PDB Chemical Component GMP
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 GMP
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O5' |
C5' |
1.432 |
1.430 |
| O5' |
HO5' |
0.950 |
0.966 |
| C5' |
C4' |
1.534 |
1.530 |
| C5' |
H5'1 |
1.101 |
1.090 |
| C5' |
H5'2 |
1.100 |
1.090 |
| C4' |
O4' |
1.437 |
1.437 |
| C4' |
C3' |
1.529 |
1.541 |
| C4' |
H4' |
1.100 |
1.089 |
| O4' |
C1' |
1.440 |
1.444 |
| C3' |
O3' |
1.432 |
1.428 |
| C3' |
C2' |
1.527 |
1.548 |
| C3' |
H3' |
1.100 |
1.090 |
| O3' |
HO3' |
0.950 |
0.967 |
| C2' |
O2' |
1.431 |
1.430 |
| C2' |
C1' |
1.531 |
1.550 |
| C2' |
H2' |
1.100 |
1.090 |
| O2' |
HO2' |
0.950 |
0.967 |
| C1' |
N9 |
1.482 |
1.465 |
| C1' |
H1' |
1.100 |
1.089 |
| N9 |
C8 |
1.333 |
1.365 |
| N9 |
C4 |
1.327 |
1.368 |
| C8 |
N7 |
1.331 |
1.301 |
| C8 |
H8 |
1.080 |
1.080 |
| N7 |
C5 |
1.331 |
1.355 |
| C5 |
C6 |
1.391 |
1.414 |
| C5 |
C4 |
1.390 |
1.399 |
| C6 |
O6 |
1.233 |
1.220 |
| C6 |
N1 |
1.397 |
1.351 |
| N1 |
C2 |
1.402 |
1.363 |
| N1 |
HN1 |
1.000 |
0.970 |
| C2 |
N2 |
1.329 |
1.373 |
| C2 |
N3 |
1.339 |
1.313 |
| N2 |
HN21 |
1.000 |
0.970 |
| N2 |
HN22 |
1.000 |
0.970 |
| N3 |
C4 |
1.342 |
1.338 |
Bond Angles for GMP
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C5' |
O5' |
HO5' |
109.5 |
114.0 |
| O5' |
C5' |
C4' |
112.0 |
109.5 |
| O5' |
C5' |
H5'1 |
108.6 |
109.5 |
| O5' |
C5' |
H5'2 |
108.1 |
109.4 |
| C4' |
C5' |
H5'1 |
108.6 |
109.5 |
| C4' |
C5' |
H5'2 |
108.0 |
109.5 |
| C5' |
C4' |
O4' |
109.3 |
109.9 |
| C5' |
C4' |
C3' |
112.2 |
109.9 |
| C5' |
C4' |
H4' |
106.2 |
109.9 |
| H5'1 |
C5' |
H5'2 |
111.5 |
109.4 |
| O4' |
C4' |
C3' |
104.2 |
107.3 |
| O4' |
C4' |
H4' |
113.9 |
109.9 |
| C4' |
O4' |
C1' |
108.5 |
107.0 |
| C3' |
C4' |
H4' |
111.1 |
110.0 |
| C4' |
C3' |
O3' |
110.1 |
110.5 |
| C4' |
C3' |
C2' |
99.9 |
104.2 |
| C4' |
C3' |
H3' |
115.0 |
110.5 |
| O4' |
C1' |
C2' |
106.7 |
103.5 |
| O4' |
C1' |
N9 |
107.2 |
110.6 |
| O4' |
C1' |
H1' |
113.8 |
110.6 |
| O3' |
C3' |
C2' |
109.1 |
110.5 |
| O3' |
C3' |
H3' |
106.7 |
110.4 |
