PDB Chemical Component DDN
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 DDN
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
OP3 |
P |
1.522 |
1.480 |
P |
OP1 |
1.501 |
1.610 |
P |
OP2 |
1.518 |
1.610 |
P |
O5' |
1.632 |
1.610 |
OP1 |
H1P |
0.950 |
0.967 |
OP2 |
H2P |
0.950 |
0.967 |
O5' |
C5' |
1.442 |
1.428 |
C5' |
C4' |
1.519 |
1.530 |
C5' |
H5' |
1.115 |
1.090 |
C5' |
H5'' |
1.115 |
1.090 |
C4' |
O4' |
1.427 |
1.446 |
C4' |
C3' |
1.539 |
1.545 |
C4' |
H4' |
1.115 |
1.091 |
O4' |
C1' |
1.434 |
1.445 |
C3' |
O3' |
1.398 |
1.430 |
C3' |
C2' |
1.478 |
1.545 |
C3' |
H3' |
1.115 |
1.091 |
O3' |
H1 |
0.950 |
0.967 |
C2' |
C1' |
1.499 |
1.545 |
C2' |
H2' |
1.115 |
1.090 |
C2' |
H2'' |
1.115 |
1.089 |
C1' |
N1 |
1.636 |
1.465 |
C1' |
H1' |
1.115 |
1.090 |
N1 |
C2 |
1.411 |
1.340 |
N1 |
C6 |
1.379 |
1.386 |
C2 |
O2 |
1.231 |
1.216 |
C2 |
N3 |
1.398 |
1.349 |
N3 |
C4 |
1.574 |
1.472 |
N3 |
HN3 |
1.020 |
0.970 |
C4 |
O4 |
1.435 |
1.428 |
C4 |
C5 |
1.552 |
1.515 |
C4 |
H4 |
1.115 |
1.091 |
O4 |
HO4 |
0.950 |
0.967 |
C5 |
C6 |
1.367 |
1.321 |
C5 |
H5 |
1.103 |
1.079 |
C6 |
H6 |
1.103 |
1.080 |
Bond Angles for DDN
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
OP3 |
P |
OP1 |
112.6 |
109.5 |
OP3 |
P |
OP2 |
111.5 |
109.4 |
OP3 |
P |
O5' |
107.2 |
109.5 |
OP1 |
P |
OP2 |
114.4 |
109.5 |
OP1 |
P |
O5' |
105.0 |
109.5 |
P |
OP1 |
H1P |
112.7 |
106.8 |
OP2 |
P |
O5' |
105.5 |
109.4 |
P |
OP2 |
H2P |
111.5 |
106.8 |
P |
O5' |
C5' |
121.0 |
106.8 |
O5' |
C5' |
C4' |
109.2 |
109.5 |
O5' |
C5' |
H5' |
112.3 |
109.5 |
O5' |
C5' |
H5'' |
112.3 |
109.5 |
C4' |
C5' |
H5' |
112.3 |
109.4 |
C4' |
C5' |
H5'' |
112.3 |
109.4 |
C5' |
C4' |
O4' |
111.6 |
110.4 |
C5' |
C4' |
C3' |
114.7 |
110.7 |
C5' |
C4' |
H4' |
103.3 |
110.3 |
H5' |
C5' |
H5'' |
98.1 |
109.5 |
O4' |
C4' |
C3' |
106.4 |
104.7 |
O4' |
C4' |
H4' |
112.1 |
110.4 |
C4' |
O4' |
C1' |
102.4 |
105.4 |
C3' |
C4' |
H4' |
108.8 |
110.2 |
C4' |
C3' |
O3' |
110.5 |
110.5 |
C4' |
C3' |
C2' |
107.2 |
104.2 |
C4' |
C3' |
H3' |
110.4 |
110.5 |
