PDB Chemical Component ONE
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 ONE
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| OP3 |
P |
1.604 |
1.610 |
| OP3 |
HOP3 |
0.950 |
0.967 |
| P |
OP1 |
1.488 |
1.480 |
| P |
OP2 |
1.482 |
1.609 |
| P |
O5' |
1.588 |
1.609 |
| OP2 |
HOP2 |
0.951 |
0.966 |
| O5' |
C5' |
1.419 |
1.428 |
| C5' |
C4' |
1.501 |
1.530 |
| C5' |
H5'' |
1.115 |
1.090 |
| C5' |
H5' |
1.114 |
1.091 |
| C4' |
O4' |
1.452 |
1.445 |
| C4' |
C3' |
1.516 |
1.543 |
| C4' |
H4' |
1.115 |
1.090 |
| O4' |
C1' |
1.417 |
1.445 |
| C3' |
C2' |
1.528 |
1.544 |
| C3' |
O3' |
1.426 |
1.429 |
| C3' |
H3' |
1.115 |
1.090 |
| C2' |
O2' |
1.413 |
1.429 |
| C2' |
C1' |
1.531 |
1.544 |
| C2' |
H2' |
1.115 |
1.090 |
| O2' |
HO2 |
0.951 |
0.966 |
| O3' |
HO3 |
0.950 |
0.968 |
| C1' |
N1 |
1.471 |
1.465 |
| C1' |
H1' |
1.115 |
1.090 |
| N1 |
C6 |
1.372 |
1.356 |
| N1 |
C2 |
1.366 |
1.356 |
| C6 |
C5 |
1.336 |
1.350 |
| C6 |
H6 |
1.102 |
1.080 |
| C2 |
C3 |
1.336 |
1.350 |
| C2 |
H2 |
1.103 |
1.079 |
| C3 |
C4 |
1.443 |
1.415 |
| C3 |
H3 |
1.104 |
1.080 |
| C4 |
O4 |
1.231 |
1.222 |
| C4 |
C5 |
1.444 |
1.414 |
| C5 |
H5 |
1.103 |
1.080 |
Bond Angles for ONE
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| P |
OP3 |
HOP3 |
110.1 |
106.8 |
| OP3 |
P |
OP1 |
110.1 |
109.4 |
| OP3 |
P |
OP2 |
107.7 |
109.5 |
| OP3 |
P |
O5' |
102.6 |
109.5 |
| OP1 |
P |
OP2 |
119.6 |
109.5 |
| OP1 |
P |
O5' |
109.5 |
109.5 |
| OP2 |
P |
O5' |
105.9 |
109.5 |
| P |
OP2 |
HOP2 |
107.8 |
106.9 |
| P |
O5' |
C5' |
118.9 |
106.9 |
| O5' |
C5' |
C4' |
111.4 |
109.5 |
| O5' |
C5' |
H5'' |
111.5 |
109.5 |
| O5' |
C5' |
H5' |
111.5 |
109.4 |
| C4' |
C5' |
H5'' |
111.5 |
109.5 |
| C4' |
C5' |
H5' |
111.5 |
109.5 |
| C5' |
C4' |
O4' |
110.0 |
110.3 |
| C5' |
C4' |
C3' |
112.2 |
110.7 |
| C5' |
C4' |
H4' |
106.4 |
110.3 |
| H5'' |
C5' |
H5' |
98.9 |
109.5 |
| O4' |
C4' |
C3' |
106.5 |
104.8 |
| O4' |
C4' |
H4' |
112.1 |
110.4 |
| C4' |
O4' |
C1' |
109.7 |
105.3 |
| C3' |
C4' |
H4' |
109.8 |
110.3 |
| C4' |
C3' |
C2' |
102.2 |
104.2 |
| C4' |
C3' |
O3' |
