PDB Chemical Component GNG
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 GNG
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O5' |
C5' |
1.430 |
1.429 |
| O5' |
H5' |
0.949 |
0.967 |
| C5' |
C4' |
1.516 |
1.529 |
| C5' |
H5'1 |
1.115 |
1.089 |
| C5' |
H5'2 |
1.114 |
1.089 |
| C4' |
O4' |
1.454 |
1.445 |
| C4' |
C3' |
1.527 |
1.549 |
| C4' |
H4' |
1.116 |
1.090 |
| O4' |
C1' |
1.431 |
1.437 |
| C1' |
N9 |
1.464 |
1.465 |
| C1' |
C2' |
1.519 |
1.539 |
| C1' |
H1' |
1.115 |
1.091 |
| N9 |
C8 |
1.375 |
1.363 |
| N9 |
C4 |
1.383 |
1.360 |
| C8 |
N7 |
1.305 |
1.302 |
| C8 |
H8 |
1.102 |
1.079 |
| N7 |
C5 |
1.383 |
1.353 |
| C5 |
C4 |
1.386 |
1.388 |
| C5 |
C6 |
1.416 |
1.466 |
| C4 |
N3 |
1.347 |
1.371 |
| N3 |
C2 |
1.333 |
1.359 |
| N3 |
HN3 |
1.021 |
0.969 |
| C2 |
N1 |
1.377 |
1.315 |
| C2 |
N2 |
1.344 |
1.369 |
| N1 |
C6 |
1.390 |
1.341 |
| C6 |
O6 |
1.237 |
1.222 |
| N2 |
HN21 |
1.020 |
0.970 |
| N2 |
HN22 |
1.021 |
0.970 |
| C2' |
C3' |
1.515 |
1.549 |
| C2' |
H2'1 |
1.115 |
1.090 |
| C2' |
H2'2 |
1.114 |
1.090 |
| C3' |
O3' |
1.429 |
1.429 |
| C3' |
H3' |
1.115 |
1.091 |
| O3' |
H1 |
0.950 |
0.966 |
Bond Angles for GNG
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C5' |
O5' |
H5' |
111.0 |
106.8 |
| O5' |
C5' |
C4' |
111.0 |
109.4 |
| O5' |
C5' |
H5'1 |
111.7 |
109.4 |
| O5' |
C5' |
H5'2 |
111.7 |
109.5 |
| C4' |
C5' |
H5'1 |
111.6 |
109.5 |
| C4' |
C5' |
H5'2 |
111.6 |
109.4 |
| C5' |
C4' |
O4' |
110.8 |
110.8 |
| C5' |
C4' |
C3' |
112.9 |
110.6 |
| C5' |
C4' |
H4' |
105.0 |
110.6 |
| H5'1 |
C5' |
H5'2 |
98.8 |
109.6 |
| O4' |
C4' |
C3' |
105.6 |
103.6 |
| O4' |
C4' |
H4' |
112.4 |
110.5 |
| C4' |
O4' |
C1' |
111.2 |
106.9 |
| C3' |
C4' |
H4' |
110.3 |
110.5 |
| C4' |
C3' |
C2' |
104.0 |
102.1 |
| C4' |
C3' |
O3' |
112.2 |
111.0 |
| C4' |
C3' |
H3' |
111.5 |
110.9 |
| O4' |
C1' |
N9 |
107.7 |
109.9 |
| O4' |
C1' |
C2' |
106.0 |
107.4 |
| O4' |
C1' |
H1' |
113.2 |
109.9 |
| N9 |
C1' |
C2' |
110.3 |
109.9 |
| N9 |
C1' |
