PDB Chemical Component JSQ
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 JSQ
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O1G |
PG |
1.512 |
1.480 |
| PG |
O3G |
1.505 |
1.611 |
| PG |
O3B |
1.610 |
1.610 |
| PG |
O2G |
1.509 |
1.610 |
| O1B |
PB |
1.514 |
1.480 |
| O3B |
PB |
1.613 |
1.610 |
| O2B |
PB |
1.497 |
1.610 |
| PB |
O3A |
1.612 |
1.610 |
| O2A |
PA |
1.518 |
1.481 |
| O3A |
PA |
1.615 |
1.609 |
| O3' |
C3' |
1.423 |
1.430 |
| C5' |
C4' |
1.532 |
1.530 |
| C5' |
O5' |
1.426 |
1.429 |
| PA |
O5' |
1.617 |
1.610 |
| PA |
O1A |
1.503 |
1.609 |
| C4' |
C3' |
1.539 |
1.542 |
| C4' |
O4' |
1.442 |
1.438 |
| C3' |
C2' |
1.540 |
1.548 |
| O2' |
C2' |
1.426 |
1.429 |
| O4' |
C1' |
1.440 |
1.443 |
| C2' |
C1' |
1.540 |
1.550 |
| C1' |
N9 |
1.455 |
1.465 |
| N9 |
C8 |
1.360 |
1.364 |
| N9 |
C4 |
1.358 |
1.372 |
| C8 |
N7 |
1.297 |
1.301 |
| N7 |
C5 |
1.351 |
1.355 |
| C4 |
N3 |
1.322 |
1.330 |
| C4 |
C5 |
1.398 |
1.404 |
| N3 |
C2 |
1.312 |
1.319 |
| C5 |
C6 |
1.396 |
1.405 |
| C2 |
F2 |
1.361 |
1.350 |
| C2 |
N1 |
1.318 |
1.322 |
| C6 |
N1 |
1.324 |
1.329 |
| C6 |
N6 |
1.380 |
1.384 |
| C1' |
H1' |
1.100 |
1.090 |
| C2' |
H2' |
1.100 |
1.090 |
| C3' |
H3' |
1.100 |
1.090 |
| C4' |
H4' |
1.100 |
1.090 |
| C5' |
H5'2 |
1.100 |
1.090 |
| C5' |
H5'1 |
1.100 |
1.090 |
| C8 |
H8 |
1.080 |
1.080 |
| N6 |
HN62 |
1.000 |
0.969 |
| N6 |
HN61 |
1.000 |
0.970 |
| O1A |
H1 |
0.950 |
0.968 |
| O2' |
HO2' |
0.950 |
0.967 |
| O2B |
H2 |
0.950 |
0.967 |
| O2G |
H3 |
0.950 |
0.967 |
| O3' |
HO3' |
0.950 |
0.967 |
| O3G |
H4 |
0.950 |
0.967 |
Bond Angles for JSQ
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O1G |
PG |
O3G |
110.6 |
109.5 |
| O1G |
PG |
O3B |
107.8 |
109.5 |
| O1G |
PG |
O2G |
110.1 |
109.5 |
| PG |
O3G |
H4 |
109.5 |
114.0 |
| PG |
O2G |
H3 |
109.5 |
114.0 |
| O1B |
PB |
O3B |
112.1 |
109.4 |
| O1B |
PB |
O2B |
110.2 |
109.5 |
| O1B |
PB |
O3A |
113.8 |
109.5 |
| O2B |
PB |
O3B |
103.4 |
109.5 |
| O2B |
PB |
O3A |
105.9 |
109.5 |
| PB |
O2B |
H2 |
109.5 |
114.0 |
| O2A |
PA |
O3A |
112.6 |
109.4 |
| O2A |
PA |
O5' |
111.3 |
109.4 |
| O3A |
PA |
O5' |
108.9 |
109.5 |
| O3' |
C3' |
H3' |
111.9 |
110.4 |
| C5' |
C4' |
O4' |
110.6 |
110.0 |
| C5' |
C4' |
H4' |
110.1 |
110.0 |
| O5' |
C5' |
H5'2 |
109.5 |
109.5 |
| O5' |
C5' |
H5'1 |
109.6 |
109.4 |
| PA |
O1A |
H1 |
109.5 |
114.0 |
| C4' |
C3' |
H3' |
110.1 |
110.5 |
| O4' |
C4' |
H4' |
111.4 |
109.7 |
| C3' |
C2' |
H2' |
109.9 |
110.9 |
| O2' |
C2' |
