PDB Chemical Component HDV
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 HDV
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O3G |
PG |
1.494 |
1.480 |
| O2B |
PB |
1.483 |
1.479 |
| O1G |
PG |
1.493 |
1.610 |
| O1B |
PB |
1.450 |
1.610 |
| PG |
O3B |
1.633 |
1.611 |
| PG |
O2G |
1.436 |
1.609 |
| PB |
O3B |
1.566 |
1.610 |
| PB |
O3A |
1.571 |
1.610 |
| O3A |
PA |
1.623 |
1.610 |
| O2A |
PA |
1.429 |
1.480 |
| PA |
O5' |
1.634 |
1.611 |
| PA |
O1A |
1.455 |
1.610 |
| O5' |
C5' |
1.412 |
1.429 |
| F2' |
C2' |
1.441 |
1.399 |
| C3' |
O3' |
1.453 |
1.429 |
| C3' |
C2' |
1.500 |
1.548 |
| C3' |
C4' |
1.514 |
1.549 |
| C5' |
C4' |
1.540 |
1.531 |
| C2' |
C1' |
1.492 |
1.541 |
| C4' |
O4' |
1.470 |
1.444 |
| O4' |
C1' |
1.469 |
1.437 |
| C8 |
N9 |
1.381 |
1.364 |
| C8 |
N7 |
1.358 |
1.301 |
| C1' |
N9 |
1.449 |
1.465 |
| N9 |
C4 |
1.338 |
1.372 |
| N7 |
C5 |
1.433 |
1.355 |
| C4 |
C5 |
1.423 |
1.404 |
| C4 |
N3 |
1.308 |
1.329 |
| C5 |
C6 |
1.400 |
1.406 |
| N3 |
C2 |
1.358 |
1.316 |
| C6 |
N6 |
1.414 |
1.384 |
| C6 |
N1 |
1.279 |
1.329 |
| C2 |
N1 |
1.315 |
1.321 |
| C2 |
CL2 |
1.498 |
1.507 |
| O1A |
H1 |
0.949 |
0.966 |
| O1B |
H2 |
0.950 |
0.967 |
| O2G |
H3 |
0.950 |
0.967 |
| O1G |
H4 |
0.950 |
0.967 |
| C5' |
H5 |
1.100 |
1.090 |
| C5' |
H6 |
1.100 |
1.089 |
| C4' |
H7 |
1.100 |
1.090 |
| C3' |
H8 |
1.100 |
1.090 |
| O3' |
H9 |
0.950 |
0.967 |
| C2' |
H10 |
1.100 |
1.091 |
| C1' |
H11 |
1.100 |
1.090 |
| C8 |
H12 |
1.080 |
1.080 |
| CL2 |
H13 |
1.100 |
1.089 |
| CL2 |
H14 |
1.100 |
1.091 |
| CL2 |
H15 |
1.100 |
1.090 |
| N6 |
H16 |
1.000 |
0.971 |
| N6 |
H17 |
1.000 |
0.971 |
Bond Angles for HDV
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O3G |
PG |
O2G |
108.9 |
109.5 |
| O2B |
PB |
O3B |
114.3 |
109.5 |
| O1B |
PB |
O3B |
108.7 |
109.5 |
| PG |
O2G |
H3 |
109.5 |
114.0 |
| O3A |
PA |
O5' |
96.1 |
109.5 |
| O2A |
PA |
O5' |
105.4 |
109.5 |
| O2A |
PA |
O1A |
117.9 |
109.5 |
| O1A |
PA |
O5' |
114.8 |
109.4 |
| PA |
O5' |
C5' |
116.3 |
123.0 |
| PA |
O1A |
H1 |
109.5 |
114.0 |
| O5' |
C5' |
C4' |
107.3 |
109.5 |
| O5' |
C5' |
H5 |
110.0 |
109.4 |
| O5' |
C5' |
