PDB Chemical Component DC
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 DC
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| OP3 |
P |
1.631 |
1.610 |
| OP3 |
HOP3 |
0.951 |
0.967 |
| P |
OP1 |
1.460 |
1.480 |
| P |
OP2 |
1.432 |
1.609 |
| P |
O5' |
1.615 |
1.611 |
| OP2 |
HOP2 |
0.951 |
0.967 |
| O5' |
C5' |
1.406 |
1.428 |
| C5' |
C4' |
1.509 |
1.530 |
| C5' |
H5' |
1.115 |
1.090 |
| C5' |
H5'' |
1.115 |
1.089 |
| C4' |
O4' |
1.444 |
1.445 |
| C4' |
C3' |
1.540 |
1.549 |
| C4' |
H4' |
1.115 |
1.090 |
| O4' |
C1' |
1.436 |
1.437 |
| C3' |
O3' |
1.452 |
1.429 |
| C3' |
C2' |
1.511 |
1.547 |
| C3' |
H3' |
1.115 |
1.090 |
| O3' |
HO3' |
0.949 |
0.968 |
| C2' |
C1' |
1.547 |
1.541 |
| C2' |
H2' |
1.114 |
1.089 |
| C2' |
H2'' |
1.114 |
1.091 |
| C1' |
N1 |
1.457 |
1.465 |
| C1' |
H1' |
1.116 |
1.090 |
| N1 |
C2 |
1.391 |
1.344 |
| N1 |
C6 |
1.380 |
1.362 |
| C2 |
O2 |
1.236 |
1.220 |
| C2 |
N3 |
1.352 |
1.332 |
| N3 |
C4 |
1.346 |
1.326 |
| C4 |
N4 |
1.324 |
1.376 |
| C4 |
C5 |
1.419 |
1.410 |
| N4 |
H41 |
1.020 |
0.970 |
| N4 |
H42 |
1.019 |
0.970 |
| C5 |
C6 |
1.320 |
1.353 |
| C5 |
H5 |
1.103 |
1.081 |
| C6 |
H6 |
1.102 |
1.080 |
Bond Angles for DC
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| P |
OP3 |
HOP3 |
109.4 |
106.8 |
| OP3 |
P |
OP1 |
109.4 |
109.4 |
| OP3 |
P |
OP2 |
110.8 |
109.5 |
| OP3 |
P |
O5' |
102.6 |
109.5 |
| OP1 |
P |
OP2 |
121.1 |
109.5 |
| OP1 |
P |
O5' |
108.9 |
109.5 |
| OP2 |
P |
O5' |
102.2 |
109.5 |
| P |
OP2 |
HOP2 |
121.1 |
106.8 |
| P |
O5' |
C5' |
119.2 |
106.8 |
| O5' |
C5' |
C4' |
107.1 |
109.5 |
| O5' |
C5' |
H5' |
113.1 |
109.5 |
| O5' |
C5' |
H5'' |
113.1 |
109.6 |
| C4' |
C5' |
H5' |
113.1 |
109.4 |
| C4' |
C5' |
H5'' |
113.1 |
109.4 |
| C5' |
C4' |
O4' |
109.5 |
110.8 |
| C5' |
C4' |
C3' |
115.9 |
110.7 |
| C5' |
C4' |
H4' |
103.3 |
110.5 |
| H5' |
C5' |
H5'' |
97.3 |
109.4 |
| O4' |
C4' |
C3' |
103.3 |
103.6 |
| O4' |
C4' |
H4' |
115.8 |
110.5 |
| C4' |
O4' |
C1' |
103.5 |
106.9 |
| C3' |
C4' |
H4' |
109.5 |
