PDB Chemical Component HPD
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 HPD
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| P |
O5' |
1.614 |
1.609 |
| P |
O1P |
1.492 |
1.480 |
| P |
O2P |
1.531 |
1.610 |
| P |
O3P |
1.519 |
1.609 |
| O5' |
C5' |
1.440 |
1.427 |
| O2P |
HOP2 |
0.950 |
0.967 |
| O3P |
HOP3 |
0.950 |
0.967 |
| C5' |
C4' |
1.541 |
1.529 |
| C5' |
H5'1 |
1.114 |
1.090 |
| C5' |
H5'2 |
1.115 |
1.090 |
| O4' |
C4' |
1.411 |
1.429 |
| O4' |
HO'4 |
0.950 |
0.966 |
| O3' |
C3' |
1.411 |
1.429 |
| O3' |
HO'3 |
0.949 |
0.967 |
| C1' |
O1' |
1.388 |
1.429 |
| C1' |
C2' |
1.526 |
1.529 |
| C1' |
H1'1 |
1.115 |
1.090 |
| C1' |
H1'2 |
1.115 |
1.090 |
| O1' |
HO'1 |
0.949 |
0.966 |
| C3' |
C4' |
1.554 |
1.530 |
| C3' |
C2' |
1.547 |
1.530 |
| C3' |
H3' |
1.114 |
1.090 |
| C4' |
H4' |
1.116 |
1.090 |
| C2' |
H2'1 |
1.115 |
1.090 |
| C2' |
H2'2 |
1.116 |
1.090 |
Bond Angles for HPD
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O5' |
P |
O1P |
109.6 |
109.5 |
| O5' |
P |
O2P |
103.7 |
109.5 |
| O5' |
P |
O3P |
106.8 |
109.5 |
| P |
O5' |
C5' |
118.6 |
106.9 |
| O1P |
P |
O2P |
111.4 |
109.4 |
| O1P |
P |
O3P |
110.8 |
109.4 |
| O2P |
P |
O3P |
114.3 |
109.5 |
| P |
O2P |
HOP2 |
103.7 |
106.8 |
| P |
O3P |
HOP3 |
106.7 |
106.8 |
| O5' |
C5' |
C4' |
108.2 |
109.6 |
| O5' |
C5' |
H5'1 |
112.7 |
109.5 |
| O5' |
C5' |
H5'2 |
112.7 |
109.5 |
| C4' |
C5' |
H5'1 |
112.7 |
109.5 |
| C4' |
C5' |
H5'2 |
112.7 |
109.4 |
| C5' |
C4' |
O4' |
107.4 |
109.5 |
| C5' |
C4' |
C3' |
116.6 |
109.5 |
| C5' |
C4' |
H4' |
106.3 |
109.5 |
| H5'1 |
C5' |
H5'2 |
97.8 |
109.4 |
| C4' |
O4' |
HO'4 |
107.4 |
106.8 |
| O4' |
C4' |
C3' |
110.5 |
109.4 |
| O4' |
C4' |
H4' |
112.9 |
109.5 |
| C3' |
O3' |
HO'3 |
107.9 |
106.8 |
| O3' |
C3' |
C4' |
107.9 |
109.4 |
| O3' |
C3' |
C2' |
108.8 |
109.5 |
| O3' |
C3' |
H3' |
111.5 |
109.4 |
| O1' |
C1' |
C2' |
112.5 |
109.5 |
| O1' |
C1' |
H1'1 |
111.2 |
109.4 |
| O1' |
C1' |
H1'2 |
111.1 |
109.4 |
| C1' |
O1' |
HO'1 |
112.4 |
106.9 |
| C2' |
C1' |
H1'1 |
111.1 |
109.5 |
| C2' |
C1' |
H1'2 |
111.1 |
109.5 |
| C1' |
C2' |
C3' |
115.6 |
109.5 |
| C1' |
C2' |
H2'1 |
110.0 |
109.5 |
| C1' |
C2' |
H2'2 |
110.0 |
109.5 |
| H1'1 |
C1' |
H1'2 |
99.2 |
109.5 |
| C4' |
C3' |
C2' |
111.2 |
109.5 |
| C4' |
C3' |
H3' |
109.1 |
109.5 |
| C3' |
C4' |
H4' |
103.0 |
109.5 |