H2' |
111.6 |
110.8 |
| O4' |
C1' |
H1' |
111.3 |
110.6 |
| C2' |
C1' |
N9 |
105.9 |
110.6 |
| C2' |
C1' |
H1' |
109.9 |
110.6 |
| C1' |
N9 |
C8 |
125.5 |
126.2 |
| N9 |
C1' |
H1' |
111.1 |
110.6 |
| N9 |
C8 |
H8 |
125.1 |
125.1 |
| N7 |
C8 |
H8 |
125.0 |
125.0 |
| C4 |
C5 |
C6 |
118.0 |
118.2 |
| N3 |
C2 |
F2 |
118.5 |
118.8 |
| N3 |
C2 |
N1 |
123.2 |
122.3 |
| C5 |
C6 |
N1 |
118.6 |
118.5 |
| C5 |
C6 |
N6 |
119.9 |
120.8 |
| F2 |
C2 |
N1 |
118.3 |
118.9 |
| C2 |
N1 |
C6 |
120.7 |
121.2 |
| N1 |
C6 |
N6 |
121.5 |
120.7 |
| C6 |
N6 |
HN62 |
109.5 |
120.0 |
| C6 |
N6 |
HN61 |
109.5 |
120.0 |
| H5'2 |
C5' |
H5'1 |
109.5 |
109.5 |
| HN62 |
N6 |
HN61 |
109.5 |
120.0 |
Torsion Angles for JSQ
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O1G |
PG |
O3G |
H4 |
0.0 |
60.0 |
| O1G |
PG |
O2G |
H3 |
0.0 |
180.0 |
| O1G |
PG |
O3G |
O3B |
239.8 |
240.0 |
| O1G |
PG |
O3G |
O2G |
121.3 |
120.0 |
| O3G |
PG |
O2G |
H3 |
121.6 |
300.0 |
| O1G |
PG |
O3B |
O3G |
121.9 |
120.0 |
| O1G |
PG |
O3B |
O2G |
241.5 |
240.0 |
| O3B |
PG |
O2G |
H3 |
243.0 |
60.0 |
| O1G |
PG |
O2G |
O3G |
238.4 |
240.0 |
| O1G |
PG |
O2G |
O3B |
117.1 |
120.0 |
| O2B |
PB |
O1B |
O3B |
114.6 |
120.0 |
| O2B |
PB |
O1B |
O3A |
241.3 |
240.0 |
| O1B |
PB |
O2B |
H2 |
0.0 |
180.0 |
| O1G |
PG |
O3B |
PB |
124.6 |
320.0 |
| O1B |
PB |
O3B |
O2B |
118.7 |
119.9 |
| O1B |
PB |
O3B |
O3A |
231.8 |
240.0 |
| O2B |
PB |
O3B |
O3A |
113.0 |
120.0 |
| O3B |
PB |
O2B |
H2 |
120.0 |
299.9 |
| O1B |
PB |
O2B |
O3B |
240.0 |
240.1 |
| O1B |
PB |
O2B |
O3A |
123.4 |
120.0 |
| O1B |
PB |
O3A |
O3B |
127.3 |
120.0 |
| O1B |
PB |
O3A |
O2B |
238.8 |
240.0 |
| O2B |
PB |
O3A |
O3B |
248.5 |
240.0 |
| O3A |
PB |
O2B |
H2 |
236.6 |
60.0 |
| O3A |
PA |
O2A |
O5' |
237.5 |
240.0 |
| O2A |
PA |
O1A |
H1 |
0.0 |
179.9 |
| O1B |
PB |
O3A |
PA |
5.5 |
320.0 |
| O2B |
PB |
O3A |
PA |
126.7 |
80.0 |
| O2A |
PA |
O3A |
O5' |
123.9 |
120.0 |
| O3A |
PA |
O1A |
H1 |
237.5 |
60.0 |
| C4' |
C3' |
O3' |
H3' |
236.5 |
237.4 |
| O3' |
C3' |
C2' |
H2' |
263.9 |
216.1 |
| C5' |
C4' |
C3' |
H3' |
324.2 |
357.2 |
| O4' |
C4' |
C5' |
H4' |
123.5 |
121.0 |
| O2A |
PA |
O5' |
C5' |
312.5 |
55.1 |
| O3A |
PA |
O5' |
C5' |
77.2 |
175.0 |
| O5' |
C5' |
C4' |
O4' |
302.7 |
67.0 |
| O5' |
C5' |
C4' |
H4' |
179.2 |
306.0 |
| H5'2 |
C5' |
O5' |
H5'1 |
120.1 |
120.0 |
| O2A |
PA |
O5' |
O3A |
235.4 |
240.0 |
| PA |
O5' |
C5' |
H5'2 |
102.5 |
59.9 |
| PA |
O5' |
C5' |
H5'1 |
342.3 |
299.9 |
| O5' |
PA |
O1A |