H1' |
109.0 |
109.8 |
| C1' |
N9 |
C8 |
125.8 |
126.2 |
| C1' |
N9 |
C4 |
127.8 |
126.3 |
| C2' |
C1' |
H1' |
110.6 |
109.9 |
| C1' |
C2' |
C3' |
104.0 |
104.2 |
| C1' |
C2' |
H2'1 |
114.3 |
110.5 |
| C1' |
C2' |
H2'2 |
114.3 |
110.5 |
| C8 |
N9 |
C4 |
106.4 |
107.5 |
| N9 |
C8 |
N7 |
113.3 |
109.5 |
| N9 |
C8 |
H8 |
125.6 |
125.3 |
| N9 |
C4 |
C5 |
104.8 |
106.4 |
| N9 |
C4 |
N3 |
126.6 |
134.7 |
| N7 |
C8 |
H8 |
121.1 |
125.2 |
| C8 |
N7 |
C5 |
104.4 |
109.1 |
| N7 |
C5 |
C4 |
111.1 |
107.4 |
| N7 |
C5 |
C6 |
129.8 |
134.5 |
| C4 |
C5 |
C6 |
119.1 |
118.2 |
| C5 |
C4 |
N3 |
128.5 |
118.9 |
| C5 |
C6 |
N1 |
111.7 |
118.6 |
| C5 |
C6 |
O6 |
128.2 |
120.7 |
| C4 |
N3 |
C2 |
111.7 |
120.5 |
| C4 |
N3 |
HN3 |
111.4 |
119.8 |
| C2 |
N3 |
HN3 |
111.3 |
119.7 |
| N3 |
C2 |
N1 |
124.0 |
122.5 |
| N3 |
C2 |
N2 |
120.3 |
118.7 |
| N1 |
C2 |
N2 |
115.7 |
118.8 |
| C2 |
N1 |
C6 |
124.9 |
121.4 |
| C2 |
N2 |
HN21 |
120.4 |
120.0 |
| C2 |
N2 |
HN22 |
108.4 |
120.0 |
| N1 |
C6 |
O6 |
120.1 |
120.7 |
| HN21 |
N2 |
HN22 |
108.3 |
120.0 |
| C3' |
C2' |
H2'1 |
114.3 |
110.5 |
| C3' |
C2' |
H2'2 |
114.3 |
110.4 |
| C2' |
C3' |
O3' |
109.8 |
110.9 |
| C2' |
C3' |
H3' |
113.8 |
110.9 |
| H2'1 |
C2' |
H2'2 |
96.2 |
110.6 |
| O3' |
C3' |
H3' |
105.7 |
110.8 |
| C3' |
O3' |
H1 |
112.2 |
106.8 |
Torsion Angles for GNG
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C4' |
C5' |
O5' |
H5'1 |
234.8 |
119.9 |
| C4' |
C5' |
O5' |
H5'2 |
125.2 |
240.1 |
| O5' |
C5' |
C4' |
O4' |
60.4 |
65.8 |
| O5' |
C5' |
C4' |
C3' |
178.6 |
180.0 |
| O5' |
C5' |
C4' |
H4' |
298.7 |
302.8 |
| H5'1 |
C5' |
O5' |
H5'2 |
250.4 |
120.1 |
| H5' |
O5' |
C5' |
C4' |
180.0 |
180.0 |
| H5' |
O5' |
C5' |
H5'1 |
305.2 |
60.1 |
| H5' |
O5' |
C5' |
H5'2 |
54.8 |
300.0 |
| C4' |
C5' |
O5' |
H5' |
180.0 |
180.0 |
| O5' |
C5' |
C4' |
H5'1 |
125.3 |
240.1 |
| O5' |
C5' |
C4' |
H5'2 |
234.7 |
119.9 |
| H5'1 |
C5' |
C4' |
H5'2 |
109.5 |
239.9 |
| O4' |
C4' |
C5' |
C3' |
241.8 |
245.7 |
| O4' |
C4' |
C5' |
