PDB Chemical Component 3D1
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 3D1
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O5' |
C5' |
1.433 |
1.428 |
| O5' |
H5' |
0.950 |
0.967 |
| C5' |
C4' |
1.553 |
1.531 |
| C5' |
H5'1 |
1.100 |
1.090 |
| C5' |
H5'2 |
1.100 |
1.090 |
| C4' |
O4' |
1.445 |
1.444 |
| C4' |
C3' |
1.537 |
1.550 |
| C4' |
H4' |
1.100 |
1.090 |
| O4' |
C1' |
1.447 |
1.438 |
| C1' |
N9 |
1.698 |
1.465 |
| C1' |
C2' |
1.517 |
1.540 |
| C1' |
H1' |
1.100 |
1.090 |
| N9 |
C4 |
1.392 |
1.371 |
| N9 |
C8 |
1.459 |
1.364 |
| C4 |
N3 |
1.376 |
1.328 |
| C4 |
C5 |
1.422 |
1.405 |
| N3 |
C2 |
1.369 |
1.317 |
| C2 |
N1 |
1.379 |
1.321 |
| C2 |
H2 |
1.080 |
1.080 |
| N1 |
C6 |
1.412 |
1.329 |
| C6 |
N6 |
1.325 |
1.384 |
| C6 |
C5 |
1.403 |
1.406 |
| N6 |
HN61 |
1.000 |
0.970 |
| N6 |
HN62 |
1.000 |
0.969 |
| C5 |
N7 |
1.395 |
1.354 |
| N7 |
C8 |
1.293 |
1.301 |
| C8 |
H8 |
1.080 |
1.079 |
| C2' |
C3' |
1.509 |
1.548 |
| C2' |
H2'1 |
1.100 |
1.091 |
| C2' |
H2'2 |
1.100 |
1.091 |
| C3' |
O3' |
1.439 |
1.429 |
| C3' |
H3' |
1.100 |
1.090 |
| O3' |
H1 |
0.950 |
0.967 |
Bond Angles for 3D1
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C5' |
O5' |
H5' |
109.5 |
113.9 |
| O5' |
C5' |
C4' |
112.9 |
109.5 |
| O5' |
C5' |
H5'1 |
108.3 |
109.5 |
| O5' |
C5' |
H5'2 |
107.6 |
109.5 |
| C4' |
C5' |
H5'1 |
108.3 |
109.4 |
| C4' |
C5' |
H5'2 |
107.6 |
109.5 |
| C5' |
C4' |
O4' |
112.5 |
110.6 |
| C5' |
C4' |
C3' |
108.6 |
110.6 |
| C5' |
C4' |
H4' |
107.4 |
110.5 |
| H5'1 |
C5' |
H5'2 |
112.2 |
109.4 |
| O4' |
C4' |
C3' |
107.6 |
103.5 |
| O4' |
C4' |
H4' |
108.4 |
110.7 |
| C4' |
O4' |
C1' |
107.8 |
106.9 |
| C3' |
C4' |
H4' |
112.4 |
110.8 |
| C4' |
C3' |
C2' |
104.6 |
102.0 |
| C4' |
C3' |
O3' |
113.5 |
110.9 |
| C4' |
C3' |
H3' |
109.6 |
110.9 |
| O4' |
C1' |
N9 |
110.4 |
109.9 |
| O4' |
C1' |
C2' |
107.1 |
107.3 |
| O4' |
C1' |
H1' |
109.4 |
109.9 |
| N9 |
