
112.4 |
110.7 |
| N14 |
C19 |
C18 |
109.3 |
109.3 |
| N14 |
C19 |
H19 |
109.6 |
109.4 |
| N14 |
C19 |
H19A |
109.5 |
109.5 |
| N14 |
C15 |
C16 |
109.6 |
109.3 |
| N14 |
C15 |
H15 |
109.4 |
109.5 |
| N14 |
C15 |
H15A |
109.4 |
109.5 |
| C16 |
C15 |
H15 |
109.4 |
109.5 |
| C16 |
C15 |
H15A |
109.4 |
109.5 |
| C15 |
C16 |
O17 |
111.6 |
109.2 |
| C15 |
C16 |
H16 |
108.8 |
109.5 |
| C15 |
C16 |
H16A |
108.8 |
109.5 |
| H15 |
C15 |
H15A |
109.5 |
109.5 |
| O17 |
C16 |
H16 |
108.8 |
109.5 |
| O17 |
C16 |
H16A |
108.8 |
109.5 |
| H16 |
C16 |
H16A |
110.2 |
109.6 |
| C19 |
C18 |
H18 |
108.8 |
109.5 |
| C19 |
C18 |
H18A |
108.8 |
109.6 |
| H18 |
C18 |
H18A |
110.1 |
109.5 |
| H19 |
C19 |
H19A |
109.4 |
109.5 |
| N20 |
C21 |
C22 |
109.4 |
109.2 |
| N20 |
C21 |
H21 |
109.5 |
109.6 |
| N20 |
C21 |
H21A |
109.5 |
109.5 |
| C22 |
C21 |
H21 |
109.5 |
109.5 |
| C22 |
C21 |
H21A |
109.5 |
109.5 |
| C21 |
C22 |
H22 |
108.8 |
109.5 |
| C21 |
C22 |
H22A |
108.8 |
109.5 |
| H21 |
C21 |
H21A |
109.5 |
109.5 |
| O23 |
C22 |
H22 |
108.8 |
109.5 |
| O23 |
C22 |
H22A |
108.8 |
109.6 |
| H22 |
C22 |
H22A |
110.1 |
109.5 |
| C25 |
C24 |
H24 |
108.8 |
109.5 |
| C25 |
C24 |
H24A |
108.8 |
109.5 |
| H24 |
C24 |
H24A |
110.2 |
109.5 |
| H25 |
C25 |
H25A |
109.6 |
109.5 |
| F27 |
C26 |
F28 |
105.4 |
109.5 |
Torsion Angles for SD5
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| HN01 |
N01 |
C02 |
HN0A |
240.0 |
180.2 |
| C03 |
C02 |
N01 |
N07 |
179.4 |
180.3 |
| N01 |
C02 |
N07 |
C06 |
178.9 |
179.7 |
| C02 |
N01 |
HN01 |
HN0A |
120.0 |
179.8 |
| HN01 |
N01 |
C02 |
N07 |
0.0 |
359.9 |
| C02 |
N01 |
HN0A |
HN01 |
240.0 |
180.2 |
| HN0A |
N01 |
C02 |
N07 |
120.0 |
179.7 |
| C03 |
C02 |
N01 |
HN01 |
179.4 |
180.2 |
| C03 |
C02 |
N01 |
HN0A |
299.4 |
0.0 |
| N01 |
C02 |
C03 |
N07 |
180.6 |
179.7 |
| C03 |
C02 |
N07 |
C06 |
359.5 |
359.4 |
| N07 |
C02 |
N01 |
HN01 |
0.0 |
359.9 |
| N07 |
C02 |
N01 |
HN0A |
120.0 |
179.7 |
| C02 |
N07 |
C06 |
H06 |
180.0 |
180.4 |
| C04 |
C03 |
C02 |
N07 |
0.6 |
0.3 |
| C03 |
C04 |
C05 |
C08 |
177.7 |
180.0 |
| C03 |
C04 |
C05 |
C06 |
359.7 |
360.0 |
| H03 |
C03 |
C02 |
N07 |
180.6 |
180.3 |
| H03 |
C03 |
C04 |
C05 |
179.8 |
