PDB Chemical Component DNR
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 DNR
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
P |
OP1 |
1.481 |
1.501 |
P |
OP2 |
1.480 |
1.618 |
P |
O5' |
1.616 |
1.619 |
P |
OP3 |
|
1.616 |
OP2 |
HOP2 |
0.949 |
0.981 |
O5' |
C5' |
1.433 |
1.418 |
C5' |
C4' |
1.524 |
1.523 |
C5' |
H5' |
1.085 |
1.092 |
C5' |
H5'' |
1.091 |
1.093 |
C4' |
O4' |
1.450 |
1.441 |
C4' |
C3' |
1.520 |
1.522 |
C4' |
H4' |
1.088 |
1.094 |
O4' |
C1' |
1.445 |
1.434 |
C1' |
N1 |
1.484 |
1.434 |
C1' |
C2' |
1.513 |
1.520 |
C1' |
H1' |
1.079 |
1.095 |
N1 |
C6 |
1.361 |
1.390 |
N1 |
C2 |
1.396 |
1.406 |
C6 |
C5 |
1.344 |
1.335 |
C6 |
H6 |
1.086 |
1.085 |
C2 |
O2 |
1.230 |
1.224 |
C2 |
N3 |
1.368 |
1.447 |
N3 |
C4 |
1.344 |
1.329 |
N3 |
HN3 |
1.021 |
1.017 |
C4 |
N4 |
1.330 |
1.323 |
C4 |
C5 |
1.429 |
1.483 |
N4 |
H41 |
1.009 |
1.016 |
N4 |
H42 |
1.010 |
1.017 |
C5 |
H5 |
1.090 |
1.084 |
C2' |
C3' |
1.499 |
1.511 |
C2' |
H2' |
1.088 |
1.097 |
C2' |
H2'' |
1.080 |
1.095 |
C3' |
O3' |
1.435 |
1.426 |
C3' |
H3' |
1.093 |
1.094 |
O3' |
HO3' |
0.950 |
0.973 |
OP3 |
HOP3 |
|
0.981 |
Bond Angles for DNR
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
OP1 |
P |
OP2 |
119.8 |
115.3 |
OP1 |
P |
O5' |
108.1 |
115.0 |
OP1 |
P |
OP3 |
|
115.0 |
OP2 |
P |
O5' |
108.1 |
103.7 |
OP2 |
P |
OP3 |
|
103.3 |
P |
OP2 |
HOP2 |
119.8 |
118.9 |
O5' |
P |
OP3 |
|
102.9 |
P |
O5' |
C5' |
120.5 |
118.5 |
P |
OP3 |
HOP3 |
|
118.9 |
O5' |
C5' |
C4' |
112.4 |
108.9 |
O5' |
C5' |
H5' |
108.9 |
109.0 |
O5' |
C5' |
H5'' |
109.2 |
108.9 |
C4' |
C5' |
H5' |
108.1 |
110.3 |
C4' |
C5' |
H5'' |
109.1 |
110.3 |
C5' |
C4' |
O4' |
110.9 |
107.9 |
C5' |
C4' |
C3' |
111.7 |
112.9 |
C5' |
C4' |
H4' |
109.1 |
109.5 |
H5' |
C5' |
H5'' |
109.0 |
109.3 |
O4' |
C4' |
C3' |
107.4 |
106.2 |
O4' |
C4' |
H4' |
108.7 |
107.9 |
C4' |
O4' |
C1' |
109.6 |
109.3 |
C3' |
C4' |
H4' |
109.0 |
112.2 |
C4' |
C3' |
C2' |
104.4 |
103.1 |
C4' |
C3' |
O3' |
