PDB Chemical Component DN
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 DN
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| OP3 |
P |
1.476 |
1.610 |
| OP3 |
HOP3 |
0.950 |
0.967 |
| P |
OP1 |
1.473 |
1.480 |
| P |
OP2 |
1.463 |
1.610 |
| P |
O5' |
1.562 |
1.610 |
| OP2 |
HOP2 |
0.950 |
0.967 |
| O5' |
C5' |
1.421 |
1.429 |
| C5' |
C4' |
1.485 |
1.530 |
| C5' |
H5' |
1.100 |
1.090 |
| C5' |
H5'' |
1.100 |
1.089 |
| C4' |
O4' |
1.436 |
1.432 |
| C4' |
C3' |
1.489 |
1.544 |
| C4' |
H4' |
1.100 |
1.090 |
| O4' |
C1' |
1.429 |
1.437 |
| C3' |
O3' |
1.438 |
1.428 |
| C3' |
C2' |
1.496 |
1.554 |
| C3' |
H3' |
1.100 |
1.090 |
| O3' |
HO3' |
0.950 |
0.967 |
| C2' |
H2'2 |
1.101 |
1.090 |
| C2' |
C1' |
1.536 |
1.550 |
| C2' |
H2' |
1.099 |
1.090 |
| C1' |
H1' |
1.100 |
1.091 |
| C1' |
H1'2 |
1.100 |
1.090 |
Bond Angles for DN
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| P |
OP3 |
HOP3 |
109.5 |
114.0 |
| OP3 |
P |
OP1 |
111.1 |
109.5 |
| OP3 |
P |
OP2 |
114.6 |
109.4 |
| OP3 |
P |
O5' |
100.9 |
109.5 |
| OP1 |
P |
OP2 |
112.9 |
109.5 |
| OP1 |
P |
O5' |
104.2 |
109.5 |
| OP2 |
P |
O5' |
112.0 |
109.5 |
| P |
OP2 |
HOP2 |
109.5 |
114.0 |
| P |
O5' |
C5' |
126.9 |
123.0 |
| O5' |
C5' |
C4' |
107.2 |
109.5 |
| O5' |
C5' |
H5' |
110.2 |
109.5 |
| O5' |
C5' |
H5'' |
110.2 |
109.4 |
| C4' |
C5' |
H5' |
110.2 |
109.5 |
| C4' |
C5' |
H5'' |
110.2 |
109.5 |
| C5' |
C4' |
O4' |
112.3 |
109.8 |
| C5' |
C4' |
C3' |
110.6 |
109.8 |
| C5' |
C4' |
H4' |
106.2 |
109.8 |
| H5' |
C5' |
H5'' |
108.7 |
109.5 |
| O4' |
C4' |
C3' |
107.5 |
107.7 |
| O4' |
C4' |
H4' |
109.3 |
109.8 |
| C4' |
O4' |
C1' |
113.1 |
109.9 |
| C3' |
C4' |
H4' |
111.1 |
109.9 |
| C4' |
C3' |
O3' |
109.0 |
110.9 |
| C4' |
C3' |
C2' |
104.9 |
102.2 |
| C4' |
C3' |
H3' |
113.5 |
110.8 |
| O4' |
C1' |
C2' |
103.8 |
105.1 |
| O4' |
C1' |
H1' |
111.4 |
110.3 |
| O4' |
C1' |
H1'2 |
111.4 |
110.3 |
| O3' |
C3' |
C2' |
111.5 |
110.9 |
| O3' |
C3' |
H3' |
107.1 |
110.8 |
| C3' |
O3' |
HO3' |
109.5 |
114.0 |
| C2' |
C3' |
H3' |
111.0 |
111.0 |
| C3' |
C2' |
H2'2 |
109.9 |
111.1 |
| C3' |
C2' |
C1' |
108.3 |
100.9 |
| C3' |
C2' |
H2' |
109.9 |
111.1 |
| C1' |
C2' |
H2'2 |
109.9 |
111.2 |
| H2' |
