PDB Chemical Component CDP
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 CDP
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
O3B |
PB |
1.601 |
1.610 |
PB |
O1B |
1.448 |
1.480 |
PB |
O2B |
1.592 |
1.610 |
PB |
O3A |
1.616 |
1.610 |
O3A |
PA |
1.584 |
1.610 |
PA |
O1A |
1.486 |
1.480 |
PA |
O2A |
1.530 |
1.610 |
PA |
O5' |
1.589 |
1.610 |
O5' |
C5' |
1.424 |
1.429 |
C5' |
C4' |
1.533 |
1.529 |
C5' |
H5'1 |
1.100 |
1.090 |
C5' |
H5'2 |
1.100 |
1.090 |
C4' |
O4' |
1.411 |
1.437 |
C4' |
C3' |
1.536 |
1.541 |
C4' |
H4' |
1.100 |
1.090 |
O4' |
C1' |
1.435 |
1.445 |
C3' |
O3' |
1.438 |
1.428 |
C3' |
C2' |
1.517 |
1.548 |
C3' |
H3' |
1.100 |
1.090 |
O3' |
HA |
0.950 |
0.968 |
C2' |
O2' |
1.422 |
1.429 |
C2' |
C1' |
1.531 |
1.549 |
C2' |
H2' |
1.100 |
1.090 |
O2' |
HB |
0.950 |
0.967 |
C1' |
N1 |
1.484 |
1.464 |
C1' |
H1' |
1.100 |
1.091 |
N1 |
C2 |
1.396 |
1.346 |
N1 |
C6 |
1.362 |
1.363 |
C2 |
O2 |
1.235 |
1.220 |
C2 |
N3 |
1.365 |
1.332 |
N3 |
C4 |
1.369 |
1.327 |
C4 |
N4 |
1.331 |
1.375 |
C4 |
C5 |
1.426 |
1.410 |
N4 |
H4N1 |
1.000 |
0.970 |
N4 |
H4N2 |
1.000 |
0.970 |
C5 |
C6 |
1.401 |
1.355 |
C5 |
H5 |
1.080 |
1.080 |
C6 |
H6 |
1.081 |
1.079 |
HO1 |
O2A |
0.950 |
0.967 |
HO2 |
O2B |
0.950 |
0.967 |
HO3 |
O3B |
0.950 |
0.967 |
Bond Angles for CDP
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
O3B |
PB |
O1B |
100.6 |
109.5 |
O3B |
PB |
O2B |
106.8 |
109.4 |
O3B |
PB |
O3A |
103.2 |
109.5 |
O1B |
PB |
O2B |
119.1 |
109.5 |
O1B |
PB |
O3A |
105.5 |
109.5 |
O2B |
PB |
O3A |
119.0 |
109.5 |
PB |
O3A |
PA |
136.1 |
134.0 |
O3A |
PA |
O1A |
110.5 |
109.4 |
O3A |
PA |
O2A |
118.6 |
109.5 |
O3A |
PA |
O5' |
96.6 |
109.5 |
O1A |
PA |
O2A |
114.3 |
109.5 |
O1A |
PA |
O5' |
106.6 |
109.5 |
O2A |
PA |
O5' |
108.0 |
109.5 |
PA |
O5' |
C5' |
117.8 |
123.0 |
O5' |
C5' |
C4' |
111.7 |
109.5 |
O5' |
C5' |
H5'1 |
108.7 |
109.4 |
O5' |
C5' |
H5'2 |
108.3 |
109.5 |
C4' |
C5' |
H5'1 |
108.7 |
109.4 |
C4' |
C5' |
H5'2 |
108.2 |
109.5 |
C5' |
C4' |
O4' |
110.5 |
109.9 |
C5' |
C4' |
C3' |
115.0 |