O4' |
C1' |
C2' |
116.3 |
104.8 |
O4' |
C1' |
N1 |
97.8 |
110.5 |
O4' |
C1' |
H1' |
149.1 |
110.4 |
O3' |
C3' |
C2' |
109.8 |
110.5 |
O3' |
C3' |
H3' |
107.8 |
110.4 |
C3' |
O3' |
H1 |
110.5 |
106.8 |
C2' |
C3' |
H3' |
111.1 |
110.5 |
C3' |
C2' |
C1' |
99.1 |
104.0 |
C3' |
C2' |
H2' |
116.2 |
110.5 |
C3' |
C2' |
H2'' |
116.2 |
110.5 |
C1' |
C2' |
H2' |
116.2 |
110.5 |
C1' |
C2' |
H2'' |
116.2 |
110.5 |
C2' |
C1' |
N1 |
143.2 |
110.4 |
C2' |
C1' |
H1' |
60.3 |
110.4 |
H2' |
C2' |
H2'' |
94.2 |
110.6 |
N1 |
C1' |
H1' |
97.4 |
110.4 |
C1' |
N1 |
C2 |
118.0 |
118.3 |
C1' |
N1 |
C6 |
106.5 |
118.3 |
C2 |
N1 |
C6 |
124.4 |
123.4 |
N1 |
C2 |
O2 |
123.9 |
119.1 |
N1 |
C2 |
N3 |
114.4 |
121.8 |
N1 |
C6 |
C5 |
120.7 |
121.3 |
N1 |
C6 |
H6 |
120.1 |
119.4 |
O2 |
C2 |
N3 |
121.3 |
119.2 |
C2 |
N3 |
C4 |
123.4 |
118.3 |
C2 |
N3 |
HN3 |
112.0 |
120.8 |
C4 |
N3 |
HN3 |
124.6 |
120.9 |
N3 |
C4 |
O4 |
113.0 |
107.9 |
N3 |
C4 |
C5 |
111.0 |
117.2 |
N3 |
C4 |
H4 |
105.1 |
107.9 |
O4 |
C4 |
C5 |
106.7 |
107.9 |
O4 |
C4 |
H4 |
109.5 |
107.8 |
C4 |
O4 |
HO4 |
113.1 |
106.8 |
C5 |
C4 |
H4 |
111.6 |
107.9 |
C4 |
C5 |
C6 |
120.7 |
118.1 |
C4 |
C5 |
H5 |
126.0 |
120.9 |
C6 |
C5 |
H5 |
113.3 |
121.0 |
C5 |
C6 |
H6 |
119.2 |
119.4 |
Torsion Angles for DDN
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
OP1 |
P |
OP3 |
OP2 |
229.9 |
120.0 |
OP1 |
P |
OP3 |
O5' |
115.0 |
239.9 |
OP3 |
P |
OP1 |
H1P |
180.0 |
300.0 |
OP2 |
P |
OP3 |
O5' |
245.1 |
120.0 |
OP3 |
P |
OP2 |
H2P |
180.0 |
179.9 |
OP3 |
P |
O5' |
C5' |
169.8 |
55.0 |
OP3 |
P |
OP1 |
OP2 |
128.6 |
240.1 |
OP3 |
P |
OP1 |
O5' |
243.7 |
120.1 |
OP2 |
P |
OP1 |
O5' |
115.1 |
240.0 |
OP1 |
P |
OP2 |
H2P |
309.2 |
60.0 |
OP1 |
P |
O5' |
C5' |
49.8 |
175.0 |
OP3 |
P |
OP2 |
OP1 |
230.8 |
120.0 |
OP3 |
P |
OP2 |
O5' |
116.0 |
240.0 |
OP1 |
P |
OP2 |
O5' |
245.2 |
120.0 |
OP2 |
P |
OP1 |
H1P |
51.4 |
60.0 |
OP2 |
P |
O5' |
C5' |
288.6 |
295.0 |
OP3 |
P |
O5' |
OP1 |
120.0 |
240.0 |
OP3 |
P |
O5' |
OP2 |
241.1 |
120.0 |
OP1 |
P |
O5' |
OP2 |
121.1 |
240.0 |
