PDB Chemical Component AAB
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 AAB
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| P |
O1P |
1.419 |
1.610 |
| P |
O2P |
1.404 |
1.479 |
| P |
O3P |
1.544 |
1.610 |
| P |
O5' |
1.537 |
1.610 |
| O1P |
H1P |
0.950 |
0.967 |
| O3P |
H3P |
0.950 |
0.967 |
| O5' |
C5' |
1.406 |
1.429 |
| C5' |
C4' |
1.520 |
1.530 |
| C5' |
H5'1 |
1.100 |
1.090 |
| C5' |
H5'2 |
1.100 |
1.090 |
| C4' |
O4' |
1.409 |
1.444 |
| C4' |
C3' |
1.503 |
1.551 |
| C4' |
H4' |
1.100 |
1.090 |
| O4' |
C1' |
1.407 |
1.437 |
| C1' |
O1' |
1.391 |
1.430 |
| C1' |
C2' |
1.500 |
1.541 |
| C1' |
H1' |
1.100 |
1.091 |
| O1' |
HO1' |
0.950 |
0.967 |
| C2' |
C3' |
1.512 |
1.548 |
| C2' |
H2'1 |
1.100 |
1.089 |
| C2' |
H2'2 |
1.099 |
1.091 |
| C3' |
O3' |
1.433 |
1.428 |
| C3' |
H3' |
1.100 |
1.090 |
| O3' |
HO3' |
0.950 |
0.967 |
Bond Angles for AAB
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O1P |
P |
O2P |
120.8 |
109.5 |
| O1P |
P |
O3P |
108.8 |
109.5 |
| O1P |
P |
O5' |
107.4 |
109.5 |
| P |
O1P |
H1P |
109.5 |
114.0 |
| O2P |
P |
O3P |
107.0 |
109.5 |
| O2P |
P |
O5' |
107.6 |
109.5 |
| O3P |
P |
O5' |
104.0 |
109.5 |
| P |
O3P |
H3P |
109.5 |
114.0 |
| P |
O5' |
C5' |
127.5 |
123.0 |
| O5' |
C5' |
C4' |
111.8 |
109.4 |
| O5' |
C5' |
H5'1 |
108.9 |
109.4 |
| O5' |
C5' |
H5'2 |
108.9 |
109.5 |
| C4' |
C5' |
H5'1 |
108.9 |
109.5 |
| C4' |
C5' |
H5'2 |
108.9 |
109.5 |
| C5' |
C4' |
O4' |
111.9 |
110.6 |
| C5' |
C4' |
C3' |
110.0 |
110.6 |
| C5' |
C4' |
H4' |
108.5 |
110.6 |
| H5'1 |
C5' |
H5'2 |
109.5 |
109.5 |
| O4' |
C4' |
C3' |
107.8 |
103.5 |
| O4' |
C4' |
H4' |
110.0 |
110.6 |
| C4' |
O4' |
C1' |
108.2 |
107.0 |
| C3' |
C4' |
H4' |
108.6 |
110.8 |
| C4' |
C3' |
C2' |
95.9 |
102.1 |
| C4' |
C3' |
O3' |
110.8 |
110.9 |
| C4' |
C3' |
H3' |
111.9 |
110.9 |
| O4' |
C1' |
O1' |
110.1 |
109.9 |
| O4' |
C1' |
C2' |
98.7 |
107.3 |
| O4' |
C1' |
H1' |
112.8 |
109.9 |
| O1' |
C1' |
C2' |
109.8 |
109.9 |
| O1' |
C1' |
H1' |
113.1 |
109.8 |
| C1' |
O1' |
HO1' |
109.5 |
114.0 |
| C2' |
C1' |
H1' |
111.4 |
110.0 |
| C1' |
C2' |
C3' |
100.2 |
104.2 |
| C1' |
C2' |
H2'1 |
111.7 |
110.5 |
| C1' |
C2' |
H2'2 |
111.7 |
110.5 |
| C3' |
C2' |
H2'1 |
111.8 |
110.5 |
| C3' |
C2' |
H2'2 |
111.7 |
110.5 |
| C2' |
C3' |
O3' |
112.2 |