| C3' |
O3' |
HO3' |
109.5 |
114.1 |
| C2' |
C3' |
H3' |
115.9 |
110.6 |
| C3' |
C2' |
O2' |
110.7 |
110.9 |
| C3' |
C2' |
C1' |
100.8 |
102.1 |
| C3' |
C2' |
H2' |
113.9 |
111.0 |
| O2' |
C2' |
C1' |
108.6 |
110.9 |
| O2' |
C2' |
H2' |
106.8 |
110.8 |
| C2' |
O2' |
HO2' |
109.5 |
113.9 |
| C1' |
C2' |
H2' |
115.9 |
111.0 |
| C2' |
C1' |
N9 |
112.4 |
110.6 |
| C2' |
C1' |
H1' |
108.7 |
110.6 |
| N9 |
C1' |
H1' |
108.2 |
110.7 |
| C1' |
N9 |
C8 |
127.7 |
126.3 |
| C1' |
N9 |
C4 |
124.1 |
126.2 |
| C8 |
N9 |
C4 |
108.1 |
107.5 |
| N9 |
C8 |
N7 |
109.3 |
109.8 |
| N9 |
C8 |
H8 |
125.3 |
125.1 |
| N9 |
C4 |
C5 |
107.4 |
106.1 |
| N9 |
C4 |
N3 |
130.7 |
134.2 |
| N7 |
C8 |
H8 |
125.4 |
125.1 |
| C8 |
N7 |
C5 |
108.3 |
109.3 |
| N7 |
C5 |
C6 |
134.6 |
134.2 |
| N7 |
C5 |
C4 |
106.9 |
107.3 |
| C6 |
C5 |
C4 |
118.5 |
118.6 |
| C5 |
C6 |
O6 |
121.8 |
120.8 |
| C5 |
C6 |
N1 |
118.8 |
118.4 |
| C5 |
C4 |
N3 |
121.9 |
119.7 |
| O6 |
C6 |
N1 |
119.3 |
120.8 |
| C6 |
N1 |
C2 |
120.1 |
120.3 |
| C6 |
N1 |
HN1 |
119.9 |
119.9 |
| C2 |
N1 |
HN1 |
120.0 |
119.8 |
| N1 |
C2 |
N2 |
120.1 |
119.1 |
| N1 |
C2 |
N3 |
119.5 |
121.9 |
| N2 |
C2 |
N3 |
120.5 |
119.0 |
| C2 |
N2 |
HN21 |
109.5 |
120.0 |
| C2 |
N2 |
HN22 |
109.5 |
120.0 |
| C2 |
N3 |
C4 |
121.3 |
121.1 |
| HN21 |
N2 |
HN22 |
109.5 |
120.0 |
Torsion Angles for GMP
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C4' |
C5' |
O5' |
H5'1 |
240.0 |
240.0 |
| C4' |
C5' |
O5' |
H5'2 |
118.9 |
120.0 |
| O5' |
C5' |
C4' |
O4' |
298.8 |
66.5 |
| O5' |
C5' |
C4' |
C3' |
53.8 |
184.3 |
| O5' |
C5' |
C4' |
H4' |
175.4 |
305.5 |
| H5'1 |
C5' |
O5' |
H5'2 |
238.9 |
240.1 |
| HO5' |
O5' |
C5' |
C4' |
232.9 |
180.0 |
| HO5' |
O5' |
C5' |
H5'1 |
352.9 |
300.1 |
| HO5' |
O5' |
C5' |
H5'2 |
114.0 |
60.0 |
| C4' |
C5' |
O5' |
HO5' |
232.9 |
180.0 |
| O5' |
C5' |
C4' |
H5'1 |
120.0 |
120.0 |
| O5' |
C5' |
C4' |
H5'2 |
241.1 |
240.0 |
| H5'1 |
C5' |
C4' |
H5'2 |
121.1 |
120.0 |
| O4' |
C4' |
C5' |
C3' |
244.9 |
242.2 |
| O4' |
C4' |
C5' |
H4' |
123.3 |
121.0 |
| C5' |
C4' |