| C2' |
C3' |
H3' |
108.2 |
109.5 |
| C3' |
C2' |
H2'1 |
110.0 |
109.5 |
| C3' |
C2' |
H2'2 |
110.0 |
109.4 |
| H2'1 |
C2' |
H2'2 |
100.2 |
109.5 |
Torsion Angles for HPD
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O1P |
P |
O5' |
O2P |
119.0 |
240.0 |
| O1P |
P |
O5' |
O3P |
240.0 |
120.0 |
| O2P |
P |
O5' |
O3P |
121.0 |
240.0 |
| O5' |
P |
O2P |
HOP2 |
180.0 |
180.0 |
| O5' |
P |
O3P |
HOP3 |
180.0 |
300.0 |
| P |
O5' |
C5' |
C4' |
201.2 |
180.0 |
| P |
O5' |
C5' |
H5'1 |
326.5 |
59.9 |
| P |
O5' |
C5' |
H5'2 |
76.0 |
300.0 |
| O5' |
P |
O1P |
O2P |
245.9 |
120.0 |
| O5' |
P |
O1P |
O3P |
117.5 |
240.0 |
| O1P |
P |
O5' |
C5' |
308.9 |
60.0 |
| O2P |
P |
O1P |
O3P |
231.6 |
119.9 |
| O1P |
P |
O2P |
HOP2 |
62.3 |
300.0 |
| O1P |
P |
O3P |
HOP3 |
299.2 |
180.0 |
| O5' |
P |
O2P |
O1P |
117.7 |
240.0 |
| O5' |
P |
O2P |
O3P |
244.2 |
120.1 |
| O2P |
P |
O5' |
C5' |
189.9 |
180.0 |
| O1P |
P |
O2P |
O3P |
126.5 |
240.1 |
| O2P |
P |
O3P |
HOP3 |
66.0 |
60.1 |
| O5' |
P |
O3P |
O1P |
240.7 |
120.0 |
| O5' |
P |
O3P |
O2P |
114.0 |
239.9 |
| O3P |
P |
O5' |
C5' |
68.9 |
300.0 |
| O1P |
P |
O3P |
O2P |
233.2 |
119.9 |
| O3P |
P |
O2P |
HOP2 |
295.8 |
60.0 |
| C5' |
O5' |
P |
O1P |
308.9 |
60.0 |
| C5' |
O5' |
P |
O2P |
189.9 |
180.0 |
| C5' |
O5' |
P |
O3P |
68.9 |
300.0 |
| C4' |
C5' |
O5' |
H5'1 |
234.7 |
120.1 |
| C4' |
C5' |
O5' |
H5'2 |
125.2 |
240.0 |
| O5' |
C5' |
C4' |
O4' |
69.8 |
60.0 |
| O5' |
C5' |
C4' |
C3' |
194.5 |
180.0 |
| O5' |
C5' |
C4' |
H4' |
308.6 |
300.0 |
| H5'1 |
C5' |
O5' |
H5'2 |
250.5 |
119.9 |
| HOP2 |
O2P |
P |
O3P |
295.8 |
60.0 |
| O5' |
C5' |
C4' |
H5'1 |
125.3 |
239.9 |
| O5' |
C5' |
C4' |
H5'2 |
234.8 |
120.0 |
| H5'1 |
C5' |
C4' |
H5'2 |
109.5 |
240.1 |
| C5' |
C4' |
O4' |
HO'4 |
180.0 |
60.0 |
| O4' |
C4' |
C5' |
C3' |
235.4 |
240.0 |
| O4' |
C4' |
C5' |
H4' |
121.2 |
120.0 |
| O3' |
C3' |
C4' |
C5' |
54.6 |
60.0 |
| C5' |
C4' |
C3' |
C2' |
173.9 |
180.0 |
| C5' |
C4' |
C3' |
H3' |
293.3 |
300.0 |
| C3' |
C4' |
C5' |
H4' |
245.8 |
240.0 |
| O5' |
C5' |
H5'1 |
C4' |
237.2 |
120.1 |
| O5' |
C5' |
H5'1 |
H5'2 |
118.6 |
240.0 |
| C4' |
C5' |
H5'1 |
H5'2 |
241.4 |
119.9 |
| H5'1 |
C5' |
C4' |
O4' |
304.5 |
180.1 |
| H5'1 |
C5' |
C4' |
C3' |
69.2 |
300.0 |
| H5'1 |
C5' |
C4' |
H4' |
183.4 |
60.1 |
| O5' |
C5' |
H5'2 |
C4' |
122.8 |
239.9 |
| O5' |
C5' |