H4' |
121.6 |
122.9 |
| C5' |
C4' |
O4' |
C1' |
115.9 |
158.5 |
| C3' |
C4' |
C5' |
H4' |
239.8 |
237.2 |
| C5' |
C4' |
C3' |
C2' |
261.9 |
204.3 |
| C5' |
C4' |
C3' |
O3' |
143.3 |
86.1 |
| C5' |
C4' |
C3' |
H3' |
24.9 |
322.5 |
| H5'1 |
C5' |
O5' |
H5' |
305.2 |
60.1 |
| O5' |
C5' |
H5'1 |
C4' |
235.1 |
119.9 |
| O5' |
C5' |
H5'1 |
H5'2 |
117.6 |
240.0 |
| C4' |
C5' |
H5'1 |
H5'2 |
242.5 |
120.0 |
| H5'1 |
C5' |
C4' |
O4' |
295.1 |
185.7 |
| H5'1 |
C5' |
C4' |
C3' |
53.3 |
300.0 |
| H5'1 |
C5' |
C4' |
H4' |
173.5 |
62.7 |
| H5'2 |
C5' |
O5' |
H5' |
54.8 |
300.0 |
| O5' |
C5' |
H5'2 |
C4' |
124.9 |
240.1 |
| O5' |
C5' |
H5'2 |
H5'1 |
242.4 |
120.0 |
| C4' |
C5' |
H5'2 |
H5'1 |
117.5 |
239.9 |
| H5'2 |
C5' |
C4' |
O4' |
185.6 |
305.8 |
| H5'2 |
C5' |
C4' |
C3' |
303.8 |
60.1 |
| H5'2 |
C5' |
C4' |
H4' |
64.0 |
182.9 |
| O4' |
C4' |
C5' |
H5'1 |
295.1 |
185.7 |
| O4' |
C4' |
C5' |
H5'2 |
185.6 |
305.8 |
| C5' |
C4' |
O4' |
C3' |
122.6 |
118.6 |
| C5' |
C4' |
O4' |
H4' |
242.8 |
237.0 |
| C3' |
C4' |
O4' |
H4' |
120.2 |
118.4 |
| O4' |
C4' |
C3' |
C2' |
23.2 |
323.1 |
| O4' |
C4' |
C3' |
O3' |
264.5 |
204.9 |
| O4' |
C4' |
C3' |
H3' |
146.1 |
81.3 |
| C4' |
O4' |
C1' |
N9 |
229.4 |
214.2 |
| C4' |
O4' |
C1' |
C2' |
347.4 |
333.7 |
| C4' |
O4' |
C1' |
H1' |
108.8 |
93.2 |
| C3' |
C4' |
C5' |
H5'1 |
53.3 |
300.0 |
| C3' |
C4' |
C5' |
H5'2 |
303.8 |
60.1 |
| C5' |
C4' |
C3' |
O4' |
238.8 |
241.2 |
| C5' |
C4' |
C3' |
H4' |
117.1 |
122.8 |
| O4' |
C4' |
C3' |
H4' |
238.3 |
241.6 |
| C3' |
C4' |
O4' |
C1' |
353.3 |
39.8 |
| C1' |
C2' |
C3' |
C4' |
329.7 |
20.9 |
| C4' |
C3' |
C2' |
H2'1 |
204.5 |
139.6 |
| C4' |
C3' |
C2' |
H2'2 |
95.0 |
262.2 |
| C2' |
C3' |
C4' |
O3' |
118.6 |
118.2 |
| C2' |
C3' |
C4' |
H3' |
237.0 |
241.8 |
| O3' |
C3' |
C4' |
H3' |
118.4 |
123.6 |
| C4' |
C3' |
O3' |
H1 |
180.0 |
174.2 |
| H4' |
C4' |
C5' |
H5'1 |
173.5 |
62.7 |
| H4' |
C4' |
C5' |
H5'2 |
64.0 |
182.9 |
| C5' |
C4' |
H4' |
O4' |
120.6 |
123.1 |
| C5' |
C4' |