109.9 |
C5' |
C4' |
H4' |
103.0 |
109.9 |
H5'1 |
C5' |
H5'2 |
111.2 |
109.5 |
O4' |
C4' |
C3' |
102.6 |
107.3 |
O4' |
C4' |
H4' |
115.3 |
109.9 |
C4' |
O4' |
C1' |
112.1 |
107.0 |
C3' |
C4' |
H4' |
110.8 |
110.0 |
C4' |
C3' |
O3' |
113.9 |
110.5 |
C4' |
C3' |
C2' |
103.9 |
104.2 |
C4' |
C3' |
H3' |
111.5 |
110.5 |
O4' |
C1' |
C2' |
106.4 |
103.5 |
O4' |
C1' |
N1 |
108.8 |
110.6 |
O4' |
C1' |
H1' |
114.1 |
110.6 |
O3' |
C3' |
C2' |
112.7 |
110.5 |
O3' |
C3' |
H3' |
102.5 |
110.5 |
C3' |
O3' |
HA |
109.5 |
114.0 |
C2' |
C3' |
H3' |
112.7 |
110.6 |
C3' |
C2' |
O2' |
106.3 |
110.9 |
C3' |
C2' |
C1' |
101.6 |
102.1 |
C3' |
C2' |
H2' |
116.5 |
110.9 |
O2' |
C2' |
C1' |
110.0 |
110.9 |
O2' |
C2' |
H2' |
108.9 |
110.8 |
C2' |
O2' |
HB |
109.5 |
114.0 |
C1' |
C2' |
H2' |
113.2 |
110.9 |
C2' |
C1' |
N1 |
115.3 |
110.7 |
C2' |
C1' |
H1' |
107.4 |
110.6 |
N1 |
C1' |
H1' |
105.0 |
110.7 |
C1' |
N1 |
C2 |
115.5 |
119.9 |
C1' |
N1 |
C6 |
123.3 |
119.8 |
C2 |
N1 |
C6 |
119.5 |
120.3 |
N1 |
C2 |
O2 |
120.2 |
119.4 |
N1 |
C2 |
N3 |
121.7 |
121.1 |
N1 |
C6 |
C5 |
119.2 |
119.3 |
N1 |
C6 |
H6 |
120.4 |
120.4 |
O2 |
C2 |
N3 |
118.0 |
119.5 |
C2 |
N3 |
C4 |
120.5 |
120.7 |
N3 |
C4 |
N4 |
117.7 |
120.2 |
N3 |
C4 |
C5 |
118.0 |
119.7 |
N4 |
C4 |
C5 |
124.3 |
120.2 |
C4 |
N4 |
H4N1 |
109.7 |
120.0 |
C4 |
N4 |
H4N2 |
125.2 |
120.0 |
C4 |
C5 |
C6 |
120.6 |
119.0 |
C4 |
C5 |
H5 |
119.7 |
120.6 |
H4N1 |
N4 |
H4N2 |
125.2 |
120.0 |
C6 |
C5 |
H5 |
119.7 |
120.5 |
C5 |
C6 |
H6 |
120.4 |
120.3 |
Torsion Angles for CDP
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
O1B |
PB |
O3B |
O2B |
235.1 |
240.0 |
O1B |
PB |
O3B |
O3A |
108.8 |
120.0 |
O2B |
PB |
O3B |
O3A |
233.7 |
240.0 |
O3B |
PB |
O3A |
PA |
122.5 |
80.0 |
O3B |
PB |
O1B |
O2B |
116.1 |
120.0 |
O3B |
PB |
O1B |
O3A |
253.0 |
240.0 |
O2B |
PB |
O1B |
O3A |
136.8 |
120.0 |
O1B |
PB |
O3A |
PA |
17.4 |
320.0 |
O3B |
PB |
O2B |
O1B |
247.2 |
240.0 |
O3B |
PB |
O2B |
O3A |
116.2 |
120.0 |
O1B |
PB |
O2B |
O3A |
228.9 |
240.0 |
O2B |
PB |
O3A |
PA |
240.5 |
200.0 |
O3B |