O5' |
P |
OP1 |
H1P |
296.2 |
180.0 |
O5' |
P |
OP2 |
H2P |
64.1 |
299.9 |
P |
O5' |
C5' |
C4' |
156.0 |
180.0 |
P |
O5' |
C5' |
H5' |
30.7 |
60.1 |
P |
O5' |
C5' |
H5'' |
281.3 |
300.0 |
H1P |
OP1 |
P |
OP2 |
51.4 |
60.0 |
H1P |
OP1 |
P |
O5' |
296.2 |
180.0 |
H2P |
OP2 |
P |
O5' |
64.1 |
299.9 |
C4' |
C5' |
O5' |
H5' |
125.3 |
120.0 |
C4' |
C5' |
O5' |
H5'' |
234.7 |
240.0 |
O5' |
C5' |
C4' |
O4' |
158.7 |
66.4 |
O5' |
C5' |
C4' |
C3' |
279.8 |
181.9 |
O5' |
C5' |
C4' |
H4' |
38.1 |
304.2 |
H5' |
C5' |
O5' |
H5'' |
109.5 |
120.1 |
O5' |
C5' |
C4' |
H5' |
234.7 |
240.0 |
O5' |
C5' |
C4' |
H5'' |
125.3 |
120.0 |
H5' |
C5' |
C4' |
H5'' |
250.5 |
240.1 |
O4' |
C4' |
C5' |
C3' |
238.9 |
244.6 |
O4' |
C4' |
C5' |
H4' |
120.6 |
122.3 |
C5' |
C4' |
O4' |
C1' |
99.7 |
159.5 |
C3' |
C4' |
C5' |
H4' |
241.7 |
237.7 |
C5' |
C4' |
C3' |
O3' |
147.1 |
98.5 |
C5' |
C4' |
C3' |
C2' |
266.8 |
217.3 |
C5' |
C4' |
C3' |
H3' |
28.0 |
336.0 |
O5' |
C5' |
H5' |
C4' |
123.5 |
120.0 |
O5' |
C5' |
H5' |
H5'' |
241.8 |
239.9 |
C4' |
C5' |
H5' |
H5'' |
118.2 |
119.9 |
H5' |
C5' |
C4' |
O4' |
284.0 |
186.5 |
H5' |
C5' |
C4' |
C3' |
45.1 |
301.9 |
H5' |
C5' |
C4' |
H4' |
163.3 |
64.2 |
O5' |
C5' |
H5'' |
C4' |
236.5 |
240.0 |
O5' |
C5' |
H5'' |
H5' |
118.2 |
120.1 |
C4' |
C5' |
H5'' |
H5' |
241.7 |
240.1 |
H5'' |
C5' |
C4' |
O4' |
33.4 |
306.4 |
H5'' |
C5' |
C4' |
C3' |
154.5 |
61.9 |
H5'' |
C5' |
C4' |
H4' |
272.8 |
184.2 |
O4' |
C4' |
C5' |
H5' |
284.0 |
186.5 |
O4' |
C4' |
C5' |
H5'' |
33.4 |
306.4 |
C5' |
C4' |
O4' |
C3' |
125.8 |
119.2 |
C5' |
C4' |
O4' |
H4' |
244.7 |
237.8 |
C3' |
C4' |
O4' |
H4' |
118.9 |
118.6 |
O4' |
C4' |
C3' |
O3' |
271.1 |
217.5 |
O4' |
C4' |
C3' |
C2' |
30.7 |
336.2 |
O4' |
C4' |
C3' |
H3' |
151.9 |
94.9 |
C4' |
O4' |
C1' |
C2' |
14.6 |
319.6 |
C4' |
O4' |
C1' |
N1 |
208.9 |
200.7 |
C4' |
O4' |
C1' |
H1' |
90.1 |
78.4 |
C3' |
C4' |
C5' |
H5' |
45.1 |
301.9 |
C3' |
C4' |
C5' |
H5'' |
154.5 |
61.9 |
C5' |
C4' |
C3' |
O4' |
236.1 |
241.1 |
C5' |
C4' |
C3' |
H4' |
115.1 |
122.4 |
O4' |