110.6 |
| C4' |
C3' |
O3' |
104.9 |
110.9 |
| C4' |
C3' |
C2' |
104.6 |
102.1 |
| C4' |
C3' |
H3' |
117.0 |
110.9 |
| O4' |
C1' |
C2' |
105.0 |
107.4 |
| O4' |
C1' |
N1 |
107.4 |
109.9 |
| O4' |
C1' |
H1' |
115.6 |
109.9 |
| O3' |
C3' |
C2' |
114.1 |
110.9 |
| O3' |
C3' |
H3' |
108.1 |
110.8 |
| C3' |
O3' |
HO3' |
104.9 |
106.7 |
| C2' |
C3' |
H3' |
108.3 |
110.9 |
| C3' |
C2' |
C1' |
103.4 |
104.2 |
| C3' |
C2' |
H2' |
114.5 |
110.5 |
| C3' |
C2' |
H2'' |
114.5 |
110.5 |
| C1' |
C2' |
H2' |
114.5 |
110.5 |
| C1' |
C2' |
H2'' |
114.5 |
110.4 |
| C2' |
C1' |
N1 |
114.9 |
109.9 |
| C2' |
C1' |
H1' |
108.3 |
109.8 |
| H2' |
C2' |
H2'' |
96.0 |
110.5 |
| N1 |
C1' |
H1' |
105.9 |
109.9 |
| C1' |
N1 |
C2 |
119.4 |
119.8 |
| C1' |
N1 |
C6 |
119.7 |
119.8 |
| C2 |
N1 |
C6 |
120.8 |
120.3 |
| N1 |
C2 |
O2 |
119.4 |
119.5 |
| N1 |
C2 |
N3 |
118.8 |
121.1 |
| N1 |
C6 |
C5 |
120.0 |
119.3 |
| N1 |
C6 |
H6 |
122.2 |
120.4 |
| O2 |
C2 |
N3 |
121.8 |
119.5 |
| C2 |
N3 |
C4 |
120.3 |
120.7 |
| N3 |
C4 |
N4 |
116.9 |
120.2 |
| N3 |
C4 |
C5 |
120.7 |
119.6 |
| N4 |
C4 |
C5 |
122.4 |
120.2 |
| C4 |
N4 |
H41 |
122.4 |
120.0 |
| C4 |
N4 |
H42 |
107.6 |
120.0 |
| C4 |
C5 |
C6 |
119.1 |
119.0 |
| C4 |
C5 |
H5 |
123.9 |
120.5 |
| H41 |
N4 |
H42 |
107.6 |
120.0 |
| C6 |
C5 |
H5 |
116.9 |
120.5 |
| C5 |
C6 |
H6 |
117.8 |
120.4 |
Torsion Angles for DC
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP1 |
P |
OP3 |
OP2 |
136.0 |
240.0 |
| OP1 |
P |
OP3 |
O5' |
244.5 |
119.9 |
| OP2 |
P |
OP3 |
O5' |
108.5 |
240.0 |
| OP3 |
P |
OP2 |
HOP2 |
310.1 |
60.0 |
| OP3 |
P |
O5' |
C5' |
290.3 |
180.0 |
| HOP3 |
OP3 |
P |
OP1 |
180.0 |
300.0 |
| HOP3 |
OP3 |
P |
OP2 |
44.0 |
60.0 |
| HOP3 |
OP3 |
P |
O5' |
295.5 |
180.0 |
| OP1 |
P |
OP3 |
HOP3 |
180.0 |
300.0 |
| OP3 |
P |
OP1 |
OP2 |
229.3 |
120.0 |
| OP3 |
P |
OP1 |
O5' |
111.4 |
240.1 |
| OP2 |
P |
OP1 |
O5' |
242.1 |
120.1 |
| OP1 |
P |
OP2 |
HOP2 |
180.0 |
180.0 |
| OP1 |
P |
O5' |
C5' |
46.1 |
60.0 |
| OP2 |
P |
OP3 |
HOP3 |
44.0 |
60.0 |
| OP3 |