180.0 |
| C26 |
C04 |
C03 |
H03 |
359.2 |
360.0 |
| C05 |
C04 |
C03 |
H03 |
179.8 |
180.0 |
| C06 |
C05 |
C04 |
C08 |
182.1 |
180.0 |
| C04 |
C05 |
C08 |
N13 |
133.0 |
0.0 |
| C04 |
C05 |
C06 |
H06 |
180.4 |
180.0 |
| C04 |
C05 |
C08 |
C06 |
182.2 |
180.0 |
| C08 |
C05 |
C06 |
H06 |
2.4 |
360.0 |
| C09 |
C08 |
C05 |
N13 |
179.2 |
180.2 |
| C05 |
C08 |
N13 |
C12 |
179.0 |
179.8 |
| C02 |
N07 |
C06 |
C05 |
0.0 |
0.6 |
| C04 |
C05 |
C06 |
C08 |
178.0 |
180.0 |
| C06 |
C05 |
C08 |
N13 |
310.9 |
180.0 |
| N07 |
C06 |
C05 |
H06 |
180.0 |
179.8 |
| N07 |
C06 |
C05 |
C08 |
182.4 |
179.8 |
| C05 |
C06 |
N07 |
H06 |
180.0 |
180.2 |
| H06 |
C06 |
C05 |
C08 |
2.4 |
360.0 |
| C05 |
C08 |
C09 |
N13 |
180.9 |
179.8 |
| C09 |
C08 |
N13 |
C12 |
359.8 |
359.6 |
| C08 |
N13 |
C12 |
N14 |
181.7 |
180.2 |
| C10 |
C09 |
C08 |
N13 |
360.0 |
0.2 |
| C09 |
C10 |
N11 |
C12 |
0.1 |
359.9 |
| H09 |
C09 |
C08 |
N13 |
180.0 |
180.2 |
| H09 |
C09 |
C10 |
N11 |
180.1 |
180.1 |
| N20 |
C10 |
C09 |
H09 |
359.9 |
360.0 |
| N11 |
C10 |
C09 |
H09 |
180.1 |
180.1 |
| C10 |
N11 |
C12 |
N14 |
178.4 |
180.0 |
| C08 |
N13 |
C12 |
N11 |
0.4 |
0.5 |
| N13 |
C12 |
N11 |
N14 |
181.3 |
179.8 |
| N11 |
C12 |
N14 |
C19 |
18.0 |
180.0 |
| N11 |
C12 |
N14 |
C15 |
179.8 |
303.6 |
| N11 |
C12 |
N13 |
N14 |
178.7 |
180.2 |
| N13 |
C12 |
N14 |
C19 |
196.8 |
0.3 |
| N13 |
C12 |
N14 |
C15 |
358.7 |
123.9 |
| C15 |
N14 |
C12 |
C19 |
161.8 |
123.6 |
| C12 |
N14 |
C19 |
C18 |
217.6 |
182.4 |
| C12 |
N14 |
C19 |
H19 |
337.6 |
302.3 |
| C12 |
N14 |
C19 |
H19A |
97.6 |
62.4 |
| C12 |
N14 |
C15 |
C16 |
143.2 |
177.6 |
| C12 |
N14 |
C15 |
H15 |
263.2 |
297.6 |
| C12 |
N14 |
C15 |
H15A |
23.2 |
57.6 |
| C12 |
N14 |
C19 |
C15 |
163.6 |
123.8 |
| C19 |
N14 |
C15 |
C16 |
306.6 |
301.4 |
| C19 |
N14 |
C15 |
H15 |
66.5 |
61.4 |
| C19 |
N14 |
C15 |
H15A |
186.6 |
181.4 |
| N14 |
C19 |
C18 |
H18 |
183.0 |
183.2 |
| N14 |
C19 |
C18 |
H18A |
63.0 |
63.1 |
| H19 |
C19 |
N14 |
H19A |
240.0 |
239.9 |
| C12 |
N14 |
C15 |
C19 |
196.6 |
236.2 |
| C15 |
N14 |
C19 |
C18 |
54.0 |
58.6 |
| C15 |
N14 |
C19 |
H19 |
174.0 |
178.6 |
| C15 |
N14 |
C19 |
H19A |
293.9 |
298.6 |
| C16 |
C15 |
N14 |
H15 |
240.0 |
240.0 |