C2' |
H2'2 |
109.1 |
111.0 |
| C1' |
C2' |
H2' |
109.9 |
111.2 |
| C2' |
C1' |
H1' |
111.4 |
110.3 |
| C2' |
C1' |
H1'2 |
111.4 |
110.3 |
| H1' |
C1' |
H1'2 |
107.5 |
110.4 |
Torsion Angles for DN
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP1 |
P |
OP3 |
OP2 |
230.5 |
240.0 |
| OP1 |
P |
OP3 |
O5' |
110.1 |
120.0 |
| OP2 |
P |
OP3 |
O5' |
239.5 |
240.0 |
| OP3 |
P |
OP2 |
HOP2 |
231.5 |
60.0 |
| OP3 |
P |
O5' |
C5' |
232.7 |
175.0 |
| HOP3 |
OP3 |
P |
OP1 |
0.0 |
300.0 |
| HOP3 |
OP3 |
P |
OP2 |
129.5 |
60.0 |
| HOP3 |
OP3 |
P |
O5' |
250.0 |
180.0 |
| OP1 |
P |
OP3 |
HOP3 |
0.0 |
300.0 |
| OP3 |
P |
OP1 |
OP2 |
130.3 |
120.0 |
| OP3 |
P |
OP1 |
O5' |
252.1 |
240.0 |
| OP2 |
P |
OP1 |
O5' |
121.8 |
120.0 |
| OP1 |
P |
OP2 |
HOP2 |
0.0 |
180.0 |
| OP1 |
P |
O5' |
C5' |
117.4 |
55.0 |
| OP2 |
P |
OP3 |
HOP3 |
129.5 |
60.0 |
| OP3 |
P |
OP2 |
OP1 |
231.4 |
240.0 |
| OP3 |
P |
OP2 |
O5' |
114.1 |
120.0 |
| OP1 |
P |
OP2 |
O5' |
242.7 |
240.0 |
| OP2 |
P |
O5' |
C5' |
355.0 |
295.0 |
| O5' |
P |
OP3 |
HOP3 |
250.0 |
180.0 |
| OP3 |
P |
O5' |
OP1 |
115.3 |
120.0 |
| OP3 |
P |
O5' |
OP2 |
237.7 |
240.0 |
| OP1 |
P |
O5' |
OP2 |
122.4 |
120.0 |
| O5' |
P |
OP2 |
HOP2 |
117.3 |
300.0 |
| P |
O5' |
C5' |
C4' |
132.4 |
180.0 |
| P |
O5' |
C5' |
H5' |
252.4 |
300.0 |
| P |
O5' |
C5' |
H5'' |
12.4 |
60.0 |
| HOP2 |
OP2 |
P |
O5' |
117.3 |
300.0 |
| C4' |
C5' |
O5' |
H5' |
240.0 |
240.0 |
| C4' |
C5' |
O5' |
H5'' |
120.0 |
120.0 |
| O5' |
C5' |
C4' |
O4' |
59.9 |
66.4 |
| O5' |
C5' |
C4' |
C3' |
179.9 |
184.6 |
| O5' |
C5' |
C4' |
H4' |
300.5 |
305.5 |
| 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 |
120.0 |
| O4' |
C4' |
C5' |
C3' |
240.0 |
241.8 |
| O4' |
C4' |
C5' |
H4' |
119.4 |
120.9 |
| C5' |
C4' |
O4' |
C1' |
112.4 |
117.8 |
| C3' |
C4' |
C5' |
H4' |
239.4 |
239.1 |
| C5' |
C4' |
C3' |
O3' |
132.5 |
100.9 |
| C5' |
C4' |
C3' |
C2' |
252.0 |
219.1 |
| C5' |
C4' |
C3' |
H3' |
13.3 |
337.4 |
| O5' |
C5' |
H5' |
C4' |
241.8 |
240.0 |
| O5' |
C5' |
H5' |
H5'' |
120.9 |
119.9 |
| C4' |
C5' |
H5' |
H5'' |
239.1 |
239.9 |
| H5' |
C5' |
C4' |
O4' |
299.9 |
306.4 |
| H5' |
C5' |
C4' |
C3' |
60.0 |
64.6 |
| H5' |
C5' |
C4' |
H4' |
180.5 |
185.6 |
