PDB Chemical Component G5A
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 G5A
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C |
N3S |
1.331 |
1.348 |
| N |
CA |
1.449 |
1.468 |
| N |
HN |
1.000 |
1.009 |
| N |
HNA |
1.000 |
1.008 |
| O |
C |
1.223 |
1.212 |
| S |
O5' |
1.612 |
1.522 |
| S |
O2S |
1.416 |
1.421 |
| N1 |
C2 |
1.342 |
1.321 |
| C2 |
H2 |
1.080 |
1.080 |
| N3 |
C2 |
1.342 |
1.316 |
| C4 |
N3 |
1.354 |
1.330 |
| C5 |
C4 |
1.430 |
1.405 |
| C5 |
C6 |
1.440 |
1.406 |
| C6 |
N1 |
1.353 |
1.329 |
| N6 |
C6 |
1.353 |
1.384 |
| N6 |
HN6 |
1.000 |
0.970 |
| N6 |
HN6A |
1.000 |
0.970 |
| N7 |
C5 |
1.351 |
1.355 |
| N7 |
C8 |
1.360 |
1.302 |
| C8 |
N9 |
1.346 |
1.363 |
| C8 |
H8 |
1.080 |
1.080 |
| N9 |
C4 |
1.331 |
1.371 |
| N9 |
C1' |
1.485 |
1.466 |
| CA |
C |
1.517 |
1.507 |
| CA |
HA |
1.100 |
1.091 |
| CA |
HAA |
1.100 |
1.090 |
| C1' |
C2' |
1.492 |
1.550 |
| C1' |
H1' |
1.100 |
1.090 |
| O1S |
S |
1.407 |
1.421 |
| C2' |
O2' |
1.410 |
1.428 |
| C2' |
H2' |
1.100 |
1.090 |
| O2' |
HO2' |
0.950 |
0.967 |
| C3' |
C2' |
1.473 |
1.548 |
| C3' |
O3' |
1.397 |
1.429 |
| N3S |
S |
1.580 |
1.656 |
| N3S |
HN3S |
1.000 |
0.970 |
| C4' |
C3' |
1.518 |
1.541 |
| C4' |
O4' |
1.420 |
1.437 |
| C4' |
H4' |
1.100 |
1.090 |
| O4' |
C1' |
1.429 |
1.444 |
| C5' |
C4' |
1.493 |
1.530 |
| C5' |
H5' |
1.100 |
1.090 |
| C5' |
H5'A |
1.100 |
1.090 |
| O5' |
C5' |
1.420 |
1.429 |
| C3' |
H16 |
1.100 |
1.090 |
| O3' |
H17 |
0.950 |
0.967 |
Bond Angles for G5A
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O |
C |
N3S |
123.7 |
120.0 |
| CA |
C |
N3S |
115.0 |
120.0 |
| C |
N3S |
S |
121.9 |
120.0 |
| C |
N3S |
HN3S |
119.1 |
120.1 |
| CA |
N |
HN |
109.5 |
111.0 |
| CA |
N |
HNA |
109.5 |
111.0 |
| N |
CA |
HA |
108.3 |
109.5 |
| N |
CA |
HAA |
108.4 |
109.5 |
| HN |
N |
HNA |
109.4 |
111.1 |
| O2S |
S |
O5' |
104.2 |
106.4 |
| O1S |
S |
O5' |
104.5 |
106.4 |
| N3S |
S |
O5' |
104.2 |
107.2 |
| S |
O5' |
C5' |
118.2 |
114.0 |
| O1S |
S |
O2S |
115.0 |
123.1 |
| N1 |
C2 |
H2 |
118.8 |
118.8 |
| N3 |
C2 |
H2 |
118.9 |
118.8 |
| HN6 |
N6 |
HN6A |
109.5 |
120.0 |
| N7 |
C8 |
N9 |
109.6 |
109.9 |
| N7 |
C8 |
H8 |
125.2 |
125.1 |
| N9 |
C8 |
H8 |
125.2 |
125.0 |
| C8 |
N9 |
C1' |
128.1 |
126.2 |
| N9 |
C1' |
C2' |
114.3 |
110.6 |
| N9 |
C1' |
H1' |
104.2 |
110.5 |
| HA |