O4' |
C1' |
145.1 |
145.9 |
| C3' |
C4' |
C5' |
H4' |
238.4 |
238.8 |
| C5' |
C4' |
C3' |
O3' |
85.3 |
119.8 |
| C5' |
C4' |
C3' |
C2' |
200.0 |
238.6 |
| C5' |
C4' |
C3' |
H3' |
324.7 |
357.3 |
| H5'1 |
C5' |
O5' |
HO5' |
352.9 |
300.1 |
| O5' |
C5' |
H5'1 |
C4' |
237.9 |
240.0 |
| O5' |
C5' |
H5'1 |
H5'2 |
119.0 |
119.9 |
| C4' |
C5' |
H5'1 |
H5'2 |
241.1 |
239.9 |
| H5'1 |
C5' |
C4' |
O4' |
178.7 |
306.5 |
| H5'1 |
C5' |
C4' |
C3' |
293.8 |
64.3 |
| H5'1 |
C5' |
C4' |
H4' |
55.4 |
185.5 |
| H5'2 |
C5' |
O5' |
HO5' |
114.0 |
60.0 |
| O5' |
C5' |
H5'2 |
C4' |
121.4 |
120.0 |
| O5' |
C5' |
H5'2 |
H5'1 |
240.7 |
240.0 |
| C4' |
C5' |
H5'2 |
H5'1 |
119.3 |
120.1 |
| H5'2 |
C5' |
C4' |
O4' |
57.7 |
186.5 |
| H5'2 |
C5' |
C4' |
C3' |
172.7 |
304.3 |
| H5'2 |
C5' |
C4' |
H4' |
294.3 |
65.4 |
| O4' |
C4' |
C5' |
H5'1 |
178.7 |
306.5 |
| O4' |
C4' |
C5' |
H5'2 |
57.7 |
186.5 |
| C5' |
C4' |
O4' |
C3' |
120.1 |
119.4 |
| C5' |
C4' |
O4' |
H4' |
241.4 |
239.0 |
| C3' |
C4' |
O4' |
H4' |
121.3 |
119.5 |
| O4' |
C4' |
C3' |
O3' |
203.5 |
239.3 |
| O4' |
C4' |
C3' |
C2' |
318.1 |
358.0 |
| O4' |
C4' |
C3' |
H3' |
82.9 |
116.8 |
| C4' |
O4' |
C1' |
C2' |
2.3 |
319.9 |
| C4' |
O4' |
C1' |
N9 |
241.6 |
201.5 |
| C4' |
O4' |
C1' |
H1' |
122.1 |
78.4 |
| C3' |
C4' |
C5' |
H5'1 |
293.8 |
64.3 |
| C3' |
C4' |
C5' |
H5'2 |
172.7 |
304.3 |
| C5' |
C4' |
C3' |
O4' |
241.9 |
240.6 |
| C5' |
C4' |
C3' |
H4' |
118.7 |
121.1 |
| O4' |
C4' |
C3' |
H4' |
236.9 |
240.5 |
| C3' |
C4' |
O4' |
C1' |
25.1 |
26.5 |
| O3' |
C3' |
C4' |
C2' |
245.3 |
241.3 |
| O3' |
C3' |
C4' |
H3' |
120.6 |
122.5 |
| C4' |
C3' |
O3' |
HO3' |
70.9 |
298.6 |
| C2' |
C3' |
C4' |
H3' |
235.2 |
241.2 |
| C4' |
C3' |
C2' |
O2' |
286.8 |
220.9 |
| C4' |
C3' |
C2' |
C1' |
41.6 |
339.1 |
| C4' |
C3' |
C2' |
H2' |
166.5 |
97.4 |
| H4' |
C4' |
C5' |
H5'1 |
55.4 |
185.5 |
| H4' |
C4' |
C5' |
H5'2 |
294.3 |
65.4 |
| C5' |
C4' |
H4' |
O4' |
120.4 |
121.1 |
| C5' |
C4' |
H4' |
C3' |
237.7 |
238.9 |
| O4' |
C4' |
H4' |
C3' |
117.3 |
117.9 |
| H4' |
C4' |
O4' |
C1' |