109.3 |
110.5 |
| C4' |
C3' |
H3' |
116.2 |
110.5 |
| O4' |
C1' |
C2' |
106.3 |
104.8 |
| O4' |
C1' |
N1 |
107.6 |
110.5 |
| O4' |
C1' |
H1' |
114.8 |
110.4 |
| C2' |
C3' |
O3' |
114.7 |
110.5 |
| C2' |
C3' |
H3' |
110.9 |
110.5 |
| C3' |
C2' |
O2' |
115.3 |
110.5 |
| C3' |
C2' |
C1' |
101.7 |
104.1 |
| C3' |
C2' |
H2' |
112.3 |
110.5 |
| O3' |
C3' |
H3' |
104.0 |
110.5 |
| C3' |
O3' |
HO3 |
109.3 |
106.8 |
| O2' |
C2' |
C1' |
113.1 |
110.7 |
| O2' |
C2' |
H2' |
100.6 |
110.4 |
| C2' |
O2' |
HO2 |
115.2 |
106.8 |
| C1' |
C2' |
H2' |
114.4 |
110.5 |
| C2' |
C1' |
N1 |
114.8 |
110.4 |
| C2' |
C1' |
H1' |
107.5 |
110.4 |
| N1 |
C1' |
H1' |
106.2 |
110.3 |
| C1' |
N1 |
C6 |
120.9 |
119.3 |
| C1' |
N1 |
C2 |
119.6 |
119.2 |
| C6 |
N1 |
C2 |
119.5 |
121.5 |
| N1 |
C6 |
C5 |
121.9 |
120.7 |
| N1 |
C6 |
H6 |
120.4 |
119.7 |
| N1 |
C2 |
C3 |
122.0 |
120.7 |
| N1 |
C2 |
H2 |
120.2 |
119.7 |
| C5 |
C6 |
H6 |
117.7 |
119.6 |
| C6 |
C5 |
C4 |
120.4 |
119.3 |
| C6 |
C5 |
H5 |
116.0 |
120.4 |
| C3 |
C2 |
H2 |
117.8 |
119.7 |
| C2 |
C3 |
C4 |
120.4 |
119.3 |
| C2 |
C3 |
H3 |
115.9 |
120.4 |
| C4 |
C3 |
H3 |
123.6 |
120.4 |
| C3 |
C4 |
O4 |
121.9 |
120.7 |
| C3 |
C4 |
C5 |
115.8 |
118.6 |
| O4 |
C4 |
C5 |
122.3 |
120.7 |
| C4 |
C5 |
H5 |
123.6 |
120.3 |
Torsion Angles for ONE
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP1 |
P |
OP3 |
OP2 |
227.9 |
240.0 |
| OP1 |
P |
OP3 |
O5' |
116.5 |
120.0 |
| OP2 |
P |
OP3 |
O5' |
248.5 |
240.0 |
| OP3 |
P |
OP2 |
HOP2 |
180.0 |
60.0 |
| OP3 |
P |
O5' |
C5' |
323.2 |
180.0 |
| HOP3 |
OP3 |
P |
OP1 |
180.0 |
300.0 |
| HOP3 |
OP3 |
P |
OP2 |
312.1 |
59.9 |
| HOP3 |
OP3 |
P |
O5' |
63.6 |
180.0 |
| OP1 |
P |
OP3 |
HOP3 |
180.0 |
300.0 |
| OP3 |
P |
OP1 |
OP2 |
125.6 |
120.0 |
| OP3 |
P |
OP1 |
O5' |
247.9 |
240.0 |
| OP2 |
P |
OP1 |
O5' |
122.4 |
120.0 |
| OP1 |
P |
OP2 |
HOP2 |
306.7 |
180.0 |
| OP1 |
P |
O5' |
C5' |
206.3 |
60.0 |
| OP2 |
P |
OP3 |
HOP3 |
312.1 |
59.9 |
| OP3 |
P |
OP2 |
OP1 |
233.3 |
240.0 |
| OP3 |
P |
OP2 |
O5' |
109.2 |
120.1 |
| OP1 |
P |
OP2 |
O5' |
235.9 |
240.0 |
| OP2 |
P |
