PDB Chemical Component HVD
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 HVD
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O02 |
C14 |
1.406 |
1.359 |
| C14 |
C13 |
1.344 |
1.387 |
| C14 |
C15 |
1.351 |
1.387 |
| C13 |
C12 |
1.380 |
1.382 |
| C15 |
C16 |
1.378 |
1.386 |
| C12 |
C17 |
1.520 |
1.507 |
| C12 |
C08 |
1.415 |
1.382 |
| C19 |
C20 |
1.538 |
1.531 |
| C19 |
C18 |
1.530 |
1.529 |
| C17 |
C18 |
1.537 |
1.530 |
| C16 |
C08 |
1.418 |
1.388 |
| C16 |
O01 |
1.394 |
1.359 |
| C10 |
C09 |
1.526 |
1.506 |
| C08 |
C05 |
1.533 |
1.508 |
| C20 |
C21 |
1.525 |
1.529 |
| C09 |
C11 |
1.324 |
1.311 |
| C09 |
C04 |
1.526 |
1.507 |
| C05 |
C04 |
1.531 |
1.529 |
| C05 |
C06 |
1.527 |
1.500 |
| C04 |
C03 |
1.514 |
1.534 |
| C06 |
C01 |
1.322 |
1.295 |
| C03 |
C02 |
1.529 |
1.529 |
| C01 |
C02 |
1.521 |
1.501 |
| C01 |
C07 |
1.526 |
1.507 |
| C02 |
H01 |
1.100 |
1.090 |
| C02 |
H02 |
1.100 |
1.090 |
| C03 |
H04 |
1.100 |
1.090 |
| C03 |
H03 |
1.100 |
1.090 |
| C04 |
H10 |
1.101 |
1.090 |
| C05 |
H09 |
1.100 |
1.091 |
| C06 |
H08 |
1.080 |
1.080 |
| C07 |
H05 |
1.100 |
1.090 |
| C07 |
H06 |
1.100 |
1.090 |
| C07 |
H07 |
1.100 |
1.090 |
| C10 |
H11 |
1.100 |
1.090 |
| C10 |
H13 |
1.101 |
1.090 |
| C10 |
H12 |
1.100 |
1.090 |
| C11 |
H15 |
1.080 |
1.080 |
| C11 |
H14 |
1.080 |
1.080 |
| C13 |
H16 |
1.080 |
1.079 |
| C15 |
H17 |
1.080 |
1.080 |
| O01 |
H29 |
0.950 |
0.966 |
| O02 |
H30 |
0.950 |
0.967 |
| C17 |
H19 |
1.100 |
1.091 |
| C17 |
H18 |
1.100 |
1.090 |
| C18 |
H21 |
1.100 |
1.090 |
| C18 |
H20 |
1.100 |
1.090 |
| C19 |
H23 |
1.101 |
1.091 |
| C19 |
H22 |
1.100 |
1.089 |
| C20 |
H24 |
1.100 |
1.089 |
| C20 |
H25 |
1.100 |
1.090 |
| C21 |
H26 |
1.100 |
1.089 |
| C21 |
H27 |
1.100 |
1.090 |
| C21 |
H28 |
1.100 |
1.091 |
Bond Angles for HVD
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C14 |
C13 |
H16 |
119.4 |
120.0 |
| C14 |
C15 |
C16 |
120.4 |
119.9 |
| C14 |
C15 |
H17 |
119.8 |
120.0 |
| C13 |
C12 |
C17 |
118.0 |
120.0 |
| C15 |
C16 |
O01 |
120.1 |
120.0 |
| C16 |
C15 |
H17 |
119.8 |
120.1 |
| C12 |
C17 |
C18 |
111.6 |
109.5 |
| C12 |
C17 |
H19 |
109.0 |
109.4 |
| C12 |
C17 |
H18 |
109.0 |
109.5 |
| C19 |
C20 |
C21 |
110.3 |
109.5 |
| C20 |
C19 |
H23 |
109.4 |
109.4 |
| C20 |
C19 |
H22 |
109.4 |
109.5 |
| C19 |
C20 |
H24 |
109.3 |
109.5 |
| C19 |
C20 |
H25 |
109.3 |
109.5 |
| C19 |
C18 |
H21 |
108.7 |
109.5 |
| C19 |
C18 |
