PDB Chemical Component TDG
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 TDG
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O3' |
C3' |
1.432 |
1.429 |
| C3' |
C4' |
1.523 |
1.532 |
| C3' |
C2' |
1.518 |
1.531 |
| C4' |
C5' |
1.527 |
1.531 |
| C4' |
O4' |
1.433 |
1.429 |
| O2' |
C2' |
1.435 |
1.428 |
| O6' |
C6' |
1.431 |
1.429 |
| C2' |
C1' |
1.520 |
1.530 |
| C5' |
C6' |
1.529 |
1.530 |
| C5' |
O5' |
1.428 |
1.429 |
| O6 |
C6 |
1.433 |
1.428 |
| C1' |
O5' |
1.427 |
1.430 |
| C1' |
S1 |
1.756 |
1.814 |
| C6 |
C5 |
1.532 |
1.530 |
| O5 |
C5 |
1.427 |
1.429 |
| O5 |
C1 |
1.423 |
1.429 |
| S1 |
C1 |
1.756 |
1.813 |
| C5 |
C4 |
1.537 |
1.530 |
| C1 |
C2 |
1.516 |
1.531 |
| C4 |
O4 |
1.428 |
1.430 |
| C4 |
C3 |
1.521 |
1.532 |
| C2 |
O2 |
1.434 |
1.430 |
| C2 |
C3 |
1.512 |
1.532 |
| C3 |
O3 |
1.435 |
1.428 |
| C1 |
H1 |
1.101 |
1.090 |
| C2 |
H2 |
1.100 |
1.090 |
| O2 |
HO2 |
0.950 |
0.966 |
| C3 |
H3 |
1.100 |
1.090 |
| O3 |
HO3 |
0.950 |
0.967 |
| C4 |
H4 |
1.099 |
1.090 |
| O4 |
HO4 |
0.950 |
0.967 |
| C5 |
H5 |
1.100 |
1.091 |
| C6 |
H62 |
1.100 |
1.090 |
| C6 |
H61 |
1.100 |
1.090 |
| O6 |
HO6 |
0.950 |
0.967 |
| C1' |
H1' |
1.100 |
1.090 |
| C2' |
H2' |
1.100 |
1.090 |
| O2' |
HO2' |
0.950 |
0.967 |
| C3' |
H3' |
1.100 |
1.090 |
| O3' |
HO3' |
0.949 |
0.967 |
| C4' |
H4' |
1.100 |
1.091 |
| O4' |
HO4' |
0.950 |
0.968 |
| C5' |
H5' |
1.100 |
1.090 |
| C6' |
H6'2 |
1.100 |
1.091 |
| C6' |
H6'1 |
1.100 |
1.090 |
| O6' |
HO6' |
0.950 |
0.967 |
Bond Angles for TDG
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O3' |
C3' |
H3' |
109.9 |
109.6 |
| C3' |
C4' |
C5' |
111.7 |
109.1 |
| C3' |
C4' |
O4' |
109.3 |
109.5 |
| C4' |
C3' |
H3' |
108.7 |
109.5 |
| C3' |
C4' |
H4' |
108.5 |
109.5 |
| C3' |
C2' |
H2' |
108.5 |
109.5 |
| C5' |
C4' |
O4' |
109.2 |
109.5 |
| C4' |
C5' |
C6' |
111.8 |
109.5 |
| C4' |
C5' |
O5' |
111.0 |
109.4 |
| C5' |
C4' |
H4' |
108.5 |
109.5 |