O5' |
C5' |
76.1 |
300.0 |
| O5' |
P |
OP3 |
HOP3 |
63.6 |
180.0 |
| OP3 |
P |
O5' |
OP1 |
116.9 |
120.0 |
| OP3 |
P |
O5' |
OP2 |
247.2 |
240.0 |
| OP1 |
P |
O5' |
OP2 |
130.2 |
120.0 |
| O5' |
P |
OP2 |
HOP2 |
70.8 |
300.0 |
| P |
O5' |
C5' |
C4' |
172.3 |
180.0 |
| P |
O5' |
C5' |
H5'' |
297.5 |
60.0 |
| P |
O5' |
C5' |
H5' |
47.0 |
300.0 |
| HOP2 |
OP2 |
P |
O5' |
70.8 |
300.0 |
| C4' |
C5' |
O5' |
H5'' |
234.8 |
120.0 |
| C4' |
C5' |
O5' |
H5' |
125.3 |
240.0 |
| O5' |
C5' |
C4' |
O4' |
48.5 |
61.4 |
| O5' |
C5' |
C4' |
C3' |
166.8 |
176.9 |
| O5' |
C5' |
C4' |
H4' |
286.9 |
299.2 |
| H5'' |
C5' |
O5' |
H5' |
250.5 |
120.0 |
| O5' |
C5' |
C4' |
H5'' |
125.2 |
240.0 |
| O5' |
C5' |
C4' |
H5' |
234.7 |
120.0 |
| H5'' |
C5' |
C4' |
H5' |
109.5 |
240.0 |
| O4' |
C4' |
C5' |
C3' |
241.6 |
244.5 |
| O4' |
C4' |
C5' |
H4' |
121.5 |
122.2 |
| C5' |
C4' |
O4' |
C1' |
113.6 |
159.5 |
| C3' |
C4' |
C5' |
H4' |
239.9 |
237.7 |
| C5' |
C4' |
C3' |
C2' |
267.7 |
217.3 |
| C5' |
C4' |
C3' |
O3' |
145.8 |
98.5 |
| C5' |
C4' |
C3' |
H3' |
28.5 |
336.0 |
| O5' |
C5' |
H5'' |
C4' |
234.8 |
120.1 |
| O5' |
C5' |
H5'' |
H5' |
117.4 |
240.1 |
| C4' |
C5' |
H5'' |
H5' |
242.6 |
120.0 |
| H5'' |
C5' |
C4' |
O4' |
283.2 |
181.4 |
| H5'' |
C5' |
C4' |
C3' |
41.6 |
296.9 |
| H5'' |
C5' |
C4' |
H4' |
161.7 |
59.2 |
| O5' |
C5' |
H5' |
C4' |
125.2 |
239.9 |
| O5' |
C5' |
H5' |
H5'' |
242.6 |
120.0 |
| C4' |
C5' |
H5' |
H5'' |
117.4 |
240.0 |
| H5' |
C5' |
C4' |
O4' |
173.7 |
301.4 |
| H5' |
C5' |
C4' |
C3' |
292.1 |
56.9 |
| H5' |
C5' |
C4' |
H4' |
52.2 |
179.2 |
| O4' |
C4' |
C5' |
H5'' |
283.2 |
181.4 |
| O4' |
C4' |
C5' |
H5' |
173.7 |
301.4 |
| C5' |
C4' |
O4' |
C3' |
121.8 |
119.2 |
| C5' |
C4' |
O4' |
H4' |
241.9 |
237.9 |
| C3' |
C4' |
O4' |
H4' |
120.1 |
118.7 |
| O4' |
C4' |
C3' |
C2' |
28.1 |
336.2 |
| O4' |
C4' |
C3' |
O3' |
266.2 |
217.5 |
| O4' |
C4' |
C3' |
H3' |
148.9 |
94.9 |
| C4' |
O4' |
C1' |
C2' |
344.5 |
319.6 |
| C4' |
O4' |
C1' |
N1 |
221.1 |
200.7 |
| C4' |
O4' |
C1' |
H1' |
103.2 |
78.4 |
| C3' |
C4' |
C5' |
H5'' |
41.6 |
296.9 |