PB |
O3A |
O1B |
105.1 |
120.0 |
O3B |
PB |
O3A |
O2B |
241.9 |
240.0 |
O1B |
PB |
O3A |
O2B |
136.9 |
120.0 |
PB |
O3A |
PA |
O1A |
93.6 |
45.0 |
PB |
O3A |
PA |
O2A |
318.8 |
285.0 |
PB |
O3A |
PA |
O5' |
204.1 |
165.0 |
O1A |
PA |
O3A |
O2A |
134.8 |
120.0 |
O1A |
PA |
O3A |
O5' |
249.5 |
240.0 |
O2A |
PA |
O3A |
O5' |
114.7 |
120.0 |
O3A |
PA |
O5' |
C5' |
60.9 |
185.0 |
O3A |
PA |
O1A |
O2A |
223.1 |
240.0 |
O3A |
PA |
O1A |
O5' |
103.8 |
120.0 |
O2A |
PA |
O1A |
O5' |
240.7 |
240.0 |
O1A |
PA |
O5' |
C5' |
174.6 |
305.0 |
O3A |
PA |
O2A |
O1A |
133.2 |
120.0 |
O3A |
PA |
O2A |
O5' |
251.7 |
240.0 |
O1A |
PA |
O2A |
O5' |
118.5 |
120.0 |
O2A |
PA |
O5' |
C5' |
297.9 |
65.0 |
O3A |
PA |
O5' |
O1A |
246.3 |
240.1 |
O3A |
PA |
O5' |
O2A |
123.0 |
120.0 |
O1A |
PA |
O5' |
O2A |
236.7 |
240.0 |
PA |
O5' |
C5' |
C4' |
187.2 |
180.0 |
PA |
O5' |
C5' |
H5'1 |
307.2 |
300.0 |
PA |
O5' |
C5' |
H5'2 |
68.2 |
60.0 |
C4' |
C5' |
O5' |
H5'1 |
240.0 |
240.0 |
C4' |
C5' |
O5' |
H5'2 |
119.0 |
120.1 |
O5' |
C5' |
C4' |
O4' |
295.6 |
66.4 |
O5' |
C5' |
C4' |
C3' |
51.2 |
184.3 |
O5' |
C5' |
C4' |
H4' |
171.9 |
305.4 |
H5'1 |
C5' |
O5' |
H5'2 |
239.0 |
240.0 |
O5' |
C5' |
C4' |
H5'1 |
120.0 |
119.9 |
O5' |
C5' |
C4' |
H5'2 |
240.9 |
240.0 |
H5'1 |
C5' |
C4' |
H5'2 |
120.9 |
120.0 |
O4' |
C4' |
C5' |
C3' |
244.5 |
242.1 |
O4' |
C4' |
C5' |
H4' |
123.7 |
121.0 |
C5' |
C4' |
O4' |
C1' |
146.4 |
145.9 |
C3' |
C4' |
C5' |
H4' |
239.3 |
238.9 |
C5' |
C4' |
C3' |
O3' |
81.4 |
119.9 |
C5' |
C4' |
C3' |
C2' |
204.4 |
238.5 |
C5' |
C4' |
C3' |
H3' |
326.0 |
357.3 |
O5' |
C5' |
H5'1 |
C4' |
238.2 |
240.0 |
O5' |
C5' |
H5'1 |
H5'2 |
119.1 |
120.0 |
C4' |
C5' |
H5'1 |
H5'2 |
240.9 |
239.9 |
H5'1 |
C5' |
C4' |
O4' |
175.6 |
306.5 |
H5'1 |
C5' |
C4' |
C3' |
291.2 |
64.3 |
H5'1 |
C5' |
C4' |
H4' |
51.9 |
185.5 |
O5' |
C5' |
H5'2 |
C4' |
121.2 |
120.0 |
O5' |
C5' |
H5'2 |
H5'1 |
240.6 |
240.0 |
C4' |
C5' |
H5'2 |
H5'1 |
119.4 |
120.0 |
H5'2 |
C5' |
C4' |
O4' |
54.7 |
186.5 |
H5'2 |
C5' |
C4' |
C3' |
170.2 |
304.3 |
H5'2 |