H4' |
C3' |
238.1 |
237.2 |
| O4' |
C4' |
H4' |
C3' |
117.5 |
114.1 |
| H4' |
C4' |
O4' |
C1' |
233.0 |
281.4 |
| H4' |
C4' |
C3' |
C2' |
144.8 |
81.5 |
| H4' |
C4' |
C3' |
O3' |
26.2 |
323.3 |
| H4' |
C4' |
C3' |
H3' |
267.8 |
199.7 |
| C1' |
O4' |
C4' |
C3' |
353.3 |
39.8 |
| C1' |
O4' |
C4' |
H4' |
233.0 |
281.4 |
| N9 |
C1' |
O4' |
C2' |
241.9 |
240.5 |
| N9 |
C1' |
O4' |
H1' |
120.5 |
121.0 |
| O4' |
C1' |
N9 |
C8 |
35.3 |
28.2 |
| O4' |
C1' |
N9 |
C4 |
212.7 |
208.3 |
| C2' |
C1' |
O4' |
H1' |
238.6 |
240.5 |
| O4' |
C1' |
C2' |
C3' |
26.7 |
2.0 |
| O4' |
C1' |
C2' |
H2'1 |
152.0 |
243.3 |
| O4' |
C1' |
C2' |
H2'2 |
261.4 |
120.6 |
| O4' |
C1' |
N9 |
C2' |
115.2 |
118.0 |
| O4' |
C1' |
N9 |
H1' |
236.9 |
239.0 |
| C2' |
C1' |
N9 |
H1' |
121.6 |
121.0 |
| N9 |
C1' |
C2' |
C3' |
143.1 |
121.5 |
| N9 |
C1' |
C2' |
H2'1 |
268.3 |
2.8 |
| N9 |
C1' |
C2' |
H2'2 |
17.8 |
240.1 |
| C8 |
N9 |
C1' |
C4 |
182.6 |
179.9 |
| C1' |
N9 |
C8 |
N7 |
176.2 |
180.1 |
| C1' |
N9 |
C8 |
H8 |
356.3 |
0.1 |
| C1' |
N9 |
C4 |
C5 |
183.9 |
179.9 |
| C1' |
N9 |
C4 |
N3 |
2.7 |
0.3 |
| C4' |
C3' |
C2' |
C1' |
329.7 |
20.9 |
| O4' |
C1' |
C2' |
N9 |
243.7 |
240.5 |
| O4' |
C1' |
C2' |
H1' |
123.0 |
119.5 |
| N9 |
C1' |
C2' |
H1' |
239.3 |
239.1 |
| C2' |
C1' |
N9 |
C8 |
280.1 |
270.2 |
| C2' |
C1' |
N9 |
C4 |
97.5 |
90.3 |
| C3' |
C2' |
C1' |
H2'1 |
234.8 |
118.7 |
| C3' |
C2' |
C1' |
H2'2 |
125.3 |
241.4 |
| C1' |
C2' |
C3' |
O3' |
90.0 |
139.2 |
| C1' |
C2' |
C3' |
H3' |
208.3 |
262.7 |
| H2'1 |
C2' |
C1' |
H2'2 |
250.5 |
122.7 |
| O4' |
C1' |
H1' |
N9 |
119.8 |
121.0 |
| O4' |
C1' |
H1' |
C2' |
241.3 |
242.0 |
| N9 |
C1' |
H1' |
C2' |
121.5 |
121.0 |
| H1' |
C1' |
N9 |
C8 |
158.4 |
149.2 |
| H1' |
C1' |
N9 |
C4 |
335.8 |
329.3 |
| H1' |
C1' |
C2' |
C3' |
263.7 |
242.4 |
| H1' |
C1' |
C2' |
H2'1 |
29.0 |
123.8 |
| H1' |
C1' |
C2' |
H2'2 |
138.4 |
1.0 |
| C8 |
N9 |
C1' |
C2' |
280.1 |
270.2 |
| C8 |
N9 |
C1' |
H1' |
158.4 |
149.2 |
| C1' |
N9 |
C8 |
C4 |
177.9 |