| C3' |
C4' |
C5' |
H5' |
292.1 |
56.9 |
| C5' |
C4' |
C3' |
O4' |
239.6 |
241.1 |
| C5' |
C4' |
C3' |
H4' |
118.1 |
122.3 |
| O4' |
C4' |
C3' |
H4' |
238.5 |
241.2 |
| C3' |
C4' |
O4' |
C1' |
351.8 |
40.3 |
| C2' |
C3' |
C4' |
O3' |
121.9 |
118.7 |
| C2' |
C3' |
C4' |
H3' |
239.2 |
241.3 |
| C4' |
C3' |
C2' |
O2' |
201.2 |
241.1 |
| C4' |
C3' |
C2' |
C1' |
324.0 |
359.9 |
| C4' |
C3' |
C2' |
H2' |
86.8 |
118.5 |
| O3' |
C3' |
C4' |
H3' |
117.3 |
122.6 |
| C4' |
C3' |
O3' |
HO3 |
180.0 |
178.1 |
| H4' |
C4' |
C5' |
H5'' |
161.7 |
59.2 |
| H4' |
C4' |
C5' |
H5' |
52.2 |
179.2 |
| C5' |
C4' |
H4' |
O4' |
120.2 |
122.2 |
| C5' |
C4' |
H4' |
C3' |
238.4 |
237.4 |
| O4' |
C4' |
H4' |
C3' |
118.2 |
115.3 |
| H4' |
C4' |
O4' |
C1' |
231.7 |
281.6 |
| H4' |
C4' |
C3' |
C2' |
149.7 |
95.0 |
| H4' |
C4' |
C3' |
O3' |
27.7 |
336.2 |
| H4' |
C4' |
C3' |
H3' |
270.5 |
213.7 |
| C1' |
O4' |
C4' |
C3' |
351.8 |
40.3 |
| C1' |
O4' |
C4' |
H4' |
231.7 |
281.6 |
| C3' |
C2' |
C1' |
O4' |
32.5 |
24.0 |
| O2' |
C2' |
C1' |
O4' |
156.7 |
142.7 |
| O4' |
C1' |
C2' |
H2' |
271.1 |
265.3 |
| C2' |
C1' |
O4' |
N1 |
123.4 |
118.9 |
| C2' |
C1' |
O4' |
H1' |
241.3 |
241.2 |
| N1 |
C1' |
O4' |
H1' |
117.9 |
122.3 |
| O4' |
C1' |
N1 |
C6 |
21.2 |
235.5 |
| O4' |
C1' |
N1 |
C2 |
200.6 |
55.2 |
| C2' |
C3' |
C4' |
H4' |
149.7 |
95.0 |
| C4' |
C3' |
C2' |
O3' |
241.8 |
241.3 |
| C4' |
C3' |
C2' |
H3' |
124.4 |
118.7 |
| O4' |
C1' |
C2' |
C3' |
32.5 |
24.0 |
| O3' |
C3' |
C2' |
H3' |
242.6 |
237.4 |
| C2' |
C3' |
O3' |
HO3 |
65.9 |
63.3 |
| O2' |
C2' |
C3' |
C1' |
237.2 |
241.2 |
| O2' |
C2' |
C3' |
H2' |
114.4 |
122.5 |
| C3' |
C2' |
O2' |
HO2 |
180.0 |
298.6 |
| C1' |
C2' |
C3' |
H2' |
237.2 |
241.4 |
| C3' |
C2' |
C1' |
N1 |
151.2 |
143.0 |
| C3' |
C2' |
C1' |
H1' |
269.1 |
265.2 |
| O3' |
C3' |
C4' |
H4' |
27.7 |
336.2 |
| C4' |
C3' |
O3' |
C2' |
114.0 |
114.8 |
| C4' |
C3' |
O3' |
H3' |
235.3 |
237.4 |
| C2' |
C3' |
O3' |
H3' |
121.3 |
122.6 |
| O3' |
C3' |
C2' |
O2' |
319.4 |
359.8 |
| O3' |
C3' |
C2' |
C1' |
82.1 |
118.7 |
| O3' |
C3' |
C2' |
H2' |