P |
OP2 |
OP1 |
130.1 |
240.0 |
| OP3 |
P |
OP2 |
O5' |
251.3 |
120.0 |
| OP1 |
P |
OP2 |
O5' |
121.2 |
240.0 |
| OP2 |
P |
O5' |
C5' |
175.4 |
300.0 |
| O5' |
P |
OP3 |
HOP3 |
295.5 |
180.0 |
| OP3 |
P |
O5' |
OP1 |
244.2 |
119.9 |
| OP3 |
P |
O5' |
OP2 |
114.9 |
240.0 |
| OP1 |
P |
O5' |
OP2 |
230.8 |
120.1 |
| O5' |
P |
OP2 |
HOP2 |
58.8 |
300.0 |
| P |
O5' |
C5' |
C4' |
167.5 |
180.0 |
| P |
O5' |
C5' |
H5' |
292.8 |
60.0 |
| P |
O5' |
C5' |
H5'' |
42.2 |
300.0 |
| HOP2 |
OP2 |
P |
O5' |
58.8 |
300.0 |
| C4' |
C5' |
O5' |
H5' |
234.7 |
120.0 |
| C4' |
C5' |
O5' |
H5'' |
125.3 |
240.0 |
| O5' |
C5' |
C4' |
O4' |
293.5 |
65.7 |
| O5' |
C5' |
C4' |
C3' |
49.8 |
180.0 |
| O5' |
C5' |
C4' |
H4' |
169.6 |
302.9 |
| H5' |
C5' |
O5' |
H5'' |
250.5 |
120.0 |
| O5' |
C5' |
C4' |
H5' |
125.3 |
240.0 |
| O5' |
C5' |
C4' |
H5'' |
234.7 |
120.1 |
| H5' |
C5' |
C4' |
H5'' |
109.4 |
240.1 |
| O4' |
C4' |
C5' |
C3' |
243.7 |
245.7 |
| O4' |
C4' |
C5' |
H4' |
124.0 |
122.8 |
| C5' |
C4' |
O4' |
C1' |
168.6 |
158.6 |
| C3' |
C4' |
C5' |
H4' |
240.2 |
237.1 |
| C5' |
C4' |
C3' |
O3' |
90.5 |
86.1 |
| C5' |
C4' |
C3' |
C2' |
210.9 |
204.3 |
| C5' |
C4' |
C3' |
H3' |
330.7 |
322.6 |
| O5' |
C5' |
H5' |
C4' |
238.0 |
120.0 |
| O5' |
C5' |
H5' |
H5'' |
119.0 |
239.9 |
| C4' |
C5' |
H5' |
H5'' |
241.0 |
119.9 |
| H5' |
C5' |
C4' |
O4' |
168.2 |
185.7 |
| H5' |
C5' |
C4' |
C3' |
284.5 |
300.0 |
| H5' |
C5' |
C4' |
H4' |
44.3 |
62.9 |
| O5' |
C5' |
H5'' |
C4' |
122.0 |
240.0 |
| O5' |
C5' |
H5'' |
H5' |
240.9 |
120.1 |
| C4' |
C5' |
H5'' |
H5' |
119.0 |
240.1 |
| H5'' |
C5' |
C4' |
O4' |
58.8 |
305.6 |
| H5'' |
C5' |
C4' |
C3' |
175.1 |
59.9 |
| H5'' |
C5' |
C4' |
H4' |
294.9 |
182.8 |
| O4' |
C4' |
C5' |
H5' |
168.2 |
185.7 |
| O4' |
C4' |
C5' |
H5'' |
58.8 |
305.6 |
| C5' |
C4' |
O4' |
C3' |
124.0 |
118.7 |
| C5' |
C4' |
O4' |
H4' |
243.7 |
237.1 |
| C3' |
C4' |
O4' |
H4' |
119.7 |
118.5 |
| O4' |
C4' |
C3' |
O3' |
210.2 |
204.8 |
| O4' |
C4' |
C3' |
C2' |
330.6 |
323.0 |
| O4' |
C4' |