| C4' |
C5' |
H5' |
108.3 |
109.5 |
| O4' |
C4' |
H4' |
109.7 |
109.6 |
| C4' |
O4' |
HO4' |
109.5 |
114.0 |
| O2' |
C2' |
H2' |
109.6 |
109.5 |
| O6' |
C6' |
H6'2 |
109.3 |
109.4 |
| O6' |
C6' |
H6'1 |
109.3 |
109.5 |
| C2' |
C1' |
O5' |
112.1 |
109.4 |
| C2' |
C1' |
S1 |
107.2 |
109.5 |
| C2' |
C1' |
H1' |
110.5 |
109.5 |
| C6' |
C5' |
O5' |
107.8 |
109.5 |
| C6' |
C5' |
H5' |
108.3 |
109.5 |
| C5' |
C6' |
H6'2 |
109.3 |
109.5 |
| C5' |
C6' |
H6'1 |
109.3 |
109.5 |
| C1' |
O5' |
C5' |
116.4 |
114.1 |
| O5' |
C5' |
H5' |
109.6 |
109.5 |
| O6 |
C6 |
H62 |
109.3 |
109.5 |
| O6 |
C6 |
H61 |
109.3 |
109.5 |
| O5' |
C1' |
S1 |
107.4 |
109.4 |
| O5' |
C1' |
H1' |
111.9 |
109.4 |
| S1 |
C1' |
H1' |
107.6 |
109.5 |
| C6 |
C5 |
H5 |
106.7 |
109.5 |
| O5 |
C5 |
H5 |
107.9 |
109.5 |
| O5 |
C1 |
H1 |
111.7 |
109.5 |
| S1 |
C1 |
H1 |
107.5 |
109.5 |
| C5 |
C4 |
O4 |
111.8 |
109.5 |
| C5 |
C4 |
H4 |
108.5 |
109.6 |
| C1 |
C2 |
O2 |
109.3 |
109.5 |
| C1 |
C2 |
C3 |
112.0 |
109.2 |
| C2 |
C1 |
H1 |
110.4 |
109.5 |
| C1 |
C2 |
H2 |
108.2 |
109.5 |
| O4 |
C4 |
H4 |
110.0 |
109.5 |
| C4 |
O4 |
HO4 |
109.5 |
114.0 |
| C4 |
C3 |
O3 |
111.7 |
109.6 |
| C4 |
C3 |
H3 |
109.8 |
109.6 |
| C3 |
C2 |
O2 |
109.8 |
109.5 |
| O2 |
C2 |
H2 |
109.2 |
109.5 |
| C2 |
O2 |
HO2 |
109.5 |
114.1 |
| C2 |
C3 |
O3 |
105.4 |
109.6 |
| C3 |
C2 |
H2 |
108.2 |
109.6 |
| C2 |
C3 |
H3 |
109.9 |
109.6 |
| O3 |
C3 |
H3 |
111.1 |
109.5 |
| C3 |
O3 |
HO3 |
109.5 |
114.0 |
| H61 |
C6 |
H62 |
109.5 |
109.5 |
| H6'1 |
C6' |
H6'2 |
109.5 |
109.4 |
Torsion Angles for TDG
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O3' |
C3' |
C4' |
O4' |
54.8 |
57.0 |
| C4' |
C3' |
O3' |
H3' |
119.5 |
120.2 |
| O3' |
C3' |
C4' |
H4' |
295.2 |
296.8 |
| O3' |
C3' |
C2' |
H2' |
301.4 |
303.1 |
| O3' |
C3' |
C4' |
H3' |
239.8 |
239.7 |
| C4' |
C3' |
C2' |
H2' |
62.3 |
62.9 |
| C5' |
C4' |
C3' |
O4' |
120.9 |
119.9 |
| C3' |
C4' |
C5' |
C6' |
188.3 |