204.9 |
237.3 |
| H3' |
C3' |
C4' |
H4' |
270.5 |
213.7 |
| C4' |
C3' |
H3' |
C2' |
244.0 |
245.2 |
| C4' |
C3' |
H3' |
O3' |
120.2 |
122.6 |
| C2' |
C3' |
H3' |
O3' |
236.2 |
237.4 |
| H3' |
C3' |
C2' |
O2' |
76.8 |
122.4 |
| H3' |
C3' |
C2' |
C1' |
199.6 |
241.2 |
| H3' |
C3' |
C2' |
H2' |
322.4 |
359.9 |
| H3' |
C3' |
O3' |
HO3 |
304.7 |
300.7 |
| O4' |
C1' |
C2' |
O2' |
156.7 |
142.7 |
| O2' |
C2' |
C3' |
O3' |
319.4 |
359.8 |
| O2' |
C2' |
C3' |
H3' |
76.8 |
122.4 |
| C3' |
C2' |
O2' |
C1' |
116.4 |
114.7 |
| C3' |
C2' |
O2' |
H2' |
238.9 |
237.4 |
| C1' |
C2' |
O2' |
H2' |
122.5 |
122.7 |
| O2' |
C2' |
C1' |
N1 |
275.4 |
261.7 |
| O2' |
C2' |
C1' |
H1' |
33.3 |
23.9 |
| O4' |
C1' |
C2' |
N1 |
241.3 |
241.0 |
| O4' |
C1' |
C2' |
H1' |
123.4 |
118.8 |
| C1' |
C2' |
C3' |
O3' |
82.1 |
118.7 |
| C1' |
C2' |
C3' |
H3' |
199.6 |
241.2 |
| C3' |
C2' |
C1' |
O2' |
235.8 |
241.3 |
| C3' |
C2' |
C1' |
H2' |
121.4 |
118.7 |
| O2' |
C2' |
C1' |
H2' |
245.6 |
237.4 |
| C1' |
C2' |
O2' |
HO2 |
63.5 |
183.8 |
| N1 |
C1' |
C2' |
H1' |
242.1 |
237.8 |
| C2' |
C1' |
N1 |
C6 |
263.2 |
120.0 |
| C2' |
C1' |
N1 |
C2 |
82.6 |
299.7 |
| H2' |
C2' |
C3' |
O3' |
204.9 |
237.3 |
| H2' |
C2' |
C3' |
H3' |
322.4 |
359.9 |
| C3' |
C2' |
H2' |
O2' |
123.1 |
122.6 |
| C3' |
C2' |
H2' |
C1' |
244.7 |
245.3 |
| O2' |
C2' |
H2' |
C1' |
121.6 |
122.8 |
| H2' |
C2' |
O2' |
HO2 |
301.0 |
61.2 |
| H2' |
C2' |
C1' |
N1 |
29.8 |
24.3 |
| H2' |
C2' |
C1' |
H1' |
147.7 |
146.5 |
| HO2 |
O2' |
C2' |
C1' |
63.5 |
183.8 |
| HO2 |
O2' |
C2' |
H2' |
301.0 |
61.2 |
| HO3 |
O3' |
C3' |
H3' |
304.7 |
300.7 |
| O4' |
C1' |
N1 |
C2' |
118.0 |
115.5 |
| O4' |
C1' |
N1 |
H1' |
236.6 |
237.7 |
| N1 |
C1' |
C2' |
H2' |
29.8 |
24.3 |
| C2' |
C1' |
N1 |
H1' |
118.6 |
122.2 |
| C6 |
N1 |
C1' |
C2 |
180.6 |
180.3 |
| C1' |
N1 |
C6 |
C5 |
179.8 |
179.9 |
| C1' |
N1 |
C6 |
H6 |
359.9 |
0.0 |
| C1' |
N1 |
C2 |
C3 |
180.2 |
179.8 |
| C1' |
N1 |
C2 |
H2 |
0.1 |
0.3 |
| O4' |
C1' |
H1' |
C2' |
242.0 |
244.6 |
| O4' |
C1' |
H1' |
N1 |
118.7 |
122.4 |
| H1' |
C1' |
C2' |
H2' |
147.7 |
146.5 |