111.0 |
109.9 |
C4' |
C3' |
H3' |
109.8 |
113.5 |
O4' |
C1' |
N1 |
110.9 |
109.3 |
O4' |
C1' |
C2' |
106.4 |
107.4 |
O4' |
C1' |
H1' |
109.1 |
108.0 |
N1 |
C1' |
C2' |
112.2 |
112.8 |
N1 |
C1' |
H1' |
109.5 |
107.8 |
C1' |
N1 |
C6 |
120.4 |
118.3 |
C1' |
N1 |
C2 |
118.2 |
120.7 |
C2' |
C1' |
H1' |
108.7 |
111.5 |
C1' |
C2' |
C3' |
105.2 |
102.5 |
C1' |
C2' |
H2' |
111.2 |
110.6 |
C1' |
C2' |
H2'' |
109.6 |
111.7 |
C6 |
N1 |
C2 |
121.4 |
121.0 |
N1 |
C6 |
C5 |
120.9 |
122.7 |
N1 |
C6 |
H6 |
119.5 |
116.1 |
N1 |
C2 |
O2 |
120.2 |
126.8 |
N1 |
C2 |
N3 |
118.3 |
115.0 |
C5 |
C6 |
H6 |
119.6 |
121.2 |
C6 |
C5 |
C4 |
117.8 |
119.3 |
C6 |
C5 |
H5 |
121.1 |
121.1 |
O2 |
C2 |
N3 |
121.5 |
118.2 |
C2 |
N3 |
C4 |
120.4 |
125.3 |
C2 |
N3 |
HN3 |
119.7 |
118.6 |
C4 |
N3 |
HN3 |
119.7 |
116.1 |
N3 |
C4 |
N4 |
119.6 |
125.3 |
N3 |
C4 |
C5 |
121.2 |
116.8 |
N4 |
C4 |
C5 |
119.2 |
118.0 |
C4 |
N4 |
H41 |
119.8 |
120.6 |
C4 |
N4 |
H42 |
120.1 |
120.5 |
C4 |
C5 |
H5 |
121.1 |
119.6 |
H41 |
N4 |
H42 |
120.1 |
118.8 |
C3' |
C2' |
H2' |
110.4 |
109.7 |
C3' |
C2' |
H2'' |
109.8 |
114.1 |
C2' |
C3' |
O3' |
111.3 |
109.7 |
C2' |
C3' |
H3' |
109.9 |
113.2 |
H2' |
C2' |
H2'' |
110.5 |
108.3 |
O3' |
C3' |
H3' |
110.2 |
107.4 |
C3' |
O3' |
HO3' |
111.0 |
107.3 |
Torsion Angles for DNR
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
OP2 |
P |
OP1 |
O5' |
124.3 |
120.6 |
OP2 |
P |
OP1 |
OP3 |
|
239.9 |
OP1 |
P |
OP2 |
HOP2 |
180.0 |
48.8 |
O5' |
P |
OP1 |
OP3 |
|
119.3 |
OP1 |
P |
O5' |
C5' |
181.7 |
179.9 |
OP1 |
P |
OP3 |
HOP3 |
|
312.0 |
OP1 |
P |
OP2 |
O5' |
235.7 |
233.4 |
OP1 |
P |
OP2 |
OP3 |
|
126.3 |
O5' |
P |
OP2 |
OP3 |
|
252.9 |
OP2 |
P |
O5' |
C5' |
50.7 |
53.2 |
OP2 |
P |
OP3 |
HOP3 |
|
78.5 |
OP1 |
P |
O5' |
OP2 |
131.0 |
126.8 |
OP1 |
P |
O5' |
OP3 |
|
234.2 |
OP2 |
P |
O5' |
OP3 |
|
107.4 |
O5' |
P |
OP2 |
HOP2 |
304.3 |
175.4 |
O5' |
P |
OP3 |
HOP3 |
|
186.2 |
P |
O5' |
C5' |
C4' |
181.9 |
180.0 |
P |
O5' |
C5' |
H5' |
62.1 |