| O5' |
C5' |
H5'' |
C4' |
118.2 |
120.0 |
| O5' |
C5' |
H5'' |
H5' |
239.1 |
240.0 |
| C4' |
C5' |
H5'' |
H5' |
120.9 |
120.0 |
| H5'' |
C5' |
C4' |
O4' |
179.9 |
186.4 |
| H5'' |
C5' |
C4' |
C3' |
299.9 |
304.6 |
| H5'' |
C5' |
C4' |
H4' |
60.5 |
65.5 |
| O4' |
C4' |
C5' |
H5' |
299.9 |
306.4 |
| O4' |
C4' |
C5' |
H5'' |
179.9 |
186.4 |
| C5' |
C4' |
O4' |
C3' |
121.8 |
119.6 |
| C5' |
C4' |
O4' |
H4' |
242.5 |
239.2 |
| C3' |
C4' |
O4' |
H4' |
120.7 |
119.6 |
| O4' |
C4' |
C3' |
O3' |
255.3 |
220.5 |
| O4' |
C4' |
C3' |
C2' |
14.9 |
338.7 |
| O4' |
C4' |
C3' |
H3' |
136.1 |
97.0 |
| C4' |
O4' |
C1' |
C2' |
359.8 |
24.5 |
| C4' |
O4' |
C1' |
H1' |
119.8 |
143.3 |
| C4' |
O4' |
C1' |
H1'2 |
239.8 |
265.5 |
| C3' |
C4' |
C5' |
H5' |
60.0 |
64.6 |
| C3' |
C4' |
C5' |
H5'' |
299.9 |
304.6 |
| C5' |
C4' |
C3' |
O4' |
237.1 |
240.4 |
| C5' |
C4' |
C3' |
H4' |
117.6 |
120.8 |
| O4' |
C4' |
C3' |
H4' |
240.5 |
240.4 |
| C3' |
C4' |
O4' |
C1' |
350.6 |
358.3 |
| O3' |
C3' |
C4' |
C2' |
240.5 |
241.8 |
| O3' |
C3' |
C4' |
H3' |
119.2 |
123.5 |
| C4' |
C3' |
O3' |
HO3' |
180.0 |
180.0 |
| C2' |
C3' |
C4' |
H3' |
238.7 |
241.7 |
| C4' |
C3' |
C2' |
H2'2 |
104.9 |
276.2 |
| C4' |
C3' |
C2' |
C1' |
344.9 |
34.1 |
| C4' |
C3' |
C2' |
H2' |
224.9 |
152.1 |
| H4' |
C4' |
C5' |
H5' |
180.5 |
185.6 |
| H4' |
C4' |
C5' |
H5'' |
60.5 |
65.5 |
| C5' |
C4' |
H4' |
O4' |
121.3 |
120.9 |
| C5' |
C4' |
H4' |
C3' |
239.8 |
239.1 |
| O4' |
C4' |
H4' |
C3' |
118.5 |
118.3 |
| H4' |
C4' |
O4' |
C1' |
229.9 |
238.6 |
| H4' |
C4' |
C3' |
O3' |
14.9 |
340.1 |
| H4' |
C4' |
C3' |
C2' |
134.4 |
98.3 |
| H4' |
C4' |
C3' |
H3' |
255.7 |
216.6 |
| C1' |
O4' |
C4' |
C3' |
350.6 |
358.3 |
| C1' |
O4' |
C4' |
H4' |
229.9 |
238.6 |
| C3' |
C2' |
C1' |
O4' |
9.7 |
323.5 |
| O4' |
C1' |
C2' |
H2'2 |
249.7 |
81.4 |
| O4' |
C1' |
C2' |
H2' |
129.7 |
205.6 |
| C2' |
C1' |
O4' |
H1' |
240.0 |
241.1 |
| C2' |
C1' |
O4' |
H1'2 |
120.0 |
118.9 |
| H1' |
C1' |
O4' |
H1'2 |
240.0 |
237.8 |
| O3' |
C3' |
C4' |
H4' |
14.9 |
340.1 |
| C4' |
C3' |
O3' |
C2' |
115.3 |
112.8 |
| C4' |
C3' |
O3' |
H3' |
236.9 |
236.5 |
| C2' |
C3' |
O3' |
H3' |
121.6 |
123.7 |
| O3' |
C3' |
C2' |
H2'2 |
222.6 |
34.4 |
| O3' |