C5' |
C4' |
H4' |
291.0 |
65.4 |
O4' |
C4' |
C5' |
H5'1 |
175.6 |
306.5 |
O4' |
C4' |
C5' |
H5'2 |
54.7 |
186.5 |
C5' |
C4' |
O4' |
C3' |
123.1 |
119.4 |
C5' |
C4' |
O4' |
H4' |
243.7 |
239.0 |
C3' |
C4' |
O4' |
H4' |
120.6 |
119.6 |
O4' |
C4' |
C3' |
O3' |
201.4 |
239.3 |
O4' |
C4' |
C3' |
C2' |
324.4 |
358.0 |
O4' |
C4' |
C3' |
H3' |
86.0 |
116.8 |
C4' |
O4' |
C1' |
C2' |
358.2 |
320.0 |
C4' |
O4' |
C1' |
N1 |
233.4 |
201.4 |
C4' |
O4' |
C1' |
H1' |
116.5 |
78.5 |
C3' |
C4' |
C5' |
H5'1 |
291.2 |
64.3 |
C3' |
C4' |
C5' |
H5'2 |
170.2 |
304.3 |
C5' |
C4' |
C3' |
O4' |
240.0 |
240.5 |
C5' |
C4' |
C3' |
H4' |
116.3 |
121.1 |
O4' |
C4' |
C3' |
H4' |
236.3 |
240.5 |
C3' |
C4' |
O4' |
C1' |
23.3 |
26.5 |
O3' |
C3' |
C4' |
C2' |
237.0 |
241.4 |
O3' |
C3' |
C4' |
H3' |
115.4 |
122.5 |
C4' |
C3' |
O3' |
HA |
38.7 |
180.0 |
C2' |
C3' |
C4' |
H3' |
238.3 |
241.2 |
C4' |
C3' |
C2' |
O2' |
278.9 |
220.9 |
C4' |
C3' |
C2' |
C1' |
34.0 |
339.1 |
C4' |
C3' |
C2' |
H2' |
157.4 |
97.4 |
H4' |
C4' |
C5' |
H5'1 |
51.9 |
185.5 |
H4' |
C4' |
C5' |
H5'2 |
291.0 |
65.4 |
C5' |
C4' |
H4' |
O4' |
120.5 |
121.0 |
C5' |
C4' |
H4' |
C3' |
236.5 |
239.0 |
O4' |
C4' |
H4' |
C3' |
116.0 |
117.9 |
H4' |
C4' |
O4' |
C1' |
262.7 |
266.9 |
H4' |
C4' |
C3' |
O3' |
325.1 |
358.8 |
H4' |
C4' |
C3' |
C2' |
88.0 |
117.5 |
H4' |
C4' |
C3' |
H3' |
209.7 |
236.3 |
C1' |
O4' |
C4' |
C3' |
23.3 |
26.5 |
C1' |
O4' |
C4' |
H4' |
262.7 |
266.9 |
C3' |
C2' |
C1' |
O4' |
339.4 |
37.0 |
O2' |
C2' |
C1' |
O4' |
91.7 |
155.2 |
O4' |
C1' |
C2' |
H2' |
213.8 |
278.8 |
C2' |
C1' |
O4' |
N1 |
124.8 |
118.5 |
C2' |
C1' |
O4' |
H1' |
241.7 |
241.5 |
N1 |
C1' |
O4' |
H1' |
116.9 |
122.9 |
O4' |
C1' |
N1 |
C2 |
233.2 |
53.6 |
O4' |
C1' |
N1 |
C6 |
38.4 |
233.3 |
O3' |
C3' |
C4' |
H4' |
325.1 |
358.8 |
C4' |
C3' |
O3' |
C2' |
118.0 |
114.7 |
C4' |
C3' |
O3' |
H3' |
239.4 |
237.4 |
C2' |
C3' |
O3' |
H3' |
121.4 |
122.7 |
O3' |
C3' |
C2' |
O2' |
42.6 |
339.5 |
O3' |
C3' |
C2' |
C1' |
157.7 |
97.8 |
O3' |
C3' |
C2' |
H2' |
281.1 |
216.0 |
C2' |
C3' |
C4' |