CA |
HAA |
110.6 |
109.4 |
| C2' |
C1' |
H1' |
109.8 |
110.7 |
| C1' |
C2' |
O2' |
110.9 |
110.9 |
| C1' |
C2' |
H2' |
108.0 |
110.9 |
| O4' |
C1' |
H1' |
114.0 |
110.7 |
| O2' |
C2' |
H2' |
108.9 |
110.8 |
| C2' |
O2' |
HO2' |
109.5 |
114.0 |
| C3' |
C2' |
H2' |
109.8 |
111.0 |
| O3' |
C3' |
H16 |
83.3 |
110.5 |
| C3' |
O3' |
H17 |
109.5 |
114.0 |
| C4' |
C3' |
H16 |
113.5 |
110.6 |
| O4' |
C4' |
H4' |
107.8 |
109.9 |
| C5' |
C4' |
H4' |
92.0 |
110.0 |
| H5' |
C5' |
H5'A |
108.1 |
109.5 |
| O5' |
C5' |
H5' |
110.8 |
109.5 |
| O5' |
C5' |
H5'A |
110.8 |
109.4 |
Torsion Angles for G5A
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C |
N3S |
S |
O5' |
290.9 |
65.0 |
| N |
CA |
C |
N3S |
174.4 |
180.0 |
| HN |
N |
CA |
HNA |
240.0 |
235.9 |
| HA |
CA |
N |
HAA |
240.0 |
120.0 |
| CA |
N |
HN |
HNA |
120.0 |
124.0 |
| HN |
N |
CA |
HA |
300.0 |
296.0 |
| HN |
N |
CA |
HAA |
60.0 |
176.0 |
| CA |
N |
HNA |
HN |
240.0 |
236.0 |
| HNA |
N |
CA |
HA |
60.0 |
60.0 |
| HNA |
N |
CA |
HAA |
180.0 |
300.1 |
| CA |
C |
O |
N3S |
179.5 |
180.2 |
| O |
C |
N3S |
S |
5.0 |
359.9 |
| O |
C |
N3S |
HN3S |
185.0 |
180.0 |
| O1S |
S |
O5' |
O2S |
121.0 |
132.9 |
| S |
O5' |
C5' |
H5' |
115.4 |
60.0 |
| S |
O5' |
C5' |
H5'A |
355.4 |
300.0 |
| C |
N3S |
S |
O2S |
178.1 |
311.5 |
| O1S |
S |
O2S |
O5' |
246.3 |
237.1 |
| N3S |
S |
O2S |
O5' |
112.8 |
114.1 |
| O2S |
S |
O5' |
C5' |
65.7 |
188.5 |
| N3 |
C2 |
N1 |
H2 |
180.0 |
180.1 |
| N1 |
C2 |
N3 |
H2 |
180.0 |
179.9 |
| C4 |
N3 |
C2 |
H2 |
179.9 |
180.0 |
| C6 |
N1 |
C2 |
H2 |
180.2 |
180.0 |
| N9 |
C8 |
N7 |
H8 |
180.0 |
180.0 |
| N7 |
C8 |
N9 |
C1' |
181.1 |
180.1 |
| N7 |
C8 |
N9 |
H8 |
180.0 |
180.0 |
| C8 |
N9 |
C1' |
C2' |
288.4 |
264.9 |
| C8 |
N9 |
C1' |
H1' |
168.4 |
142.1 |
| N7 |
C8 |
H8 |
N9 |
180.0 |
180.0 |
| H8 |
C8 |
N9 |
C1' |
1.1 |
0.1 |
| C1' |
N9 |
C8 |
H8 |
1.1 |
0.1 |
| C2' |
C1' |
N9 |
H1' |
119.9 |
122.9 |
| N9 |
C1' |
C2' |
O2' |
218.7 |
273.7 |
| N9 |
C1' |
C2' |
H2' |
338.0 |
37.3 |
| O4' |
C1' |
N9 |
H1' |
237.3 |
237.0 |
| O |
C |
CA |
N3S |
180.4 |
179.8 |
| CA |
C |
N3S |
S |
185.4 |
179.7 |
| CA |
C |
N3S |
HN3S |
5.4 |
359.8 |
| HA |
CA |
C |
N3S |
54.4 |
300.0 |
| HA |
CA |
N |
HN |
300.0 |
296.0 |
| HA |
CA |
N |
HNA |
60.0 |
60.0 |
| N |
CA |
HA |
HAA |
118.6 |
239.9 |
| HAA |
CA |
C |
N3S |
294.4 |
