PDB Chemical Component 0DC
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 0DC
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| OP3 |
P |
1.608 |
1.610 |
| OP3 |
HOP3 |
0.950 |
0.968 |
| P |
OP1 |
1.487 |
1.479 |
| P |
OP2 |
1.485 |
1.610 |
| P |
O5' |
1.594 |
1.610 |
| OP2 |
HOP2 |
0.950 |
0.968 |
| O5' |
C5' |
1.430 |
1.428 |
| C5' |
C4' |
1.511 |
1.530 |
| C5' |
H5' |
1.100 |
1.091 |
| C5' |
H5'' |
1.100 |
1.090 |
| C4' |
O4' |
1.448 |
1.444 |
| C4' |
C3' |
1.527 |
1.545 |
| C4' |
H4' |
1.100 |
1.090 |
| O4' |
C1' |
1.421 |
1.444 |
| C3' |
O3' |
1.432 |
1.428 |
| C3' |
C2' |
1.516 |
1.546 |
| C3' |
H3' |
1.100 |
1.089 |
| O3' |
HO3' |
0.950 |
0.968 |
| C2' |
C1' |
1.520 |
1.545 |
| C2' |
H2' |
1.100 |
1.089 |
| C2' |
H2'' |
1.100 |
1.090 |
| C1' |
N1 |
1.472 |
1.466 |
| C1' |
H1' |
1.100 |
1.090 |
| N1 |
C2 |
1.398 |
1.346 |
| N1 |
C6 |
1.367 |
1.363 |
| C2 |
O2 |
1.240 |
1.220 |
| C2 |
N3 |
1.352 |
1.331 |
| N3 |
C4 |
1.335 |
1.326 |
| C4 |
N4 |
1.333 |
1.376 |
| C4 |
C5 |
1.424 |
1.409 |
| N4 |
H41 |
1.000 |
0.970 |
| N4 |
H42 |
1.000 |
0.970 |
| C5 |
C6 |
1.338 |
1.354 |
| C5 |
H5 |
1.080 |
1.081 |
| C6 |
H6 |
1.080 |
1.079 |
Bond Angles for 0DC
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| P |
OP3 |
HOP3 |
109.5 |
114.0 |
| OP3 |
P |
OP1 |
107.7 |
109.5 |
| OP3 |
P |
OP2 |
108.2 |
109.5 |
| OP3 |
P |
O5' |
104.1 |
109.5 |
| OP1 |
P |
OP2 |
119.5 |
109.5 |
| OP1 |
P |
O5' |
108.1 |
109.5 |
| OP2 |
P |
O5' |
108.1 |
109.4 |
| P |
OP2 |
HOP2 |
109.5 |
114.0 |
| P |
O5' |
C5' |
121.2 |
123.0 |
| O5' |
C5' |
C4' |
110.2 |
109.5 |
| O5' |
C5' |
H5' |
109.2 |
109.5 |
| O5' |
C5' |
H5'' |
109.2 |
109.5 |
| C4' |
C5' |
H5' |
109.2 |
109.4 |
| C4' |
C5' |
H5'' |
109.2 |
109.4 |
| C5' |
C4' |
O4' |
108.8 |
110.4 |
| C5' |
C4' |
C3' |
115.0 |
110.4 |
| C5' |
C4' |
H4' |
104.9 |
110.3 |
| H5' |
C5' |
H5'' |
109.8 |
109.5 |
| O4' |
C4' |
C3' |
105.6 |
104.8 |
| O4' |
C4' |
H4' |
114.5 |
110.3 |
| C4' |
O4' |
C1' |
110.4 |
105.3 |
| C3' |
C4' |
H4' |
108.2 |
