PDB Chemical Component GX1
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 GX1
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
OP2 |
P |
1.599 |
1.480 |
O5' |
P |
1.594 |
1.609 |
P |
OP1 |
1.482 |
1.610 |
P |
N4 |
1.627 |
1.682 |
S |
C8' |
1.831 |
1.813 |
S |
HS |
1.300 |
1.345 |
C2 |
N1 |
1.401 |
1.363 |
N1 |
C6 |
1.394 |
1.352 |
N1 |
HN1 |
1.000 |
0.970 |
N2 |
C2 |
1.327 |
1.373 |
N3 |
C2 |
1.344 |
1.314 |
N2 |
HN2 |
1.001 |
0.970 |
N2 |
HN2A |
1.000 |
0.970 |
N3 |
C4 |
1.344 |
1.338 |
N9 |
C4 |
1.333 |
1.368 |
C4 |
C5 |
1.393 |
1.400 |
N4 |
C7' |
1.474 |
1.468 |
N4 |
HN4 |
1.000 |
1.009 |
C5 |
C6 |
1.392 |
1.414 |
C5 |
N7 |
1.330 |
1.355 |
C6 |
O6 |
1.230 |
1.219 |
C8 |
N7 |
1.333 |
1.301 |
N9 |
C8 |
1.336 |
1.365 |
C8 |
H8 |
1.080 |
1.080 |
C1' |
N9 |
1.494 |
1.465 |
C2' |
C1' |
1.541 |
1.545 |
C1' |
O4' |
1.461 |
1.444 |
C1' |
H1' |
1.100 |
1.089 |
C2' |
C3' |
1.524 |
1.546 |
C2' |
H2' |
1.100 |
1.090 |
C2' |
H2'A |
1.099 |
1.090 |
O3' |
C3' |
1.428 |
1.428 |
C3' |
C4' |
1.531 |
1.545 |
C3' |
H3' |
1.100 |
1.090 |
O3' |
HO3' |
0.950 |
0.966 |
O4' |
C4' |
1.436 |
1.445 |
C4' |
C5' |
1.524 |
1.530 |
C4' |
H4' |
1.100 |
1.090 |
C5' |
O5' |
1.406 |
1.429 |
C5' |
H5' |
1.099 |
1.090 |
C5' |
H5'A |
1.100 |
1.090 |
C8' |
C7' |
1.529 |
1.530 |
C7' |
H7' |
1.100 |
1.090 |
C7' |
H7'A |
1.101 |
1.090 |
C8' |
H8' |
1.100 |
1.091 |
C8' |
H8'A |
1.100 |
1.090 |
OP1 |
HOP1 |
0.950 |
0.966 |
Bond Angles for GX1
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
OP2 |
P |
OP1 |
107.4 |
109.5 |
OP2 |
P |
N4 |
119.3 |
109.5 |
O5' |
P |
OP1 |
107.5 |
109.5 |
N4 |
P |
OP1 |
110.4 |
109.5 |
P |
OP1 |
HOP1 |
109.5 |
114.0 |
P |
N4 |
C7' |
121.7 |
111.0 |
P |
N4 |
HN4 |
105.6 |
111.0 |
C8' |
S |
HS |
102.0 |
103.0 |
S |
C8' |
C7' |
113.5 |
109.5 |
S |
C8' |
H8' |
108.2 |
109.5 |
S |
C8' |
H8'A |
108.2 |
109.5 |
C2 |
N1 |
C6 |
119.1 |
120.3 |
C2 |
N1 |
HN1 |
120.4 |
119.9 |
C6 |
N1 |
HN1 |
120.5 |
119.8 |
N1 |
C6 |
C5 |
118.6 |
118.3 |
N1 |
C6 |
O6 |
120.3 |
120.8 |
HN2 |
N2 |
HN2A |
120.0 |
119.9 |
N3 |
C4 |
C5 |
120.3 |
119.7 |
C4 |
C5 |
C6 |
120.1 |
118.6 |
C4 |
C5 |
N7 |
107.3 |
107.3 |
C7' |
N4 |
HN4 |
105.6 |
111.0 |
N4 |
C7' |
H7' |
109.2 |
109.5 |
N4 |
C7' |
H7'A |
109.2 |
109.5 |
C6 |
C5 |
N7 |
132.6 |
134.1 |
C5 |
C6 |
O6 |
121.1 |
120.9 |
N9 |
C8 |
H8 |
125.1 |
125.1 |
C2' |
C1' |
O4' |
105.9 |
104.8 |
C2' |
C1' |
H1' |
114.1 |
110.5 |