C4' |
C3' |
H4' |
239.0 |
241.3 |
C3' |
C4' |
O4' |
C1' |
333.9 |
40.3 |
O3' |
C3' |
C4' |
C2' |
240.3 |
241.3 |
O3' |
C3' |
C4' |
H3' |
119.2 |
122.5 |
C4' |
C3' |
O3' |
H1 |
180.0 |
178.2 |
C2' |
C3' |
C4' |
H3' |
238.8 |
241.3 |
C4' |
C3' |
C2' |
C1' |
340.2 |
359.9 |
C4' |
C3' |
C2' |
H2' |
214.9 |
118.5 |
C4' |
C3' |
C2' |
H2'' |
105.5 |
241.3 |
H4' |
C4' |
C5' |
H5' |
163.3 |
64.2 |
H4' |
C4' |
C5' |
H5'' |
272.8 |
184.2 |
C5' |
C4' |
H4' |
O4' |
120.3 |
122.3 |
C5' |
C4' |
H4' |
C3' |
237.7 |
237.4 |
O4' |
C4' |
H4' |
C3' |
117.4 |
115.2 |
H4' |
C4' |
O4' |
C1' |
215.0 |
281.7 |
H4' |
C4' |
C3' |
O3' |
32.0 |
336.2 |
H4' |
C4' |
C3' |
C2' |
151.7 |
94.9 |
H4' |
C4' |
C3' |
H3' |
272.9 |
213.6 |
C1' |
O4' |
C4' |
C3' |
333.9 |
40.3 |
C1' |
O4' |
C4' |
H4' |
215.0 |
281.7 |
C3' |
C2' |
C1' |
O4' |
3.9 |
24.0 |
O4' |
C1' |
C2' |
H2' |
129.2 |
265.4 |
O4' |
C1' |
C2' |
H2'' |
238.6 |
142.6 |
C2' |
C1' |
O4' |
N1 |
165.7 |
118.9 |
C2' |
C1' |
O4' |
H1' |
284.5 |
241.2 |
N1 |
C1' |
O4' |
H1' |
118.8 |
122.3 |
O4' |
C1' |
N1 |
C2 |
236.2 |
50.1 |
O4' |
C1' |
N1 |
C6 |
90.7 |
230.4 |
O3' |
C3' |
C4' |
H4' |
32.0 |
336.2 |
C4' |
C3' |
O3' |
C2' |
118.1 |
114.9 |
C4' |
C3' |
O3' |
H3' |
239.3 |
237.4 |
C2' |
C3' |
O3' |
H3' |
121.2 |
122.6 |
O3' |
C3' |
C2' |
C1' |
100.4 |
118.7 |
O3' |
C3' |
C2' |
H2' |
335.1 |
237.3 |
O3' |
C3' |
C2' |
H2'' |
225.6 |
0.0 |
C2' |
C3' |
C4' |
H4' |
151.7 |
94.9 |
C4' |
C3' |
C2' |
O3' |
239.9 |
241.3 |
C4' |
C3' |
C2' |
H3' |
120.7 |
118.7 |
O4' |
C1' |
C2' |
C3' |
3.9 |
24.0 |
O3' |
C3' |
C2' |
H3' |
240.8 |
237.4 |
C2' |
C3' |
O3' |
H1 |
61.9 |
63.3 |
C1' |
C2' |
C3' |
H2' |
125.3 |
241.4 |
C1' |
C2' |
C3' |
H2'' |
234.8 |
118.6 |
C3' |
C2' |
C1' |
N1 |
159.8 |
142.9 |
C3' |
C2' |
C1' |
H1' |
218.8 |
265.2 |
H2' |
C2' |
C3' |
H2'' |
109.5 |
237.3 |
H3' |
C3' |
C4' |
H4' |
272.9 |
213.6 |
C4' |
C3' |
H3' |
O3' |
120.8 |
122.6 |
C4' |
C3' |
H3' |
C2' |
241.2 |
245.2 |
O3' |
C3' |
H3' |
C2' |
120.3 |
122.6 |
H3' |
C3' |
O3' |
H1 |
300.8 |
300.7 |
H3' |