H5'2 |
H5'1 |
241.4 |
120.0 |
| C4' |
C5' |
H5'2 |
H5'1 |
118.6 |
240.1 |
| H5'2 |
C5' |
C4' |
O4' |
195.1 |
300.0 |
| H5'2 |
C5' |
C4' |
C3' |
319.7 |
59.9 |
| H5'2 |
C5' |
C4' |
H4' |
73.9 |
180.0 |
| O4' |
C4' |
C5' |
H5'1 |
304.5 |
180.1 |
| O4' |
C4' |
C5' |
H5'2 |
195.1 |
300.0 |
| C5' |
C4' |
O4' |
C3' |
128.2 |
120.0 |
| C5' |
C4' |
O4' |
H4' |
243.0 |
240.0 |
| O3' |
C3' |
C4' |
O4' |
177.7 |
180.0 |
| O4' |
C4' |
C3' |
C2' |
297.0 |
300.0 |
| O4' |
C4' |
C3' |
H3' |
56.3 |
60.0 |
| C3' |
C4' |
O4' |
H4' |
114.8 |
119.9 |
| HO'4 |
O4' |
C4' |
C3' |
51.8 |
300.0 |
| HO'4 |
O4' |
C4' |
H4' |
297.0 |
180.0 |
| C5' |
C4' |
C3' |
O3' |
54.6 |
60.0 |
| O4' |
C4' |
C3' |
O3' |
177.7 |
180.0 |
| C1' |
C2' |
C3' |
O3' |
297.0 |
300.0 |
| C4' |
C3' |
O3' |
C2' |
120.8 |
120.1 |
| C4' |
C3' |
O3' |
H3' |
240.1 |
240.1 |
| O3' |
C3' |
C4' |
H4' |
298.6 |
299.9 |
| C2' |
C3' |
O3' |
H3' |
119.4 |
120.0 |
| O3' |
C3' |
C2' |
H2'1 |
171.7 |
180.0 |
| O3' |
C3' |
C2' |
H2'2 |
62.3 |
60.0 |
| HO'3 |
O3' |
C3' |
C4' |
179.9 |
60.1 |
| HO'3 |
O3' |
C3' |
C2' |
59.1 |
300.0 |
| HO'3 |
O3' |
C3' |
H3' |
299.8 |
180.0 |
| C2' |
C1' |
O1' |
H1'1 |
234.8 |
240.0 |
| C2' |
C1' |
O1' |
H1'2 |
125.2 |
120.0 |
| O1' |
C1' |
C2' |
C3' |
315.0 |
180.0 |
| O1' |
C1' |
C2' |
H2'1 |
80.3 |
300.0 |
| O1' |
C1' |
C2' |
H2'2 |
189.7 |
60.1 |
| H1'1 |
C1' |
O1' |
H1'2 |
250.5 |
240.1 |
| O3' |
C3' |
C2' |
C1' |
297.0 |
300.0 |
| O1' |
C1' |
C2' |
H1'1 |
125.3 |
120.0 |
| O1' |
C1' |
C2' |
H1'2 |
234.7 |
240.0 |
| C2' |
C1' |
O1' |
HO'1 |
180.0 |
180.0 |
| H1'1 |
C1' |
C2' |
H1'2 |
109.4 |
120.0 |
| C4' |
C3' |
C2' |
C1' |
178.3 |
180.0 |
| C1' |
C2' |
C3' |
H3' |
58.4 |
60.0 |
| C3' |
C2' |
C1' |
H2'1 |
234.7 |
239.9 |
| C3' |
C2' |
C1' |
H2'2 |
125.3 |
119.9 |
| H2'1 |
C2' |
C1' |
H2'2 |
250.6 |
240.0 |
| O1' |
C1' |
H1'1 |
C2' |
234.0 |
240.0 |
| O1' |
C1' |
H1'1 |
H1'2 |
117.0 |
119.9 |
| H1'1 |
C1' |
O1' |
HO'1 |
305.3 |
300.0 |
| C2' |
C1' |
H1'1 |
H1'2 |
243.1 |
240.0 |
| H1'1 |
C1' |
C2' |
C3' |
189.7 |
60.0 |
| H1'1 |
C1' |
C2' |
H2'1 |
315.0 |
180.0 |
| H1'1 |
C1' |
C2' |
H2'2 |
64.4 |
300.1 |
| O1' |
C1' |
H1'2 |
C2' |
126.0 |
120.0 |
| O1' |
C1' |
H1'2 |
H1'1 |
242.9 |
240.1 |
| H1'2 |
C1' |
O1' |
HO'1 |
54.8 |
59.9 |
| C2' |
C1' |
H1'2 |
H1'1 |
116.9 |
120.0 |
| H1'2 |
C1' |
C2' |
C3' |
80.3 |
300.0 |
| H1'2 |