O4' |
C1' |
H1' |
108.9 |
110.4 |
C1' |
O4' |
C4' |
105.8 |
105.3 |
C3' |
C2' |
H2' |
111.2 |
110.5 |
C3' |
C2' |
H2'A |
111.2 |
110.5 |
C2' |
C3' |
C4' |
102.7 |
104.0 |
C2' |
C3' |
H3' |
114.6 |
110.5 |
H2' |
C2' |
H2'A |
107.7 |
110.5 |
O3' |
C3' |
C4' |
109.6 |
110.5 |
O3' |
C3' |
H3' |
108.3 |
110.6 |
C4' |
C3' |
H3' |
113.3 |
110.5 |
C3' |
C4' |
C5' |
113.9 |
110.4 |
C3' |
C4' |
H4' |
109.5 |
110.4 |
O4' |
C4' |
C5' |
104.3 |
110.4 |
O4' |
C4' |
H4' |
118.3 |
110.4 |
C5' |
C4' |
H4' |
108.1 |
110.3 |
C4' |
C5' |
O5' |
114.0 |
109.5 |
C4' |
C5' |
H5' |
108.0 |
109.5 |
C4' |
C5' |
H5'A |
108.0 |
109.5 |
O5' |
C5' |
H5' |
108.0 |
109.5 |
O5' |
C5' |
H5'A |
108.0 |
109.5 |
H5' |
C5' |
H5'A |
110.9 |
109.4 |
C8' |
C7' |
H7' |
109.3 |
109.4 |
C8' |
C7' |
H7'A |
109.2 |
109.4 |
H7' |
C7' |
H7'A |
109.7 |
109.4 |
H8' |
C8' |
H8'A |
110.8 |
109.5 |
Torsion Angles for GX1
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
O5' |
P |
OP2 |
OP1 |
113.0 |
120.0 |
N4 |
P |
OP2 |
OP1 |
233.4 |
240.0 |
OP2 |
P |
OP1 |
HOP1 |
360.0 |
180.0 |
OP2 |
P |
N4 |
C7' |
127.1 |
180.0 |
OP2 |
P |
N4 |
HN4 |
247.0 |
303.9 |
OP2 |
P |
O5' |
OP1 |
247.1 |
240.0 |
N4 |
P |
O5' |
OP1 |
119.9 |
120.0 |
O5' |
P |
OP1 |
HOP1 |
250.7 |
60.0 |
O5' |
P |
N4 |
C7' |
243.9 |
300.0 |
O5' |
P |
N4 |
HN4 |
3.9 |
63.9 |
OP2 |
P |
OP1 |
N4 |
228.3 |
240.0 |
OP1 |
P |
N4 |
C7' |
1.9 |
60.0 |
OP1 |
P |
N4 |
HN4 |
121.9 |
183.9 |
OP2 |
P |
N4 |
OP1 |
125.1 |
120.0 |
O5' |
P |
N4 |
OP1 |
241.9 |
240.0 |
N4 |
P |
OP1 |
HOP1 |
131.6 |
300.0 |
C7' |
N4 |
P |
HN4 |
240.0 |
236.1 |
P |
N4 |
C7' |
H7' |
194.7 |
255.0 |
P |
N4 |
C7' |
H7'A |
314.7 |
15.0 |
S |
C8' |
C7' |
H7' |
271.6 |
59.9 |
S |
C8' |
C7' |
H7'A |
151.6 |
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 |
C6 |
N1 |
C2 |
HN1 |
180.0 |
180.2 |
C2 |
N1 |
C6 |
C5 |
359.9 |
0.0 |
C2 |
N1 |
C6 |
O6 |
180.0 |
179.7 |
C2 |
N1 |
C6 |
HN1 |
180.0 |
179.8 |
C4 |
C5 |
C6 |
N1 |
0.1 |
359.9 |
N1 |
C6 |
C5 |
N7 |
180.1 |
180.0 |
C5 |
C6 |
N1 |
O6 |
179.9 |
180.4 |
C2 |
N1 |
HN1 |
C6 |
180.0 |
180.2 |
HN1 |
N1 |
C6 |
C5 |
179.9 |
180.3 |
HN1 |
N1 |
C6 |
O6 |
360.0 |
359.9 |
N2 |
C2 |
N1 |
C6 |
180.1 |
180.0 |
N2 |
C2 |
N1 |
HN1 |
0.1 |
359.7 |
N3 |
C2 |
N1 |
C6 |
360.0 |
360.0 |
N3 |
C2 |
N1 |
HN1 |
180.0 |
179.7 |
N3 |
C4 |
C5 |
C6 |
360.0 |
0.1 |
N3 |
C4 |
C5 |
N7 |
180.0 |
180.0 |
N1 |
C6 |
C5 |
C4 |
0.1 |
359.9 |
C6 |
C5 |