300.4 |
P |
O5' |
C5' |
H5'' |
303.1 |
59.6 |
OP1 |
P |
OP3 |
OP2 |
|
233.5 |
OP1 |
P |
OP3 |
O5' |
|
125.8 |
OP2 |
P |
OP3 |
O5' |
|
252.3 |
OP3 |
P |
OP2 |
HOP2 |
|
282.5 |
OP3 |
P |
O5' |
C5' |
|
305.8 |
HOP2 |
OP2 |
P |
O5' |
304.3 |
175.4 |
HOP2 |
OP2 |
P |
OP3 |
|
282.5 |
C5' |
O5' |
P |
OP3 |
|
305.8 |
C4' |
C5' |
O5' |
H5' |
119.8 |
239.6 |
C4' |
C5' |
O5' |
H5'' |
238.8 |
120.4 |
O5' |
C5' |
C4' |
O4' |
305.9 |
62.4 |
O5' |
C5' |
C4' |
C3' |
65.7 |
179.5 |
O5' |
C5' |
C4' |
H4' |
186.2 |
305.3 |
H5' |
C5' |
O5' |
H5'' |
118.9 |
240.8 |
O5' |
C5' |
C4' |
H5' |
239.7 |
119.6 |
O5' |
C5' |
C4' |
H5'' |
121.3 |
240.5 |
H5' |
C5' |
C4' |
H5'' |
241.6 |
120.9 |
O4' |
C4' |
C5' |
C3' |
240.2 |
242.9 |
O4' |
C4' |
C5' |
H4' |
119.7 |
117.1 |
C5' |
C4' |
O4' |
C1' |
120.1 |
108.6 |
C3' |
C4' |
C5' |
H4' |
239.5 |
234.2 |
C5' |
C4' |
C3' |
C2' |
255.9 |
271.2 |
C5' |
C4' |
C3' |
O3' |
135.9 |
154.2 |
C5' |
C4' |
C3' |
H3' |
13.7 |
34.0 |
O5' |
C5' |
H5' |
C4' |
122.5 |
240.5 |
O5' |
C5' |
H5' |
H5'' |
241.0 |
119.0 |
C4' |
C5' |
H5' |
H5'' |
118.5 |
238.5 |
H5' |
C5' |
C4' |
O4' |
66.2 |
302.9 |
H5' |
C5' |
C4' |
C3' |
186.0 |
60.0 |
H5' |
C5' |
C4' |
H4' |
306.5 |
185.7 |
O5' |
C5' |
H5'' |
C4' |
236.8 |
119.4 |
O5' |
C5' |
H5'' |
H5' |
118.9 |
241.0 |
C4' |
C5' |
H5'' |
H5' |
242.1 |
121.5 |
H5'' |
C5' |
C4' |
O4' |
184.6 |
181.9 |
H5'' |
C5' |
C4' |
C3' |
304.4 |
299.0 |
H5'' |
C5' |
C4' |
H4' |
64.9 |
64.8 |
O4' |
C4' |
C5' |
H5' |
66.2 |
302.9 |
O4' |
C4' |
C5' |
H5'' |
184.6 |
181.9 |
C5' |
C4' |
O4' |
C3' |
122.4 |
121.4 |
C5' |
C4' |
O4' |
H4' |
240.1 |
241.8 |
C3' |
C4' |
O4' |
H4' |
117.8 |
120.5 |
O4' |
C4' |
C3' |
C2' |
17.7 |
29.2 |
O4' |
C4' |
C3' |
O3' |
257.7 |
272.3 |
O4' |
C4' |
C3' |
H3' |
135.5 |
152.1 |
C4' |
O4' |
C1' |
N1 |
223.7 |
228.3 |
C4' |
O4' |
C1' |
C2' |
345.9 |
351.0 |
C4' |
O4' |
C1' |
H1' |
103.0 |
111.3 |
C3' |
C4' |
C5' |
H5' |
186.0 |
60.0 |
C3' |
C4' |
C5' |
H5'' |
304.4 |