C3' |
H3' |
90.4 |
81.3 |
| C4' |
O4' |
C1' |
C2' |
317.7 |
333.7 |
| C4' |
O4' |
C1' |
N1 |
195.0 |
214.2 |
| C4' |
O4' |
C1' |
H1' |
77.0 |
93.1 |
| C3' |
C4' |
C5' |
H5' |
284.5 |
300.0 |
| C3' |
C4' |
C5' |
H5'' |
175.1 |
59.9 |
| C5' |
C4' |
C3' |
O4' |
240.3 |
241.3 |
| C5' |
C4' |
C3' |
H4' |
116.3 |
122.9 |
| O4' |
C4' |
C3' |
H4' |
236.0 |
241.6 |
| C3' |
C4' |
O4' |
C1' |
44.5 |
39.9 |
| O3' |
C3' |
C4' |
C2' |
239.6 |
241.8 |
| O3' |
C3' |
C4' |
H3' |
119.8 |
123.5 |
| C4' |
C3' |
O3' |
HO3' |
180.0 |
174.2 |
| C2' |
C3' |
C4' |
H3' |
240.2 |
241.7 |
| C4' |
C3' |
C2' |
C1' |
4.2 |
20.9 |
| C4' |
C3' |
C2' |
H2' |
129.4 |
262.2 |
| C4' |
C3' |
C2' |
H2'' |
238.9 |
139.5 |
| H4' |
C4' |
C5' |
H5' |
44.3 |
62.9 |
| H4' |
C4' |
C5' |
H5'' |
294.9 |
182.8 |
| C5' |
C4' |
H4' |
O4' |
119.7 |
123.0 |
| C5' |
C4' |
H4' |
C3' |
236.0 |
237.1 |
| O4' |
C4' |
H4' |
C3' |
116.3 |
114.1 |
| H4' |
C4' |
O4' |
C1' |
284.8 |
281.4 |
| H4' |
C4' |
C3' |
O3' |
334.2 |
323.2 |
| H4' |
C4' |
C3' |
C2' |
94.6 |
81.4 |
| H4' |
C4' |
C3' |
H3' |
214.4 |
199.7 |
| C1' |
O4' |
C4' |
C3' |
44.5 |
39.9 |
| C1' |
O4' |
C4' |
H4' |
284.8 |
281.4 |
| C3' |
C2' |
C1' |
O4' |
22.7 |
1.9 |
| O4' |
C1' |
C2' |
H2' |
257.4 |
120.6 |
| O4' |
C1' |
C2' |
H2'' |
147.9 |
243.3 |
| C2' |
C1' |
O4' |
N1 |
122.7 |
119.5 |
| C2' |
C1' |
O4' |
H1' |
240.7 |
240.6 |
| N1 |
C1' |
O4' |
H1' |
118.0 |
121.1 |
| O4' |
C1' |
N1 |
C2 |
232.8 |
58.3 |
| O4' |
C1' |
N1 |
C6 |
49.1 |
238.3 |
| O3' |
C3' |
C4' |
H4' |
334.2 |
323.2 |
| C4' |
C3' |
O3' |
C2' |
113.9 |
112.7 |
| C4' |
C3' |
O3' |
H3' |
234.5 |
236.4 |
| C2' |
C3' |
O3' |
H3' |
120.5 |
123.6 |
| O3' |
C3' |
C2' |
C1' |
118.2 |
139.1 |
| O3' |
C3' |
C2' |
H2' |
243.5 |
20.4 |
| O3' |
C3' |
C2' |
H2'' |
353.0 |
257.7 |
| C2' |
C3' |
C4' |
H4' |
94.6 |
81.4 |
| C4' |
C3' |
C2' |
O3' |
245.9 |
241.8 |
| C4' |
C3' |
C2' |
H3' |
125.5 |
118.2 |
| O4' |
C1' |
C2' |
C3' |
22.7 |
1.9 |
| O3' |
C3' |
C2' |
H3' |
239.6 |
236.5 |
| C2' |
C3' |
O3' |
HO3' |