| C2' |
C1' |
H1' |
N1 |
236.7 |
237.8 |
| H1' |
C1' |
N1 |
C6 |
144.5 |
357.8 |
| H1' |
C1' |
N1 |
C2 |
323.9 |
177.5 |
| C6 |
N1 |
C1' |
H1' |
144.5 |
357.8 |
| C1' |
N1 |
C6 |
C2 |
179.4 |
179.7 |
| C6 |
N1 |
C2 |
C3 |
359.6 |
359.5 |
| C6 |
N1 |
C2 |
H2 |
179.5 |
179.9 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
179.9 |
| N1 |
C6 |
C5 |
C4 |
359.7 |
0.0 |
| N1 |
C6 |
C5 |
H5 |
179.7 |
179.9 |
| C2 |
N1 |
C1' |
H1' |
323.9 |
177.5 |
| C1' |
N1 |
C2 |
C6 |
180.6 |
180.3 |
| C2 |
N1 |
C6 |
C5 |
0.4 |
0.3 |
| C2 |
N1 |
C6 |
H6 |
180.4 |
180.4 |
| C3 |
C2 |
N1 |
H2 |
180.0 |
179.5 |
| N1 |
C2 |
C3 |
C4 |
0.3 |
0.5 |
| N1 |
C2 |
C3 |
H3 |
180.3 |
180.3 |
| C5 |
C6 |
N1 |
C2 |
0.4 |
0.3 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.1 |
| C3 |
C4 |
C5 |
C6 |
0.2 |
360.0 |
| O4 |
C4 |
C5 |
C6 |
177.9 |
180.0 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
180.1 |
| H6 |
C6 |
N1 |
C2 |
180.4 |
180.4 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
179.9 |
| H6 |
C6 |
C5 |
C4 |
179.7 |
179.9 |
| H6 |
C6 |
C5 |
H5 |
359.7 |
359.9 |
| N1 |
C2 |
C3 |
H2 |
180.0 |
180.5 |
| C4 |
C3 |
C2 |
H3 |
180.0 |
180.2 |
| C2 |
C3 |
C4 |
O4 |
182.1 |
179.7 |
| C2 |
C3 |
C4 |
C5 |
359.8 |
359.8 |
| N1 |
C2 |
H2 |
C3 |
180.0 |
179.5 |
| H2 |
C2 |
C3 |
C4 |
180.3 |
180.0 |
| H2 |
C2 |
C3 |
H3 |
0.3 |
359.8 |
| C6 |
C5 |
C4 |
C3 |
0.2 |
360.0 |
| C4 |
C3 |
C2 |
H2 |
180.3 |
180.0 |
| C2 |
C3 |
C4 |
H3 |
180.0 |
179.8 |
| O4 |
C4 |
C3 |
C5 |
182.3 |
179.9 |
| C3 |
C4 |
C5 |
H5 |
180.2 |
180.0 |
| H3 |
C3 |
C2 |
H2 |
0.3 |
359.8 |
| C2 |
C3 |
H3 |
C4 |
180.0 |
180.2 |
| H3 |
C3 |
C4 |
O4 |
2.2 |
360.0 |
| H3 |
C3 |
C4 |
C5 |
179.9 |
180.0 |
| C6 |
C5 |
C4 |
O4 |
177.9 |
180.0 |
| O4 |
C4 |
C3 |
H3 |
2.2 |
360.0 |
| C3 |
C4 |
O4 |
C5 |
177.6 |
180.1 |
| O4 |
C4 |
C5 |
H5 |
357.9 |
0.1 |
| C4 |
C5 |
C6 |
H6 |
179.7 |
179.9 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
179.9 |
| C5 |
C4 |
C3 |
H3 |
179.9 |
180.0 |
| C3 |
C4 |
C5 |
O4 |
182.3 |
179.9 |
| H5 |
C5 |
C6 |
H6 |
359.7 |
359.9 |
| C6 |
C5 |
H5 |
C4 |
180.0 |
180.1 |