C3' |
C2' |
C1' |
219.5 |
241.2 |
H3' |
C3' |
C2' |
H2' |
94.2 |
359.8 |
H3' |
C3' |
C2' |
H2'' |
344.8 |
122.6 |
H1 |
O3' |
C3' |
C2' |
61.9 |
63.3 |
H1 |
O3' |
C3' |
H3' |
300.8 |
300.7 |
O4' |
C1' |
C2' |
N1 |
204.1 |
241.1 |
O4' |
C1' |
C2' |
H1' |
145.1 |
118.8 |
C1' |
C2' |
C3' |
H3' |
219.5 |
241.2 |
C3' |
C2' |
C1' |
H2' |
234.7 |
118.6 |
C3' |
C2' |
C1' |
H2'' |
125.3 |
241.4 |
H2' |
C2' |
C1' |
H2'' |
250.5 |
122.7 |
N1 |
C1' |
C2' |
H1' |
301.0 |
237.7 |
C2' |
C1' |
N1 |
C2 |
78.0 |
294.7 |
C2' |
C1' |
N1 |
C6 |
292.4 |
115.0 |
H2' |
C2' |
C3' |
H3' |
94.2 |
359.8 |
C3' |
C2' |
H2' |
C1' |
116.0 |
245.4 |
C3' |
C2' |
H2' |
H2'' |
238.0 |
122.7 |
C1' |
C2' |
H2' |
H2'' |
122.0 |
237.3 |
H2' |
C2' |
C1' |
N1 |
285.1 |
24.3 |
H2' |
C2' |
C1' |
H1' |
344.1 |
146.6 |
H2'' |
C2' |
C3' |
H3' |
344.8 |
122.6 |
C3' |
C2' |
H2'' |
C1' |
244.0 |
114.6 |
C3' |
C2' |
H2'' |
H2' |
122.0 |
237.3 |
C1' |
C2' |
H2'' |
H2' |
238.0 |
122.7 |
H2'' |
C2' |
C1' |
N1 |
34.5 |
261.6 |
H2'' |
C2' |
C1' |
H1' |
93.6 |
23.8 |
O4' |
C1' |
N1 |
C2' |
158.3 |
115.4 |
O4' |
C1' |
N1 |
H1' |
207.0 |
237.7 |
N1 |
C1' |
C2' |
H2' |
285.1 |
24.3 |
N1 |
C1' |
C2' |
H2'' |
34.5 |
261.6 |
C2' |
C1' |
N1 |
H1' |
48.7 |
122.2 |
C2 |
N1 |
C1' |
C6 |
145.6 |
179.7 |
C1' |
N1 |
C2 |
O2 |
5.7 |
0.3 |
C1' |
N1 |
C2 |
N3 |
193.2 |
179.7 |
C1' |
N1 |
C6 |
C5 |
168.0 |
180.0 |
C1' |
N1 |
C6 |
H6 |
348.0 |
359.9 |
O4' |
C1' |
H1' |
C2' |
267.7 |
244.7 |
O4' |
C1' |
H1' |
N1 |
118.9 |
122.4 |
H1' |
C1' |
C2' |
H2' |
344.1 |
146.6 |
H1' |
C1' |
C2' |
H2'' |
93.6 |
23.8 |
C2' |
C1' |
H1' |
N1 |
211.2 |
237.8 |
H1' |
C1' |
N1 |
C2 |
29.2 |
172.5 |
H1' |
C1' |
N1 |
C6 |
243.7 |
352.8 |
C2 |
N1 |
C1' |
H1' |
29.2 |
172.5 |
C1' |
N1 |
C2 |
C6 |
221.1 |
180.3 |
C2 |
N1 |
C6 |
C5 |
25.2 |
0.4 |
C2 |
N1 |
C6 |
H6 |
205.2 |
180.3 |
O2 |
C2 |
N1 |
N3 |
172.5 |
180.5 |
N1 |
C2 |
N3 |
C4 |
19.0 |
0.6 |
N1 |
C2 |
N3 |
HN3 |
199.0 |
180.3 |
C6 |
N1 |
C1' |
H1' |
243.7 |
352.8 |
C1' |
N1 |
C6 |
C2 |
142.8 |
179.7 |
C6 |
N1 |
C2 |
O2 |
144.7 |