C1' |
C2' |
106.2 |
109.9 |
| N9 |
C1' |
H1' |
110.3 |
109.9 |
| C1' |
N9 |
C4 |
129.9 |
126.3 |
| C1' |
N9 |
C8 |
128.7 |
126.3 |
| C2' |
C1' |
H1' |
113.4 |
110.0 |
| C1' |
C2' |
C3' |
106.8 |
104.2 |
| C1' |
C2' |
H2'1 |
110.4 |
110.5 |
| C1' |
C2' |
H2'2 |
110.9 |
110.5 |
| C4 |
N9 |
C8 |
101.4 |
107.4 |
| N9 |
C4 |
N3 |
127.0 |
134.9 |
| N9 |
C4 |
C5 |
105.8 |
106.0 |
| N9 |
C8 |
N7 |
118.5 |
109.9 |
| N9 |
C8 |
H8 |
120.7 |
125.0 |
| N3 |
C4 |
C5 |
127.2 |
119.1 |
| C4 |
N3 |
C2 |
112.0 |
120.7 |
| C4 |
C5 |
C6 |
116.5 |
118.2 |
| C4 |
C5 |
N7 |
113.9 |
107.2 |
| N3 |
C2 |
N1 |
126.6 |
122.4 |
| N3 |
C2 |
H2 |
116.7 |
118.8 |
| N1 |
C2 |
H2 |
116.7 |
118.7 |
| C2 |
N1 |
C6 |
119.0 |
121.2 |
| N1 |
C6 |
N6 |
123.6 |
120.8 |
| N1 |
C6 |
C5 |
118.6 |
118.5 |
| N6 |
C6 |
C5 |
117.7 |
120.8 |
| C6 |
N6 |
HN61 |
109.5 |
119.9 |
| C6 |
N6 |
HN62 |
109.5 |
120.0 |
| C6 |
C5 |
N7 |
129.6 |
134.7 |
| HN61 |
N6 |
HN62 |
109.4 |
120.1 |
| C5 |
N7 |
C8 |
100.4 |
109.5 |
| N7 |
C8 |
H8 |
120.8 |
125.1 |
| C3' |
C2' |
H2'1 |
110.4 |
110.5 |
| C3' |
C2' |
H2'2 |
111.0 |
110.5 |
| C2' |
C3' |
O3' |
107.9 |
110.9 |
| C2' |
C3' |
H3' |
115.0 |
110.9 |
| H2'1 |
C2' |
H2'2 |
107.4 |
110.4 |
| O3' |
C3' |
H3' |
106.4 |
110.9 |
| C3' |
O3' |
H1 |
109.5 |
114.0 |
Torsion Angles for 3D1
| 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 |
118.5 |
120.0 |
| O5' |
C5' |
C4' |
O4' |
59.8 |
66.4 |
| O5' |
C5' |
C4' |
C3' |
178.8 |
180.6 |
| O5' |
C5' |
C4' |
H4' |
300.6 |
303.6 |
| H5'1 |
C5' |
O5' |
H5'2 |
238.5 |
240.0 |
| H5' |
O5' |
C5' |
C4' |
178.4 |
180.0 |
| H5' |
O5' |
C5' |
H5'1 |
298.4 |
300.0 |
| H5' |
O5' |
C5' |
H5'2 |
59.9 |
60.0 |
| C4' |
C5' |
O5' |
H5' |
178.4 |
180.0 |
| O5' |
C5' |
C4' |
H5'1 |
120.0 |
120.0 |
| O5' |
C5' |
C4' |
H5'2 |
241.5 |
239.9 |
| H5'1 |
C5' |
C4' |
H5'2 |
121.5 |
119.9 |
| O4' |
C4' |
C5' |
C3' |
241.0 |
245.9 |
| O4' |
C4' |
C5' |
H4' |
