PDB Chemical Component OGX
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 OGX
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| P |
OP2 |
1.586 |
1.480 |
| O5' |
P |
1.612 |
1.611 |
| P |
N4 |
1.614 |
1.682 |
| P |
OP1 |
1.483 |
1.610 |
| S |
C8' |
1.832 |
1.814 |
| S |
HS |
1.300 |
1.345 |
| C6 |
N1 |
1.395 |
1.351 |
| N1 |
C2 |
1.382 |
1.361 |
| N1 |
HN1 |
1.000 |
0.970 |
| N3 |
C2 |
1.329 |
1.315 |
| C2 |
N2 |
1.346 |
1.372 |
| N2 |
HN2 |
1.000 |
0.970 |
| N2 |
HN2A |
1.000 |
0.971 |
| C4 |
N3 |
1.356 |
1.338 |
| N9 |
C4 |
1.381 |
1.380 |
| C5 |
C4 |
1.375 |
1.389 |
| N4 |
C7' |
1.461 |
1.469 |
| N4 |
HN4 |
1.000 |
1.010 |
| N7 |
C5 |
1.391 |
1.397 |
| C5 |
C6 |
1.415 |
1.402 |
| O6 |
C6 |
1.235 |
1.221 |
| C8 |
N7 |
1.306 |
1.348 |
| N7 |
HN7 |
1.000 |
0.970 |
| O8 |
C8 |
1.231 |
1.217 |
| C8 |
N9 |
1.380 |
1.347 |
| N9 |
C1' |
1.456 |
1.465 |
| C1' |
C2' |
1.525 |
1.541 |
| C1' |
O4' |
1.447 |
1.438 |
| C1' |
H1' |
1.100 |
1.090 |
| C2' |
C3' |
1.527 |
1.548 |
| C2' |
H2' |
1.100 |
1.090 |
| C2' |
H2'A |
1.100 |
1.090 |
| O3' |
C3' |
1.448 |
1.430 |
| C3' |
C4' |
1.523 |
1.549 |
| C3' |
H3' |
1.100 |
1.091 |
| O3' |
HO3' |
0.950 |
0.967 |
| O4' |
C4' |
1.455 |
1.443 |
| C4' |
C5' |
1.532 |
1.530 |
| C4' |
H4' |
1.100 |
1.091 |
| C5' |
O5' |
1.401 |
1.430 |
| C5' |
H5' |
1.100 |
1.090 |
| C5' |
H5'A |
1.100 |
1.089 |
| C8' |
C7' |
1.524 |
1.530 |
| C7' |
H7' |
1.100 |
1.090 |
| C7' |
H7'A |
1.101 |
1.089 |
| C8' |
H8' |
1.100 |
1.089 |
| C8' |
H8'A |
1.100 |
1.090 |
| OP1 |
HOP1 |
0.950 |
0.967 |
Bond Angles for OGX
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O5' |
P |
OP1 |
109.6 |
109.4 |
| N4 |
P |
OP1 |
114.8 |
109.5 |
| P |
N4 |
C7' |
120.7 |
111.0 |
| P |
N4 |
HN4 |
105.9 |
111.0 |
| P |
OP1 |
HOP1 |
109.5 |
114.1 |
| C8' |
S |
HS |
102.0 |
103.0 |
| S |
C8' |
C7' |
112.6 |
109.5 |
| S |
C8' |
H8' |
108.5 |
109.5 |
| S |
C8' |
H8'A |
108.4 |
109.5 |
| C6 |
N1 |
HN1 |
117.7 |
119.9 |
| C2 |
N1 |
HN1 |
117.7 |
120.0 |
| N1 |
C2 |
N2 |
117.5 |
119.1 |
| C2 |
N2 |
HN2 |
120.0 |
120.1 |
| C2 |
N2 |
HN2A |
120.0 |
120.0 |
| HN2 |
N2 |
HN2A |
120.0 |
119.9 |
| C7' |
N4 |
HN4 |
105.9 |
111.0 |
| N4 |
C7' |
H7' |
110.1 |
109.4 |
| N4 |
C7' |
H7'A |
110.1 |
109.5 |