66.1 |
61.5 |
| C1' |
C2' |
C3' |
H2' |
234.8 |
118.7 |
| C1' |
C2' |
C3' |
H2'' |
125.2 |
241.4 |
| C3' |
C2' |
C1' |
N1 |
140.4 |
121.5 |
| C3' |
C2' |
C1' |
H1' |
258.6 |
242.5 |
| H2' |
C2' |
C3' |
H2'' |
250.5 |
122.7 |
| H3' |
C3' |
C4' |
H4' |
214.4 |
199.7 |
| C4' |
C3' |
H3' |
O3' |
118.0 |
123.6 |
| C4' |
C3' |
H3' |
C2' |
242.1 |
247.2 |
| O3' |
C3' |
H3' |
C2' |
124.1 |
123.6 |
| H3' |
C3' |
O3' |
HO3' |
305.5 |
297.8 |
| H3' |
C3' |
C2' |
C1' |
238.7 |
262.7 |
| H3' |
C3' |
C2' |
H2' |
3.9 |
143.9 |
| H3' |
C3' |
C2' |
H2'' |
113.4 |
21.3 |
| HO3' |
O3' |
C3' |
C2' |
66.1 |
61.5 |
| HO3' |
O3' |
C3' |
H3' |
305.5 |
297.8 |
| O4' |
C1' |
C2' |
N1 |
242.2 |
240.5 |
| O4' |
C1' |
C2' |
H1' |
124.1 |
119.5 |
| C1' |
C2' |
C3' |
H3' |
238.7 |
262.7 |
| C3' |
C2' |
C1' |
H2' |
125.3 |
241.3 |
| C3' |
C2' |
C1' |
H2'' |
234.7 |
118.7 |
| H2' |
C2' |
C1' |
H2'' |
109.5 |
237.4 |
| N1 |
C1' |
C2' |
H1' |
241.9 |
239.0 |
| C2' |
C1' |
N1 |
C2 |
116.3 |
300.3 |
| C2' |
C1' |
N1 |
C6 |
292.7 |
120.3 |
| H2' |
C2' |
C3' |
H3' |
3.9 |
143.9 |
| C3' |
C2' |
H2' |
C1' |
240.8 |
114.8 |
| C3' |
C2' |
H2' |
H2'' |
120.4 |
237.3 |
| C1' |
C2' |
H2' |
H2'' |
239.6 |
122.6 |
| H2' |
C2' |
C1' |
N1 |
15.2 |
240.2 |
| H2' |
C2' |
C1' |
H1' |
133.3 |
1.2 |
| H2'' |
C2' |
C3' |
H3' |
113.4 |
21.3 |
| C3' |
C2' |
H2'' |
C1' |
119.2 |
245.3 |
| C3' |
C2' |
H2'' |
H2' |
239.6 |
122.6 |
| C1' |
C2' |
H2'' |
H2' |
120.4 |
237.4 |
| H2'' |
C2' |
C1' |
N1 |
265.7 |
2.8 |
| H2'' |
C2' |
C1' |
H1' |
23.8 |
123.8 |
| O4' |
C1' |
N1 |
C2' |
116.4 |
118.0 |
| O4' |
C1' |
N1 |
H1' |
235.9 |
238.9 |
| N1 |
C1' |
C2' |
H2' |
15.2 |
240.2 |
| N1 |
C1' |
C2' |
H2'' |
265.7 |
2.8 |
| C2' |
C1' |
N1 |
H1' |
119.5 |
121.0 |
| C2 |
N1 |
C1' |
C6 |
183.6 |
180.0 |
| C1' |
N1 |
C2 |
O2 |
353.4 |
360.0 |
| C1' |
N1 |
C2 |
N3 |
170.3 |
180.0 |
| C1' |
N1 |
C6 |
C5 |
186.7 |
179.8 |
| C1' |
N1 |
C6 |
H6 |
6.6 |
359.9 |
| O4' |
C1' |
H1' |
C2' |
242.5 |
242.1 |
| O4' |
C1' |
H1' |
N1 |
118.8 |
121.1 |
| H1' |