182.4 |
| C3' |
C4' |
C5' |
O5' |
308.7 |
302.4 |
| C5' |
C4' |
C3' |
H4' |
240.5 |
240.1 |
| C3' |
C4' |
C5' |
H5' |
69.1 |
62.4 |
| O4' |
C4' |
C3' |
H4' |
119.6 |
120.2 |
| C3' |
C4' |
O4' |
HO4' |
180.0 |
300.0 |
| O2' |
C2' |
C3' |
H2' |
120.2 |
120.1 |
| C3' |
C2' |
C1' |
O5' |
55.3 |
57.6 |
| C3' |
C2' |
C1' |
S1 |
172.9 |
177.6 |
| C3' |
C2' |
C1' |
H1' |
289.8 |
297.6 |
| C3' |
C4' |
C5' |
O4' |
239.0 |
240.1 |
| C5' |
C4' |
C3' |
H3' |
295.9 |
297.1 |
| C3' |
C4' |
C5' |
H4' |
119.5 |
119.9 |
| O4' |
C4' |
C5' |
H4' |
240.5 |
239.8 |
| C5' |
C4' |
O4' |
HO4' |
57.6 |
180.3 |
| C6' |
C5' |
C4' |
O5' |
239.6 |
240.0 |
| C6' |
C5' |
C4' |
H5' |
119.2 |
120.0 |
| C4' |
C5' |
C6' |
H6'2 |
165.7 |
305.0 |
| C4' |
C5' |
C6' |
H6'1 |
45.9 |
64.9 |
| C1' |
O5' |
C5' |
C4' |
52.0 |
61.1 |
| O5' |
C5' |
C4' |
H5' |
239.6 |
240.0 |
| C3' |
C4' |
O4' |
C5' |
122.4 |
119.7 |
| O4' |
C4' |
C3' |
H3' |
175.0 |
177.2 |
| C3' |
C4' |
O4' |
H4' |
241.2 |
239.9 |
| O4' |
C4' |
C5' |
C6' |
309.3 |
302.3 |
| O4' |
C4' |
C5' |
O5' |
69.7 |
62.3 |
| C5' |
C4' |
O4' |
H4' |
118.7 |
120.2 |
| O4' |
C4' |
C5' |
H5' |
190.1 |
182.3 |
| C3' |
C2' |
O2' |
H2' |
240.5 |
239.9 |
| O2' |
C2' |
C1' |
O5' |
177.0 |
177.6 |
| O2' |
C2' |
C1' |
S1 |
294.6 |
297.5 |
| O2' |
C2' |
C1' |
H1' |
51.6 |
57.6 |
| O6' |
C6' |
C5' |
H5' |
45.0 |
305.0 |
| C5' |
C6' |
O6' |
H6'2 |
239.9 |
120.0 |
| C5' |
C6' |
O6' |
H6'1 |
120.1 |
239.9 |
| H6'1 |
C6' |
O6' |
H6'2 |
119.8 |
240.1 |
| C2' |
C1' |
O5' |
C5' |
305.0 |
298.9 |
| O5' |
C1' |
C2' |
S1 |
242.4 |
240.0 |
| O5' |
C1' |
C2' |
H1' |
125.5 |
120.0 |
| S1 |
C1' |
C2' |
H1' |
243.1 |
239.9 |
| C6' |
C5' |
C4' |
O4' |
309.3 |
302.3 |
| C4' |
C5' |
C6' |
O5' |
122.3 |
119.9 |
| C6' |
C5' |
C4' |
H4' |
68.8 |
62.6 |
| C4' |
C5' |
C6' |
H5' |
240.8 |
240.0 |
| O6' |
C6' |
C5' |
H6'2 |
120.1 |
240.0 |
| O6' |
C6' |
C5' |
H6'1 |
239.9 |
120.1 |
| C1' |
O5' |
C5' |
C6' |