H20 |
108.7 |
109.5 |
| C18 |
C17 |
H19 |
108.9 |
109.5 |
| C18 |
C17 |
H18 |
108.9 |
109.5 |
| C17 |
C18 |
H21 |
108.7 |
109.4 |
| C17 |
C18 |
H20 |
108.7 |
109.5 |
| C16 |
O01 |
H29 |
109.5 |
114.0 |
| C10 |
C09 |
C11 |
120.3 |
120.0 |
| C08 |
C05 |
H09 |
107.8 |
109.2 |
| C21 |
C20 |
H24 |
109.3 |
109.5 |
| C21 |
C20 |
H25 |
109.3 |
109.5 |
| C20 |
C21 |
H26 |
109.5 |
109.5 |
| C20 |
C21 |
H27 |
109.5 |
109.5 |
| C20 |
C21 |
H28 |
109.5 |
109.5 |
| C09 |
C11 |
H15 |
120.0 |
120.0 |
| C09 |
C11 |
H14 |
120.0 |
120.0 |
| C09 |
C04 |
H10 |
109.0 |
109.6 |
| C05 |
C04 |
H10 |
108.9 |
109.7 |
| C06 |
C05 |
H09 |
107.9 |
109.2 |
| C05 |
C06 |
H08 |
118.8 |
118.0 |
| C04 |
C03 |
H04 |
109.3 |
109.6 |
| C04 |
C03 |
H03 |
109.3 |
109.8 |
| C06 |
C01 |
C07 |
120.4 |
118.0 |
| C03 |
C02 |
H01 |
108.3 |
109.4 |
| C03 |
C02 |
H02 |
108.2 |
109.3 |
| C02 |
C01 |
C07 |
118.4 |
118.0 |
| C01 |
C02 |
H01 |
108.2 |
109.3 |
| C01 |
C02 |
H02 |
108.2 |
109.4 |
| C01 |
C07 |
H05 |
109.5 |
109.5 |
| C01 |
C07 |
H06 |
109.5 |
109.4 |
| C01 |
C07 |
H07 |
109.5 |
109.5 |
| H01 |
C02 |
H02 |
109.5 |
109.3 |
| H04 |
C03 |
H03 |
109.4 |
109.6 |
| H05 |
C07 |
H06 |
109.5 |
109.5 |
| H05 |
C07 |
H07 |
109.4 |
109.5 |
| H06 |
C07 |
H07 |
109.5 |
109.5 |
| H11 |
C10 |
H13 |
109.5 |
109.5 |
| H11 |
C10 |
H12 |
109.5 |
109.5 |
| H13 |
C10 |
H12 |
109.5 |
109.5 |
| H15 |
C11 |
H14 |
120.0 |
120.0 |
| H19 |
C17 |
H18 |
109.5 |
109.4 |
| H21 |
C18 |
H20 |
109.5 |
109.5 |
| H23 |
C19 |
H22 |
109.5 |
109.5 |
| H24 |
C20 |
H25 |
109.4 |
109.5 |
| H26 |
C21 |
H27 |
109.5 |
109.5 |
| H26 |
C21 |
H28 |
109.5 |
109.5 |
| H27 |
C21 |
H28 |
109.5 |
109.4 |
Torsion Angles for HVD
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O02 |
C14 |
C13 |
H16 |
359.7 |
359.9 |
| O02 |
C14 |
C15 |
H17 |
359.8 |
0.1 |
| C14 |
C13 |
C12 |
C17 |
178.8 |
180.0 |
| C15 |
C14 |
C13 |
H16 |
181.1 |
180.0 |
| C14 |
C15 |
C16 |
O01 |
181.0 |
180.1 |
| C16 |
C15 |
C14 |
H17 |
180.0 |
179.7 |
| C13 |
C12 |
C17 |
C18 |
255.1 |
260.9 |
| C13 |
C12 |
C17 |
H19 |
15.4 |
21.0 |
| C13 |
C12 |
C17 |
H18 |
134.7 |
140.9 |
| C14 |
C15 |
C16 |
H17 |
180.0 |
180.3 |
| C15 |
C16 |
O01 |
H29 |
180.0 |
90.0 |
| C18 |
C17 |
C12 |
H19 |
239.7 |
240.0 |
| C18 |
C17 |
C12 |
H18 |
120.3 |
120.1 |
| C12 |
C17 |
C18 |
H21 |
306.1 |
300.0 |
| C12 |
C17 |
C18 |
H20 |
187.0 |
60.0 |
| H19 |
C17 |
C12 |
H18 |
240.6 |
240.1 |
| C12 |