180.1 |
| C8 |
N9 |
C4 |
C5 |
1.8 |
360.0 |
| C8 |
N9 |
C4 |
N3 |
180.5 |
180.3 |
| N7 |
C8 |
N9 |
H8 |
180.0 |
180.0 |
| N9 |
C8 |
N7 |
C5 |
0.7 |
0.0 |
| C4 |
N9 |
C1' |
C2' |
97.5 |
90.3 |
| C4 |
N9 |
C1' |
H1' |
335.8 |
329.3 |
| C1' |
N9 |
C4 |
C8 |
182.2 |
179.9 |
| C4 |
N9 |
C8 |
N7 |
358.4 |
0.0 |
| C4 |
N9 |
C8 |
H8 |
178.4 |
180.0 |
| N7 |
C5 |
C4 |
N9 |
358.6 |
0.0 |
| N9 |
C4 |
C5 |
C6 |
178.1 |
179.9 |
| C5 |
C4 |
N9 |
N3 |
181.3 |
179.6 |
| N9 |
C4 |
N3 |
C2 |
181.7 |
180.2 |
| N9 |
C4 |
N3 |
HN3 |
56.4 |
360.0 |
| N7 |
C8 |
N9 |
C4 |
358.4 |
0.0 |
| N9 |
C8 |
N7 |
H8 |
180.0 |
180.0 |
| C8 |
N7 |
C5 |
C4 |
0.5 |
360.0 |
| C8 |
N7 |
C5 |
C6 |
181.0 |
180.1 |
| H8 |
C8 |
N9 |
C4 |
178.4 |
180.0 |
| N9 |
C8 |
H8 |
N7 |
180.0 |
180.0 |
| H8 |
C8 |
N7 |
C5 |
180.7 |
180.1 |
| N9 |
C4 |
C5 |
N7 |
358.6 |
0.0 |
| C5 |
N7 |
C8 |
H8 |
180.7 |
180.1 |
| C4 |
C5 |
N7 |
C6 |
179.5 |
179.9 |
| N7 |
C5 |
C4 |
N3 |
179.9 |
179.7 |
| N7 |
C5 |
C6 |
N1 |
180.4 |
179.9 |
| N7 |
C5 |
C6 |
O6 |
1.4 |
359.9 |
| N9 |
C4 |
C5 |
N3 |
178.7 |
180.3 |
| N7 |
C5 |
C4 |
C6 |
180.5 |
180.1 |
| C4 |
C5 |
C6 |
N1 |
1.0 |
0.1 |
| C4 |
C5 |
C6 |
O6 |
182.0 |
180.0 |
| C5 |
C4 |
N3 |
C2 |
0.1 |
0.6 |
| C5 |
C4 |
N3 |
HN3 |
234.9 |
180.4 |
| N7 |
C5 |
C6 |
C4 |
179.4 |
179.8 |
| C6 |
C5 |
C4 |
N3 |
359.4 |
359.6 |
| C2 |
N1 |
C6 |
C5 |
359.0 |
360.0 |
| N1 |
C6 |
C5 |
O6 |
179.0 |
180.1 |
| N9 |
C4 |
N3 |
C5 |
181.6 |
179.6 |
| N3 |
C4 |
C5 |
C6 |
359.4 |
359.6 |
| C2 |
N3 |
C4 |
HN3 |
125.3 |
180.2 |
| C4 |
N3 |
C2 |
N1 |
359.9 |
359.5 |
| C4 |
N3 |
C2 |
N2 |
179.6 |
179.7 |
| C4 |
N3 |
C2 |
HN3 |
234.7 |
179.8 |
| N1 |
C2 |
N3 |
N2 |
180.3 |
179.8 |
| N3 |
C2 |
N1 |
C6 |
0.6 |
0.2 |
| N3 |
C2 |
N2 |
HN21 |
180.0 |
179.8 |
| N3 |
C2 |
N2 |
HN22 |
54.7 |
359.4 |
| C4 |
N3 |
HN3 |
C2 |
125.5 |
180.2 |
| HN3 |
N3 |
C2 |
N1 |
125.2 |
179.7 |
| HN3 |
N3 |
C2 |
N2 |
304.9 |
359.9 |
| C5 |
C6 |
N1 |
C2 |
359.0 |
360.0 |
| N1 |
C2 |
N3 |
HN3 |
125.2 |
179.7 |
| N3 |
C2 |