H6 |
110.0 |
109.6 |
| F2' |
C2' |
C1' |
109.1 |
110.5 |
| F2' |
C2' |
H10 |
110.9 |
110.5 |
| O3' |
C3' |
C2' |
109.4 |
110.9 |
| O3' |
C3' |
H8 |
111.0 |
110.8 |
| C3' |
O3' |
H9 |
109.5 |
114.0 |
| C3' |
C2' |
C1' |
104.9 |
104.2 |
| C2' |
C3' |
H8 |
110.3 |
111.0 |
| C3' |
C2' |
H10 |
110.1 |
110.5 |
| C3' |
C4' |
O4' |
101.8 |
103.5 |
| C3' |
C4' |
H7 |
110.4 |
110.8 |
| C5' |
C4' |
O4' |
104.7 |
110.6 |
| C4' |
C5' |
H5 |
110.0 |
109.4 |
| C4' |
C5' |
H6 |
110.0 |
109.5 |
| C5' |
C4' |
H7 |
110.0 |
110.5 |
| C2' |
C1' |
N9 |
121.0 |
109.9 |
| C1' |
C2' |
H10 |
110.2 |
110.5 |
| C2' |
C1' |
H11 |
110.2 |
109.9 |
| C4' |
O4' |
C1' |
113.6 |
106.9 |
| O4' |
C4' |
H7 |
111.0 |
110.6 |
| O4' |
C1' |
N9 |
100.4 |
109.9 |
| O4' |
C1' |
H11 |
110.5 |
110.0 |
| C1' |
N9 |
C4 |
121.1 |
126.3 |
| N9 |
C1' |
H11 |
110.8 |
109.8 |
| N9 |
C4 |
C5 |
105.9 |
106.0 |
| N9 |
C4 |
N3 |
134.5 |
134.9 |
| N7 |
C5 |
C6 |
129.4 |
134.7 |
| C5 |
C4 |
N3 |
119.5 |
119.1 |
| C4 |
C5 |
C6 |
121.6 |
118.2 |
| C4 |
N3 |
C2 |
113.4 |
120.6 |
| C5 |
C6 |
N6 |
121.0 |
120.8 |
| C5 |
C6 |
N1 |
116.8 |
118.5 |
| N3 |
C2 |
N1 |
129.7 |
122.5 |
| N3 |
C2 |
CL2 |
117.3 |
118.8 |
| C6 |
N6 |
H16 |
109.5 |
120.0 |
| C6 |
N6 |
H17 |
109.5 |
120.0 |
| CL2 |
C2 |
N1 |
113.0 |
118.8 |
| C2 |
CL2 |
H13 |
109.5 |
109.5 |
| C2 |
CL2 |
H14 |
109.5 |
109.5 |
| C2 |
CL2 |
H15 |
109.5 |
109.4 |
| H5 |
C5' |
H6 |
109.5 |
109.5 |
| H13 |
CL2 |
H14 |
109.4 |
109.5 |
| H13 |
CL2 |
H15 |
109.5 |
109.5 |
| H14 |
CL2 |
H15 |
109.5 |
109.4 |
| H16 |
N6 |
H17 |
109.5 |
119.9 |
Torsion Angles for HDV
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O3G |
PG |
O2G |
H3 |
360.0 |
180.0 |
| O1B |
PB |
O2B |
O3B |
128.1 |
120.1 |
| O1G |
PG |
O2G |
H3 |
230.3 |
300.0 |
| O2B |
PB |
O1B |
O3B |
229.2 |
239.9 |
| PB |
O3A |
PA |
O5' |
119.0 |
165.0 |
| O2A |
PA |
O3A |
O5' |
250.0 |
240.0 |
| O1A |
PA |
O3A |
O5' |
118.0 |
119.9 |
| O3A |
PA |
O5' |
C5' |
76.1 |
185.0 |
| O3A |
PA |
O1A |
H1 |
130.1 |
300.0 |
| O3A |
PA |
O2A |
O5' |
104.4 |
120.0 |
| O1A |
PA |
O2A |
O5' |
230.4 |
240.1 |
| O2A |
PA |
O5' |
C5' |
193.8 |
305.1 |
| O2A |