299.0 |
C5' |
C4' |
C3' |
O4' |
238.2 |
241.9 |
C5' |
C4' |
C3' |
H4' |
120.6 |
124.3 |
O4' |
C4' |
C3' |
H4' |
242.4 |
242.4 |
C3' |
C4' |
O4' |
C1' |
357.7 |
347.3 |
C1' |
C2' |
C3' |
C4' |
334.2 |
326.6 |
C4' |
C3' |
C2' |
H2' |
94.3 |
84.1 |
C4' |
C3' |
C2' |
H2'' |
216.4 |
205.7 |
C2' |
C3' |
C4' |
O3' |
120.0 |
116.9 |
C2' |
C3' |
C4' |
H3' |
242.2 |
237.2 |
O3' |
C3' |
C4' |
H3' |
122.2 |
120.2 |
C4' |
C3' |
O3' |
HO3' |
180.0 |
232.0 |
H4' |
C4' |
C5' |
H5' |
306.5 |
185.7 |
H4' |
C4' |
C5' |
H5'' |
64.9 |
64.8 |
C5' |
C4' |
H4' |
O4' |
121.0 |
117.1 |
C5' |
C4' |
H4' |
C3' |
237.8 |
233.8 |
O4' |
C4' |
H4' |
C3' |
116.8 |
116.7 |
H4' |
C4' |
O4' |
C1' |
240.0 |
226.8 |
H4' |
C4' |
C3' |
C2' |
135.3 |
146.9 |
H4' |
C4' |
C3' |
O3' |
15.3 |
29.9 |
H4' |
C4' |
C3' |
H3' |
253.1 |
269.7 |
C1' |
O4' |
C4' |
C3' |
357.7 |
347.3 |
C1' |
O4' |
C4' |
H4' |
240.0 |
226.8 |
N1 |
C1' |
O4' |
C2' |
237.8 |
237.3 |
N1 |
C1' |
O4' |
H1' |
120.7 |
117.0 |
O4' |
C1' |
N1 |
C6 |
53.4 |
32.9 |
O4' |
C1' |
N1 |
C2 |
235.7 |
212.9 |
C2' |
C1' |
O4' |
H1' |
242.9 |
239.7 |
O4' |
C1' |
C2' |
C3' |
25.0 |
26.9 |
O4' |
C1' |
C2' |
H2' |
265.4 |
270.0 |
O4' |
C1' |
C2' |
H2'' |
143.0 |
149.4 |
O4' |
C1' |
N1 |
C2' |
118.8 |
119.4 |
O4' |
C1' |
N1 |
H1' |
239.6 |
242.9 |
C2' |
C1' |
N1 |
H1' |
120.8 |
123.5 |
N1 |
C1' |
C2' |
C3' |
146.4 |
147.4 |
N1 |
C1' |
C2' |
H2' |
26.8 |
30.6 |
N1 |
C1' |
C2' |
H2'' |
264.4 |
269.9 |
C6 |
N1 |
C1' |
C2 |
177.7 |
180.0 |
C1' |
N1 |
C6 |
C5 |
182.8 |
180.0 |
C1' |
N1 |
C6 |
H6 |
3.5 |
360.0 |
C1' |
N1 |
C2 |
O2 |
357.7 |
359.9 |
C1' |
N1 |
C2 |
N3 |
177.3 |
180.0 |
C4' |
C3' |
C2' |
C1' |
334.2 |
326.6 |
O4' |
C1' |
C2' |
N1 |
238.6 |
239.5 |
O4' |
C1' |
C2' |
H1' |
117.3 |
118.1 |
N1 |
C1' |
C2' |
H1' |
238.7 |
238.6 |
C2' |
C1' |
N1 |
C6 |
294.6 |
273.5 |
C2' |
C1' |
N1 |
C2 |
116.9 |
93.5 |
C3' |
C2' |
C1' |
H2' |
119.6 |
116.9 |
C3' |
C2' |
C1' |
H2'' |
242.0 |
237.5 |
C1' |
C2' |
C3' |
O3' |