C4 |
N7 |
180.0 |
180.1 |
C4 |
C5 |
C6 |
O6 |
180.0 |
180.3 |
C7' |
N4 |
P |
OP1 |
1.9 |
60.0 |
P |
N4 |
C7' |
HN4 |
120.0 |
124.0 |
S |
C8' |
C7' |
N4 |
31.6 |
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 |
121.9 |
183.9 |
P |
N4 |
HN4 |
C7' |
229.9 |
236.0 |
HN4 |
N4 |
C7' |
H7' |
74.7 |
131.0 |
HN4 |
N4 |
C7' |
H7'A |
194.7 |
251.0 |
C5 |
C6 |
N1 |
HN1 |
179.9 |
180.3 |
N1 |
C6 |
C5 |
O6 |
180.1 |
179.6 |
C4 |
C5 |
C6 |
N7 |
180.0 |
179.9 |
C4 |
C5 |
N7 |
C6 |
180.0 |
180.1 |
N7 |
C5 |
C6 |
O6 |
0.0 |
0.4 |
O6 |
C6 |
N1 |
HN1 |
360.0 |
359.9 |
N1 |
C6 |
O6 |
C5 |
179.9 |
180.4 |
O6 |
C6 |
C5 |
N7 |
0.0 |
0.4 |
C1' |
N9 |
C8 |
H8 |
359.6 |
0.0 |
O4' |
C1' |
C2' |
H1' |
119.8 |
118.9 |
C2' |
C1' |
O4' |
C4' |
29.2 |
319.5 |
C2' |
C1' |
O4' |
H1' |
236.9 |
241.1 |
C1' |
O4' |
C4' |
C5' |
76.1 |
159.3 |
C1' |
O4' |
C4' |
H4' |
196.2 |
281.6 |
C2' |
C1' |
H1' |
O4' |
118.0 |
115.4 |
H1' |
C1' |
O4' |
C4' |
152.2 |
78.4 |
C3' |
C2' |
C1' |
O4' |
356.6 |
24.0 |
C3' |
C2' |
C1' |
H1' |
236.8 |
265.1 |
H2' |
C2' |
C3' |
H2'A |
120.0 |
122.7 |
O3' |
C3' |
C2' |
C4' |
115.8 |
118.6 |
O3' |
C3' |
C2' |
H3' |
239.1 |
237.2 |
C4' |
C3' |
C2' |
H3' |
123.3 |
118.6 |
C2' |
C3' |
C4' |
C5' |
287.3 |
217.2 |
C2' |
C3' |
C4' |
H4' |
166.1 |
95.0 |
H2' |
C2' |
C1' |
O4' |
116.6 |
142.6 |
H2' |
C2' |
C1' |
H1' |
356.8 |
23.7 |
C3' |
C2' |
H2' |
H2'A |
237.9 |
237.4 |
H2' |
C2' |
C3' |
C4' |
218.6 |
241.3 |
H2' |
C2' |
C3' |
H3' |
95.3 |
122.8 |
H2'A |
C2' |
C1' |
O4' |
236.6 |
265.3 |
H2'A |
C2' |
C1' |
H1' |
116.8 |
146.5 |
C3' |
C2' |
H2'A |
H2' |
122.1 |
122.6 |
H2'A |
C2' |
C3' |
C4' |
98.6 |
118.7 |
H2'A |
C2' |
C3' |
H3' |
335.3 |
0.1 |
O3' |
C3' |
C2' |
H2' |
334.5 |
360.0 |
O3' |
C3' |
C2' |
H2'A |
214.4 |
237.3 |
C2' |
C3' |
O3' |
C4' |
248.7 |
245.4 |
C2' |
C3' |
O3' |
H3' |
124.7 |
122.7 |
C4' |
C3' |
O3' |
H3' |
236.0 |
237.3 |
O3' |
C3' |
C4' |
C5' |
172.5 |
98.6 |
O3' |
C3' |
C4' |
H4' |
51.4 |
336.3 |
C1' |
O4' |
C4' |
C3' |
317.0 |
40.5 |
C4' |
C3' |
C2' |
H2' |
218.6 |
241.3 |
C4' |
C3' |
C2' |
H2'A |
98.6 |
118.7 |
C2' |
C3' |
C4' |
H3' |
235.8 |
241.4 |
O3' |
C3' |
C4' |
H3' |
121.0 |
122.8 |
O4' |
C4' |
C3' |
C5' |
112.2 |
118.8 |
O4' |
C4' |
C3' |
H4' |
233.4 |
241.1 |
C5' |
C4' |
C3' |
H4' |
121.2 |
122.2 |
C3' |
C4' |
C5' |
O5' |
285.8 |
185.0 |
C3' |
C4' |
C5' |
H5' |
45.8 |
305.0 |
C3' |
C4' |
C5' |
H5'A |
165.8 |
65.0 |
H3' |