179.9 |
C6 |
N1 |
C2 |
N3 |
332.1 |
359.4 |
C4 |
C5 |
C6 |
N1 |
348.1 |
359.9 |
N1 |
C6 |
C5 |
H5 |
168.1 |
180.0 |
C5 |
C6 |
N1 |
H6 |
180.0 |
180.1 |
O2 |
C2 |
N1 |
C6 |
144.7 |
179.9 |
N1 |
C2 |
O2 |
N3 |
188.0 |
179.5 |
O2 |
C2 |
N3 |
C4 |
206.3 |
180.0 |
O2 |
C2 |
N3 |
HN3 |
26.3 |
359.7 |
N3 |
C2 |
N1 |
C6 |
332.1 |
359.4 |
N1 |
C2 |
N3 |
O2 |
172.7 |
180.5 |
C4 |
N3 |
C2 |
HN3 |
180.0 |
180.3 |
C2 |
N3 |
C4 |
O4 |
111.6 |
121.7 |
C2 |
N3 |
C4 |
C5 |
351.8 |
359.7 |
C2 |
N3 |
C4 |
H4 |
231.0 |
237.8 |
C2 |
N3 |
C4 |
HN3 |
180.0 |
179.7 |
O4 |
C4 |
N3 |
C5 |
119.8 |
122.0 |
O4 |
C4 |
N3 |
H4 |
240.7 |
243.8 |
N3 |
C4 |
O4 |
HO4 |
180.0 |
52.5 |
C5 |
C4 |
N3 |
H4 |
120.8 |
121.9 |
N3 |
C4 |
C5 |
C6 |
3.9 |
0.1 |
N3 |
C4 |
C5 |
H5 |
183.9 |
180.0 |
C2 |
N3 |
HN3 |
C4 |
180.0 |
180.3 |
HN3 |
N3 |
C4 |
O4 |
291.6 |
301.9 |
HN3 |
N3 |
C4 |
C5 |
171.8 |
180.0 |
HN3 |
N3 |
C4 |
H4 |
51.0 |
58.1 |
O4 |
C4 |
N3 |
HN3 |
291.6 |
301.9 |
N3 |
C4 |
O4 |
C5 |
237.8 |
232.5 |
N3 |
C4 |
O4 |
H4 |
116.8 |
116.2 |
C5 |
C4 |
O4 |
H4 |
239.0 |
243.8 |
O4 |
C4 |
C5 |
C6 |
240.4 |
238.1 |
O4 |
C4 |
C5 |
H5 |
60.3 |
58.1 |
N1 |
C6 |
C5 |
C4 |
348.1 |
359.9 |
C5 |
C4 |
N3 |
HN3 |
171.8 |
180.0 |
N3 |
C4 |
C5 |
O4 |
123.5 |
122.0 |
N3 |
C4 |
C5 |
H4 |
243.1 |
238.1 |
O4 |
C4 |
C5 |
H4 |
119.6 |
116.2 |
C5 |
C4 |
O4 |
HO4 |
302.3 |
180.0 |
C6 |
C5 |
C4 |
H5 |
180.0 |
180.1 |
C4 |
C5 |
C6 |
H6 |
168.1 |
180.0 |
H4 |
C4 |
N3 |
HN3 |
51.0 |
58.1 |
N3 |
C4 |
H4 |
O4 |
238.3 |
243.7 |
N3 |
C4 |
H4 |
C5 |
120.4 |
127.5 |
O4 |
C4 |
H4 |
C5 |
242.1 |
243.7 |
H4 |
C4 |
O4 |
HO4 |
63.2 |
296.2 |
H4 |
C4 |
C5 |
C6 |
120.8 |
121.9 |
H4 |
C4 |
C5 |
H5 |
300.8 |
301.9 |
HO4 |
O4 |
C4 |
C5 |
302.3 |
180.0 |
HO4 |
O4 |
C4 |
H4 |
63.2 |
296.2 |
N1 |
C6 |
C5 |
H6 |
180.0 |
179.9 |
C6 |
C5 |
C4 |
H4 |
120.8 |
121.9 |
C4 |
C5 |
C6 |
H5 |
180.0 |
179.9 |
H5 |
C5 |
C4 |
H4 |
300.8 |
301.9 |
C4 |
C5 |
H5 |
C6 |
180.0 |
180.1 |
H5 |
C5 |
C6 |
H6 |
348.1 |
0.1 |
N1 |
C6 |
H6 |
C5 |
180.0 |
180.1 |
H6 |
C6 |
C5 |
H5 |
348.1 |
0.1 |