110.9 |
| C2' |
C3' |
H3' |
111.8 |
110.9 |
| H2'1 |
C2' |
H2'2 |
109.5 |
110.5 |
| O3' |
C3' |
H3' |
113.1 |
110.9 |
| C3' |
O3' |
HO3' |
109.5 |
114.0 |
Torsion Angles for AAB
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O2P |
P |
O1P |
O3P |
124.2 |
240.0 |
| O2P |
P |
O1P |
O5' |
236.3 |
120.0 |
| O3P |
P |
O1P |
O5' |
112.0 |
240.0 |
| O1P |
P |
O3P |
H3P |
132.0 |
60.0 |
| O1P |
P |
O5' |
C5' |
26.1 |
175.0 |
| O1P |
P |
O2P |
O3P |
234.9 |
120.0 |
| O1P |
P |
O2P |
O5' |
123.7 |
240.0 |
| O2P |
P |
O1P |
H1P |
0.0 |
300.0 |
| O3P |
P |
O2P |
O5' |
248.8 |
120.0 |
| O2P |
P |
O3P |
H3P |
360.0 |
180.0 |
| O2P |
P |
O5' |
C5' |
157.6 |
55.0 |
| O1P |
P |
O3P |
O2P |
132.1 |
240.0 |
| O1P |
P |
O3P |
O5' |
245.7 |
120.0 |
| O3P |
P |
O1P |
H1P |
235.8 |
60.0 |
| O2P |
P |
O3P |
O5' |
113.7 |
240.0 |
| O3P |
P |
O5' |
C5' |
270.8 |
295.0 |
| O1P |
P |
O5' |
O2P |
228.5 |
120.0 |
| O1P |
P |
O5' |
O3P |
115.3 |
240.0 |
| O5' |
P |
O1P |
H1P |
123.8 |
180.0 |
| O2P |
P |
O5' |
O3P |
246.8 |
120.0 |
| O5' |
P |
O3P |
H3P |
246.3 |
300.0 |
| P |
O5' |
C5' |
C4' |
196.1 |
180.0 |
| P |
O5' |
C5' |
H5'1 |
316.4 |
299.9 |
| P |
O5' |
C5' |
H5'2 |
75.8 |
60.0 |
| H1P |
O1P |
P |
O2P |
0.0 |
300.0 |
| H1P |
O1P |
P |
O3P |
235.8 |
60.0 |
| H1P |
O1P |
P |
O5' |
123.8 |
180.0 |
| H3P |
O3P |
P |
O5' |
246.3 |
300.0 |
| C4' |
C5' |
O5' |
H5'1 |
239.7 |
240.0 |
| C4' |
C5' |
O5' |
H5'2 |
120.4 |
120.0 |
| O5' |
C5' |
C4' |
O4' |
298.0 |
66.5 |
| O5' |
C5' |
C4' |
C3' |
57.9 |
180.5 |
| O5' |
C5' |
C4' |
H4' |
176.6 |
303.6 |
| H5'1 |
C5' |
O5' |
H5'2 |
240.7 |
240.0 |
| O5' |
C5' |
C4' |
H5'1 |
120.4 |
119.9 |
| O5' |
C5' |
C4' |
H5'2 |
239.6 |
240.0 |
| H5'1 |
C5' |
C4' |
H5'2 |
119.3 |
120.1 |
| O4' |
C4' |
C5' |
C3' |
240.1 |
246.0 |
| O4' |
C4' |
C5' |
H4' |
121.4 |
122.9 |
| C5' |
C4' |
O4' |
C1' |
124.7 |
158.5 |
| C3' |
C4' |
C5' |
H4' |
241.3 |
236.9 |
| C5' |
C4' |
C3' |
C2' |
265.9 |
204.5 |
| C5' |
C4' |
C3' |
O3' |
149.5 |
86.3 |
| C5' |
C4' |
C3' |
H3' |
22.3 |
322.7 |
| O5' |
C5' |
H5'1 |
C4' |
237.9 |
240.1 |
| O5' |
C5' |
H5'1 |
H5'2 |
118.9 |
120.0 |
| C4' |
C5' |
H5'1 |
H5'2 |
241.1 |
239.9 |
| H5'1 |
C5' |
C4' |
O4' |
177.7 |
306.5 |
| H5'1 |
C5' |
C4' |
C3' |
297.5 |
60.6 |
| H5'1 |
C5' |
C4' |
H4' |
56.2 |
183.6 |
