PDB Chemical Component A5O
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 A5O
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| OP2 |
P |
1.477 |
1.481 |
| P |
OP1 |
1.477 |
1.610 |
| P |
O5' |
1.605 |
1.610 |
| P |
OP3 |
1.611 |
1.610 |
| C6 |
N1 |
1.336 |
1.328 |
| N1 |
C2 |
1.324 |
1.321 |
| N3 |
C2 |
1.324 |
1.317 |
| C2 |
H2 |
1.080 |
1.079 |
| C4 |
N3 |
1.360 |
1.330 |
| C5 |
C4 |
1.367 |
1.405 |
| N9 |
C4 |
1.368 |
1.372 |
| N7 |
C5 |
1.400 |
1.354 |
| C5 |
C6 |
1.416 |
1.405 |
| N6 |
C6 |
1.321 |
1.384 |
| HN6 |
N6 |
1.000 |
0.970 |
| N6 |
HN6A |
1.000 |
0.969 |
| N7 |
C8 |
1.310 |
1.301 |
| H8 |
C8 |
1.080 |
1.081 |
| C8 |
N9 |
1.369 |
1.363 |
| N9 |
C1' |
1.476 |
1.465 |
| C2' |
C1' |
1.517 |
1.544 |
| C1' |
H1' |
1.100 |
1.090 |
| C1' |
O4' |
1.413 |
1.444 |
| O2' |
C2' |
1.419 |
1.429 |
| H2' |
C2' |
1.100 |
1.089 |
| C2' |
C3' |
1.536 |
1.545 |
| O2' |
HO2' |
0.950 |
0.967 |
| H3' |
C3' |
1.100 |
1.089 |
| C3' |
O3' |
1.421 |
1.429 |
| C3' |
C4' |
1.533 |
1.545 |
| O3' |
HO3' |
0.950 |
0.967 |
| C5' |
C4' |
1.525 |
1.530 |
| O4' |
C4' |
1.416 |
1.445 |
| C4' |
H4' |
1.100 |
1.090 |
| O5' |
C5' |
1.422 |
1.428 |
| C5' |
H5'A |
1.100 |
1.090 |
| C5' |
H5' |
1.100 |
1.090 |
| OP1 |
HOP1 |
0.950 |
0.967 |
| OP3 |
HOP3 |
0.950 |
0.967 |
Bond Angles for A5O
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP2 |
P |
OP3 |
109.3 |
109.5 |
| O5' |
P |
OP1 |
108.4 |
109.5 |
| OP1 |
P |
OP3 |
108.4 |
109.4 |
| P |
OP1 |
HOP1 |
109.5 |
114.0 |
| O5' |
P |
OP3 |
98.7 |
109.5 |
| P |
O5' |
C5' |
118.9 |
123.0 |
| P |
OP3 |
HOP3 |
109.5 |
114.0 |
| N1 |
C2 |
H2 |
116.0 |
118.8 |
| N3 |
C2 |
H2 |
116.0 |
118.7 |
| HN6 |
N6 |
HN6A |
109.5 |
120.0 |
| N7 |
C8 |
N9 |
114.7 |
110.0 |
| C8 |
N9 |
C1' |
129.9 |
126.3 |
| N9 |
C1' |
H1' |
103.4 |
110.3 |
| N9 |
C1' |
O4' |
111.0 |
110.4 |
| C2' |
C1' |
H1' |
108.3 |
110.4 |
| C2' |
C1' |
O4' |
106.4 |
104.9 |
| O4' |
C1' |
H1' |
112.8 |
110.3 |
| C1' |
O4' |
C4' |
108.1 |
105.2 |
| O2' |
C2' |
C3' |
112.1 |
110.5 |
| C2' |
C3' |
O3' |
115.1 |
110.5 |
| C2' |
C3' |
C4' |
103.4 |
104.1 |
| O3' |
C3' |
C4' |
109.2 |
110.5 |
| C3' |
O3' |
HO3' |
109.5 |
114.0 |
| C3' |
C4' |
H4' |
108.3 |
110.3 |
| C5' |
C4' |
H4' |
107.4 |
110.3 |
| O4' |
C4' |
H4' |
111.3 |
110.3 |
| O5' |
C5' |
H5'A |
108.7 |
109.5 |
| O5' |
C5' |
H5' |
108.7 |
109.5 |
| H5' |
C5' |
H5'A |
110.2 |
109.4 |
Torsion Angles for A5O
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP1 |
P |
OP2 |
OP3 |
233.2 |
240.1 |
| OP2 |
P |
OP1 |
HOP1 |
360.0 |
59.9 |
| O5' |
P |
OP2 |
OP3 |
106.8 |
120.1 |
| OP2 |
P |
OP3 |
HOP3 |
0.0 |
180.0 |
| OP2 |
P |
OP1 |
OP3 |
127.3 |
120.0 |
| O5' |
P |
OP1 |
OP3 |
253.9 |
240.0 |
| OP1 |
P |
O5' |
C5' |
51.8 |