119.3 |
122.8 |
| C5' |
C4' |
O4' |
C1' |
95.0 |
158.6 |
| C3' |
C4' |
C5' |
H4' |
238.2 |
237.0 |
| C5' |
C4' |
C3' |
C2' |
252.9 |
204.5 |
| C5' |
C4' |
C3' |
O3' |
135.6 |
86.3 |
| C5' |
C4' |
C3' |
H3' |
16.8 |
322.6 |
| H5'1 |
C5' |
O5' |
H5' |
298.4 |
300.0 |
| O5' |
C5' |
H5'1 |
C4' |
237.2 |
240.0 |
| O5' |
C5' |
H5'1 |
H5'2 |
118.6 |
120.1 |
| C4' |
C5' |
H5'1 |
H5'2 |
241.4 |
240.1 |
| H5'1 |
C5' |
C4' |
O4' |
299.8 |
306.4 |
| H5'1 |
C5' |
C4' |
C3' |
58.8 |
60.5 |
| H5'1 |
C5' |
C4' |
H4' |
180.6 |
183.6 |
| H5'2 |
C5' |
O5' |
H5' |
59.9 |
60.0 |
| O5' |
C5' |
H5'2 |
C4' |
121.9 |
120.0 |
| O5' |
C5' |
H5'2 |
H5'1 |
241.0 |
239.9 |
| C4' |
C5' |
H5'2 |
H5'1 |
119.1 |
119.9 |
| H5'2 |
C5' |
C4' |
O4' |
178.4 |
186.5 |
| H5'2 |
C5' |
C4' |
C3' |
297.3 |
300.6 |
| H5'2 |
C5' |
C4' |
H4' |
59.1 |
63.6 |
| O4' |
C4' |
C5' |
H5'1 |
299.8 |
306.4 |
| O4' |
C4' |
C5' |
H5'2 |
178.4 |
186.5 |
| C5' |
C4' |
O4' |
C3' |
119.6 |
118.5 |
| C5' |
C4' |
O4' |
H4' |
241.3 |
237.3 |
| C3' |
C4' |
O4' |
H4' |
121.8 |
118.7 |
| O4' |
C4' |
C3' |
C2' |
15.0 |
323.0 |
| O4' |
C4' |
C3' |
O3' |
257.6 |
204.8 |
| O4' |
C4' |
C3' |
H3' |
138.8 |
81.1 |
| C4' |
O4' |
C1' |
N9 |
269.1 |
214.1 |
| C4' |
O4' |
C1' |
C2' |
24.2 |
333.5 |
| C4' |
O4' |
C1' |
H1' |
147.5 |
93.1 |
| C3' |
C4' |
C5' |
H5'1 |
58.8 |
60.5 |
| C3' |
C4' |
C5' |
H5'2 |
297.3 |
300.6 |
| C5' |
C4' |
C3' |
O4' |
237.9 |
241.5 |
| C5' |
C4' |
C3' |
H4' |
118.7 |
122.9 |
| O4' |
C4' |
C3' |
H4' |
240.7 |
241.4 |
| C3' |
C4' |
O4' |
C1' |
335.4 |
40.1 |
| C1' |
C2' |
C3' |
C4' |
359.7 |
20.9 |
| C4' |
C3' |
C2' |
H2'1 |
239.6 |
262.1 |
| C4' |
C3' |
C2' |
H2'2 |
120.7 |
139.6 |
| C2' |
C3' |
C4' |
O3' |
117.4 |
118.2 |
| C2' |
C3' |
C4' |
H3' |
236.1 |
241.9 |
| O3' |
C3' |
C4' |
H3' |
118.8 |
123.7 |
| C4' |
C3' |
O3' |
H1 |
61.2 |
180.0 |
| H4' |
C4' |
C5' |
H5'1 |
180.6 |
183.6 |
| H4' |
C4' |
C5' |
H5'2 |
59.1 |
63.6 |