110.4 |
| C4' |
C3' |
O3' |
110.5 |
110.5 |
| C4' |
C3' |
C2' |
103.1 |
104.0 |
| C4' |
C3' |
H3' |
113.4 |
110.5 |
| O4' |
C1' |
C2' |
106.6 |
104.8 |
| O4' |
C1' |
N1 |
108.0 |
110.4 |
| O4' |
C1' |
H1' |
114.1 |
110.4 |
| O3' |
C3' |
C2' |
110.6 |
110.5 |
| O3' |
C3' |
H3' |
106.2 |
110.5 |
| C3' |
O3' |
HO3' |
109.5 |
114.0 |
| C2' |
C3' |
H3' |
113.2 |
110.6 |
| C3' |
C2' |
C1' |
102.5 |
104.0 |
| C3' |
C2' |
H2' |
111.9 |
110.5 |
| C3' |
C2' |
H2'' |
111.9 |
110.5 |
| C1' |
C2' |
H2' |
111.9 |
110.5 |
| C1' |
C2' |
H2'' |
111.9 |
110.5 |
| C2' |
C1' |
N1 |
114.3 |
110.3 |
| C2' |
C1' |
H1' |
107.8 |
110.4 |
| H2' |
C2' |
H2'' |
106.9 |
110.6 |
| N1 |
C1' |
H1' |
106.3 |
110.4 |
| C1' |
N1 |
C2 |
118.9 |
119.8 |
| C1' |
N1 |
C6 |
120.7 |
119.8 |
| C2 |
N1 |
C6 |
120.3 |
120.4 |
| N1 |
C2 |
O2 |
119.0 |
119.4 |
| N1 |
C2 |
N3 |
119.2 |
121.1 |
| N1 |
C6 |
C5 |
121.1 |
119.2 |
| N1 |
C6 |
H6 |
119.4 |
120.4 |
| O2 |
C2 |
N3 |
121.8 |
119.5 |
| C2 |
N3 |
C4 |
120.0 |
120.7 |
| N3 |
C4 |
N4 |
117.9 |
120.2 |
| N3 |
C4 |
C5 |
122.0 |
119.6 |
| N4 |
C4 |
C5 |
120.1 |
120.1 |
| C4 |
N4 |
H41 |
120.0 |
119.9 |
| C4 |
N4 |
H42 |
120.0 |
120.0 |
| C4 |
C5 |
C6 |
117.4 |
119.0 |
| C4 |
C5 |
H5 |
121.3 |
120.5 |
| H41 |
N4 |
H42 |
120.0 |
120.0 |
| C6 |
C5 |
H5 |
121.3 |
120.5 |
| C5 |
C6 |
H6 |
119.5 |
120.4 |
Torsion Angles for 0DC
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP1 |
P |
OP3 |
OP2 |
229.5 |
240.0 |
| OP1 |
P |
OP3 |
O5' |
114.6 |
120.0 |
| OP2 |
P |
OP3 |
O5' |
245.1 |
240.0 |
| OP3 |
P |
OP2 |
HOP2 |
236.3 |
60.0 |
| OP3 |
P |
O5' |
C5' |
85.4 |
175.0 |
| HOP3 |
OP3 |
P |
OP1 |
0.0 |
300.0 |
| HOP3 |
OP3 |
P |
OP2 |
130.5 |
60.0 |
| HOP3 |
OP3 |
P |
O5' |
245.4 |
180.0 |
| OP1 |
P |
OP3 |
HOP3 |
0.0 |
300.0 |
| OP3 |
P |
OP1 |
OP2 |
123.9 |
120.0 |
| OP3 |
P |
OP1 |
O5' |
248.1 |
240.0 |
| OP2 |
P |
OP1 |
O5' |
124.2 |
120.0 |
| OP1 |
P |
OP2 |
HOP2 |
0.0 |
180.0 |
| OP1 |
P |
O5' |
C5' |
331.0 |
54.9 |
| OP2 |
P |
OP3 |
HOP3 |
130.5 |
60.0 |
| OP3 |