| O5' |
C5' |
H5'2 |
C4' |
122.1 |
120.0 |
| O5' |
C5' |
H5'2 |
H5'1 |
241.0 |
240.0 |
| C4' |
C5' |
H5'2 |
H5'1 |
118.9 |
120.1 |
| H5'2 |
C5' |
C4' |
O4' |
58.4 |
186.4 |
| H5'2 |
C5' |
C4' |
C3' |
178.2 |
300.5 |
| H5'2 |
C5' |
C4' |
H4' |
296.9 |
63.5 |
| O4' |
C4' |
C5' |
H5'1 |
177.7 |
306.5 |
| O4' |
C4' |
C5' |
H5'2 |
58.4 |
186.4 |
| C5' |
C4' |
O4' |
C3' |
121.2 |
118.5 |
| C5' |
C4' |
O4' |
H4' |
239.4 |
237.1 |
| C3' |
C4' |
O4' |
H4' |
118.3 |
118.7 |
| O4' |
C4' |
C3' |
C2' |
28.2 |
323.0 |
| O4' |
C4' |
C3' |
O3' |
271.8 |
204.8 |
| O4' |
C4' |
C3' |
H3' |
144.5 |
81.2 |
| C4' |
O4' |
C1' |
O1' |
210.9 |
214.0 |
| C4' |
O4' |
C1' |
C2' |
325.8 |
333.5 |
| C4' |
O4' |
C1' |
H1' |
83.5 |
93.1 |
| C3' |
C4' |
C5' |
H5'1 |
297.5 |
60.6 |
| C3' |
C4' |
C5' |
H5'2 |
178.2 |
300.5 |
| C5' |
C4' |
C3' |
O4' |
237.7 |
241.5 |
| C5' |
C4' |
C3' |
H4' |
118.6 |
122.9 |
| O4' |
C4' |
C3' |
H4' |
240.9 |
241.4 |
| C3' |
C4' |
O4' |
C1' |
3.6 |
40.1 |
| C1' |
C2' |
C3' |
C4' |
311.9 |
20.9 |
| C4' |
C3' |
C2' |
H2'1 |
193.5 |
262.2 |
| C4' |
C3' |
C2' |
H2'2 |
70.4 |
139.5 |
| C2' |
C3' |
C4' |
O3' |
116.5 |
118.2 |
| C2' |
C3' |
C4' |
H3' |
243.7 |
241.8 |
| O3' |
C3' |
C4' |
H3' |
127.2 |
123.6 |
| C4' |
C3' |
O3' |
HO3' |
180.0 |
180.0 |
| H4' |
C4' |
C5' |
H5'1 |
56.2 |
183.6 |
| H4' |
C4' |
C5' |
H5'2 |
296.9 |
63.5 |
| C5' |
C4' |
H4' |
O4' |
122.6 |
122.9 |
| C5' |
C4' |
H4' |
C3' |
240.4 |
237.0 |
| O4' |
C4' |
H4' |
C3' |
117.8 |
114.1 |
| H4' |
C4' |
O4' |
C1' |
245.3 |
281.4 |
| H4' |
C4' |
C3' |
C2' |
147.3 |
81.5 |
| H4' |
C4' |
C3' |
O3' |
30.9 |
323.3 |
| H4' |
C4' |
C3' |
H3' |
263.7 |
199.7 |
| C1' |
O4' |
C4' |
C3' |
3.6 |
40.1 |
| C1' |
O4' |
C4' |
H4' |
245.3 |
281.4 |
| O1' |
C1' |
O4' |
C2' |
245.1 |
240.5 |
| O1' |
C1' |
O4' |
H1' |
127.4 |
121.0 |
| O4' |
C1' |
O1' |
HO1' |
180.0 |
298.6 |
| C2' |
C1' |
O4' |
H1' |
242.3 |
240.4 |
| O4' |
C1' |
C2' |
C3' |
52.2 |
2.0 |
| O4' |
C1' |
C2' |
H2'1 |
170.7 |
120.7 |
| O4' |
C1' |
C2' |
H2'2 |
293.7 |
243.4 |
| O4' |
C1' |
O1' |
C2' |
107.7 |
117.9 |
| O4' |
C1' |
O1' |
H1' |
232.8 |
239.0 |
| C2' |
C1' |
O1' |
H1' |
125.1 |
121.1 |
| O1' |
C1' |
C2' |
C3' |
167.3 |
121.5 |
| O1' |
C1' |
C2' |
H2'1 |
285.8 |
240.2 |
| O1' |
C1' |
C2' |
H2'2 |
48.8 |
2.8 |
| C4' |