| C8 |
N7 |
HN7 |
125.5 |
126.0 |
| O8 |
C8 |
N9 |
123.2 |
125.2 |
| C8 |
N9 |
C1' |
123.1 |
125.6 |
| N9 |
C1' |
C2' |
124.8 |
109.9 |
| N9 |
C1' |
O4' |
94.4 |
109.9 |
| N9 |
C1' |
H1' |
107.9 |
109.9 |
| C2' |
C1' |
O4' |
101.5 |
107.3 |
| C2' |
C1' |
H1' |
101.6 |
109.9 |
| C1' |
C2' |
C3' |
100.1 |
104.2 |
| C1' |
C2' |
H2' |
112.7 |
110.5 |
| C1' |
C2' |
H2'A |
112.7 |
110.5 |
| O4' |
C1' |
H1' |
129.3 |
110.0 |
| C1' |
O4' |
C4' |
110.5 |
106.9 |
| C3' |
C2' |
H2' |
112.7 |
110.5 |
| C3' |
C2' |
H2'A |
112.8 |
110.5 |
| C2' |
C3' |
C4' |
99.2 |
102.1 |
| C2' |
C3' |
H3' |
115.9 |
110.9 |
| H2' |
C2' |
H2'A |
106.0 |
110.5 |
| O3' |
C3' |
C4' |
111.9 |
110.9 |
| O3' |
C3' |
H3' |
104.1 |
110.8 |
| C4' |
C3' |
H3' |
115.0 |
110.9 |
| C3' |
C4' |
C5' |
113.1 |
110.6 |
| C3' |
C4' |
H4' |
111.8 |
110.6 |
| O4' |
C4' |
C5' |
111.8 |
110.6 |
| O4' |
C4' |
H4' |
113.0 |
110.8 |
| C5' |
C4' |
H4' |
103.7 |
110.5 |
| C4' |
C5' |
O5' |
108.3 |
109.5 |
| C4' |
C5' |
H5' |
109.9 |
109.5 |
| C4' |
C5' |
H5'A |
109.9 |
109.5 |
| O5' |
C5' |
H5' |
109.9 |
109.4 |
| O5' |
C5' |
H5'A |
109.9 |
109.4 |
| H5' |
C5' |
H5'A |
109.1 |
109.5 |
| C8' |
C7' |
H7' |
110.1 |
109.5 |
| C8' |
C7' |
H7'A |
110.1 |
109.5 |
| H7' |
C7' |
H7'A |
108.8 |
109.5 |
| H8' |
C8' |
H8'A |
110.5 |
109.5 |
Torsion Angles for OGX
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| N4 |
P |
O5' |
OP1 |
121.7 |
120.0 |
| O5' |
P |
N4 |
C7' |
211.8 |
300.0 |
| O5' |
P |
N4 |
HN4 |
331.8 |
64.0 |
| O5' |
P |
OP1 |
HOP1 |
244.8 |
60.0 |
| O5' |
P |
N4 |
OP1 |
242.0 |
240.0 |
| N4 |
P |
OP1 |
HOP1 |
131.5 |
300.0 |
| C7' |
N4 |
P |
HN4 |
240.0 |
236.0 |
| P |
N4 |
C7' |
H7' |
235.4 |
255.0 |
| P |
N4 |
C7' |
H7'A |
355.4 |
15.0 |
| OP1 |
P |
N4 |
C7' |
329.8 |
60.0 |
| OP1 |
P |
N4 |
HN4 |
89.8 |
183.9 |
| S |
C8' |
C7' |
H7' |
265.3 |
60.0 |
| S |
C8' |
C7' |
H7'A |
145.3 |
300.0 |
| H8' |
C8' |
S |
H8'A |
240.0 |
240.0 |
| HS |
S |
C8' |
C7' |
180.0 |
180.0 |
| HS |
S |
C8' |
H8' |
300.0 |
300.0 |
| HS |
S |
C8' |
H8'A |
60.0 |
60.0 |
| C2 |
N1 |
C6 |
HN1 |
180.0 |
179.8 |
| C6 |
N1 |
C2 |
HN1 |
180.0 |
180.2 |
| N1 |
C2 |
N2 |
HN2 |
179.9 |
359.9 |
| N1 |
C2 |
N2 |
HN2A |
359.8 |
180.0 |
| HN1 |
N1 |
C2 |
N2 |
0.1 |
0.0 |
| N3 |