174.8 |
181.1 |
| O5' |
C5' |
C6' |
H5' |
118.5 |
120.0 |
| H6'1 |
C6' |
C5' |
H6'2 |
240.2 |
119.9 |
| O5' |
C5' |
C4' |
O4' |
69.7 |
62.3 |
| C4' |
C5' |
O5' |
C6' |
237.2 |
240.0 |
| O5' |
C5' |
C4' |
H4' |
189.2 |
182.5 |
| C4' |
C5' |
O5' |
H5' |
119.6 |
120.0 |
| C6' |
C5' |
O5' |
H5' |
242.4 |
240.0 |
| O5' |
C5' |
C6' |
H6'2 |
43.4 |
185.1 |
| O5' |
C5' |
C6' |
H6'1 |
283.6 |
305.0 |
| C5' |
O5' |
C1' |
S1 |
187.5 |
178.9 |
| C5' |
O5' |
C1' |
H1' |
69.7 |
58.9 |
| O6 |
C6 |
C5 |
H5 |
281.1 |
305.0 |
| H61 |
C6 |
O6 |
H62 |
119.8 |
240.0 |
| C4' |
C5' |
O5' |
C1' |
52.0 |
61.1 |
| C2' |
C1' |
O5' |
S1 |
117.5 |
120.0 |
| C2' |
C1' |
O5' |
H1' |
235.3 |
240.0 |
| C6' |
C5' |
O5' |
C1' |
174.8 |
181.1 |
| C1' |
O5' |
C5' |
H5' |
292.5 |
301.1 |
| S1 |
C1' |
O5' |
H1' |
117.8 |
120.0 |
| C2' |
C1' |
S1 |
O5' |
239.4 |
240.0 |
| C2' |
C1' |
S1 |
H1' |
118.8 |
120.1 |
| S1 |
C1' |
O5' |
C5' |
187.5 |
178.9 |
| O5' |
C1' |
S1 |
H1' |
239.4 |
240.0 |
| C1' |
S1 |
C1 |
H1 |
24.3 |
55.0 |
| O5 |
C5 |
C6 |
H5 |
116.5 |
120.0 |
| C6 |
C5 |
C4 |
O4 |
298.1 |
302.3 |
| C6 |
C5 |
C4 |
H4 |
59.6 |
62.4 |
| C6 |
C5 |
O5 |
H5 |
244.2 |
240.0 |
| C5 |
O5 |
C1 |
H1 |
62.9 |
58.8 |
| O5 |
C5 |
C4 |
H4 |
184.4 |
182.4 |
| S1 |
C1 |
O5 |
H1 |
119.3 |
120.1 |
| C2 |
C1 |
O5 |
H1 |
235.9 |
240.1 |
| O5 |
C1 |
C2 |
H2 |
297.6 |
297.6 |
| O5 |
C1 |
S1 |
H1 |
238.1 |
239.9 |
| C2 |
C1 |
S1 |
H1 |
117.7 |
120.0 |
| S1 |
C1 |
C2 |
H2 |
56.9 |
57.6 |
| O4 |
C4 |
C5 |
H4 |
238.6 |
239.9 |
| C5 |
C4 |
O4 |
HO4 |
180.0 |
180.3 |
| C5 |
C4 |
C3 |
O3 |
165.9 |
176.8 |
| C5 |
C4 |
C3 |
H3 |
289.5 |
297.0 |
| O5 |
C1 |
C2 |
H1 |
124.9 |
119.9 |
| S1 |
C1 |
C2 |
H1 |
244.2 |
240.0 |
| C3 |
C2 |
C1 |
O2 |
238.1 |
240.1 |
| O2 |
C2 |
C1 |
H2 |
241.2 |
239.9 |
| C1 |
C2 |
O2 |
HO2 |
180.0 |
59.9 |
| C1 |
C2 |
C3 |
O3 |
189.7 |
183.1 |
| C3 |
C2 |
C1 |
H2 |
119.2 |
120.0 |
| C1 |
C2 |
C3 |
H3 |
70.0 |
62.9 |
| C5 |