PA |
O1A |
H1 |
0.0 |
180.0 |
| O2A |
PA |
O5' |
O1A |
228.6 |
240.0 |
| O5' |
PA |
O1A |
H1 |
234.9 |
60.0 |
| PA |
O5' |
C5' |
C4' |
150.8 |
180.0 |
| PA |
O5' |
C5' |
H5 |
270.5 |
299.9 |
| PA |
O5' |
C5' |
H6 |
31.1 |
59.9 |
| O3A |
PA |
O1A |
O5' |
255.2 |
240.0 |
| O2A |
PA |
O1A |
O5' |
125.1 |
120.0 |
| O1A |
PA |
O5' |
C5' |
325.2 |
65.1 |
| O5' |
C5' |
C4' |
O4' |
295.9 |
66.4 |
| C4' |
C5' |
O5' |
H5 |
240.3 |
240.1 |
| C4' |
C5' |
O5' |
H6 |
119.6 |
120.0 |
| O5' |
C5' |
C4' |
H7 |
176.5 |
303.6 |
| H5 |
C5' |
O5' |
H6 |
239.3 |
239.9 |
| C3' |
C2' |
F2' |
C1' |
244.7 |
245.2 |
| F2' |
C2' |
C3' |
H8 |
329.1 |
21.3 |
| C3' |
C2' |
F2' |
H10 |
123.1 |
122.7 |
| F2' |
C2' |
C1' |
N9 |
19.6 |
2.8 |
| C1' |
C2' |
F2' |
H10 |
238.4 |
237.4 |
| F2' |
C2' |
C1' |
H11 |
151.1 |
123.8 |
| O3' |
C3' |
C2' |
C1' |
88.9 |
139.1 |
| C2' |
C3' |
O3' |
H8 |
121.9 |
123.7 |
| O3' |
C3' |
C2' |
H10 |
330.3 |
20.4 |
| O3' |
C3' |
C4' |
O4' |
257.4 |
204.8 |
| O3' |
C3' |
C4' |
H7 |
15.3 |
323.4 |
| F2' |
C2' |
C3' |
C1' |
117.9 |
118.7 |
| F2' |
C2' |
C3' |
H10 |
236.4 |
237.3 |
| O3' |
C3' |
C2' |
H8 |
237.7 |
236.5 |
| C2' |
C3' |
O3' |
H9 |
180.0 |
61.5 |
| C2' |
C3' |
C4' |
O4' |
15.6 |
323.0 |
| C2' |
C3' |
C4' |
H7 |
133.5 |
81.6 |
| C3' |
C2' |
C1' |
N9 |
139.1 |
121.5 |
| C1' |
C2' |
C3' |
H10 |
118.6 |
118.6 |
| C3' |
C2' |
C1' |
H11 |
270.5 |
242.5 |
| C5' |
C4' |
C3' |
O4' |
245.9 |
241.5 |
| C3' |
C4' |
C5' |
H5 |
288.7 |
60.6 |
| C3' |
C4' |
C5' |
H6 |
168.0 |
300.6 |
| C5' |
C4' |
C3' |
H7 |
128.0 |
122.9 |
| C3' |
C4' |
O4' |
C1' |
3.0 |
40.0 |
| O4' |
C4' |
C3' |
H7 |
242.1 |
241.4 |
| O5' |
C5' |
C4' |
H5 |
119.7 |
119.9 |
| O5' |
C5' |
C4' |
H6 |
240.4 |
239.9 |
| C3' |
C4' |
C5' |
O4' |
112.5 |
114.1 |
| C3' |
C4' |
C5' |
H7 |
231.9 |
236.9 |
| C5' |
C4' |
O4' |
C1' |
126.8 |
158.6 |
| O4' |
C4' |
C5' |
H7 |
119.4 |
122.8 |
| H5 |
C5' |
C4' |
H6 |
120.7 |
120.0 |
| F2' |
C2' |
C1' |
H10 |
122.0 |
122.6 |
| C1' |
C2' |
C3' |
H8 |
211.2 |
262.6 |
| C3' |
C2' |
C1' |
H10 |
241.5 |
241.3 |
| C4' |
O4' |
C1' |
C2' |
340.0 |
333.5 |
| O4' |
C1' |
C2' |
N9 |
249.3 |
240.5 |