C2 |
N1 |
HN1 |
180.0 |
180.0 |
| N3 |
C2 |
N2 |
HN2 |
0.0 |
180.0 |
| N3 |
C2 |
N2 |
HN2A |
180.0 |
0.1 |
| N2 |
C2 |
N1 |
HN1 |
0.1 |
0.0 |
| HN2 |
N2 |
C2 |
HN2A |
180.1 |
179.9 |
| C2 |
N2 |
HN2 |
HN2A |
179.9 |
180.1 |
| C2 |
N2 |
HN2A |
HN2 |
180.1 |
179.9 |
| C7' |
N4 |
P |
OP1 |
329.8 |
60.0 |
| P |
N4 |
C7' |
HN4 |
120.0 |
124.0 |
| S |
C8' |
C7' |
N4 |
25.3 |
180.0 |
| C8' |
C7' |
N4 |
H7' |
240.0 |
240.0 |
| C8' |
C7' |
N4 |
H7'A |
120.0 |
120.0 |
| H7' |
C7' |
N4 |
H7'A |
240.0 |
240.0 |
| HN4 |
N4 |
P |
OP1 |
89.8 |
183.9 |
| P |
N4 |
HN4 |
C7' |
230.7 |
236.0 |
| HN4 |
N4 |
C7' |
H7' |
115.4 |
131.0 |
| HN4 |
N4 |
C7' |
H7'A |
235.4 |
251.0 |
| C5 |
C6 |
N1 |
HN1 |
179.0 |
179.8 |
| O6 |
C6 |
N1 |
HN1 |
359.3 |
0.2 |
| O8 |
C8 |
N7 |
HN7 |
0.8 |
0.0 |
| O8 |
C8 |
N9 |
C1' |
355.8 |
359.9 |
| N9 |
C8 |
N7 |
HN7 |
180.2 |
180.0 |
| C8 |
N9 |
C1' |
C2' |
173.9 |
295.0 |
| C8 |
N9 |
C1' |
O4' |
281.2 |
52.8 |
| C8 |
N9 |
C1' |
H1' |
55.1 |
173.9 |
| C2' |
C1' |
N9 |
O4' |
252.7 |
242.2 |
| C2' |
C1' |
N9 |
H1' |
118.9 |
121.1 |
| N9 |
C1' |
C2' |
C3' |
147.0 |
121.5 |
| N9 |
C1' |
C2' |
H2' |
267.0 |
240.1 |
| N9 |
C1' |
C2' |
H2'A |
27.0 |
2.7 |
| O4' |
C1' |
N9 |
H1' |
226.2 |
238.9 |
| N9 |
C1' |
O4' |
C4' |
211.9 |
214.0 |
| N9 |
C1' |
C2' |
O4' |
103.7 |
119.4 |
| N9 |
C1' |
C2' |
H1' |
238.3 |
238.9 |
| O4' |
C1' |
C2' |
H1' |
134.6 |
119.5 |
| C2' |
C1' |
O4' |
C4' |
338.8 |
333.5 |
| C3' |
C2' |
C1' |
H2' |
240.0 |
241.3 |
| C3' |
C2' |
C1' |
H2'A |
120.0 |
118.7 |
| C1' |
C2' |
C3' |
C4' |
311.3 |
20.9 |
| C1' |
C2' |
C3' |
H3' |
187.6 |
262.7 |
| H2' |
C2' |
C1' |
H2'A |
240.0 |
237.4 |
| N9 |
C1' |
O4' |
C2' |
233.1 |
240.6 |
| N9 |
C1' |
O4' |
H1' |
117.5 |
121.1 |
| C2' |
C1' |
O4' |
H1' |
244.4 |
240.5 |
| O4' |
C1' |
C2' |
C3' |
43.3 |
2.1 |
| O4' |
C1' |
C2' |
H2' |
163.3 |
120.7 |
| O4' |
C1' |
C2' |
H2'A |
283.3 |
243.3 |
| C1' |
O4' |
C4' |
C5' |
112.5 |
158.6 |
| C1' |
O4' |
C4' |
H4' |
229.1 |
281.5 |
| N9 |
C1' |
H1' |
C2' |
132.8 |
121.1 |
| N9 |
C1' |
H1' |
O4' |
248.3 |
239.0 |
| C2' |
C1' |
H1' |
O4' |
115.5 |
117.9 |
| H1' |
C1' |
C2' |
C3' |
268.7 |
242.5 |
| H1' |
C1' |
C2' |
H2' |
28.7 |
1.2 |
| H1' |
C1' |
C2' |
H2'A |
148.7 |
123.8 |
| H1' |
C1' |