C3' |
C2' |
C1' |
102.7 |
152.3 |
| O3' |
C3' |
C2' |
H2' |
342.7 |
270.3 |
| C2' |
C3' |
C4' |
H4' |
134.4 |
98.3 |
| C4' |
C3' |
C2' |
O3' |
242.2 |
241.8 |
| C4' |
C3' |
C2' |
H3' |
122.9 |
118.2 |
| O4' |
C1' |
C2' |
C3' |
9.7 |
323.5 |
| O3' |
C3' |
C2' |
H3' |
240.7 |
236.4 |
| C2' |
C3' |
O3' |
HO3' |
64.7 |
67.1 |
| C1' |
C2' |
C3' |
H2'2 |
240.0 |
117.9 |
| H2' |
C2' |
C3' |
H2'2 |
120.0 |
235.9 |
| C1' |
C2' |
C3' |
H2' |
120.0 |
242.1 |
| C3' |
C2' |
C1' |
H1' |
249.7 |
204.6 |
| C3' |
C2' |
C1' |
H1'2 |
129.7 |
82.5 |
| H3' |
C3' |
C4' |
H4' |
255.7 |
216.6 |
| C4' |
C3' |
H3' |
O3' |
120.3 |
123.5 |
| C4' |
C3' |
H3' |
C2' |
242.2 |
247.1 |
| O3' |
C3' |
H3' |
C2' |
121.9 |
123.6 |
| H3' |
C3' |
O3' |
HO3' |
303.1 |
303.4 |
| H3' |
C3' |
C2' |
H2'2 |
341.9 |
158.0 |
| H3' |
C3' |
C2' |
C1' |
221.9 |
275.9 |
| H3' |
C3' |
C2' |
H2' |
101.9 |
33.8 |
| HO3' |
O3' |
C3' |
C2' |
64.7 |
67.1 |
| HO3' |
O3' |
C3' |
H3' |
303.1 |
303.4 |
| H2'2 |
C2' |
C3' |
H3' |
341.9 |
158.0 |
| C3' |
C2' |
H2'2 |
C1' |
241.0 |
111.5 |
| C3' |
C2' |
H2'2 |
H2' |
120.5 |
235.8 |
| C1' |
C2' |
H2'2 |
H2' |
239.5 |
124.3 |
| H2'2 |
C2' |
C1' |
H1' |
129.7 |
322.5 |
| H2'2 |
C2' |
C1' |
H1'2 |
9.7 |
200.3 |
| O4' |
C1' |
C2' |
H1' |
120.0 |
118.9 |
| O4' |
C1' |
C2' |
H1'2 |
240.0 |
241.1 |
| C1' |
C2' |
C3' |
H3' |
221.9 |
275.9 |
| C3' |
C2' |
C1' |
H2'2 |
120.0 |
242.1 |
| C3' |
C2' |
C1' |
H2' |
240.0 |
117.9 |
| H2' |
C2' |
C1' |
H2'2 |
240.0 |
124.2 |
| H1' |
C1' |
C2' |
H1'2 |
120.0 |
122.2 |
| H2' |
C2' |
C3' |
H3' |
101.9 |
33.8 |
| C3' |
C2' |
H2' |
H2'2 |
239.5 |
124.1 |
| C3' |
C2' |
H2' |
C1' |
119.0 |
248.4 |
| C1' |
C2' |
H2' |
H2'2 |
120.5 |
235.7 |
| H2' |
C2' |
C1' |
H1' |
9.7 |
86.7 |
| H2' |
C2' |
C1' |
H1'2 |
249.7 |
324.6 |
| O4' |
C1' |
H1' |
C2' |
244.6 |
244.3 |
| O4' |
C1' |
H1' |
H1'2 |
122.3 |
122.2 |
| H1' |
C1' |
C2' |
H2'2 |
129.7 |
322.5 |
| H1' |
C1' |
C2' |
H2' |
9.7 |
86.7 |
| C2' |
C1' |
H1' |
H1'2 |
237.7 |
237.9 |
| O4' |
C1' |
H1'2 |
C2' |
115.4 |
115.7 |
| O4' |
C1' |
H1'2 |
H1' |
237.7 |
237.8 |
| H1'2 |
C1' |
C2' |
H2'2 |
9.7 |
200.3 |
| H1'2 |
C1' |
C2' |
H2' |
249.7 |
324.6 |
| C2' |
C1' |
H1'2 |
H1' |
122.3 |
122.1 |