| O4' |
C1' |
C2' |
H11 |
117.9 |
119.6 |
| C2' |
C1' |
N9 |
C4 |
146.5 |
85.0 |
| N9 |
C1' |
C2' |
H11 |
228.6 |
239.1 |
| C3' |
C4' |
O4' |
H7 |
117.4 |
118.8 |
| O4' |
C4' |
C5' |
H5 |
176.2 |
306.5 |
| O4' |
C4' |
C5' |
H6 |
55.5 |
186.5 |
| C5' |
C4' |
O4' |
H7 |
241.3 |
237.3 |
| C4' |
O4' |
C1' |
N9 |
214.6 |
214.1 |
| C4' |
O4' |
C1' |
H11 |
97.6 |
93.0 |
| C2' |
C1' |
O4' |
N9 |
125.4 |
119.4 |
| O4' |
C1' |
C2' |
H10 |
146.9 |
120.7 |
| C2' |
C1' |
O4' |
H11 |
242.4 |
240.5 |
| C1' |
O4' |
C4' |
H7 |
245.5 |
281.3 |
| O4' |
C1' |
N9 |
C4 |
258.5 |
202.9 |
| N9 |
C1' |
O4' |
H11 |
117.0 |
121.1 |
| C8 |
N9 |
C1' |
H11 |
192.4 |
143.7 |
| C8 |
N9 |
C4 |
N3 |
180.7 |
180.2 |
| C8 |
N7 |
C5 |
C6 |
177.4 |
179.7 |
| N9 |
C1' |
C2' |
H10 |
257.6 |
240.2 |
| C2' |
C1' |
N9 |
H11 |
131.2 |
121.0 |
| O4' |
C1' |
N9 |
H11 |
243.2 |
238.8 |
| C1' |
N9 |
C4 |
C5 |
177.8 |
180.0 |
| C1' |
N9 |
C4 |
N3 |
358.2 |
359.9 |
| C4 |
N9 |
C1' |
H11 |
15.4 |
324.1 |
| C5 |
C4 |
N9 |
N3 |
179.6 |
180.1 |
| N9 |
C4 |
C5 |
C6 |
181.8 |
180.0 |
| N9 |
C4 |
N3 |
C2 |
179.4 |
180.1 |
| N7 |
C5 |
C4 |
N3 |
180.4 |
180.0 |
| C4 |
C5 |
N7 |
C6 |
181.1 |
180.0 |
| N7 |
C5 |
C6 |
N6 |
0.9 |
0.0 |
| N7 |
C5 |
C6 |
N1 |
179.1 |
180.0 |
| N9 |
C4 |
C5 |
N3 |
180.4 |
179.9 |
| N7 |
C5 |
C4 |
C6 |
179.0 |
180.0 |
| C5 |
C4 |
N3 |
C2 |
359.9 |
360.0 |
| C4 |
C5 |
C6 |
N6 |
179.7 |
180.0 |
| C4 |
C5 |
C6 |
N1 |
357.9 |
360.0 |
| N9 |
C4 |
N3 |
C5 |
179.5 |
180.1 |
| N3 |
C4 |
C5 |
C6 |
1.4 |
0.0 |
| C4 |
N3 |
C2 |
N1 |
359.4 |
360.0 |
| C4 |
N3 |
C2 |
CL2 |
181.4 |
180.0 |
| C6 |
C5 |
C4 |
N3 |
1.4 |
0.0 |
| C5 |
C6 |
N6 |
H16 |
178.1 |
0.0 |
| C5 |
C6 |
N6 |
H17 |
298.1 |
180.0 |
| CL2 |
C2 |
N3 |
N1 |
182.0 |
180.0 |
| N3 |
C2 |
CL2 |
H13 |
360.0 |
90.0 |
| N3 |
C2 |
CL2 |
H14 |
120.0 |
210.0 |
| N3 |
C2 |
CL2 |
H15 |
240.0 |
330.0 |
| C5 |
C6 |
N6 |
N1 |
178.1 |
180.0 |
| H16 |
N6 |
C6 |
H17 |
240.0 |
180.0 |
| C5 |
C6 |
N1 |
N6 |
181.8 |
180.0 |
| C5 |
C6 |
N1 |
C2 |
1.5 |
360.0 |
| N3 |
C2 |
N1 |
CL2 |
181.9 |
180.0 |
| N1 |
C2 |
CL2 |
H13 |
181.6 |
270.1 |
| N1 |
C2 |
CL2 |
H14 |
301.6 |
30.1 |
| N1 |
C2 |