C4 |
O4 |
H4 |
120.6 |
120.2 |
| O4 |
C4 |
C3 |
O3 |
43.9 |
56.9 |
| O4 |
C4 |
C3 |
H3 |
167.6 |
177.2 |
| C4 |
C3 |
C2 |
O2 |
188.1 |
183.2 |
| C2 |
C3 |
C4 |
O3 |
244.0 |
240.1 |
| C4 |
C3 |
C2 |
H2 |
68.9 |
63.0 |
| C2 |
C3 |
C4 |
H3 |
120.4 |
119.9 |
| O3 |
C3 |
C4 |
H3 |
236.3 |
239.8 |
| C4 |
C3 |
O3 |
HO3 |
180.0 |
180.5 |
| C1 |
C2 |
O2 |
C3 |
236.8 |
240.3 |
| O2 |
C2 |
C1 |
H1 |
53.8 |
57.6 |
| C1 |
C2 |
O2 |
H2 |
118.2 |
120.1 |
| O2 |
C2 |
C3 |
O3 |
68.1 |
63.2 |
| C3 |
C2 |
O2 |
H2 |
241.4 |
239.8 |
| O2 |
C2 |
C3 |
H3 |
308.4 |
303.0 |
| C1 |
C2 |
C3 |
O2 |
121.6 |
119.9 |
| C3 |
C2 |
C1 |
H1 |
291.9 |
297.6 |
| C1 |
C2 |
C3 |
H2 |
240.8 |
240.0 |
| C4 |
C3 |
C2 |
O3 |
120.0 |
119.9 |
| C4 |
C3 |
C2 |
H3 |
239.7 |
240.1 |
| O2 |
C2 |
C3 |
H2 |
119.2 |
120.1 |
| C3 |
C2 |
O2 |
HO2 |
303.2 |
179.7 |
| O3 |
C3 |
C2 |
H3 |
119.7 |
120.2 |
| C2 |
C3 |
O3 |
HO3 |
298.1 |
300.0 |
| C4 |
C3 |
O3 |
H3 |
122.9 |
120.2 |
| O3 |
C3 |
C2 |
O2 |
68.1 |
63.2 |
| O3 |
C3 |
C2 |
H2 |
308.9 |
303.1 |
| C2 |
C3 |
O3 |
H3 |
241.0 |
239.8 |
| H1 |
C1 |
C2 |
O2 |
53.8 |
57.6 |
| H1 |
C1 |
C2 |
C3 |
291.9 |
297.6 |
| H1 |
C1 |
C2 |
H2 |
172.7 |
177.6 |
| C1 |
C2 |
H2 |
O2 |
241.1 |
239.9 |
| C1 |
C2 |
H2 |
C3 |
121.6 |
119.8 |
| H2 |
C2 |
C1 |
H1 |
172.7 |
177.6 |
| C3 |
C2 |
H2 |
O2 |
119.5 |
120.2 |
| H2 |
C2 |
O2 |
HO2 |
61.8 |
299.9 |
| H2 |
C2 |
C3 |
O3 |
308.9 |
303.1 |
| H2 |
C2 |
C3 |
H3 |
189.2 |
182.9 |
| HO2 |
O2 |
C2 |
H2 |
61.8 |
299.9 |
| C4 |
C3 |
H3 |
O3 |
235.9 |
239.8 |
| H3 |
C3 |
C2 |
O2 |
308.4 |
303.0 |
| C2 |
C3 |
H3 |
O3 |
116.2 |
120.2 |
| H3 |
C3 |
C2 |
H2 |
189.2 |
182.9 |
| H3 |
C3 |
O3 |
HO3 |
57.0 |
60.2 |
| HO3 |
O3 |
C3 |
H3 |
57.0 |
60.2 |
| C5 |
C4 |
H4 |
O4 |
237.5 |
239.9 |
| H4 |
C4 |
O4 |
HO4 |
59.4 |
60.1 |
| H4 |
C4 |
C3 |
O3 |
286.0 |
296.9 |
| H4 |
C4 |
C3 |
H3 |
49.7 |
57.1 |
| HO4 |
O4 |
C4 |
H4 |
59.4 |
60.1 |
| H5 |
C5 |
C4 |
O4 |
180.1 |