| C5' |
C4' |
H4' |
O4' |
121.9 |
122.8 |
| C5' |
C4' |
H4' |
C3' |
240.6 |
237.0 |
| O4' |
C4' |
H4' |
C3' |
118.8 |
114.2 |
| H4' |
C4' |
O4' |
C1' |
213.7 |
281.4 |
| H4' |
C4' |
C3' |
C2' |
134.2 |
81.6 |
| H4' |
C4' |
C3' |
O3' |
16.9 |
323.4 |
| H4' |
C4' |
C3' |
H3' |
258.1 |
199.7 |
| C1' |
O4' |
C4' |
C3' |
335.4 |
40.1 |
| C1' |
O4' |
C4' |
H4' |
213.7 |
281.4 |
| N9 |
C1' |
O4' |
C2' |
244.8 |
240.6 |
| N9 |
C1' |
O4' |
H1' |
121.5 |
121.0 |
| O4' |
C1' |
N9 |
C4 |
163.3 |
203.6 |
| O4' |
C1' |
N9 |
C8 |
343.6 |
23.2 |
| C2' |
C1' |
O4' |
H1' |
236.7 |
240.4 |
| O4' |
C1' |
C2' |
C3' |
345.7 |
2.0 |
| O4' |
C1' |
C2' |
H2'1 |
105.7 |
120.8 |
| O4' |
C1' |
C2' |
H2'2 |
224.7 |
243.3 |
| O4' |
C1' |
N9 |
C2' |
115.8 |
117.8 |
| O4' |
C1' |
N9 |
H1' |
239.0 |
239.0 |
| C2' |
C1' |
N9 |
H1' |
123.2 |
121.2 |
| N9 |
C1' |
C2' |
C3' |
103.6 |
121.5 |
| N9 |
C1' |
C2' |
H2'1 |
223.7 |
240.2 |
| N9 |
C1' |
C2' |
H2'2 |
342.6 |
2.7 |
| C4 |
N9 |
C1' |
C8 |
179.7 |
180.4 |
| C1' |
N9 |
C4 |
N3 |
0.5 |
360.0 |
| C1' |
N9 |
C4 |
C5 |
180.6 |
180.0 |
| C1' |
N9 |
C8 |
N7 |
179.4 |
179.8 |
| C1' |
N9 |
C8 |
H8 |
359.4 |
0.0 |
| C4' |
C3' |
C2' |
C1' |
359.7 |
20.9 |
| O4' |
C1' |
C2' |
N9 |
242.0 |
240.6 |
| O4' |
C1' |
C2' |
H1' |
120.8 |
119.5 |
| N9 |
C1' |
C2' |
H1' |
238.7 |
238.9 |
| C2' |
C1' |
N9 |
C4 |
47.5 |
85.8 |
| C2' |
C1' |
N9 |
C8 |
227.8 |
265.4 |
| C3' |
C2' |
C1' |
H2'1 |
240.0 |
241.3 |
| C3' |
C2' |
C1' |
H2'2 |
121.0 |
118.7 |
| C1' |
C2' |
C3' |
O3' |
120.8 |
139.0 |
| C1' |
C2' |
C3' |
H3' |
239.3 |
262.7 |
| H2'1 |
C2' |
C1' |
H2'2 |
241.1 |
237.4 |
| O4' |
C1' |
H1' |
N9 |
121.6 |
121.0 |
| O4' |
C1' |
H1' |
C2' |
240.5 |
242.1 |
| N9 |
C1' |
H1' |
C2' |
118.9 |
121.1 |
| H1' |
C1' |
N9 |
C4 |
284.3 |
324.6 |
| H1' |
C1' |
N9 |
C8 |
104.6 |
144.2 |
| H1' |
C1' |
C2' |
C3' |
224.9 |
242.5 |
| H1' |
C1' |
C2' |
H2'1 |
344.9 |
1.3 |
| H1' |
C1' |