263.8 |
267.0 |
| H4' |
C4' |
C3' |
O3' |
326.6 |
358.7 |
| H4' |
C4' |
C3' |
C2' |
81.2 |
117.5 |
| H4' |
C4' |
C3' |
H3' |
206.0 |
236.2 |
| C1' |
O4' |
C4' |
C3' |
25.1 |
26.5 |
| C1' |
O4' |
C4' |
H4' |
263.8 |
267.0 |
| C3' |
C2' |
C1' |
O4' |
331.7 |
37.1 |
| O2' |
C2' |
C1' |
O4' |
88.1 |
155.2 |
| O4' |
C1' |
C2' |
H2' |
208.2 |
278.8 |
| C2' |
C1' |
O4' |
N9 |
120.7 |
118.5 |
| C2' |
C1' |
O4' |
H1' |
240.2 |
241.5 |
| N9 |
C1' |
O4' |
H1' |
119.5 |
123.0 |
| O4' |
C1' |
N9 |
C8 |
33.4 |
23.5 |
| O4' |
C1' |
N9 |
C4 |
216.4 |
203.3 |
| O3' |
C3' |
C4' |
H4' |
326.6 |
358.7 |
| C4' |
C3' |
O3' |
C2' |
108.7 |
114.8 |
| C4' |
C3' |
O3' |
H3' |
234.6 |
237.5 |
| C2' |
C3' |
O3' |
H3' |
125.9 |
122.7 |
| O3' |
C3' |
C2' |
O2' |
42.3 |
339.6 |
| O3' |
C3' |
C2' |
C1' |
157.1 |
97.8 |
| O3' |
C3' |
C2' |
H2' |
281.9 |
216.1 |
| C2' |
C3' |
C4' |
H4' |
81.2 |
117.5 |
| C4' |
C3' |
C2' |
O3' |
244.5 |
241.3 |
| C4' |
C3' |
C2' |
H3' |
124.1 |
118.7 |
| O4' |
C1' |
C2' |
C3' |
331.7 |
37.1 |
| O3' |
C3' |
C2' |
H3' |
239.6 |
237.4 |
| C2' |
C3' |
O3' |
HO3' |
322.2 |
183.8 |
| O2' |
C2' |
C3' |
C1' |
245.2 |
241.8 |
| O2' |
C2' |
C3' |
H2' |
120.4 |
123.5 |
| C3' |
C2' |
O2' |
HO2' |
149.8 |
298.6 |
| C1' |
C2' |
C3' |
H2' |
235.2 |
241.7 |
| C3' |
C2' |
C1' |
N9 |
88.9 |
155.5 |
| C3' |
C2' |
C1' |
H1' |
208.6 |
278.6 |
| H3' |
C3' |
C4' |
H4' |
206.0 |
236.2 |
| C4' |
C3' |
H3' |
O3' |
122.4 |
122.6 |
| C4' |
C3' |
H3' |
C2' |
244.1 |
245.2 |
| O3' |
C3' |
H3' |
C2' |
121.6 |
122.6 |
| H3' |
C3' |
O3' |
HO3' |
196.4 |
61.1 |
| H3' |
C3' |
C2' |
O2' |
162.7 |
102.2 |
| H3' |
C3' |
C2' |
C1' |
277.5 |
220.3 |
| H3' |
C3' |
C2' |
H2' |
42.3 |
338.7 |
| HO3' |
O3' |
C3' |
C2' |
322.2 |
183.8 |
| HO3' |
O3' |
C3' |
H3' |
196.4 |
61.1 |
| O4' |
C1' |
C2' |
O2' |
88.1 |
155.2 |
| O2' |
C2' |
C3' |
H3' |
162.7 |
102.2 |
| C3' |
C2' |
O2' |
C1' |
109.8 |
112.7 |
| C3' |
C2' |
O2' |
H2' |
235.5 |
236.4 |
| C1' |
C2' |
O2' |
H2' |
125.7 |
123.7 |
| O2' |
C2' |
C1' |
N9 |
205.3 |
273.7 |
| O2' |
C2' |
C1' |