P |
OP2 |
OP1 |
236.3 |
240.0 |
| OP3 |
P |
OP2 |
O5' |
112.2 |
120.0 |
| OP1 |
P |
OP2 |
O5' |
235.9 |
240.0 |
| OP2 |
P |
O5' |
C5' |
200.3 |
294.9 |
| O5' |
P |
OP3 |
HOP3 |
245.4 |
180.0 |
| OP3 |
P |
O5' |
OP1 |
114.4 |
120.0 |
| OP3 |
P |
O5' |
OP2 |
245.1 |
240.0 |
| OP1 |
P |
O5' |
OP2 |
130.7 |
120.0 |
| O5' |
P |
OP2 |
HOP2 |
124.2 |
300.0 |
| P |
O5' |
C5' |
C4' |
220.3 |
180.0 |
| P |
O5' |
C5' |
H5' |
340.3 |
300.0 |
| P |
O5' |
C5' |
H5'' |
100.3 |
60.1 |
| HOP2 |
OP2 |
P |
O5' |
124.2 |
300.0 |
| C4' |
C5' |
O5' |
H5' |
240.0 |
240.0 |
| C4' |
C5' |
O5' |
H5'' |
120.0 |
120.0 |
| O5' |
C5' |
C4' |
O4' |
148.2 |
293.6 |
| O5' |
C5' |
C4' |
C3' |
30.0 |
178.2 |
| O5' |
C5' |
C4' |
H4' |
271.2 |
55.8 |
| H5' |
C5' |
O5' |
H5'' |
240.0 |
240.0 |
| O5' |
C5' |
C4' |
H5' |
120.0 |
120.0 |
| O5' |
C5' |
C4' |
H5'' |
240.0 |
240.0 |
| H5' |
C5' |
C4' |
H5'' |
120.0 |
119.9 |
| O4' |
C4' |
C5' |
C3' |
118.3 |
115.5 |
| O4' |
C4' |
C5' |
H4' |
237.1 |
237.8 |
| C5' |
C4' |
O4' |
C1' |
244.7 |
200.6 |
| C3' |
C4' |
C5' |
H4' |
118.8 |
122.3 |
| C5' |
C4' |
C3' |
O3' |
211.3 |
261.5 |
| C5' |
C4' |
C3' |
C2' |
93.1 |
142.8 |
| C5' |
C4' |
C3' |
H3' |
330.4 |
24.1 |
| O5' |
C5' |
H5' |
C4' |
239.4 |
240.0 |
| O5' |
C5' |
H5' |
H5'' |
119.7 |
120.0 |
| C4' |
C5' |
H5' |
H5'' |
240.3 |
240.1 |
| H5' |
C5' |
C4' |
O4' |
28.3 |
173.6 |
| H5' |
C5' |
C4' |
C3' |
270.0 |
58.1 |
| H5' |
C5' |
C4' |
H4' |
151.2 |
295.8 |
| O5' |
C5' |
H5'' |
C4' |
120.6 |
120.0 |
| O5' |
C5' |
H5'' |
H5' |
240.3 |
240.0 |
| C4' |
C5' |
H5'' |
H5' |
119.7 |
119.9 |
| H5'' |
C5' |
C4' |
O4' |
268.2 |
53.6 |
| H5'' |
C5' |
C4' |
C3' |
150.0 |
298.2 |
| H5'' |
C5' |
C4' |
H4' |
31.2 |
175.8 |
| O4' |
C4' |
C5' |
H5' |
28.3 |
173.6 |
| O4' |
C4' |
C5' |
H5'' |
268.2 |
53.6 |
| C5' |
C4' |
O4' |
C3' |
236.0 |
241.1 |
| C5' |
C4' |
O4' |
H4' |
117.0 |
122.2 |
| C3' |
C4' |
O4' |
H4' |
241.1 |
241.1 |
| O4' |
C4' |
C3' |
O3' |
91.3 |
142.6 |
| O4' |
C4' |
C3' |
C2' |
333.1 |
24.0 |
| O4' |
C4' |