H1 |
121.5 |
299.9 |
| O3' |
C3' |
C4' |
H3' |
124.5 |
122.6 |
| C4' |
C3' |
C2' |
H2' |
145.3 |
97.3 |
| C5' |
C4' |
O4' |
H4' |
237.2 |
238.8 |
| O4' |
C4' |
C3' |
H3' |
83.0 |
116.8 |
| C4' |
O4' |
C1' |
H1' |
113.1 |
78.7 |
| O2' |
C2' |
C3' |
H2' |
124.5 |
123.6 |
| C3' |
C2' |
C1' |
N9 |
104.2 |
155.5 |
| C3' |
C2' |
C1' |
H1' |
224.3 |
278.4 |
| C3' |
C2' |
O2' |
H2' |
236.5 |
236.4 |
| O2' |
C2' |
C1' |
H1' |
343.7 |
36.6 |
| C2' |
C1' |
O4' |
H1' |
238.7 |
241.5 |
| N9 |
C1' |
O4' |
H1' |
123.3 |
122.9 |
| O4' |
C1' |
C2' |
H1' |
122.2 |
118.5 |
| C2' |
C1' |
N9 |
C8 |
292.4 |
267.1 |
| N9 |
C1' |
C2' |
H1' |
239.9 |
237.2 |
| O4' |
C1' |
N9 |
H1' |
236.6 |
237.1 |
| C2' |
C1' |
N9 |
H1' |
119.3 |
122.8 |
| C1' |
N9 |
C8 |
H8 |
359.5 |
0.0 |
| C8 |
N9 |
C1' |
H1' |
173.2 |
144.3 |
| N7 |
C8 |
N9 |
H8 |
180.0 |
179.9 |
| C1' |
N9 |
C8 |
N7 |
179.5 |
180.0 |
| N9 |
C8 |
N7 |
H8 |
180.0 |
180.1 |
| C4 |
N3 |
C2 |
F2 |
180.0 |
180.0 |
| C4 |
N3 |
C2 |
N1 |
0.0 |
0.0 |
| C4 |
C5 |
C6 |
N1 |
359.9 |
359.9 |
| C4 |
C5 |
C6 |
N6 |
180.1 |
180.0 |
| F2 |
C2 |
N3 |
N1 |
180.0 |
179.9 |
| N3 |
C2 |
N1 |
C6 |
359.9 |
359.9 |
| C2 |
N1 |
C6 |
C5 |
0.1 |
0.1 |
| N1 |
C6 |
C5 |
N6 |
179.8 |
179.9 |
| C5 |
C6 |
N6 |
HN62 |
179.8 |
359.9 |
| C5 |
C6 |
N6 |
HN61 |
299.8 |
180.0 |
| N3 |
C2 |
F2 |
N1 |
180.0 |
180.0 |
| F2 |
C2 |
N1 |
C6 |
179.9 |
180.0 |
| N3 |
C2 |
N1 |
F2 |
180.0 |
179.9 |
| C5 |
C6 |
N1 |
C2 |
0.1 |
0.1 |
| C2 |
N1 |
C6 |
N6 |
179.9 |
180.0 |
| C5 |
C6 |
N1 |
N6 |
180.2 |
180.1 |
| N1 |
C6 |
N6 |
HN62 |
360.0 |
180.0 |
| N1 |
C6 |
N6 |
HN61 |
120.0 |
0.0 |
| C5 |
C6 |
N6 |
N1 |
179.8 |
179.9 |
| HN62 |
N6 |
C6 |
HN61 |
239.9 |
180.0 |
| C2' |
C1' |
H1' |
N9 |
243.1 |
237.1 |
| H1' |
C1' |
N9 |
C8 |
173.2 |
144.3 |
| H2' |
C2' |
C1' |
N9 |
347.3 |
37.4 |
| H2' |
C2' |
C1' |
H1' |
107.4 |
160.2 |
| H3' |
C3' |
C2' |
H2' |
27.9 |
338.6 |
| C5' |
C4' |
H4' |
O4' |
123.0 |
121.2 |
| H4' |
C4' |
C3' |
H3' |
203.1 |
236.1 |
| H5'2 |
C5' |
C4' |
O4' |
62.6 |
187.1 |
| H5'2 |
C5' |
C4' |
H4' |
299.1 |
66.1 |
| O5' |
C5' |
H5'2 |
H5'1 |
239.8 |
240.0 |
| H5'1 |
C5' |
C4' |
O4' |
182.8 |
307.1 |
| H5'1 |
C5' |
C4' |
H4' |
59.2 |
186.1 |
| O5' |
C5' |
H5'1 |
H5'2 |
120.2 |
120.0 |
| C6 |
N6 |
HN62 |
HN61 |
120.0 |
180.0 |
| C6 |
N6 |
HN61 |
HN62 |
240.0 |
180.0 |
| HO2' |
O2' |
C2' |
H2' |
303.5 |
56.3 |
| H2 |
O2B |
PB |
O3B |
120.0 |
299.9 |
| H2 |
O2B |
PB |
O3A |
236.6 |
60.0 |
| HO3' |
O3' |
C3' |
H3' |
303.5 |
298.9 |