H1' |
325.0 |
36.7 |
| O4' |
C1' |
C2' |
N9 |
242.8 |
241.5 |
| O4' |
C1' |
C2' |
H1' |
123.1 |
118.5 |
| C1' |
C2' |
C3' |
H3' |
277.5 |
220.3 |
| C3' |
C2' |
C1' |
O2' |
243.6 |
241.8 |
| C3' |
C2' |
C1' |
H2' |
123.4 |
118.3 |
| O2' |
C2' |
C1' |
H2' |
239.8 |
236.5 |
| C1' |
C2' |
O2' |
HO2' |
40.0 |
185.9 |
| N9 |
C1' |
C2' |
H1' |
240.3 |
237.0 |
| C2' |
C1' |
N9 |
C8 |
276.5 |
269.5 |
| C2' |
C1' |
N9 |
C4 |
99.5 |
89.2 |
| H2' |
C2' |
C3' |
H3' |
42.3 |
338.7 |
| C3' |
C2' |
H2' |
O2' |
122.6 |
123.6 |
| C3' |
C2' |
H2' |
C1' |
243.7 |
247.2 |
| O2' |
C2' |
H2' |
C1' |
121.1 |
123.6 |
| H2' |
C2' |
O2' |
HO2' |
274.4 |
62.2 |
| H2' |
C2' |
C1' |
N9 |
325.4 |
37.2 |
| H2' |
C2' |
C1' |
H1' |
85.2 |
160.3 |
| HO2' |
O2' |
C2' |
C1' |
40.0 |
185.9 |
| HO2' |
O2' |
C2' |
H2' |
274.4 |
62.2 |
| O4' |
C1' |
N9 |
C2' |
116.9 |
114.0 |
| O4' |
C1' |
N9 |
H1' |
236.9 |
237.0 |
| N9 |
C1' |
C2' |
H2' |
325.4 |
37.2 |
| C2' |
C1' |
N9 |
H1' |
120.0 |
123.0 |
| C8 |
N9 |
C1' |
C4 |
177.0 |
180.3 |
| C1' |
N9 |
C8 |
N7 |
182.3 |
180.0 |
| C1' |
N9 |
C8 |
H8 |
2.3 |
360.0 |
| C1' |
N9 |
C4 |
C5 |
178.0 |
179.9 |
| C1' |
N9 |
C4 |
N3 |
359.4 |
0.7 |
| O4' |
C1' |
H1' |
C2' |
241.3 |
246.0 |
| O4' |
C1' |
H1' |
N9 |
119.0 |
123.0 |
| H1' |
C1' |
C2' |
H2' |
85.2 |
160.3 |
| C2' |
C1' |
H1' |
N9 |
237.7 |
237.0 |
| H1' |
C1' |
N9 |
C8 |
156.4 |
146.5 |
| H1' |
C1' |
N9 |
C4 |
339.4 |
326.3 |
| C8 |
N9 |
C1' |
H1' |
156.4 |
146.5 |
| C1' |
N9 |
C8 |
C4 |
182.6 |
179.8 |
| C8 |
N9 |
C4 |
C5 |
0.5 |
359.6 |
| C8 |
N9 |
C4 |
N3 |
181.9 |
180.5 |
| N7 |
C8 |
N9 |
H8 |
180.0 |
180.0 |
| N9 |
C8 |
N7 |
C5 |
0.0 |
360.0 |
| C4 |
N9 |
C1' |
H1' |
339.4 |
326.3 |
| C1' |
N9 |
C4 |
C8 |
177.5 |
180.2 |
| C4 |
N9 |
C8 |
N7 |
359.7 |
0.3 |
| C4 |
N9 |
C8 |
H8 |
179.7 |
180.2 |
| N7 |
C5 |
C4 |
N9 |
359.6 |
0.4 |
| C6 |
C5 |
C4 |
N9 |
181.0 |
180.1 |
| C5 |
C4 |
N9 |
N3 |
178.5 |
179.1 |
| C2 |
N3 |
C4 |
N9 |
178.3 |
179.6 |
| N7 |
C8 |
N9 |
C4 |
359.7 |
0.3 |
| N9 |
C8 |
N7 |
H8 |
180.0 |
180.0 |
| C8 |
N7 |
C5 |