C3' |
H3' |
210.3 |
265.2 |
| C4' |
O4' |
C1' |
C2' |
13.3 |
40.5 |
| C4' |
O4' |
C1' |
N1 |
136.6 |
159.3 |
| C4' |
O4' |
C1' |
H1' |
254.5 |
281.6 |
| C3' |
C4' |
C5' |
H5' |
270.0 |
58.1 |
| C3' |
C4' |
C5' |
H5'' |
150.0 |
298.2 |
| C5' |
C4' |
C3' |
O4' |
120.0 |
118.9 |
| C5' |
C4' |
C3' |
H4' |
243.0 |
237.7 |
| O4' |
C4' |
C3' |
H4' |
123.0 |
118.9 |
| C3' |
C4' |
O4' |
C1' |
8.7 |
319.5 |
| O3' |
C3' |
C4' |
C2' |
118.2 |
118.6 |
| O3' |
C3' |
C4' |
H3' |
241.0 |
237.4 |
| C4' |
C3' |
O3' |
HO3' |
180.0 |
180.0 |
| C2' |
C3' |
C4' |
H3' |
122.8 |
118.7 |
| C4' |
C3' |
C2' |
C1' |
33.9 |
0.0 |
| C4' |
C3' |
C2' |
H2' |
153.9 |
118.7 |
| C4' |
C3' |
C2' |
H2'' |
273.9 |
241.4 |
| H4' |
C4' |
C5' |
H5' |
151.2 |
295.8 |
| H4' |
C4' |
C5' |
H5'' |
31.2 |
175.8 |
| C5' |
C4' |
H4' |
O4' |
240.8 |
237.8 |
| C5' |
C4' |
H4' |
C3' |
123.3 |
122.3 |
| O4' |
C4' |
H4' |
C3' |
242.5 |
244.5 |
| H4' |
C4' |
O4' |
C1' |
127.6 |
78.4 |
| H4' |
C4' |
C3' |
O3' |
328.3 |
23.7 |
| H4' |
C4' |
C3' |
C2' |
210.1 |
265.1 |
| H4' |
C4' |
C3' |
H3' |
87.3 |
146.4 |
| C1' |
O4' |
C4' |
C3' |
8.7 |
319.5 |
| C1' |
O4' |
C4' |
H4' |
127.6 |
78.4 |
| C3' |
C2' |
C1' |
O4' |
330.3 |
336.0 |
| O4' |
C1' |
C2' |
H2' |
210.3 |
217.4 |
| O4' |
C1' |
C2' |
H2'' |
90.3 |
94.6 |
| C2' |
C1' |
O4' |
N1 |
236.7 |
241.2 |
| C2' |
C1' |
O4' |
H1' |
118.8 |
118.9 |
| N1 |
C1' |
O4' |
H1' |
242.1 |
237.7 |
| O4' |
C1' |
N1 |
C2 |
151.4 |
181.5 |
| O4' |
C1' |
N1 |
C6 |
331.4 |
1.2 |
| O3' |
C3' |
C4' |
H4' |
328.3 |
23.7 |
| C4' |
C3' |
O3' |
C2' |
246.5 |
245.4 |
| C4' |
C3' |
O3' |
H3' |
123.3 |
122.6 |
| C2' |
C3' |
O3' |
H3' |
236.8 |
237.2 |
| O3' |
C3' |
C2' |
C1' |
275.8 |
241.4 |
| O3' |
C3' |
C2' |
H2' |
35.8 |
0.0 |
| O3' |
C3' |
C2' |
H2'' |
155.8 |
122.8 |
| C2' |
C3' |
C4' |
H4' |
210.1 |
265.1 |
| C4' |
C3' |
C2' |
O3' |
118.1 |
118.6 |
| C4' |
C3' |
C2' |
H3' |
237.1 |
241.4 |
| O4' |
C1' |
C2' |
C3' |
330.3 |
336.0 |
| O3' |
C3' |
C2' |
H3' |
119.0 |
122.7 |
| C2' |
C3' |
O3' |
HO3' |