| C16 |
C15 |
N14 |
H15A |
120.0 |
120.0 |
| N14 |
C15 |
C16 |
O17 |
56.0 |
56.9 |
| N14 |
C15 |
C16 |
H16 |
176.0 |
176.8 |
| N14 |
C15 |
C16 |
H16A |
296.0 |
297.0 |
| H15 |
C15 |
N14 |
H15A |
240.0 |
240.0 |
| C16 |
C15 |
N14 |
C19 |
306.6 |
301.4 |
| N14 |
C15 |
C16 |
H15 |
120.0 |
120.0 |
| N14 |
C15 |
C16 |
H15A |
240.0 |
240.1 |
| H15 |
C15 |
C16 |
H15A |
120.0 |
120.1 |
| O17 |
C16 |
C15 |
H16 |
240.0 |
240.1 |
| O17 |
C16 |
C15 |
H16A |
120.0 |
119.9 |
| H16 |
C16 |
C15 |
H16A |
240.0 |
239.8 |
| H15 |
C15 |
N14 |
C19 |
66.5 |
61.4 |
| N14 |
C15 |
H15 |
C16 |
239.9 |
240.2 |
| N14 |
C15 |
H15 |
H15A |
119.9 |
120.0 |
| C16 |
C15 |
H15 |
H15A |
240.0 |
239.9 |
| H15 |
C15 |
C16 |
O17 |
296.0 |
296.9 |
| H15 |
C15 |
C16 |
H16 |
56.0 |
56.8 |
| H15 |
C15 |
C16 |
H16A |
176.0 |
177.0 |
| H15A |
C15 |
N14 |
C19 |
186.6 |
181.4 |
| N14 |
C15 |
H15A |
C16 |
120.1 |
119.8 |
| N14 |
C15 |
H15A |
H15 |
240.0 |
240.0 |
| C16 |
C15 |
H15A |
H15 |
120.0 |
120.1 |
| H15A |
C15 |
C16 |
O17 |
176.0 |
176.8 |
| H15A |
C15 |
C16 |
H16 |
296.0 |
296.7 |
| H15A |
C15 |
C16 |
H16A |
56.0 |
56.9 |
| O17 |
C16 |
C15 |
H15 |
296.0 |
296.9 |
| O17 |
C16 |
C15 |
H15A |
176.0 |
176.8 |
| C15 |
C16 |
O17 |
H16 |
120.0 |
119.9 |
| C15 |
C16 |
O17 |
H16A |
240.0 |
240.1 |
| H16 |
C16 |
O17 |
H16A |
120.0 |
120.2 |
| H16 |
C16 |
C15 |
H15 |
56.0 |
56.8 |
| H16 |
C16 |
C15 |
H15A |
296.0 |
296.7 |
| C15 |
C16 |
H16 |
O17 |
238.3 |
240.3 |
| C15 |
C16 |
H16 |
H16A |
119.1 |
120.1 |
| O17 |
C16 |
H16 |
H16A |
240.9 |
239.8 |
| H16A |
C16 |
C15 |
H15 |
176.0 |
177.0 |
| H16A |
C16 |
C15 |
H15A |
56.0 |
56.9 |
| C15 |
C16 |
H16A |
O17 |
121.7 |
119.7 |
| C15 |
C16 |
H16A |
H16 |
240.9 |
239.9 |
| O17 |
C16 |
H16A |
H16 |
119.1 |
120.2 |
| N14 |
C19 |
C18 |
O17 |
303.0 |
303.1 |
| C18 |
O17 |
C16 |
H16 |
180.2 |
181.4 |
| C18 |
O17 |
C16 |
H16A |
60.2 |
61.2 |
| N14 |
C19 |
C18 |
H19 |
120.0 |
119.9 |
| N14 |
C19 |
C18 |
H19A |
240.0 |
240.0 |
| H18 |
C18 |
C19 |
H18A |
120.0 |
120.1 |
| C19 |
C18 |
H18 |
H18A |
240.8 |
239.8 |
| C19 |
C18 |
H18A |
H18 |
119.2 |
120.1 |
| N14 |
C19 |
H19 |
C18 |
240.2 |
240.2 |
| N14 |
C19 |
H19 |
H19A |
120.1 |
120.1 |