C6 |
178.5 |
180.1 |
| C8 |
N7 |
C5 |
C4 |
0.2 |
359.8 |
| H8 |
C8 |
N9 |
C4 |
179.7 |
180.2 |
| N9 |
C8 |
H8 |
N7 |
180.0 |
180.0 |
| H8 |
C8 |
N7 |
C5 |
180.0 |
180.0 |
| N9 |
C4 |
C5 |
N7 |
359.6 |
0.4 |
| C5 |
N7 |
C8 |
H8 |
180.0 |
180.0 |
| C6 |
C5 |
N7 |
C4 |
178.2 |
180.3 |
| N7 |
C5 |
C6 |
O6 |
3.9 |
360.0 |
| N7 |
C5 |
C6 |
N1 |
182.5 |
180.0 |
| N7 |
C5 |
C4 |
N3 |
178.2 |
179.7 |
| N9 |
C4 |
C5 |
C6 |
181.0 |
180.1 |
| N7 |
C5 |
C6 |
C4 |
181.9 |
179.7 |
| C6 |
C5 |
C4 |
N3 |
359.7 |
359.4 |
| O6 |
C6 |
C5 |
N1 |
181.4 |
180.0 |
| C5 |
C6 |
N1 |
C2 |
359.6 |
0.0 |
| C5 |
C6 |
N1 |
HN1 |
179.6 |
180.0 |
| N9 |
C4 |
C5 |
N3 |
181.3 |
180.7 |
| N7 |
C5 |
C4 |
C6 |
178.6 |
180.2 |
| C4 |
C5 |
C6 |
O6 |
181.9 |
180.3 |
| C4 |
C5 |
C6 |
N1 |
0.5 |
0.3 |
| C2 |
N3 |
C4 |
C5 |
360.0 |
0.6 |
| O6 |
C6 |
C5 |
C4 |
181.9 |
180.3 |
| C5 |
C6 |
O6 |
N1 |
178.6 |
180.0 |
| O6 |
C6 |
N1 |
C2 |
178.2 |
180.0 |
| O6 |
C6 |
N1 |
HN1 |
358.2 |
359.9 |
| N1 |
C6 |
C5 |
C4 |
0.5 |
0.3 |
| C5 |
C6 |
N1 |
O6 |
181.4 |
180.0 |
| C2 |
N1 |
C6 |
HN1 |
180.0 |
180.1 |
| C6 |
N1 |
C2 |
N2 |
180.1 |
180.0 |
| C6 |
N1 |
C2 |
N3 |
0.0 |
359.9 |
| C6 |
N1 |
C2 |
HN1 |
180.0 |
179.9 |
| N2 |
C2 |
N1 |
N3 |
180.1 |
180.0 |
| N1 |
C2 |
N2 |
HN21 |
338.6 |
360.0 |
| N1 |
C2 |
N2 |
HN22 |
98.6 |
179.9 |
| N1 |
C2 |
N3 |
C4 |
0.2 |
359.7 |
| C6 |
N1 |
HN1 |
C2 |
180.0 |
180.1 |
| HN1 |
N1 |
C2 |
N2 |
0.2 |
0.1 |
| HN1 |
N1 |
C2 |
N3 |
180.1 |
180.0 |
| N2 |
C2 |
N1 |
HN1 |
0.2 |
0.1 |
| N1 |
C2 |
N2 |
N3 |
179.9 |
180.0 |
| N2 |
C2 |
N3 |
C4 |
180.1 |
179.7 |
| HN21 |
N2 |
C2 |
HN22 |
240.0 |
180.1 |
| N9 |
C4 |
N3 |
C2 |
178.3 |
179.6 |
| C5 |
C4 |
N3 |
C2 |
360.0 |
0.6 |
| N3 |
C2 |
N1 |
HN1 |
180.1 |
180.0 |
| N1 |
C2 |
N3 |
N2 |
180.1 |
180.0 |
| N3 |
C2 |
N2 |
HN21 |
158.7 |
180.0 |
| N3 |
C2 |
N2 |
HN22 |
278.7 |
360.0 |
| HN21 |
N2 |
C2 |
N3 |
158.7 |
180.0 |
| C2 |
N2 |
HN21 |
HN22 |
120.0 |
179.9 |
| HN22 |
N2 |
C2 |
N3 |
278.7 |
360.0 |
| C2 |
N2 |
HN22 |
HN21 |
240.0 |
180.1 |
| N9 |
C4 |
N3 |
C5 |
178.3 |
179.0 |