293.5 |
294.7 |
| C1' |
C2' |
C3' |
H2' |
240.0 |
241.4 |
| C1' |
C2' |
C3' |
H2'' |
120.0 |
118.6 |
| C3' |
C2' |
C1' |
N1 |
211.1 |
217.2 |
| C3' |
C2' |
C1' |
H1' |
93.2 |
94.9 |
| H2' |
C2' |
C3' |
H2'' |
240.0 |
237.3 |
| H3' |
C3' |
C4' |
H4' |
87.3 |
146.4 |
| C4' |
C3' |
H3' |
O3' |
238.5 |
237.4 |
| C4' |
C3' |
H3' |
C2' |
117.0 |
114.7 |
| O3' |
C3' |
H3' |
C2' |
238.4 |
237.3 |
| H3' |
C3' |
O3' |
HO3' |
56.7 |
57.4 |
| H3' |
C3' |
C2' |
C1' |
156.8 |
118.7 |
| H3' |
C3' |
C2' |
H2' |
276.8 |
237.3 |
| H3' |
C3' |
C2' |
H2'' |
36.8 |
0.0 |
| HO3' |
O3' |
C3' |
C2' |
293.5 |
294.7 |
| HO3' |
O3' |
C3' |
H3' |
56.7 |
57.4 |
| O4' |
C1' |
C2' |
N1 |
119.2 |
118.8 |
| O4' |
C1' |
C2' |
H1' |
237.1 |
241.1 |
| C1' |
C2' |
C3' |
H3' |
156.8 |
118.7 |
| C3' |
C2' |
C1' |
H2' |
120.0 |
118.6 |
| C3' |
C2' |
C1' |
H2'' |
240.0 |
241.4 |
| H2' |
C2' |
C1' |
H2'' |
120.0 |
122.8 |
| N1 |
C1' |
C2' |
H1' |
117.9 |
122.3 |
| C2' |
C1' |
N1 |
C2 |
269.8 |
296.8 |
| C2' |
C1' |
N1 |
C6 |
89.8 |
116.6 |
| H2' |
C2' |
C3' |
H3' |
276.8 |
237.3 |
| C3' |
C2' |
H2' |
C1' |
245.6 |
245.4 |
| C3' |
C2' |
H2' |
H2'' |
122.8 |
122.7 |
| C1' |
C2' |
H2' |
H2'' |
237.2 |
237.3 |
| H2' |
C2' |
C1' |
N1 |
91.1 |
98.6 |
| H2' |
C2' |
C1' |
H1' |
333.1 |
336.3 |
| H2'' |
C2' |
C3' |
H3' |
36.8 |
0.0 |
| C3' |
C2' |
H2'' |
C1' |
114.4 |
114.6 |
| C3' |
C2' |
H2'' |
H2' |
237.2 |
237.3 |
| C1' |
C2' |
H2'' |
H2' |
122.8 |
122.7 |
| H2'' |
C2' |
C1' |
N1 |
331.1 |
335.8 |
| H2'' |
C2' |
C1' |
H1' |
213.2 |
213.5 |
| O4' |
C1' |
N1 |
C2' |
241.6 |
244.6 |
| O4' |
C1' |
N1 |
H1' |
122.8 |
122.3 |
| N1 |
C1' |
C2' |
H2' |
91.1 |
98.6 |
| N1 |
C1' |
C2' |
H2'' |
331.1 |
335.8 |
| C2' |
C1' |
N1 |
H1' |
241.3 |
237.7 |
| C2 |
N1 |
C1' |
C6 |
180.1 |
180.2 |
| C1' |
N1 |
C2 |
O2 |
359.9 |
360.0 |
| C1' |
N1 |
C2 |
N3 |
179.9 |
180.0 |
| C1' |
N1 |
C6 |
C5 |
180.2 |
179.7 |
| C1' |
N1 |
C6 |
H6 |
0.2 |
359.9 |
| O4' |
C1' |
H1' |
C2' |
118.1 |
115.4 |
| O4' |
C1' |
H1' |
N1 |
241.1 |
237.7 |