O4' |
C4' |
94.4 |
93.0 |
| C3' |
C2' |
C1' |
O4' |
43.3 |
2.1 |
| C3' |
C2' |
C1' |
H1' |
268.7 |
242.5 |
| C1' |
C2' |
C3' |
H2' |
120.0 |
118.6 |
| C1' |
C2' |
C3' |
H2'A |
240.0 |
241.3 |
| H2' |
C2' |
C3' |
H2'A |
120.0 |
122.7 |
| O3' |
C3' |
C2' |
C4' |
117.9 |
118.2 |
| O3' |
C3' |
C2' |
H3' |
241.6 |
236.4 |
| C4' |
C3' |
C2' |
H3' |
123.7 |
118.2 |
| C2' |
C3' |
C4' |
C5' |
274.8 |
204.5 |
| C2' |
C3' |
C4' |
H4' |
158.2 |
81.7 |
| H2' |
C2' |
C1' |
O4' |
163.3 |
120.7 |
| H2' |
C2' |
C1' |
H1' |
28.7 |
1.2 |
| C1' |
C2' |
H2' |
C3' |
247.6 |
245.2 |
| C1' |
C2' |
H2' |
H2'A |
123.8 |
122.6 |
| C3' |
C2' |
H2' |
H2'A |
236.2 |
237.3 |
| H2' |
C2' |
C3' |
C4' |
191.4 |
262.2 |
| H2' |
C2' |
C3' |
H3' |
67.6 |
144.0 |
| H2'A |
C2' |
C1' |
O4' |
283.3 |
243.3 |
| H2'A |
C2' |
C1' |
H1' |
148.7 |
123.8 |
| C1' |
C2' |
H2'A |
C3' |
112.4 |
114.8 |
| C1' |
C2' |
H2'A |
H2' |
236.2 |
237.4 |
| C3' |
C2' |
H2'A |
H2' |
123.8 |
122.7 |
| H2'A |
C2' |
C3' |
C4' |
71.4 |
139.5 |
| H2'A |
C2' |
C3' |
H3' |
307.6 |
21.3 |
| O3' |
C3' |
C2' |
H2' |
309.2 |
20.4 |
| O3' |
C3' |
C2' |
H2'A |
189.2 |
257.8 |
| C2' |
C3' |
O3' |
C4' |
250.1 |
247.3 |
| C2' |
C3' |
O3' |
H3' |
125.3 |
123.6 |
| C4' |
C3' |
O3' |
H3' |
235.2 |
236.4 |
| O3' |
C3' |
C4' |
C5' |
157.6 |
86.2 |
| O3' |
C3' |
C4' |
H4' |
41.0 |
323.4 |
| C1' |
O4' |
C4' |
C3' |
350.4 |
40.1 |
| C4' |
C3' |
C2' |
H2' |
191.4 |
262.2 |
| C4' |
C3' |
C2' |
H2'A |
71.4 |
139.5 |
| C2' |
C3' |
C4' |
H3' |
235.7 |
241.8 |
| O3' |
C3' |
C4' |
H3' |
118.5 |
123.5 |
| O4' |
C4' |
C3' |
C5' |
121.3 |
118.5 |
| O4' |
C4' |
C3' |
H4' |
237.9 |
241.3 |
| C5' |
C4' |
C3' |
H4' |
116.6 |
122.8 |
| C3' |
C4' |
C5' |
O5' |
299.9 |
185.0 |
| C3' |
C4' |
C5' |
H5' |
59.9 |
305.0 |
| C3' |
C4' |
C5' |
H5'A |
179.9 |
65.1 |
| H3' |
C3' |
C2' |
H2' |
67.6 |
144.0 |
| H3' |
C3' |
C2' |
H2'A |
307.6 |
21.3 |
| C2' |
C3' |
H3' |
C4' |
115.0 |
112.7 |
| O3' |
C3' |
H3' |
C4' |
237.2 |
236.4 |
| H3' |
C3' |
C4' |
C5' |
39.1 |
322.7 |
| H3' |
C3' |
C4' |
H4' |
282.5 |
199.9 |
| HO3' |
O3' |
C3' |
C4' |
289.9 |
174.2 |
| HO3' |
O3' |
C3' |
H3' |
54.7 |
297.8 |
| C4' |
O4' |
C1' |
H1' |
94.4 |
93.0 |
| O4' |
C4' |
C3' |
H3' |
160.4 |
81.2 |
| C3' |
C4' |
O4' |