C1' |
C2' |
H2'1 |
205.6 |
60.0 |
| H1'2 |
C1' |
C2' |
H2'2 |
315.0 |
180.0 |
| HO'1 |
O1' |
C1' |
C2' |
180.0 |
180.0 |
| HO'1 |
O1' |
C1' |
H1'1 |
305.3 |
300.0 |
| HO'1 |
O1' |
C1' |
H1'2 |
54.8 |
59.9 |
| C3' |
C4' |
C5' |
H5'1 |
69.2 |
300.0 |
| C3' |
C4' |
C5' |
H5'2 |
319.7 |
59.9 |
| C5' |
C4' |
C3' |
O4' |
237.0 |
240.0 |
| C5' |
C4' |
C3' |
H4' |
116.0 |
120.0 |
| C3' |
C4' |
O4' |
HO'4 |
51.8 |
300.0 |
| O4' |
C4' |
C3' |
H4' |
239.1 |
240.0 |
| C4' |
C3' |
O3' |
HO'3 |
179.9 |
60.1 |
| O3' |
C3' |
C4' |
C2' |
240.7 |
240.0 |
| O3' |
C3' |
C4' |
H3' |
121.4 |
119.9 |
| C1' |
C2' |
C3' |
C4' |
178.3 |
180.0 |
| C2' |
C3' |
C4' |
H3' |
240.6 |
240.0 |
| C4' |
C3' |
C2' |
H2'1 |
53.0 |
59.9 |
| C4' |
C3' |
C2' |
H2'2 |
303.6 |
300.0 |
| C2' |
C3' |
O3' |
HO'3 |
59.1 |
300.0 |
| O3' |
C3' |
C2' |
C4' |
118.7 |
120.0 |
| O3' |
C3' |
C2' |
H3' |
238.6 |
240.0 |
| C3' |
C2' |
C1' |
H1'1 |
189.7 |
60.0 |
| C3' |
C2' |
C1' |
H1'2 |
80.3 |
300.0 |
| C1' |
C2' |
C3' |
H2'1 |
125.3 |
120.1 |
| C1' |
C2' |
C3' |
H2'2 |
234.7 |
240.0 |
| C4' |
C3' |
C2' |
H3' |
119.9 |
120.0 |
| C2' |
C3' |
C4' |
H4' |
57.9 |
60.0 |
| H2'1 |
C2' |
C3' |
H2'2 |
109.4 |
119.9 |
| H3' |
C3' |
O3' |
HO'3 |
299.8 |
180.0 |
| O3' |
C3' |
H3' |
C4' |
240.9 |
240.1 |
| O3' |
C3' |
H3' |
C2' |
119.7 |
120.0 |
| C4' |
C3' |
H3' |
C2' |
238.8 |
239.9 |
| H3' |
C3' |
C4' |
H4' |
177.2 |
180.0 |
| H3' |
C3' |
C2' |
H2'1 |
293.1 |
299.9 |
| H3' |
C3' |
C2' |
H2'2 |
183.7 |
180.0 |
| H4' |
C4' |
C5' |
H5'1 |
183.4 |
60.1 |
| H4' |
C4' |
C5' |
H5'2 |
73.9 |
180.0 |
| C5' |
C4' |
H4' |
O4' |
117.6 |
120.0 |
| C5' |
C4' |
H4' |
C3' |
236.9 |
239.9 |
| H4' |
C4' |
O4' |
HO'4 |
297.0 |
180.0 |
| O4' |
C4' |
H4' |
C3' |
119.3 |
119.9 |
| H4' |
C4' |
C3' |
C2' |
57.9 |
60.0 |
| H4' |
C4' |
C3' |
H3' |
177.2 |
180.0 |
| H2'1 |
C2' |
C1' |
H1'1 |
315.0 |
180.0 |
| H2'1 |
C2' |
C1' |
H1'2 |
205.6 |
60.0 |
| C1' |
C2' |
H2'1 |
C3' |
231.6 |
239.9 |
| C1' |
C2' |
H2'1 |
H2'2 |
115.8 |
120.0 |
| H2'1 |
C2' |
C3' |
H3' |
293.1 |
299.9 |
| C3' |
C2' |
H2'1 |
H2'2 |
244.2 |
240.1 |
| H2'2 |
C2' |
C1' |
H1'1 |
64.4 |
300.1 |
| H2'2 |
C2' |
C1' |
H1'2 |
315.0 |
180.0 |
| C1' |
C2' |
H2'2 |
C3' |
128.4 |
120.0 |
| C1' |
C2' |
H2'2 |
H2'1 |
244.2 |
239.9 |
| H2'2 |
C2' |
C3' |
H3' |
183.7 |
180.0 |
| C3' |
C2' |
H2'2 |
H2'1 |
115.8 |
120.0 |