| H1' |
C1' |
C2' |
H2' |
333.1 |
336.3 |
| H1' |
C1' |
C2' |
H2'' |
213.2 |
213.5 |
| C2' |
C1' |
H1' |
N1 |
123.0 |
122.3 |
| H1' |
C1' |
N1 |
C2 |
28.6 |
59.2 |
| H1' |
C1' |
N1 |
C6 |
208.5 |
238.9 |
| C2 |
N1 |
C1' |
H1' |
28.6 |
59.2 |
| C1' |
N1 |
C2 |
C6 |
179.9 |
179.8 |
| C2 |
N1 |
C6 |
C5 |
0.1 |
359.5 |
| C2 |
N1 |
C6 |
H6 |
180.1 |
179.7 |
| O2 |
C2 |
N1 |
N3 |
180.1 |
179.9 |
| N1 |
C2 |
N3 |
C4 |
0.0 |
360.0 |
| C6 |
N1 |
C1' |
H1' |
208.5 |
238.9 |
| C1' |
N1 |
C6 |
C2 |
180.1 |
180.2 |
| C6 |
N1 |
C2 |
O2 |
180.0 |
180.2 |
| C6 |
N1 |
C2 |
N3 |
359.9 |
0.3 |
| C4 |
C5 |
C6 |
N1 |
359.9 |
0.5 |
| N1 |
C6 |
C5 |
H5 |
179.9 |
180.3 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
179.8 |
| O2 |
C2 |
N1 |
C6 |
180.0 |
180.2 |
| N1 |
C2 |
O2 |
N3 |
179.9 |
180.1 |
| O2 |
C2 |
N3 |
C4 |
180.0 |
180.1 |
| N3 |
C2 |
N1 |
C6 |
359.9 |
0.3 |
| N1 |
C2 |
N3 |
O2 |
180.1 |
179.9 |
| C2 |
N3 |
C4 |
N4 |
180.1 |
180.1 |
| C2 |
N3 |
C4 |
C5 |
0.0 |
0.0 |
| N4 |
C4 |
N3 |
C5 |
180.1 |
180.1 |
| N3 |
C4 |
N4 |
H41 |
360.0 |
0.0 |
| N3 |
C4 |
N4 |
H42 |
180.0 |
180.0 |
| N3 |
C4 |
C5 |
C6 |
0.0 |
359.7 |
| N3 |
C4 |
C5 |
H5 |
180.0 |
180.0 |
| N3 |
C4 |
N4 |
C5 |
179.9 |
179.9 |
| N4 |
C4 |
C5 |
C6 |
179.9 |
179.7 |
| N4 |
C4 |
C5 |
H5 |
359.9 |
359.9 |
| H41 |
N4 |
C4 |
H42 |
180.0 |
180.0 |
| N1 |
C6 |
C5 |
C4 |
359.9 |
0.5 |
| N3 |
C4 |
C5 |
N4 |
180.1 |
180.1 |
| C5 |
C4 |
N4 |
H41 |
180.1 |
180.1 |
| C5 |
C4 |
N4 |
H42 |
0.1 |
0.0 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
179.8 |
| C4 |
C5 |
C6 |
H6 |
179.9 |
180.3 |
| H41 |
N4 |
C4 |
C5 |
180.1 |
180.1 |
| C4 |
N4 |
H41 |
H42 |
180.0 |
180.0 |
| H42 |
N4 |
C4 |
C5 |
0.1 |
0.0 |
| C4 |
N4 |
H42 |
H41 |
180.0 |
180.0 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.2 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
180.2 |
| C4 |
C5 |
H5 |
C6 |
180.0 |
179.8 |
| H5 |
C5 |
C6 |
H6 |
359.9 |
0.1 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
179.8 |
| H6 |
C6 |
C5 |
H5 |
359.9 |
0.1 |