C3' |
C2' |
C1' |
311.9 |
20.9 |
| O4' |
C1' |
C2' |
O1' |
244.9 |
240.5 |
| O4' |
C1' |
C2' |
H1' |
118.8 |
119.5 |
| O1' |
C1' |
C2' |
H1' |
233.9 |
239.0 |
| C2' |
C1' |
O1' |
HO1' |
72.3 |
180.7 |
| C3' |
C2' |
C1' |
H2'1 |
241.5 |
241.3 |
| C3' |
C2' |
C1' |
H2'2 |
118.5 |
118.6 |
| C1' |
C2' |
C3' |
O3' |
67.3 |
139.1 |
| C1' |
C2' |
C3' |
H3' |
195.5 |
262.8 |
| H2'1 |
C2' |
C1' |
H2'2 |
237.0 |
237.4 |
| O4' |
C1' |
H1' |
O1' |
125.8 |
121.0 |
| O4' |
C1' |
H1' |
C2' |
250.0 |
242.1 |
| O1' |
C1' |
H1' |
C2' |
124.2 |
121.1 |
| H1' |
C1' |
O1' |
HO1' |
307.2 |
59.6 |
| H1' |
C1' |
C2' |
C3' |
293.4 |
242.5 |
| H1' |
C1' |
C2' |
H2'1 |
51.9 |
1.2 |
| H1' |
C1' |
C2' |
H2'2 |
174.9 |
123.8 |
| HO1' |
O1' |
C1' |
C2' |
72.3 |
180.7 |
| HO1' |
O1' |
C1' |
H1' |
307.2 |
59.6 |
| C2' |
C3' |
C4' |
H4' |
147.3 |
81.5 |
| C4' |
C3' |
C2' |
O3' |
244.7 |
241.8 |
| C4' |
C3' |
C2' |
H3' |
116.5 |
118.2 |
| C3' |
C2' |
C1' |
H1' |
293.4 |
242.5 |
| C1' |
C2' |
C3' |
H2'1 |
118.5 |
118.7 |
| C1' |
C2' |
C3' |
H2'2 |
241.5 |
241.4 |
| H2'1 |
C2' |
C3' |
H2'2 |
123.1 |
122.6 |
| O3' |
C3' |
C2' |
H3' |
231.8 |
236.3 |
| C2' |
C3' |
O3' |
HO3' |
74.1 |
67.3 |
| H2'1 |
C2' |
C1' |
H1' |
51.9 |
1.2 |
| C1' |
C2' |
H2'1 |
C3' |
248.6 |
245.2 |
| C1' |
C2' |
H2'1 |
H2'2 |
124.3 |
122.6 |
| C3' |
C2' |
H2'1 |
H2'2 |
235.7 |
237.4 |
| H2'1 |
C2' |
C3' |
O3' |
308.8 |
20.4 |
| H2'1 |
C2' |
C3' |
H3' |
77.0 |
144.0 |
| H2'2 |
C2' |
C1' |
H1' |
174.9 |
123.8 |
| C1' |
C2' |
H2'2 |
C3' |
111.4 |
114.7 |
| C1' |
C2' |
H2'2 |
H2'1 |
235.7 |
237.4 |
| C3' |
C2' |
H2'2 |
H2'1 |
124.4 |
122.6 |
| H2'2 |
C2' |
C3' |
O3' |
185.7 |
257.7 |
| H2'2 |
C2' |
C3' |
H3' |
313.9 |
21.4 |
| O3' |
C3' |
C4' |
H4' |
30.9 |
323.3 |
| C4' |
C3' |
O3' |
C2' |
105.9 |
112.7 |
| C4' |
C3' |
O3' |
H3' |
233.4 |
236.4 |
| O3' |
C3' |
C2' |
H2'1 |
308.8 |
20.4 |
| O3' |
C3' |
C2' |
H2'2 |
185.7 |
257.7 |
| C2' |
C3' |
O3' |
H3' |
127.5 |
123.7 |
| H3' |
C3' |
C4' |
H4' |
263.7 |
199.7 |
| C4' |
C3' |
H3' |
C2' |
253.7 |
247.3 |
| C4' |
C3' |
H3' |
O3' |
126.0 |
123.6 |
| H3' |
C3' |
C2' |
H2'1 |
77.0 |
144.0 |
| H3' |
C3' |
C2' |
H2'2 |
313.9 |
21.4 |
| C2' |
C3' |
H3' |
O3' |
232.3 |
236.3 |
| H3' |
C3' |
O3' |
HO3' |
306.6 |
303.6 |
| HO3' |
O3' |
C3' |
H3' |
306.6 |
303.6 |