H4' |
88.0 |
117.5 |
C4' |
C3' |
C2' |
O3' |
236.3 |
241.3 |
C4' |
C3' |
C2' |
H3' |
120.9 |
118.7 |
O4' |
C1' |
C2' |
C3' |
339.4 |
37.0 |
O3' |
C3' |
C2' |
H3' |
244.6 |
237.4 |
C2' |
C3' |
O3' |
HA |
280.7 |
65.3 |
O2' |
C2' |
C3' |
C1' |
244.9 |
241.8 |
O2' |
C2' |
C3' |
H2' |
121.5 |
123.5 |
C3' |
C2' |
O2' |
HB |
89.3 |
298.6 |
C1' |
C2' |
C3' |
H2' |
236.6 |
241.7 |
C3' |
C2' |
C1' |
N1 |
100.1 |
155.5 |
C3' |
C2' |
C1' |
H1' |
216.8 |
278.6 |
H3' |
C3' |
C4' |
H4' |
209.7 |
236.3 |
C4' |
C3' |
H3' |
O3' |
122.2 |
122.6 |
C4' |
C3' |
H3' |
C2' |
243.6 |
245.2 |
O3' |
C3' |
H3' |
C2' |
121.4 |
122.6 |
H3' |
C3' |
O3' |
HA |
159.3 |
302.6 |
H3' |
C3' |
C2' |
O2' |
158.0 |
102.2 |
H3' |
C3' |
C2' |
C1' |
273.1 |
220.4 |
H3' |
C3' |
C2' |
H2' |
36.5 |
338.7 |
HA |
O3' |
C3' |
C2' |
280.7 |
65.3 |
HA |
O3' |
C3' |
H3' |
159.3 |
302.6 |
O4' |
C1' |
C2' |
O2' |
91.7 |
155.2 |
O2' |
C2' |
C3' |
H3' |
158.0 |
102.2 |
C3' |
C2' |
O2' |
C1' |
109.2 |
112.8 |
C3' |
C2' |
O2' |
H2' |
233.8 |
236.4 |
C1' |
C2' |
O2' |
H2' |
124.6 |
123.6 |
O2' |
C2' |
C1' |
N1 |
212.4 |
273.7 |
O2' |
C2' |
C1' |
H1' |
329.1 |
36.8 |
O4' |
C1' |
C2' |
N1 |
239.3 |
241.5 |
O4' |
C1' |
C2' |
H1' |
122.6 |
118.4 |
C1' |
C2' |
C3' |
H3' |
273.1 |
220.4 |
C3' |
C2' |
C1' |
O2' |
247.7 |
241.8 |
C3' |
C2' |
C1' |
H2' |
125.6 |
118.2 |
O2' |
C2' |
C1' |
H2' |
237.9 |
236.5 |
C1' |
C2' |
O2' |
HB |
340.0 |
185.9 |
N1 |
C1' |
C2' |
H1' |
243.3 |
236.9 |
C2' |
C1' |
N1 |
C2 |
113.8 |
299.5 |
C2' |
C1' |
N1 |
C6 |
279.0 |
119.2 |
H2' |
C2' |
C3' |
H3' |
36.5 |
338.7 |
C3' |
C2' |
H2' |
O2' |
120.1 |
123.6 |
C3' |
C2' |
H2' |
C1' |
242.8 |
247.2 |
O2' |
C2' |
H2' |
C1' |
122.7 |
123.6 |
H2' |
C2' |
O2' |
HB |
215.5 |
62.2 |
H2' |
C2' |
C1' |
N1 |
334.4 |
37.3 |
H2' |
C2' |
C1' |
H1' |
91.1 |
160.3 |
HB |
O2' |
C2' |
C1' |
340.0 |
185.9 |
HB |
O2' |
C2' |
H2' |
215.5 |
62.2 |
O4' |
C1' |
N1 |
C2' |
119.4 |
114.1 |
O4' |
C1' |
N1 |
H1' |
237.4 |
237.1 |
N1 |
C1' |
C2' |
H2' |
334.4 |
37.3 |
C2' |
C1' |
N1 |
H1' |
118.0 |
123.0 |
C2 |
