PDB Chemical Component DU
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 DU
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
OP3 |
P |
|
1.618 |
OP3 |
HOP3 |
|
0.981 |
P |
OP1 |
1.490 |
1.501 |
P |
OP2 |
1.487 |
1.616 |
P |
O5' |
1.597 |
1.619 |
OP2 |
HOP2 |
0.951 |
0.981 |
O5' |
C5' |
1.441 |
1.418 |
C5' |
C4' |
1.511 |
1.523 |
C5' |
H5' |
1.100 |
1.092 |
C5' |
H5'' |
1.100 |
1.093 |
C4' |
O4' |
1.450 |
1.441 |
C4' |
C3' |
1.529 |
1.522 |
C4' |
H4' |
1.100 |
1.094 |
O4' |
C1' |
1.425 |
1.434 |
C3' |
O3' |
1.424 |
1.426 |
C3' |
C2' |
1.523 |
1.511 |
C3' |
H3' |
1.100 |
1.094 |
O3' |
HO3' |
0.950 |
0.973 |
C2' |
C1' |
1.523 |
1.520 |
C2' |
H2' |
1.100 |
1.097 |
C2' |
H2'' |
1.100 |
1.095 |
C1' |
N1 |
1.467 |
1.434 |
C1' |
H1' |
1.100 |
1.095 |
N1 |
C2 |
1.382 |
1.412 |
N1 |
C6 |
1.372 |
1.389 |
C2 |
O2 |
1.220 |
1.233 |
C2 |
N3 |
1.379 |
1.402 |
N3 |
C4 |
1.376 |
1.386 |
N3 |
H3 |
0.999 |
1.016 |
C4 |
O4 |
1.229 |
1.227 |
C4 |
C5 |
1.426 |
1.477 |
C5 |
C6 |
1.333 |
1.336 |
C5 |
H5 |
1.080 |
1.083 |
C6 |
H6 |
1.080 |
1.085 |
Bond Angles for DU
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
P |
OP3 |
HOP3 |
|
118.9 |
OP3 |
P |
OP1 |
|
115.3 |
OP3 |
P |
OP2 |
|
103.3 |
OP3 |
P |
O5' |
|
103.7 |
OP1 |
P |
OP2 |
119.4 |
115.0 |
OP1 |
P |
O5' |
107.7 |
115.0 |
OP2 |
P |
O5' |
108.8 |
102.9 |
P |
OP2 |
HOP2 |
109.5 |
118.9 |
P |
O5' |
C5' |
120.5 |
118.5 |
O5' |
C5' |
C4' |
110.6 |
108.9 |
O5' |
C5' |
H5' |
108.8 |
109.0 |
O5' |
C5' |
H5'' |
109.1 |
108.9 |
C4' |
C5' |
H5' |
108.9 |
110.3 |
C4' |
C5' |
H5'' |
109.1 |
110.3 |
C5' |
C4' |
O4' |
110.4 |
107.9 |
C5' |
C4' |
C3' |
116.7 |
112.9 |
C5' |
C4' |
H4' |
102.6 |
109.5 |
H5' |
C5' |
H5'' |
110.4 |
109.3 |
O4' |
C4' |
C3' |
106.0 |
106.2 |
O4' |
C4' |
H4' |
114.1 |
107.9 |
C4' |
O4' |
C1' |
110.2 |
109.3 |
C3' |
C4' |
H4' |
107.3 |
112.2 |
C4' |
C3' |
O3' |
107.4 |
109.9 |
C4' |
C3' |
C2' |
103.1 |
103.1 |
C4' |
C3' |
H3' |
114.9 |
113.5 |
O4' |
C1' |
C2' |
105.6 |
107.4 |
O4' |
C1' |
N1 |
107.5 |
109.3 |
O4' |
C1' |
H1' |
115.1 |
108.0 |
O3' |
C3' |
C2' |
109.9 |
109.7 |
O3' |
C3' |
H3' |
108.7 |
107.4 |
C3' |
O3' |
HO3' |
109.5 |
107.3 |
C2' |
C3' |
H3' |
112.7 |
113.2 |
C3' |
C2' |
C1' |
102.0 |
102.5 |
C3' |
C2' |
H2' |
113.6 |
109.7 |
C3' |
C2' |
H2'' |
112.0 |
114.1 |
C1' |
C2' |
H2' |
113.6 |
110.6 |
C1' |
C2' |
H2'' |