C2' |
H2'2 |
103.9 |
123.8 |
| C4 |
N9 |
C1' |
C2' |
47.5 |
85.8 |
| C4 |
N9 |
C1' |
H1' |
284.3 |
324.6 |
| C1' |
N9 |
C4 |
C8 |
180.3 |
179.7 |
| C4 |
N9 |
C8 |
N7 |
359.7 |
359.5 |
| C4 |
N9 |
C8 |
H8 |
179.7 |
179.7 |
| N3 |
C4 |
N9 |
C5 |
179.9 |
180.0 |
| N9 |
C4 |
N3 |
C2 |
180.3 |
180.0 |
| N9 |
C4 |
C5 |
C6 |
179.6 |
180.0 |
| N9 |
C4 |
C5 |
N7 |
359.7 |
360.0 |
| C8 |
N9 |
C1' |
C2' |
227.8 |
265.4 |
| C8 |
N9 |
C1' |
H1' |
104.6 |
144.2 |
| C1' |
N9 |
C8 |
C4 |
179.8 |
180.3 |
| C8 |
N9 |
C4 |
N3 |
180.2 |
180.3 |
| C8 |
N9 |
C4 |
C5 |
0.3 |
0.3 |
| C5 |
N7 |
C8 |
N9 |
0.2 |
0.5 |
| N7 |
C8 |
N9 |
H8 |
180.0 |
179.8 |
| N3 |
C4 |
N9 |
C8 |
180.2 |
180.3 |
| N9 |
C4 |
N3 |
C5 |
180.1 |
180.0 |
| N3 |
C4 |
C5 |
C6 |
359.7 |
0.0 |
| N3 |
C4 |
C5 |
N7 |
179.8 |
180.0 |
| C4 |
N3 |
C2 |
N1 |
0.0 |
359.9 |
| C4 |
N3 |
C2 |
H2 |
180.0 |
180.0 |
| C5 |
C4 |
N9 |
C8 |
0.3 |
0.3 |
| N9 |
C4 |
C5 |
N3 |
179.9 |
180.0 |
| C5 |
C4 |
N3 |
C2 |
0.2 |
0.0 |
| N1 |
C6 |
C5 |
C4 |
0.2 |
359.9 |
| N6 |
C6 |
C5 |
C4 |
180.3 |
180.1 |
| C6 |
C5 |
C4 |
N7 |
179.8 |
180.1 |
| C4 |
C5 |
N7 |
C8 |
0.1 |
359.7 |
| C2 |
N3 |
C4 |
C5 |
0.2 |
0.0 |
| N1 |
C2 |
N3 |
H2 |
180.0 |
179.9 |
| N3 |
C2 |
N1 |
C6 |
359.9 |
0.0 |
| N3 |
C2 |
N1 |
H2 |
180.0 |
180.1 |
| C2 |
N1 |
C6 |
N6 |
179.9 |
179.9 |
| C2 |
N1 |
C6 |
C5 |
359.9 |
0.0 |
| N3 |
C2 |
H2 |
N1 |
180.0 |
179.9 |
| H2 |
C2 |
N1 |
C6 |
179.9 |
179.9 |
| C4 |
C5 |
C6 |
N1 |
0.2 |
359.9 |
| C6 |
N1 |
C2 |
H2 |
179.9 |
179.9 |
| N6 |
C6 |
N1 |
C5 |
180.0 |
179.9 |
| N1 |
C6 |
N6 |
HN61 |
283.3 |
0.1 |
| N1 |
C6 |
N6 |
HN62 |
43.3 |
180.1 |
| N1 |
C6 |
C5 |
N7 |
180.1 |
180.0 |
| C4 |
C5 |
C6 |
N6 |
180.3 |
180.1 |
| N1 |
C6 |
N6 |
C5 |
180.0 |
180.1 |
| N6 |
C6 |
C5 |
N7 |
0.1 |
0.1 |
| HN61 |
N6 |
C6 |
HN62 |
240.0 |
180.0 |
| C4 |
C5 |
C6 |
N7 |
180.2 |
179.9 |
| N1 |
C6 |
C5 |
N6 |
180.0 |
179.9 |
| C5 |
C6 |
N6 |
HN61 |
103.3 |
179.9 |