N1 |
N2 |
179.7 |
180.2 |
| N1 |
C2 |
N2 |
HN21 |
359.7 |
0.0 |
| N1 |
C2 |
N2 |
HN22 |
234.4 |
179.6 |
| C2 |
N1 |
C6 |
O6 |
178.1 |
180.1 |
| N2 |
C2 |
N3 |
HN3 |
304.9 |
359.9 |
| N3 |
C2 |
N2 |
N1 |
180.3 |
179.8 |
| N2 |
C2 |
N1 |
C6 |
180.9 |
180.0 |
| HN21 |
N2 |
C2 |
HN22 |
125.2 |
180.4 |
| C5 |
C6 |
N1 |
O6 |
180.9 |
179.9 |
| C6 |
N1 |
C2 |
N2 |
180.9 |
180.0 |
| C5 |
C6 |
O6 |
N1 |
178.9 |
180.1 |
| C2 |
N2 |
HN21 |
HN22 |
234.7 |
179.6 |
| C2 |
N2 |
HN22 |
HN21 |
132.1 |
180.4 |
| C2' |
C3' |
C4' |
H4' |
144.8 |
81.5 |
| C4' |
C3' |
C2' |
O3' |
239.7 |
241.7 |
| C4' |
C3' |
C2' |
H3' |
121.4 |
118.2 |
| C3' |
C2' |
C1' |
H1' |
263.7 |
242.4 |
| C1' |
C2' |
C3' |
H2'1 |
125.2 |
241.3 |
| C1' |
C2' |
C3' |
H2'2 |
234.7 |
118.7 |
| H2'1 |
C2' |
C3' |
H2'2 |
109.5 |
237.4 |
| O3' |
C3' |
C2' |
H3' |
241.7 |
236.5 |
| C2' |
C3' |
O3' |
H1 |
64.8 |
61.5 |
| H2'1 |
C2' |
C1' |
H1' |
29.0 |
123.8 |
| C1' |
C2' |
H2'1 |
C3' |
240.4 |
114.8 |
| C1' |
C2' |
H2'1 |
H2'2 |
120.2 |
237.3 |
| C3' |
C2' |
H2'1 |
H2'2 |
239.8 |
122.5 |
| H2'1 |
C2' |
C3' |
O3' |
324.8 |
257.9 |
| H2'1 |
C2' |
C3' |
H3' |
83.0 |
21.4 |
| H2'2 |
C2' |
C1' |
H1' |
138.4 |
1.0 |
| C1' |
C2' |
H2'2 |
C3' |
119.7 |
245.3 |
| C1' |
C2' |
H2'2 |
H2'1 |
239.8 |
122.7 |
| C3' |
C2' |
H2'2 |
H2'1 |
120.2 |
237.4 |
| H2'2 |
C2' |
C3' |
O3' |
215.3 |
20.5 |
| H2'2 |
C2' |
C3' |
H3' |
333.6 |
144.0 |
| O3' |
C3' |
C4' |
H4' |
26.2 |
323.3 |
| C4' |
C3' |
O3' |
C2' |
115.1 |
112.8 |
| C4' |
C3' |
O3' |
H3' |
238.3 |
236.4 |
| O3' |
C3' |
C2' |
H2'1 |
324.8 |
257.9 |
| O3' |
C3' |
C2' |
H2'2 |
215.3 |
20.5 |
| C2' |
C3' |
O3' |
H3' |
123.1 |
123.6 |
| H3' |
C3' |
C4' |
H4' |
267.8 |
199.7 |
| C4' |
C3' |
H3' |
C2' |
242.8 |
247.3 |
| C4' |
C3' |
H3' |
O3' |
122.2 |
123.7 |
| H3' |
C3' |
C2' |
H2'1 |
83.0 |
21.4 |
| H3' |
C3' |
C2' |
H2'2 |
333.6 |
144.0 |
| C2' |
C3' |
H3' |
O3' |
239.4 |
236.4 |
| H3' |
C3' |
O3' |
H1 |
301.7 |
297.9 |
| H1 |
O3' |
C3' |
H3' |
301.7 |
297.9 |