112.1 |
111.7 |
C2' |
C1' |
N1 |
114.6 |
112.8 |
C2' |
C1' |
H1' |
108.1 |
111.5 |
H2' |
C2' |
H2'' |
103.9 |
108.3 |
N1 |
C1' |
H1' |
106.2 |
107.8 |
C1' |
N1 |
C2 |
118.2 |
121.3 |
C1' |
N1 |
C6 |
120.8 |
118.4 |
C2 |
N1 |
C6 |
121.0 |
120.3 |
N1 |
C2 |
O2 |
122.8 |
123.8 |
N1 |
C2 |
N3 |
114.8 |
115.1 |
N1 |
C6 |
C5 |
122.8 |
123.9 |
N1 |
C6 |
H6 |
118.6 |
115.6 |
O2 |
C2 |
N3 |
122.4 |
121.1 |
C2 |
N3 |
C4 |
126.8 |
126.8 |
C2 |
N3 |
H3 |
116.6 |
116.6 |
C4 |
N3 |
H3 |
116.6 |
116.6 |
N3 |
C4 |
O4 |
119.5 |
124.5 |
N3 |
C4 |
C5 |
114.8 |
114.6 |
O4 |
C4 |
C5 |
125.7 |
120.9 |
C4 |
C5 |
C6 |
119.8 |
119.3 |
C4 |
C5 |
H5 |
120.1 |
118.8 |
C6 |
C5 |
H5 |
120.1 |
121.9 |
C5 |
C6 |
H6 |
118.6 |
120.5 |
Torsion Angles for DU
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
OP1 |
P |
OP3 |
OP2 |
|
126.3 |
OP1 |
P |
OP3 |
O5' |
|
233.4 |
OP2 |
P |
OP3 |
O5' |
|
107.1 |
OP3 |
P |
OP2 |
HOP2 |
|
78.5 |
OP3 |
P |
O5' |
C5' |
|
53.2 |
HOP3 |
OP3 |
P |
OP1 |
|
48.8 |
HOP3 |
OP3 |
P |
OP2 |
|
282.5 |
HOP3 |
OP3 |
P |
O5' |
|
175.4 |
OP1 |
P |
OP3 |
HOP3 |
|
48.8 |
OP3 |
P |
OP1 |
OP2 |
|
239.9 |
OP3 |
P |
OP1 |
O5' |
|
120.6 |
OP2 |
P |
OP1 |
O5' |
124.6 |
240.7 |
OP1 |
P |
OP2 |
HOP2 |
159.6 |
312.0 |
OP1 |
P |
O5' |
C5' |
170.6 |
179.9 |
OP2 |
P |
OP3 |
HOP3 |
|
282.5 |
OP3 |
P |
OP2 |
OP1 |
|
126.5 |
OP3 |
P |
OP2 |
O5' |
|
252.3 |
OP1 |
P |
OP2 |
O5' |
236.0 |
125.8 |
OP2 |
P |
O5' |
C5' |
39.9 |
305.8 |
O5' |
P |
OP3 |
HOP3 |
|
175.4 |
OP3 |
P |
O5' |
OP1 |
|
233.2 |
OP3 |
P |
O5' |
OP2 |
|
107.4 |
OP1 |
P |
O5' |
OP2 |
130.8 |
234.2 |
O5' |
P |
OP2 |
HOP2 |
283.6 |
186.2 |
P |
O5' |
C5' |
C4' |
208.5 |
180.0 |
P |
O5' |
C5' |
H5' |
89.0 |
300.4 |
P |
O5' |
C5' |
H5'' |
328.5 |
59.6 |
HOP2 |
OP2 |
P |
O5' |
283.6 |
186.2 |
C4' |
C5' |
O5' |
H5' |
119.5 |
239.6 |
C4' |
C5' |
O5' |
H5'' |
240.0 |
120.4 |
O5' |
C5' |
C4' |
O4' |
287.2 |
62.4 |
O5' |
C5' |
C4' |
C3' |
48.3 |
179.5 |
O5' |
C5' |
C4' |
H4' |
165.3 |
305.3 |
H5' |
C5' |
O5' |
H5'' |
120.5 |
240.8 |
O5' |
C5' |
C4' |
H5' |
240.5 |
119.6 |
O5' |
C5' |
C4' |
H5'' |
120.0 |
240.5 |
H5' |
C5' |
C4' |
H5'' |
239.5 |
120.9 |
O4' |
C4' |
C5' |
C3' |
239.0 |
242.9 |
O4' |
C4' |
C5' |
H4' |
121.9 |
117.1 |
C5' |
C4' |
O4' |
C1' |
124.5 |
108.6 |
C3' |
C4' |
C5' |
H4' |
243.0 |
234.2 |
C5' |
C4' |
C3' |
O3' |
144.5 |
154.2 |
C5' |
C4' |