182.3 |
| H5 |
C5 |
C4 |
H4 |
301.5 |
302.4 |
| O6 |
C6 |
H62 |
H61 |
119.7 |
240.0 |
| H62 |
C6 |
C5 |
H5 |
160.9 |
65.0 |
| O6 |
C6 |
H61 |
H62 |
240.3 |
120.0 |
| H61 |
C6 |
C5 |
H5 |
41.2 |
185.0 |
| HO6 |
O6 |
C6 |
H62 |
300.1 |
60.0 |
| HO6 |
O6 |
C6 |
H61 |
59.9 |
300.0 |
| C2' |
C1' |
H1' |
O5' |
125.6 |
119.9 |
| C2' |
C1' |
H1' |
S1 |
243.3 |
239.9 |
| H1' |
C1' |
O5' |
C5' |
69.7 |
58.9 |
| O5' |
C1' |
H1' |
S1 |
117.7 |
120.0 |
| H2' |
C2' |
C1' |
O5' |
297.2 |
297.7 |
| H2' |
C2' |
C1' |
S1 |
54.8 |
57.7 |
| H2' |
C2' |
C1' |
H1' |
171.7 |
177.8 |
| HO2' |
O2' |
C2' |
H2' |
299.5 |
299.8 |
| H3' |
C3' |
C4' |
C5' |
295.9 |
297.1 |
| H3' |
C3' |
C4' |
O4' |
175.0 |
177.2 |
| H3' |
C3' |
C4' |
H4' |
55.4 |
57.0 |
| H3' |
C3' |
C2' |
H2' |
181.1 |
182.8 |
| HO3' |
O3' |
C3' |
H3' |
60.5 |
59.8 |
| C3' |
C4' |
H4' |
C5' |
238.5 |
240.4 |
| C3' |
C4' |
H4' |
O4' |
119.3 |
120.1 |
| H4' |
C4' |
C3' |
H3' |
55.4 |
57.0 |
| C5' |
C4' |
H4' |
O4' |
240.8 |
239.8 |
| H4' |
C4' |
C5' |
C6' |
68.8 |
62.6 |
| H4' |
C4' |
C5' |
O5' |
189.2 |
182.5 |
| H4' |
C4' |
C5' |
H5' |
309.6 |
302.6 |
| H4' |
C4' |
O4' |
HO4' |
298.8 |
60.1 |
| HO4' |
O4' |
C4' |
H4' |
298.8 |
60.1 |
| H5' |
C5' |
C4' |
O4' |
190.1 |
182.3 |
| C4' |
C5' |
H5' |
C6' |
121.4 |
120.0 |
| C4' |
C5' |
H5' |
O5' |
238.8 |
240.0 |
| H5' |
C5' |
C4' |
H4' |
309.6 |
302.6 |
| C6' |
C5' |
H5' |
O5' |
117.4 |
120.0 |
| H5' |
C5' |
C6' |
H6'2 |
284.9 |
65.0 |
| H5' |
C5' |
C6' |
H6'1 |
165.1 |
185.0 |
| O6' |
C6' |
H6'2 |
H6'1 |
119.6 |
240.1 |
| H6'2 |
C6' |
C5' |
O5' |
43.4 |
185.1 |
| H6'2 |
C6' |
C5' |
H5' |
284.9 |
65.0 |
| C5' |
C6' |
H6'2 |
H6'1 |
240.3 |
120.0 |
| O6' |
C6' |
H6'1 |
H6'2 |
240.4 |
119.9 |
| H6'1 |
C6' |
C5' |
O5' |
283.6 |
305.0 |
| H6'1 |
C6' |
C5' |
H5' |
165.1 |
185.0 |
| C5' |
C6' |
H6'1 |
H6'2 |
119.6 |
240.0 |
| HO6' |
O6' |
C6' |
H6'2 |
300.1 |
60.0 |
| HO6' |
O6' |
C6' |
H6'1 |
59.9 |
300.1 |