C5' |
237.8 |
241.5 |
| C3' |
C4' |
O4' |
H4' |
121.3 |
118.6 |
| C5' |
C4' |
O4' |
H4' |
243.4 |
237.1 |
| O4' |
C4' |
C5' |
O5' |
183.2 |
70.9 |
| O4' |
C4' |
C5' |
H5' |
303.2 |
190.9 |
| O4' |
C4' |
C5' |
H5'A |
63.2 |
311.0 |
| C5' |
C4' |
C3' |
H3' |
39.1 |
322.7 |
| C3' |
C4' |
C5' |
H4' |
238.8 |
237.1 |
| O4' |
C4' |
C5' |
H4' |
122.1 |
123.0 |
| O5' |
C5' |
C4' |
H5' |
240.0 |
240.0 |
| O5' |
C5' |
C4' |
H5'A |
120.0 |
119.9 |
| H5' |
C5' |
C4' |
H5'A |
240.0 |
239.9 |
| H4' |
C4' |
C3' |
H3' |
282.5 |
199.9 |
| C3' |
C4' |
H4' |
C5' |
122.1 |
122.9 |
| O4' |
C4' |
H4' |
C5' |
238.7 |
237.1 |
| H4' |
C4' |
C5' |
O5' |
61.1 |
307.9 |
| H4' |
C4' |
C5' |
H5' |
181.1 |
67.9 |
| H4' |
C4' |
C5' |
H5'A |
301.1 |
187.9 |
| C5' |
O5' |
P |
OP1 |
62.2 |
170.0 |
| O5' |
C5' |
C4' |
H4' |
61.1 |
307.9 |
| C4' |
C5' |
O5' |
H5' |
120.0 |
120.0 |
| C4' |
C5' |
O5' |
H5'A |
240.0 |
240.0 |
| H5' |
C5' |
O5' |
H5'A |
120.0 |
120.0 |
| H5' |
C5' |
C4' |
H4' |
181.1 |
67.9 |
| C4' |
C5' |
H5' |
O5' |
241.0 |
240.0 |
| C4' |
C5' |
H5' |
H5'A |
120.5 |
120.0 |
| O5' |
C5' |
H5' |
H5'A |
239.5 |
240.0 |
| H5'A |
C5' |
C4' |
H4' |
301.1 |
187.9 |
| C4' |
C5' |
H5'A |
O5' |
119.0 |
120.0 |
| C4' |
C5' |
H5'A |
H5' |
239.5 |
239.9 |
| O5' |
C5' |
H5'A |
H5' |
120.5 |
120.0 |
| C7' |
C8' |
S |
HS |
180.0 |
180.0 |
| S |
C8' |
C7' |
H8' |
120.0 |
120.0 |
| S |
C8' |
C7' |
H8'A |
240.0 |
240.0 |
| C8' |
C7' |
N4 |
HN4 |
355.4 |
11.1 |
| N4 |
C7' |
C8' |
H7' |
120.0 |
120.0 |
| N4 |
C7' |
C8' |
H7'A |
240.0 |
240.0 |
| H7' |
C7' |
C8' |
H7'A |
120.0 |
120.0 |
| H7' |
C7' |
N4 |
HN4 |
115.4 |
131.0 |
| N4 |
C7' |
H7' |
H7'A |
120.8 |
120.0 |
| C8' |
C7' |
H7' |
H7'A |
239.2 |
240.0 |
| H7'A |
C7' |
N4 |
HN4 |
235.4 |
251.0 |
| N4 |
C7' |
H7'A |
H7' |
239.2 |
240.0 |
| C8' |
C7' |
H7'A |
H7' |
120.8 |
120.0 |
| H8' |
C8' |
S |
HS |
300.0 |
300.0 |
| S |
C8' |
H8' |
C7' |
237.5 |
240.0 |
| S |
C8' |
H8' |
H8'A |
118.7 |
120.1 |
| H8' |
C8' |
C7' |
H7' |
145.3 |
300.0 |
| H8' |
C8' |
C7' |
H7'A |
25.3 |
180.0 |
| H8'A |
C8' |
S |
HS |
60.0 |
60.0 |
| S |
C8' |
H8'A |
C7' |
122.5 |
120.0 |
| S |
C8' |
H8'A |
H8' |
241.3 |
240.0 |
| H8'A |
C8' |
C7' |
H7' |
25.3 |
180.0 |
| H8'A |
C8' |
C7' |
H7'A |
265.3 |
60.0 |