C3' |
C2' |
260.5 |
271.2 |
C5' |
C4' |
C3' |
H3' |
23.5 |
34.0 |
O5' |
C5' |
H5' |
C4' |
120.6 |
240.5 |
O5' |
C5' |
H5' |
H5'' |
240.3 |
119.0 |
C4' |
C5' |
H5' |
H5'' |
119.7 |
238.5 |
H5' |
C5' |
C4' |
O4' |
46.8 |
302.9 |
H5' |
C5' |
C4' |
C3' |
167.8 |
60.0 |
H5' |
C5' |
C4' |
H4' |
284.8 |
185.7 |
O5' |
C5' |
H5'' |
C4' |
239.1 |
119.4 |
O5' |
C5' |
H5'' |
H5' |
119.5 |
241.0 |
C4' |
C5' |
H5'' |
H5' |
240.4 |
121.5 |
H5'' |
C5' |
C4' |
O4' |
167.3 |
181.9 |
H5'' |
C5' |
C4' |
C3' |
288.3 |
299.0 |
H5'' |
C5' |
C4' |
H4' |
45.3 |
64.8 |
O4' |
C4' |
C5' |
H5' |
46.8 |
302.9 |
O4' |
C4' |
C5' |
H5'' |
167.3 |
181.9 |
C5' |
C4' |
O4' |
C3' |
127.2 |
121.4 |
C5' |
C4' |
O4' |
H4' |
245.1 |
241.8 |
C3' |
C4' |
O4' |
H4' |
117.8 |
120.5 |
O4' |
C4' |
C3' |
O3' |
267.9 |
272.3 |
O4' |
C4' |
C3' |
C2' |
23.9 |
29.2 |
O4' |
C4' |
C3' |
H3' |
146.8 |
152.1 |
C4' |
O4' |
C1' |
C2' |
340.2 |
351.0 |
C4' |
O4' |
C1' |
N1 |
217.4 |
228.3 |
C4' |
O4' |
C1' |
H1' |
99.3 |
111.3 |
C3' |
C4' |
C5' |
H5' |
167.8 |
60.0 |
C3' |
C4' |
C5' |
H5'' |
288.3 |
299.0 |
C5' |
C4' |
C3' |
O4' |
236.7 |
241.9 |
C5' |
C4' |
C3' |
H4' |
114.4 |
124.3 |
O4' |
C4' |
C3' |
H4' |
237.8 |
242.4 |
C3' |
C4' |
O4' |
C1' |
357.3 |
347.3 |
O3' |
C3' |
C4' |
C2' |
244.0 |
243.1 |
O3' |
C3' |
C4' |
H3' |
121.1 |
120.2 |
C4' |
C3' |
O3' |
HO3' |
231.2 |
232.0 |
C2' |
C3' |
C4' |
H3' |
237.1 |
237.2 |
C4' |
C3' |
C2' |
C1' |
325.3 |
326.6 |
C4' |
C3' |
C2' |
H2' |
202.7 |
84.1 |
C4' |
C3' |
C2' |
H2'' |
85.3 |
205.7 |
H4' |
C4' |
C5' |
H5' |
284.8 |
185.7 |
H4' |
C4' |
C5' |
H5'' |
45.3 |
64.8 |
C5' |
C4' |
H4' |
O4' |
119.4 |
117.1 |
C5' |
C4' |
H4' |
C3' |
236.5 |
233.8 |
O4' |
C4' |
H4' |
C3' |
117.0 |
116.7 |
H4' |
C4' |
O4' |
C1' |
239.5 |
226.8 |
H4' |
C4' |
C3' |
O3' |
30.1 |
29.9 |
H4' |
C4' |
C3' |
C2' |
146.1 |
146.9 |
H4' |
C4' |
C3' |
H3' |
269.0 |
269.7 |
C1' |
O4' |
C4' |
C3' |
357.3 |
347.3 |
C1' |
O4' |
C4' |
H4' |
239.5 |
226.8 |
C3' |
C2' |
C1' |
O4' |
34.0 |
26.9 |
O4' |
C1' |
C2' |
H2' |
156.7 |
270.0 |
O4' |
C1' |
C2' |
H2'' |
274.0 |
149.4 |
C2' |
C1' |
O4' |
N1 |
122.8 |
122.7 |
C2' |
C1' |
O4' |
H1' |
240.9 |
239.7 |
N1 |
C1' |
O4' |
H1' |
118.1 |
117.0 |
O4' |
C1' |
N1 |
C2 |
241.6 |
212.9 |
O4' |
C1' |
N1 |
C6 |
61.1 |
32.9 |
O3' |
C3' |
C4' |
H4' |
30.1 |
29.9 |
C4' |
C3' |
O3' |
C2' |
111.4 |
112.7 |