| H19 |
C19 |
C18 |
H18 |
62.9 |
63.4 |
| H19 |
C19 |
C18 |
H18A |
302.9 |
303.2 |
| N14 |
C19 |
H19A |
C18 |
119.8 |
119.8 |
| N14 |
C19 |
H19A |
H19 |
239.9 |
240.0 |
| H19A |
C19 |
C18 |
H18 |
303.0 |
303.2 |
| H19A |
C19 |
C18 |
H18A |
183.0 |
183.1 |
| C25 |
N20 |
C21 |
H21 |
69.1 |
178.5 |
| C25 |
N20 |
C21 |
H21A |
189.1 |
298.7 |
| C22 |
C21 |
N20 |
H21 |
240.0 |
240.1 |
| C22 |
C21 |
N20 |
H21A |
120.0 |
119.9 |
| N20 |
C21 |
C22 |
H22 |
176.0 |
63.1 |
| N20 |
C21 |
C22 |
H22A |
295.9 |
183.2 |
| H21 |
C21 |
N20 |
H21A |
240.0 |
239.8 |
| N20 |
C21 |
C22 |
H21 |
120.0 |
120.0 |
| N20 |
C21 |
C22 |
H21A |
240.0 |
240.1 |
| H21 |
C21 |
C22 |
H21A |
120.0 |
120.1 |
| O23 |
C22 |
C21 |
H22 |
240.0 |
240.0 |
| O23 |
C22 |
C21 |
H22A |
120.0 |
120.0 |
| H22 |
C22 |
C21 |
H22A |
240.0 |
239.9 |
| N20 |
C21 |
H21 |
C22 |
240.0 |
240.2 |
| N20 |
C21 |
H21 |
H21A |
120.0 |
120.2 |
| C22 |
C21 |
H21 |
H21A |
240.0 |
239.9 |
| H21 |
C21 |
C22 |
H22 |
56.0 |
303.1 |
| H21 |
C21 |
C22 |
H22A |
176.0 |
63.2 |
| N20 |
C21 |
H21A |
C22 |
120.0 |
119.7 |
| N20 |
C21 |
H21A |
H21 |
240.0 |
239.8 |
| C22 |
C21 |
H21A |
H21 |
120.0 |
120.1 |
| H21A |
C21 |
C22 |
H22 |
296.0 |
183.1 |
| H21A |
C21 |
C22 |
H22A |
55.9 |
303.1 |
| O23 |
C22 |
C21 |
H21 |
296.0 |
183.2 |
| O23 |
C22 |
C21 |
H21A |
175.9 |
63.1 |
| C21 |
C22 |
O23 |
H22 |
120.0 |
120.0 |
| C21 |
C22 |
O23 |
H22A |
240.0 |
240.0 |
| H22 |
C22 |
O23 |
H22A |
120.0 |
120.1 |
| H22 |
C22 |
C21 |
H21 |
56.0 |
303.1 |
| H22 |
C22 |
C21 |
H21A |
296.0 |
183.1 |
| C21 |
C22 |
H22 |
H22A |
119.1 |
120.1 |
| O23 |
C22 |
H22 |
H22A |
240.8 |
239.9 |
| H22A |
C22 |
C21 |
H21 |
176.0 |
63.2 |
| H22A |
C22 |
C21 |
H21A |
55.9 |
303.1 |
| C21 |
C22 |
H22A |
H22 |
240.9 |
239.9 |
| O23 |
C22 |
H22A |
H22 |
119.2 |
120.1 |
| C24 |
O23 |
C22 |
H22 |
178.2 |
298.7 |
| C24 |
O23 |
C22 |
H22A |
58.2 |
178.6 |
| H24 |
C24 |
C25 |
H24A |
120.0 |
120.1 |
| C25 |
C24 |
H24 |
H24A |
240.9 |
239.9 |
| C25 |
C24 |
H24A |
H24 |
119.1 |
120.1 |
| H25 |
C25 |
C24 |
H24 |
65.2 |
177.0 |
| H25 |
C25 |
C24 |
H24A |
305.2 |
56.9 |
| H25A |
C25 |
C24 |
H24 |
305.2 |
56.9 |
| H25A |
C25 |
C24 |
H24A |
185.2 |
296.7 |