C08 |
C05 |
H09 |
359.7 |
1.8 |
| C20 |
C19 |
C18 |
H21 |
298.2 |
60.0 |
| C20 |
C19 |
C18 |
H20 |
57.2 |
300.0 |
| C21 |
C20 |
C19 |
H24 |
239.9 |
240.0 |
| C21 |
C20 |
C19 |
H25 |
120.1 |
120.0 |
| C19 |
C20 |
C21 |
H26 |
180.0 |
60.0 |
| C19 |
C20 |
C21 |
H27 |
300.0 |
180.0 |
| C19 |
C20 |
C21 |
H28 |
60.0 |
299.9 |
| H23 |
C19 |
C20 |
H22 |
240.1 |
120.0 |
| H24 |
C20 |
C19 |
H25 |
240.3 |
240.0 |
| C19 |
C18 |
C17 |
H19 |
306.2 |
60.0 |
| C19 |
C18 |
C17 |
H18 |
186.8 |
300.0 |
| C17 |
C18 |
C19 |
H21 |
239.5 |
120.0 |
| C17 |
C18 |
C19 |
H20 |
120.5 |
240.0 |
| H21 |
C18 |
C19 |
H20 |
240.9 |
120.1 |
| C12 |
C17 |
C18 |
H19 |
120.3 |
120.0 |
| C12 |
C17 |
C18 |
H18 |
239.7 |
240.0 |
| C19 |
C18 |
C17 |
H21 |
120.4 |
240.0 |
| C19 |
C18 |
C17 |
H20 |
239.5 |
120.0 |
| H19 |
C17 |
C18 |
H18 |
119.3 |
120.0 |
| H21 |
C18 |
C17 |
H20 |
119.1 |
240.0 |
| C16 |
C08 |
C05 |
H09 |
179.7 |
181.5 |
| O01 |
C16 |
C15 |
H17 |
1.0 |
359.7 |
| C10 |
C09 |
C11 |
H15 |
180.6 |
359.9 |
| C10 |
C09 |
C11 |
H14 |
0.6 |
180.1 |
| C10 |
C09 |
C04 |
H10 |
343.4 |
173.5 |
| C08 |
C05 |
C04 |
H10 |
58.3 |
50.0 |
| C06 |
C05 |
C08 |
H09 |
242.9 |
240.5 |
| C08 |
C05 |
C06 |
H08 |
29.9 |
42.6 |
| C21 |
C20 |
C19 |
H23 |
194.0 |
60.0 |
| C21 |
C20 |
C19 |
H22 |
313.9 |
300.0 |
| C19 |
C20 |
C21 |
H24 |
120.1 |
120.0 |
| C19 |
C20 |
C21 |
H25 |
239.8 |
240.0 |
| H24 |
C20 |
C21 |
H25 |
119.7 |
120.0 |
| H26 |
C21 |
C20 |
H27 |
240.0 |
240.0 |
| H26 |
C21 |
C20 |
H28 |
120.0 |
120.1 |
| H27 |
C21 |
C20 |
H28 |
240.0 |
240.1 |
| C11 |
C09 |
C04 |
H10 |
163.9 |
353.4 |
| H15 |
C11 |
C09 |
H14 |
180.0 |
179.9 |
| C05 |
C04 |
C09 |
H10 |
119.5 |
120.6 |
| C09 |
C04 |
C03 |
H04 |
295.4 |
52.9 |
| C09 |
C04 |
C03 |
H03 |
55.2 |
292.5 |
| C09 |
C04 |
C05 |
H10 |
240.4 |
239.4 |
| C05 |
C04 |
C03 |
H04 |
56.7 |
172.9 |
| C05 |
C04 |
C03 |
H03 |
176.4 |
52.4 |
| C08 |
C05 |
C06 |
H09 |
117.0 |
119.5 |
| C06 |
C05 |
C04 |
H10 |
295.3 |
289.6 |
| C05 |
C06 |
C01 |
C07 |
187.3 |
180.2 |
| C04 |
C03 |
C02 |
H01 |
165.2 |
289.2 |
| C04 |
C03 |
C02 |
H02 |
283.7 |
169.6 |
| H04 |
C03 |
C04 |
H03 |
240.2 |
120.4 |
| C02 |
C01 |
C06 |
C07 |
178.4 |
179.8 |
| C06 |
C01 |
C02 |
H01 |
224.2 |
103.3 |
| C06 |
C01 |
C02 |
H02 |
105.6 |
223.0 |
| C06 |
C01 |
C07 |
H05 |
180.0 |
269.8 |
| C06 |
C01 |
C07 |
H06 |
300.0 |
29.8 |
| C06 |
C01 |
C07 |
H07 |
60.0 |
149.8 |
| C03 |
C02 |