59.9 |
| HAA |
CA |
N |
HN |
60.0 |
176.0 |
| HAA |
CA |
N |
HNA |
180.0 |
300.1 |
| N |
CA |
HAA |
HA |
241.4 |
120.0 |
| N9 |
C1' |
C2' |
H1' |
243.2 |
237.2 |
| O4' |
C1' |
C2' |
H1' |
122.8 |
118.7 |
| O2' |
C2' |
C1' |
H2' |
240.7 |
236.4 |
| C1' |
C2' |
O2' |
HO2' |
180.0 |
180.0 |
| C3' |
C2' |
C1' |
H2' |
119.9 |
118.2 |
| N9 |
C1' |
H1' |
C2' |
122.9 |
122.9 |
| H1' |
C1' |
C2' |
O2' |
335.4 |
36.5 |
| H1' |
C1' |
C2' |
H2' |
94.7 |
160.1 |
| C |
N3S |
S |
O1S |
44.1 |
178.6 |
| O2S |
S |
O1S |
O5' |
113.6 |
122.9 |
| N3S |
S |
O1S |
O5' |
247.0 |
245.9 |
| O1S |
S |
O5' |
C5' |
186.7 |
321.4 |
| O2' |
C2' |
C1' |
H1' |
335.4 |
36.5 |
| C1' |
C2' |
O2' |
H2' |
118.7 |
123.6 |
| C3' |
C2' |
O2' |
H2' |
240.1 |
236.3 |
| H2' |
C2' |
C1' |
H1' |
94.7 |
160.1 |
| C1' |
C2' |
H2' |
O2' |
239.5 |
236.4 |
| H2' |
C2' |
O2' |
HO2' |
61.3 |
56.4 |
| HO2' |
O2' |
C2' |
H2' |
61.3 |
56.4 |
| C3' |
C2' |
C1' |
H1' |
214.6 |
278.4 |
| C1' |
C2' |
C3' |
H2' |
241.3 |
241.8 |
| O2' |
C2' |
C3' |
H2' |
119.3 |
123.6 |
| C3' |
C2' |
O2' |
HO2' |
301.4 |
292.7 |
| O3' |
C3' |
C2' |
H2' |
282.4 |
216.0 |
| C4' |
C3' |
O3' |
H16 |
246.3 |
237.3 |
| C |
N3S |
S |
HN3S |
180.0 |
180.1 |
| O2S |
S |
N3S |
O5' |
247.2 |
246.4 |
| O1S |
S |
N3S |
O5' |
113.2 |
113.5 |
| N3S |
S |
O5' |
C5' |
306.4 |
75.0 |
| C |
N3S |
HN3S |
S |
180.0 |
179.9 |
| HN3S |
N3S |
S |
O5' |
110.9 |
245.0 |
| C4' |
C3' |
C2' |
H2' |
142.2 |
97.3 |
| O3' |
C3' |
C4' |
H16 |
97.6 |
122.6 |
| C4' |
C3' |
O3' |
H17 |
311.0 |
176.3 |
| C4' |
O4' |
C1' |
H1' |
131.1 |
78.6 |
| O4' |
C4' |
C3' |
H16 |
106.3 |
116.7 |
| C5' |
C4' |
O4' |
H4' |
257.7 |
238.8 |
| H4' |
C4' |
C3' |
H16 |
221.7 |
236.1 |
| N9 |
C1' |
O4' |
H1' |
116.8 |
122.9 |
| C2' |
C1' |
O4' |
H1' |
240.0 |
241.4 |
| O4' |
C1' |
C2' |
H2' |
217.5 |
278.8 |
| S |
O5' |
C5' |
C4' |
235.4 |
180.0 |
| C5' |
C4' |
C3' |
H16 |
322.4 |
357.3 |
| O4' |
C4' |
C5' |
H4' |
111.4 |
121.1 |
| H5' |
C5' |
C4' |
H4' |
298.0 |
66.1 |
| O5' |
C5' |
H5' |
H5'A |
238.4 |
240.0 |
| H5'A |
C5' |
C4' |
H4' |
58.0 |
186.1 |
| O5' |
C5' |
H5'A |
H5' |
121.6 |
120.0 |
| O5' |
C5' |
C4' |
H4' |
177.9 |
306.1 |
| H5' |
C5' |
O5' |
H5'A |
120.0 |
120.0 |
| H16 |
C3' |
C2' |
H2' |
20.4 |
338.5 |
| H16 |
C3' |
O3' |
H17 |
64.8 |
298.9 |
| H17 |
O3' |
C3' |
H16 |
64.8 |
298.9 |