| C5 |
C6 |
N6 |
HN62 |
223.3 |
359.9 |
| C6 |
C5 |
N7 |
C8 |
180.3 |
179.7 |
| HN61 |
N6 |
C6 |
C5 |
103.3 |
179.9 |
| C6 |
N6 |
HN61 |
HN62 |
120.0 |
180.0 |
| HN62 |
N6 |
C6 |
C5 |
223.3 |
359.9 |
| C6 |
N6 |
HN62 |
HN61 |
240.0 |
180.0 |
| N9 |
C8 |
N7 |
C5 |
0.2 |
0.5 |
| C4 |
C5 |
N7 |
C6 |
179.8 |
180.1 |
| C5 |
N7 |
C8 |
H8 |
180.2 |
180.3 |
| N9 |
C8 |
N7 |
H8 |
180.0 |
180.2 |
| N9 |
C8 |
H8 |
N7 |
180.0 |
179.8 |
| C2' |
C3' |
C4' |
H4' |
134.2 |
81.6 |
| C4' |
C3' |
C2' |
O3' |
238.9 |
241.8 |
| C4' |
C3' |
C2' |
H3' |
120.3 |
118.1 |
| C3' |
C2' |
C1' |
H1' |
224.9 |
242.5 |
| C1' |
C2' |
C3' |
H2'1 |
120.0 |
118.7 |
| C1' |
C2' |
C3' |
H2'2 |
239.0 |
241.3 |
| H2'1 |
C2' |
C3' |
H2'2 |
119.0 |
122.5 |
| O3' |
C3' |
C2' |
H3' |
241.4 |
236.3 |
| C2' |
C3' |
O3' |
H1 |
305.8 |
67.3 |
| H2'1 |
C2' |
C1' |
H1' |
344.9 |
1.3 |
| C1' |
C2' |
H2'1 |
C3' |
242.1 |
245.1 |
| C1' |
C2' |
H2'1 |
H2'2 |
121.0 |
122.6 |
| C3' |
C2' |
H2'1 |
H2'2 |
238.9 |
237.5 |
| H2'1 |
C2' |
C3' |
O3' |
0.8 |
20.3 |
| H2'1 |
C2' |
C3' |
H3' |
119.3 |
144.0 |
| H2'2 |
C2' |
C1' |
H1' |
103.9 |
123.8 |
| C1' |
C2' |
H2'2 |
C3' |
118.6 |
114.8 |
| C1' |
C2' |
H2'2 |
H2'1 |
239.3 |
237.4 |
| C3' |
C2' |
H2'2 |
H2'1 |
120.7 |
122.6 |
| H2'2 |
C2' |
C3' |
O3' |
241.8 |
257.8 |
| H2'2 |
C2' |
C3' |
H3' |
0.4 |
21.5 |
| O3' |
C3' |
C4' |
H4' |
16.9 |
323.4 |
| C4' |
C3' |
O3' |
C2' |
115.4 |
112.6 |
| C4' |
C3' |
O3' |
H3' |
239.4 |
236.3 |
| O3' |
C3' |
C2' |
H2'1 |
0.8 |
20.3 |
| O3' |
C3' |
C2' |
H2'2 |
241.8 |
257.8 |
| C2' |
C3' |
O3' |
H3' |
124.0 |
123.7 |
| H3' |
C3' |
C4' |
H4' |
258.1 |
199.7 |
| C4' |
C3' |
H3' |
C2' |
242.5 |
247.4 |
| C4' |
C3' |
H3' |
O3' |
123.1 |
123.7 |
| H3' |
C3' |
C2' |
H2'1 |
119.3 |
144.0 |
| H3' |
C3' |
C2' |
H2'2 |
0.4 |
21.5 |
| C2' |
C3' |
H3' |
O3' |
240.6 |
236.3 |
| H3' |
C3' |
O3' |
H1 |
181.8 |
303.7 |
| H1 |
O3' |
C3' |
H3' |
181.8 |
303.7 |