185.0 |
| OP1 |
P |
OP3 |
HOP3 |
133.7 |
299.9 |
| OP2 |
P |
O5' |
OP3 |
246.1 |
240.0 |
| OP1 |
P |
O5' |
OP3 |
112.8 |
120.0 |
| O5' |
P |
OP1 |
HOP1 |
126.6 |
179.9 |
| O5' |
P |
OP3 |
HOP3 |
246.4 |
60.0 |
| P |
O5' |
C5' |
H5'A |
58.9 |
300.0 |
| P |
O5' |
C5' |
H5' |
298.9 |
60.0 |
| O5' |
P |
OP3 |
OP1 |
112.7 |
120.0 |
| OP3 |
P |
OP1 |
HOP1 |
232.7 |
300.0 |
| OP3 |
P |
O5' |
C5' |
299.1 |
65.0 |
| C6 |
N1 |
C2 |
H2 |
180.2 |
180.0 |
| N3 |
C2 |
N1 |
H2 |
180.0 |
180.0 |
| N1 |
C2 |
N3 |
H2 |
180.0 |
180.0 |
| C4 |
N3 |
C2 |
H2 |
178.9 |
180.0 |
| N7 |
C8 |
N9 |
C1' |
185.0 |
180.0 |
| C8 |
N9 |
C1' |
H1' |
178.4 |
144.3 |
| C8 |
N9 |
C1' |
O4' |
57.3 |
22.1 |
| C2' |
C1' |
N9 |
H1' |
117.9 |
122.2 |
| C2' |
C1' |
N9 |
O4' |
239.1 |
244.5 |
| O4' |
C1' |
N9 |
H1' |
238.9 |
237.8 |
| N9 |
C1' |
O4' |
C4' |
202.1 |
200.7 |
| N9 |
C1' |
C2' |
H1' |
244.9 |
237.8 |
| N9 |
C1' |
C2' |
O4' |
123.4 |
118.9 |
| O4' |
C1' |
C2' |
H1' |
121.4 |
118.9 |
| C2' |
C1' |
O4' |
C4' |
328.1 |
319.6 |
| N9 |
C1' |
H1' |
O4' |
240.1 |
237.8 |
| C2' |
C1' |
H1' |
O4' |
117.4 |
115.5 |
| H1' |
C1' |
O4' |
C4' |
86.6 |
78.5 |
| N9 |
C1' |
O4' |
H1' |
115.4 |
122.2 |
| C2' |
C1' |
O4' |
H1' |
241.5 |
241.1 |
| C1' |
O4' |
C4' |
H4' |
257.3 |
281.6 |
| O2' |
C2' |
C1' |
H1' |
151.5 |
146.4 |
| O2' |
C2' |
C1' |
O4' |
272.9 |
265.3 |
| O2' |
C2' |
C3' |
O3' |
218.2 |
237.3 |
| O2' |
C2' |
C3' |
C4' |
99.2 |
118.7 |
| C3' |
C2' |
C1' |
H1' |
272.5 |
265.0 |
| C3' |
C2' |
C1' |
O4' |
33.9 |
23.9 |
| O3' |
C3' |
C2' |
C4' |
119.0 |
118.6 |
| C2' |
C3' |
O3' |
HO3' |
180.0 |
61.5 |
| C2' |
C3' |
C4' |
H4' |
126.3 |
94.8 |
| HO2' |
O2' |
C2' |
C3' |
64.7 |
65.3 |
| H3' |
C3' |
O3' |
HO3' |
59.8 |
298.9 |
| H3' |
C3' |
C4' |
H4' |
246.4 |
213.6 |
| C2' |
C3' |
O3' |
C4' |
244.2 |
245.4 |
| O3' |
C3' |
C4' |
H4' |
3.3 |
336.2 |
| C1' |
O4' |
C4' |
C3' |
16.3 |
40.4 |
| C2' |
C3' |
C4' |
O3' |
123.0 |
118.6 |
| C4' |
C3' |
O3' |
HO3' |
295.8 |
176.1 |
| C5' |
C4' |
C3' |
H4' |
118.4 |
122.2 |
| O4' |
C4' |
C3' |
H4' |
239.1 |
241.2 |
| HO3' |
O3' |
C3' |
C4' |
295.8 |
176.1 |
| P |
O5' |
C5' |
C4' |
178.9 |
180.0 |
| C3' |
C4' |
C5' |
H4' |
241.1 |
237.8 |
| O4' |
C4' |
C5' |
H4' |
120.8 |
122.3 |
| C4' |
O4' |
C1' |
H1' |
86.6 |
78.5 |
| C3' |
C4' |
O4' |
H4' |
119.0 |
118.8 |
| C5' |
C4' |
O4' |
H4' |
241.5 |
237.7 |
| C5' |
O5' |
P |
OP1 |
51.8 |
185.0 |
| C5' |
O5' |
P |
OP3 |
299.1 |
65.0 |
| O5' |
C5' |
C4' |
H4' |
177.0 |
307.2 |
| H5' |
C5' |
O5' |
H5'A |
240.0 |
120.0 |
| H5'A |
C5' |
C4' |
H4' |
297.0 |
187.2 |
| O5' |
C5' |
H5'A |
H5' |
241.0 |
120.0 |
| H5' |
C5' |
C4' |
H4' |
57.0 |
67.2 |
| O5' |
C5' |
H5' |
H5'A |
119.0 |
240.0 |
| HOP1 |
OP1 |
P |
OP3 |
232.7 |
300.0 |