C01 |
C07 |
163.4 |
162.9 |
| C01 |
C02 |
C03 |
H01 |
239.3 |
120.2 |
| C01 |
C02 |
C03 |
H02 |
120.7 |
239.8 |
| H01 |
C02 |
C03 |
H02 |
241.4 |
119.6 |
| C06 |
C01 |
C02 |
C07 |
181.5 |
180.2 |
| C03 |
C02 |
C01 |
H01 |
120.7 |
239.8 |
| C03 |
C02 |
C01 |
H02 |
239.3 |
120.1 |
| C02 |
C01 |
C07 |
H05 |
1.5 |
90.0 |
| C02 |
C01 |
C07 |
H06 |
121.6 |
210.0 |
| C02 |
C01 |
C07 |
H07 |
241.5 |
330.0 |
| H01 |
C02 |
C01 |
H02 |
118.5 |
240.3 |
| C07 |
C01 |
C02 |
H01 |
42.6 |
283.1 |
| C07 |
C01 |
C02 |
H02 |
284.1 |
42.8 |
| H05 |
C07 |
C01 |
H06 |
239.9 |
240.0 |
| H05 |
C07 |
C01 |
H07 |
120.0 |
120.0 |
| H06 |
C07 |
C01 |
H07 |
240.0 |
240.0 |
| C03 |
C02 |
H01 |
H02 |
117.8 |
240.4 |
| H01 |
C02 |
C01 |
C07 |
42.6 |
283.1 |
| C01 |
C02 |
H01 |
H02 |
242.3 |
119.7 |
| C03 |
C02 |
H02 |
H01 |
242.2 |
119.7 |
| H02 |
C02 |
C01 |
C07 |
284.1 |
42.8 |
| C01 |
C02 |
H02 |
H01 |
117.7 |
240.3 |
| C04 |
C03 |
H04 |
H03 |
119.7 |
239.4 |
| H04 |
C03 |
C02 |
H01 |
45.1 |
48.9 |
| H04 |
C03 |
C02 |
H02 |
163.7 |
289.3 |
| C04 |
C03 |
H03 |
H04 |
240.3 |
120.5 |
| H03 |
C03 |
C02 |
H01 |
285.3 |
169.3 |
| H03 |
C03 |
C02 |
H02 |
43.9 |
49.7 |
| H10 |
C04 |
C03 |
H04 |
174.7 |
292.6 |
| H10 |
C04 |
C03 |
H03 |
294.5 |
172.1 |
| H09 |
C05 |
C04 |
H10 |
176.7 |
169.6 |
| H09 |
C05 |
C06 |
H08 |
272.9 |
283.0 |
| H08 |
C06 |
C05 |
H09 |
272.9 |
283.0 |
| H08 |
C06 |
C01 |
C07 |
7.3 |
0.6 |
| C01 |
C07 |
H05 |
H06 |
120.0 |
119.9 |
| C01 |
C07 |
H05 |
H07 |
240.0 |
240.0 |
| H06 |
C07 |
H05 |
H07 |
120.0 |
120.0 |
| C01 |
C07 |
H06 |
H05 |
239.9 |
240.0 |
| C01 |
C07 |
H06 |
H07 |
120.0 |
120.0 |
| H05 |
C07 |
H06 |
H07 |
240.0 |
240.0 |
| C01 |
C07 |
H07 |
H05 |
120.0 |
120.0 |
| C01 |
C07 |
H07 |
H06 |
240.0 |
240.0 |
| H05 |
C07 |
H07 |
H06 |
120.0 |
120.0 |
| H11 |
C10 |
C09 |
C11 |
180.0 |
4.8 |
| H13 |
C10 |
H11 |
H12 |
120.0 |
120.0 |
| H13 |
C10 |
C09 |
C11 |
300.0 |
124.8 |
| H11 |
C10 |
H13 |
H12 |
240.0 |
240.0 |
| H12 |
C10 |
C09 |
C11 |
60.0 |
244.8 |
| H11 |
C10 |
H12 |
H13 |
120.0 |
120.0 |
| C09 |
C11 |
H15 |
H14 |
180.0 |
180.1 |
| C09 |
C11 |
H14 |
H15 |
180.0 |
179.9 |
| H16 |
C13 |
C12 |
C17 |
358.8 |
0.1 |
| C14 |
C15 |
H17 |
C16 |
180.0 |
179.7 |
| H17 |
C15 |
C16 |
O01 |
1.0 |
359.7 |
| C12 |
C17 |
H19 |
C18 |
238.1 |
240.0 |
| C12 |
C17 |
H19 |
H18 |
119.1 |
119.9 |
| C18 |
C17 |
H19 |
H18 |
241.0 |
240.0 |
| H19 |
C17 |
C18 |
H21 |