CL2 |
H15 |
61.6 |
150.0 |
| N3 |
C2 |
CL2 |
N1 |
178.3 |
180.0 |
| H13 |
CL2 |
C2 |
H14 |
240.0 |
240.0 |
| H13 |
CL2 |
C2 |
H15 |
120.0 |
120.0 |
| H14 |
CL2 |
C2 |
H15 |
240.0 |
240.1 |
| H1 |
O1A |
PA |
O5' |
234.9 |
60.0 |
| H2 |
O1B |
PB |
O3B |
130.8 |
300.1 |
| O5' |
C5' |
H5 |
C4' |
242.0 |
240.1 |
| O5' |
C5' |
H5 |
H6 |
121.0 |
120.1 |
| H5 |
C5' |
C4' |
O4' |
176.2 |
306.5 |
| C4' |
C5' |
H5 |
H6 |
239.0 |
240.0 |
| H5 |
C5' |
C4' |
H7 |
56.9 |
183.7 |
| O5' |
C5' |
H6 |
C4' |
118.0 |
120.0 |
| O5' |
C5' |
H6 |
H5 |
239.0 |
240.0 |
| H6 |
C5' |
C4' |
O4' |
55.5 |
186.5 |
| C4' |
C5' |
H6 |
H5 |
121.0 |
119.9 |
| H6 |
C5' |
C4' |
H7 |
296.2 |
63.7 |
| C3' |
C4' |
H7 |
O4' |
247.9 |
245.8 |
| C5' |
C4' |
H7 |
O4' |
115.5 |
122.8 |
| H7 |
C4' |
C5' |
H5 |
56.9 |
183.7 |
| H7 |
C4' |
C5' |
H6 |
296.2 |
63.7 |
| H7 |
C4' |
O4' |
C1' |
245.5 |
281.3 |
| O3' |
C3' |
H8 |
C2' |
121.4 |
123.6 |
| H8 |
C3' |
O3' |
H9 |
58.1 |
297.8 |
| H8 |
C3' |
C2' |
C1' |
211.2 |
262.6 |
| H8 |
C3' |
C2' |
H10 |
92.6 |
144.0 |
| H8 |
C3' |
C4' |
O4' |
136.2 |
81.2 |
| H8 |
C3' |
C4' |
H7 |
254.1 |
199.8 |
| H9 |
O3' |
C3' |
C2' |
180.0 |
61.5 |
| H9 |
O3' |
C3' |
H8 |
58.1 |
297.8 |
| F2' |
C2' |
H10 |
C1' |
239.1 |
237.4 |
| C3' |
C2' |
H10 |
C1' |
115.2 |
114.7 |
| H10 |
C2' |
C3' |
H8 |
92.6 |
144.0 |
| H10 |
C2' |
C1' |
N9 |
257.6 |
240.2 |
| H10 |
C2' |
C1' |
H11 |
29.0 |
1.1 |
| C2' |
C1' |
H11 |
N9 |
223.4 |
239.0 |
| H11 |
C1' |
C2' |
H10 |
29.0 |
1.1 |
| O4' |
C1' |
H11 |
N9 |
110.4 |
121.1 |
| H11 |
C1' |
N9 |
C4 |
15.4 |
324.1 |
| H13 |
CL2 |
C2 |
N1 |
181.6 |
270.1 |
| C2 |
CL2 |
H13 |
H14 |
120.0 |
120.0 |
| C2 |
CL2 |
H13 |
H15 |
240.0 |
240.0 |
| H14 |
CL2 |
H13 |
H15 |
120.0 |
120.0 |
| H14 |
CL2 |
C2 |
N1 |
301.6 |
30.1 |
| C2 |
CL2 |
H14 |
H13 |
240.0 |
240.0 |
| C2 |
CL2 |
H14 |
H15 |
120.0 |
119.9 |
| H13 |
CL2 |
H14 |
H15 |
240.0 |
239.9 |
| H15 |
CL2 |
C2 |
N1 |
61.6 |
150.0 |
| C2 |
CL2 |
H15 |
H13 |
120.1 |
120.0 |
| C2 |
CL2 |
H15 |
H14 |
240.0 |
240.0 |
| H13 |
CL2 |
H15 |
H14 |
120.0 |
120.0 |
| C6 |
N6 |
H16 |
H17 |
120.0 |
180.0 |
| C6 |
N6 |
H17 |
H16 |
239.9 |
180.0 |