N1 |
C1' |
C6 |
194.8 |
180.3 |
C1' |
N1 |
C2 |
O2 |
347.9 |
359.9 |
C1' |
N1 |
C2 |
N3 |
165.2 |
180.0 |
C1' |
N1 |
C6 |
C5 |
190.7 |
179.8 |
C1' |
N1 |
C6 |
H6 |
10.7 |
360.0 |
O4' |
C1' |
H1' |
C2' |
242.3 |
245.9 |
O4' |
C1' |
H1' |
N1 |
119.1 |
122.9 |
H1' |
C1' |
C2' |
H2' |
91.1 |
160.3 |
C2' |
C1' |
H1' |
N1 |
236.8 |
237.0 |
H1' |
C1' |
N1 |
C2 |
355.8 |
176.5 |
H1' |
C1' |
N1 |
C6 |
161.0 |
356.2 |
C2 |
N1 |
C1' |
H1' |
355.8 |
176.5 |
C1' |
N1 |
C2 |
C6 |
165.8 |
179.7 |
C2 |
N1 |
C6 |
C5 |
355.4 |
359.5 |
C2 |
N1 |
C6 |
H6 |
175.4 |
179.7 |
O2 |
C2 |
N1 |
N3 |
182.7 |
180.0 |
N1 |
C2 |
N3 |
C4 |
6.4 |
360.0 |
C6 |
N1 |
C1' |
H1' |
161.0 |
356.2 |
C1' |
N1 |
C6 |
C2 |
195.3 |
180.3 |
C6 |
N1 |
C2 |
O2 |
182.1 |
180.2 |
C6 |
N1 |
C2 |
N3 |
359.3 |
0.3 |
C4 |
C5 |
C6 |
N1 |
4.4 |
0.5 |
N1 |
C6 |
C5 |
H5 |
184.4 |
180.3 |
C5 |
C6 |
N1 |
H6 |
180.0 |
179.8 |
O2 |
C2 |
N1 |
C6 |
182.1 |
180.2 |
N1 |
C2 |
O2 |
N3 |
177.4 |
180.0 |
O2 |
C2 |
N3 |
C4 |
183.7 |
180.0 |
N3 |
C2 |
N1 |
C6 |
359.3 |
0.3 |
N1 |
C2 |
N3 |
O2 |
182.7 |
180.0 |
C2 |
N3 |
C4 |
N4 |
175.7 |
180.1 |
C2 |
N3 |
C4 |
C5 |
353.5 |
360.0 |
N4 |
C4 |
N3 |
C5 |
182.2 |
180.1 |
N3 |
C4 |
N4 |
H4N1 |
180.0 |
360.0 |
N3 |
C4 |
N4 |
H4N2 |
0.0 |
180.0 |
N3 |
C4 |
C5 |
C6 |
1.2 |
359.8 |
N3 |
C4 |
C5 |
H5 |
181.2 |
179.9 |
N3 |
C4 |
N4 |
C5 |
177.6 |
179.9 |
N4 |
C4 |
C5 |
C6 |
178.8 |
179.7 |
N4 |
C4 |
C5 |
H5 |
358.8 |
359.9 |
H4N1 |
N4 |
C4 |
H4N2 |
180.0 |
180.0 |
N1 |
C6 |
C5 |
C4 |
4.4 |
0.5 |
N3 |
C4 |
C5 |
N4 |
182.4 |
180.1 |
C5 |
C4 |
N4 |
H4N1 |
2.4 |
180.1 |
C5 |
C4 |
N4 |
H4N2 |
182.4 |
0.1 |
C6 |
C5 |
C4 |
H5 |
180.0 |
179.8 |
C4 |
C5 |
C6 |
H6 |
184.3 |
180.3 |
H4N1 |
N4 |
C4 |
C5 |
2.4 |
180.1 |
C4 |
N4 |
H4N1 |
H4N2 |
180.0 |
180.0 |
H4N2 |
N4 |
C4 |
C5 |
182.4 |
0.1 |
C4 |
N4 |
H4N2 |
H4N1 |
180.0 |
180.0 |
N1 |
C6 |
C5 |
H6 |
180.0 |
180.2 |
C4 |
C5 |
C6 |
H5 |
180.0 |
180.2 |
C4 |
C5 |
H5 |
C6 |
180.0 |
179.8 |
H5 |
C5 |
C6 |
H6 |
4.3 |
0.1 |
N1 |
C6 |
H6 |
C5 |
180.0 |
179.8 |
H6 |
C6 |
C5 |
H5 |
4.3 |
0.1 |