94.1 |
83.6 |
C1' |
C2' |
C3' |
H3' |
216.5 |
203.6 |
H2' |
C2' |
C1' |
H2'' |
122.4 |
120.7 |
O4' |
C1' |
H1' |
N1 |
121.6 |
118.0 |
O4' |
C1' |
H1' |
C2' |
244.4 |
242.3 |
N1 |
C1' |
H1' |
C2' |
122.9 |
124.3 |
H1' |
C1' |
N1 |
C6 |
173.8 |
150.0 |
H1' |
C1' |
N1 |
C2 |
356.1 |
330.0 |
H1' |
C1' |
C2' |
C3' |
267.7 |
268.8 |
H1' |
C1' |
C2' |
H2' |
148.1 |
151.9 |
H1' |
C1' |
C2' |
H2'' |
25.7 |
31.3 |
C6 |
N1 |
C1' |
C2' |
294.6 |
273.5 |
C6 |
N1 |
C1' |
H1' |
173.8 |
150.0 |
C1' |
N1 |
C6 |
C2 |
182.4 |
180.0 |
C6 |
N1 |
C2 |
O2 |
180.0 |
180.0 |
C6 |
N1 |
C2 |
N3 |
359.6 |
0.0 |
C5 |
C6 |
N1 |
H6 |
179.3 |
180.0 |
N1 |
C6 |
C5 |
C4 |
359.8 |
360.0 |
N1 |
C6 |
C5 |
H5 |
179.8 |
180.0 |
C2 |
N1 |
C1' |
C2' |
116.9 |
93.5 |
C2 |
N1 |
C1' |
H1' |
356.1 |
330.0 |
C1' |
N1 |
C2 |
C6 |
177.7 |
180.0 |
C2 |
N1 |
C6 |
C5 |
0.5 |
360.0 |
C2 |
N1 |
C6 |
H6 |
181.1 |
180.0 |
O2 |
C2 |
N1 |
N3 |
180.4 |
179.9 |
N1 |
C2 |
N3 |
C4 |
0.0 |
0.0 |
N1 |
C2 |
N3 |
HN3 |
185.5 |
179.9 |
C5 |
C6 |
N1 |
C2 |
0.5 |
360.0 |
N1 |
C6 |
C5 |
H6 |
180.7 |
180.0 |
N3 |
C4 |
C5 |
C6 |
359.8 |
0.1 |
N4 |
C4 |
C5 |
C6 |
179.7 |
180.1 |
C4 |
C5 |
C6 |
H5 |
180.0 |
180.0 |
H6 |
C6 |
N1 |
C2 |
181.1 |
180.0 |
N1 |
C6 |
H6 |
C5 |
179.4 |
180.0 |
H6 |
C6 |
C5 |
C4 |
179.2 |
180.0 |
H6 |
C6 |
C5 |
H5 |
359.1 |
0.0 |
N1 |
C2 |
O2 |
N3 |
179.6 |
180.1 |
O2 |
C2 |
N3 |
C4 |
179.6 |
180.1 |
O2 |
C2 |
N3 |
HN3 |
5.1 |
360.0 |
N1 |
C2 |
N3 |
O2 |
180.4 |
180.0 |
C4 |
N3 |
C2 |
HN3 |
174.5 |
180.1 |
C2 |
N3 |
C4 |
N4 |
180.4 |
179.9 |
C2 |
N3 |
C4 |
C5 |
0.2 |
360.0 |
C6 |
C5 |
C4 |
N3 |
359.8 |
0.1 |
C2 |
N3 |
C4 |
HN3 |
185.5 |
179.9 |
N4 |
C4 |
N3 |
C5 |
180.2 |
180.0 |
N3 |
C4 |
N4 |
H41 |
359.9 |
257.0 |
N3 |
C4 |
N4 |
H42 |
179.8 |
76.9 |
N3 |
C4 |
C5 |
H5 |
179.9 |
180.0 |
C2 |
N3 |
HN3 |
C4 |
174.6 |
180.1 |
HN3 |
N3 |
C4 |
N4 |
354.9 |
0.0 |
HN3 |
N3 |
C4 |
C5 |
174.7 |
180.0 |
C6 |
C5 |
C4 |
N4 |
179.7 |
180.1 |
N4 |
C4 |
N3 |
HN3 |
354.9 |
0.0 |