C1' |
C2' |
H2' |
133.3 |
1.2 |
| H1' |
C1' |
C2' |
H2'' |
23.8 |
123.8 |
| C2' |
C1' |
H1' |
N1 |
236.3 |
239.0 |
| H1' |
C1' |
N1 |
C2 |
356.9 |
179.3 |
| H1' |
C1' |
N1 |
C6 |
173.2 |
359.3 |
| C2 |
N1 |
C1' |
H1' |
356.9 |
179.3 |
| C1' |
N1 |
C2 |
C6 |
176.3 |
180.0 |
| C2 |
N1 |
C6 |
C5 |
3.0 |
359.7 |
| C2 |
N1 |
C6 |
H6 |
182.9 |
179.9 |
| O2 |
C2 |
N1 |
N3 |
183.1 |
180.0 |
| N1 |
C2 |
N3 |
C4 |
4.1 |
360.0 |
| C6 |
N1 |
C1' |
H1' |
173.2 |
359.3 |
| C1' |
N1 |
C6 |
C2 |
183.7 |
180.0 |
| C6 |
N1 |
C2 |
O2 |
177.0 |
180.0 |
| C6 |
N1 |
C2 |
N3 |
354.0 |
0.0 |
| C4 |
C5 |
C6 |
N1 |
1.8 |
0.4 |
| N1 |
C6 |
C5 |
H5 |
181.8 |
180.0 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
179.8 |
| O2 |
C2 |
N1 |
C6 |
177.0 |
180.0 |
| N1 |
C2 |
O2 |
N3 |
176.8 |
180.0 |
| O2 |
C2 |
N3 |
C4 |
180.9 |
180.0 |
| N3 |
C2 |
N1 |
C6 |
354.0 |
0.0 |
| N1 |
C2 |
N3 |
O2 |
183.1 |
180.0 |
| C2 |
N3 |
C4 |
N4 |
181.0 |
180.0 |
| C2 |
N3 |
C4 |
C5 |
0.7 |
0.2 |
| N4 |
C4 |
N3 |
C5 |
180.3 |
179.8 |
| N3 |
C4 |
N4 |
H41 |
359.7 |
360.0 |
| N3 |
C4 |
N4 |
H42 |
234.4 |
179.7 |
| N3 |
C4 |
C5 |
C6 |
356.2 |
359.6 |
| N3 |
C4 |
C5 |
H5 |
176.3 |
180.0 |
| N3 |
C4 |
N4 |
C5 |
179.7 |
180.2 |
| N4 |
C4 |
C5 |
C6 |
175.9 |
179.8 |
| N4 |
C4 |
C5 |
H5 |
356.0 |
0.2 |
| H41 |
N4 |
C4 |
H42 |
125.3 |
180.3 |
| N1 |
C6 |
C5 |
C4 |
1.8 |
0.4 |
| N3 |
C4 |
C5 |
N4 |
180.3 |
179.8 |
| C5 |
C4 |
N4 |
H41 |
180.0 |
179.8 |
| C5 |
C4 |
N4 |
H42 |
54.7 |
359.5 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
179.6 |
| C4 |
C5 |
C6 |
H6 |
181.9 |
180.3 |
| H41 |
N4 |
C4 |
C5 |
180.0 |
179.8 |
| C4 |
N4 |
H41 |
H42 |
234.7 |
179.7 |
| H42 |
N4 |
C4 |
C5 |
54.7 |
359.5 |
| C4 |
N4 |
H42 |
H41 |
133.7 |
180.3 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.2 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
180.4 |
| C4 |
C5 |
H5 |
C6 |
180.0 |
179.6 |
| H5 |
C5 |
C6 |
H6 |
1.8 |
359.8 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
179.8 |
| H6 |
C6 |
C5 |
H5 |
1.8 |
359.8 |