C3' |
C2' |
H2' |
95.3 |
122.8 |
H3' |
C3' |
C2' |
H2'A |
335.3 |
0.1 |
C2' |
C3' |
H3' |
C4' |
117.4 |
114.6 |
O3' |
C3' |
H3' |
C4' |
238.2 |
237.3 |
H3' |
C3' |
C4' |
C5' |
51.5 |
335.8 |
H3' |
C3' |
C4' |
H4' |
290.3 |
213.6 |
HO3' |
O3' |
C3' |
C4' |
291.2 |
176.1 |
HO3' |
O3' |
C3' |
H3' |
55.3 |
298.8 |
C4' |
O4' |
C1' |
H1' |
152.2 |
78.4 |
O4' |
C4' |
C3' |
H3' |
163.7 |
94.6 |
C3' |
C4' |
O4' |
C5' |
240.9 |
241.2 |
C3' |
C4' |
O4' |
H4' |
120.8 |
118.9 |
C5' |
C4' |
O4' |
H4' |
239.9 |
237.7 |
O4' |
C4' |
C5' |
O5' |
174.4 |
69.6 |
O4' |
C4' |
C5' |
H5' |
294.4 |
189.6 |
O4' |
C4' |
C5' |
H5'A |
54.4 |
309.6 |
C5' |
C4' |
C3' |
H3' |
51.5 |
335.8 |
C3' |
C4' |
C5' |
H4' |
238.1 |
237.7 |
O4' |
C4' |
C5' |
H4' |
126.7 |
122.3 |
O5' |
C5' |
C4' |
H5' |
240.0 |
240.0 |
O5' |
C5' |
C4' |
H5'A |
120.0 |
120.0 |
H5' |
C5' |
C4' |
H5'A |
240.0 |
240.0 |
H4' |
C4' |
C3' |
H3' |
290.3 |
213.6 |
C3' |
C4' |
H4' |
C5' |
124.6 |
122.3 |
O4' |
C4' |
H4' |
C5' |
241.9 |
237.7 |
H4' |
C4' |
C5' |
O5' |
47.7 |
307.3 |
H4' |
C4' |
C5' |
H5' |
167.7 |
67.3 |
H4' |
C4' |
C5' |
H5'A |
287.7 |
187.3 |
C5' |
O5' |
P |
OP1 |
56.3 |
170.0 |
O5' |
C5' |
C4' |
H4' |
47.7 |
307.3 |
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' |
167.7 |
67.3 |
C4' |
C5' |
H5' |
O5' |
236.3 |
240.0 |
C4' |
C5' |
H5' |
H5'A |
118.1 |
120.0 |
O5' |
C5' |
H5' |
H5'A |
241.9 |
240.0 |
H5'A |
C5' |
C4' |
H4' |
287.7 |
187.3 |
C4' |
C5' |
H5'A |
O5' |
123.7 |
120.0 |
C4' |
C5' |
H5'A |
H5' |
241.9 |
240.0 |
O5' |
C5' |
H5'A |
H5' |
118.1 |
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 |
239.9 |
C8' |
C7' |
N4 |
HN4 |
314.7 |
11.0 |
N4 |
C7' |
C8' |
H7' |
120.0 |
120.1 |
N4 |
C7' |
C8' |
H7'A |
240.0 |
240.0 |
H7' |
C7' |
C8' |
H7'A |
120.0 |
119.9 |
H7' |
C7' |
N4 |
HN4 |
74.7 |
131.0 |
N4 |
C7' |
H7' |
H7'A |
119.7 |
120.0 |
C8' |
C7' |
H7' |
H7'A |
240.3 |
240.1 |
H7'A |
C7' |
N4 |
HN4 |
194.7 |
251.0 |
N4 |
C7' |
H7'A |
H7' |
240.3 |
240.0 |
C8' |
C7' |
H7'A |
H7' |
119.8 |
119.9 |
H8' |
C8' |
S |
HS |
300.0 |
300.0 |
S |
C8' |
H8' |
C7' |
236.7 |
240.0 |
S |
C8' |
H8' |
H8'A |
118.4 |
120.1 |
H8' |
C8' |
C7' |
H7' |
151.6 |
299.9 |
H8' |
C8' |
C7' |
H7'A |
31.6 |
180.0 |
H8'A |
C8' |
S |
HS |
60.0 |
60.0 |
S |
C8' |
H8'A |
C7' |
123.3 |
120.1 |
S |
C8' |
H8'A |
H8' |
241.6 |
240.0 |
H8'A |
C8' |
C7' |
H7' |
31.6 |
180.0 |
H8'A |
C8' |
C7' |
H7'A |
271.6 |
60.1 |