N3 |
C4 |
N4 |
C5 |
179.8 |
180.0 |
N4 |
C4 |
C5 |
H5 |
359.7 |
0.0 |
H41 |
N4 |
C4 |
H42 |
180.1 |
180.0 |
C4 |
C5 |
C6 |
H6 |
179.2 |
180.0 |
C6 |
C5 |
C4 |
H5 |
180.0 |
180.0 |
C5 |
C4 |
N3 |
HN3 |
174.7 |
180.0 |
N3 |
C4 |
C5 |
N4 |
180.2 |
180.0 |
C5 |
C4 |
N4 |
H41 |
180.1 |
76.9 |
C5 |
C4 |
N4 |
H42 |
360.0 |
256.9 |
H41 |
N4 |
C4 |
C5 |
180.1 |
76.9 |
C4 |
N4 |
H41 |
H42 |
179.9 |
180.0 |
H42 |
N4 |
C4 |
C5 |
360.0 |
256.9 |
C4 |
N4 |
H42 |
H41 |
180.1 |
180.0 |
H5 |
C5 |
C6 |
H6 |
359.1 |
0.0 |
C6 |
C5 |
H5 |
C4 |
180.0 |
180.0 |
C2' |
C3' |
C4' |
H4' |
135.3 |
146.9 |
C4' |
C3' |
C2' |
O3' |
240.2 |
242.9 |
C4' |
C3' |
C2' |
H3' |
117.7 |
123.0 |
C3' |
C2' |
C1' |
H1' |
267.7 |
268.8 |
C1' |
C2' |
C3' |
H2' |
239.9 |
242.5 |
C1' |
C2' |
C3' |
H2'' |
117.9 |
120.8 |
H2' |
C2' |
C3' |
H2'' |
237.9 |
238.3 |
O3' |
C3' |
C2' |
H3' |
237.6 |
240.1 |
C2' |
C3' |
O3' |
HO3' |
64.1 |
119.3 |
H2' |
C2' |
C1' |
H1' |
148.1 |
151.9 |
C1' |
C2' |
H2' |
C3' |
116.4 |
112.3 |
C1' |
C2' |
H2' |
H2'' |
238.1 |
237.3 |
C3' |
C2' |
H2' |
H2'' |
121.7 |
125.1 |
H2' |
C2' |
C3' |
O3' |
214.2 |
201.1 |
H2' |
C2' |
C3' |
H3' |
336.6 |
321.1 |
H2'' |
C2' |
C1' |
H1' |
25.7 |
31.3 |
C1' |
C2' |
H2'' |
C3' |
244.9 |
244.4 |
C1' |
C2' |
H2'' |
H2' |
122.8 |
122.0 |
C3' |
C2' |
H2'' |
H2' |
238.0 |
237.5 |
H2'' |
C2' |
C3' |
O3' |
336.2 |
322.8 |
H2'' |
C2' |
C3' |
H3' |
98.6 |
82.7 |
O3' |
C3' |
C4' |
H4' |
15.3 |
29.9 |
C4' |
C3' |
O3' |
C2' |
115.8 |
112.7 |
C4' |
C3' |
O3' |
H3' |
238.1 |
236.1 |
O3' |
C3' |
C2' |
H2' |
214.2 |
201.1 |
O3' |
C3' |
C2' |
H2'' |
336.2 |
322.8 |
C2' |
C3' |
O3' |
H3' |
122.2 |
123.4 |
H3' |
C3' |
C4' |
H4' |
253.1 |
269.7 |
C4' |
C3' |
H3' |
C2' |
245.7 |
242.9 |
C4' |
C3' |
H3' |
O3' |
122.6 |
121.7 |
H3' |
C3' |
C2' |
H2' |
336.6 |
321.1 |
H3' |
C3' |
C2' |
H2'' |
98.6 |
82.7 |
C2' |
C3' |
H3' |
O3' |
237.0 |
238.7 |
H3' |
C3' |
O3' |
HO3' |
301.9 |
355.9 |
HO3' |
O3' |
C3' |
H3' |
301.9 |
355.9 |