185.7 |
180.0 |
| H19 |
C17 |
C18 |
H20 |
66.6 |
300.0 |
| C12 |
C17 |
H18 |
C18 |
121.9 |
120.0 |
| C12 |
C17 |
H18 |
H19 |
241.0 |
240.1 |
| C18 |
C17 |
H18 |
H19 |
119.0 |
120.0 |
| H18 |
C17 |
C18 |
H21 |
66.4 |
60.0 |
| H18 |
C17 |
C18 |
H20 |
307.3 |
180.0 |
| C19 |
C18 |
H21 |
H20 |
118.6 |
240.0 |
| H21 |
C18 |
C17 |
H19 |
185.7 |
180.0 |
| H21 |
C18 |
C17 |
H18 |
66.4 |
60.0 |
| C17 |
C18 |
H21 |
H20 |
241.4 |
120.0 |
| C19 |
C18 |
H20 |
H21 |
241.4 |
120.1 |
| H20 |
C18 |
C17 |
H19 |
66.6 |
300.0 |
| H20 |
C18 |
C17 |
H18 |
307.3 |
180.0 |
| C17 |
C18 |
H20 |
H21 |
118.6 |
240.0 |
| H23 |
C19 |
C20 |
C21 |
194.0 |
60.0 |
| C20 |
C19 |
H23 |
H22 |
119.8 |
240.0 |
| H23 |
C19 |
C20 |
H24 |
314.2 |
180.0 |
| H23 |
C19 |
C20 |
H25 |
73.9 |
300.0 |
| H23 |
C19 |
C18 |
H21 |
178.1 |
180.0 |
| H23 |
C19 |
C18 |
H20 |
297.2 |
59.9 |
| H22 |
C19 |
C20 |
C21 |
313.9 |
300.0 |
| C20 |
C19 |
H22 |
H23 |
240.2 |
119.9 |
| H22 |
C19 |
C20 |
H24 |
74.0 |
60.0 |
| H22 |
C19 |
C20 |
H25 |
193.7 |
180.1 |
| H22 |
C19 |
C18 |
H21 |
58.2 |
300.0 |
| H22 |
C19 |
C18 |
H20 |
177.3 |
180.0 |
| C19 |
C20 |
H24 |
C21 |
239.2 |
240.0 |
| H24 |
C20 |
C19 |
H23 |
314.2 |
180.0 |
| H24 |
C20 |
C19 |
H22 |
74.0 |
60.0 |
| C19 |
C20 |
H24 |
H25 |
119.6 |
120.0 |
| C21 |
C20 |
H24 |
H25 |
240.4 |
240.0 |
| H24 |
C20 |
C21 |
H26 |
59.9 |
300.0 |
| H24 |
C20 |
C21 |
H27 |
179.8 |
60.1 |
| H24 |
C20 |
C21 |
H28 |
299.8 |
180.0 |
| C19 |
C20 |
H25 |
C21 |
120.8 |
120.0 |
| H25 |
C20 |
C19 |
H23 |
73.9 |
300.0 |
| H25 |
C20 |
C19 |
H22 |
193.7 |
180.1 |
| C19 |
C20 |
H25 |
H24 |
240.4 |
240.0 |
| C21 |
C20 |
H25 |
H24 |
119.6 |
120.0 |
| H25 |
C20 |
C21 |
H26 |
300.2 |
180.0 |
| H25 |
C20 |
C21 |
H27 |
60.1 |
300.0 |
| H25 |
C20 |
C21 |
H28 |
180.1 |
59.9 |
| H26 |
C21 |
C20 |
H24 |
59.9 |
300.0 |
| H26 |
C21 |
C20 |
H25 |
300.2 |
180.0 |
| C20 |
C21 |
H26 |
H27 |
120.0 |
120.0 |
| C20 |
C21 |
H26 |
H28 |
240.0 |
239.9 |
| H27 |
C21 |
H26 |
H28 |
120.0 |
119.9 |
| H27 |
C21 |
C20 |
H24 |
179.8 |
60.1 |
| H27 |
C21 |
C20 |
H25 |
60.1 |
300.0 |
| C20 |
C21 |
H27 |
H26 |
240.0 |
239.9 |
| C20 |
C21 |
H27 |
H28 |
120.0 |
120.0 |
| H26 |
C21 |
H27 |
H28 |
240.0 |
240.0 |
| H28 |
C21 |
C20 |
H24 |
299.8 |
180.0 |
| H28 |
C21 |
C20 |
H25 |
180.1 |
59.9 |
| C20 |
C21 |
H28 |
H26 |
120.0 |
120.1 |
| C20 |
C21 |
H28 |
H27 |
240.0 |
240.0 |
| H26 |
C21 |
H28 |
H27 |
120.0 |
120.0 |