C4' |
C3' |
O3' |
H3' |
235.1 |
236.1 |
C2' |
C3' |
O3' |
H3' |
123.7 |
123.4 |
O3' |
C3' |
C2' |
C1' |
79.5 |
83.6 |
O3' |
C3' |
C2' |
H2' |
316.9 |
201.1 |
O3' |
C3' |
C2' |
H2'' |
199.5 |
322.8 |
C2' |
C3' |
C4' |
H4' |
146.1 |
146.9 |
C4' |
C3' |
C2' |
O3' |
245.8 |
242.9 |
C4' |
C3' |
C2' |
H3' |
124.5 |
123.0 |
O4' |
C1' |
C2' |
C3' |
34.0 |
26.9 |
O3' |
C3' |
C2' |
H3' |
238.6 |
240.1 |
C2' |
C3' |
O3' |
HO3' |
119.8 |
119.3 |
C1' |
C2' |
C3' |
H2' |
122.7 |
242.5 |
C1' |
C2' |
C3' |
H2'' |
240.0 |
120.8 |
C3' |
C2' |
C1' |
N1 |
152.1 |
147.4 |
C3' |
C2' |
C1' |
H1' |
270.3 |
268.8 |
H2' |
C2' |
C3' |
H2'' |
117.3 |
238.3 |
H3' |
C3' |
C4' |
H4' |
269.0 |
269.7 |
C4' |
C3' |
H3' |
O3' |
120.3 |
121.7 |
C4' |
C3' |
H3' |
C2' |
242.4 |
242.9 |
O3' |
C3' |
H3' |
C2' |
122.0 |
121.3 |
H3' |
C3' |
O3' |
HO3' |
356.1 |
355.9 |
H3' |
C3' |
C2' |
C1' |
200.9 |
203.6 |
H3' |
C3' |
C2' |
H2' |
78.2 |
321.1 |
H3' |
C3' |
C2' |
H2'' |
320.9 |
82.7 |
HO3' |
O3' |
C3' |
C2' |
119.8 |
119.3 |
HO3' |
O3' |
C3' |
H3' |
356.1 |
355.9 |
O4' |
C1' |
C2' |
N1 |
241.9 |
239.5 |
O4' |
C1' |
C2' |
H1' |
123.7 |
118.1 |
C1' |
C2' |
C3' |
H3' |
200.9 |
203.6 |
C3' |
C2' |
C1' |
H2' |
237.3 |
116.9 |
C3' |
C2' |
C1' |
H2'' |
120.0 |
237.5 |
H2' |
C2' |
C1' |
H2'' |
242.6 |
120.7 |
N1 |
C1' |
C2' |
H1' |
241.8 |
238.6 |
C2' |
C1' |
N1 |
C2 |
124.5 |
93.5 |
C2' |
C1' |
N1 |
C6 |
304.0 |
273.5 |
H2' |
C2' |
C3' |
H3' |
78.2 |
321.1 |
C3' |
C2' |
H2' |
C1' |
116.0 |
247.7 |
C3' |
C2' |
H2' |
H2'' |
238.0 |
125.1 |
C1' |
C2' |
H2' |
H2'' |
122.0 |
237.3 |
H2' |
C2' |
C1' |
N1 |
274.8 |
30.6 |
H2' |
C2' |
C1' |
H1' |
33.0 |
151.9 |
H2'' |
C2' |
C3' |
H3' |
320.9 |
82.7 |
C3' |
C2' |
H2'' |
C1' |
246.1 |
115.6 |
C3' |
C2' |
H2'' |
H2' |
123.0 |
237.5 |
C1' |
C2' |
H2'' |
H2' |
237.0 |
122.0 |
H2'' |
C2' |
C1' |
N1 |
32.2 |
269.9 |
H2'' |
C2' |
C1' |
H1' |
150.4 |
31.3 |
O4' |
C1' |
N1 |
C2' |
117.1 |
119.4 |
O4' |
C1' |
N1 |
H1' |
236.3 |
242.9 |
N1 |
C1' |
C2' |
H2' |
274.8 |
30.6 |
N1 |
C1' |
C2' |
H2'' |
32.2 |
269.9 |
C2' |
C1' |
N1 |
H1' |
119.2 |
123.5 |
C2 |
N1 |
C1' |
C6 |
180.5 |
180.0 |
C1' |
N1 |
C2 |
O2 |
359.0 |
0.0 |
C1' |
N1 |
C2 |
N3 |
179.2 |
180.0 |
C1' |
N1 |
C6 |
C5 |
180.7 |
180.0 |
C1' |
N1 |
C6 |
H6 |
0.6 |
360.0 |
O4' |
C1' |
H1' |
C2' |
242.2 |
242.3 |
O4' |
C1' |
H1' |
N1 |
118.8 |
118.0 |
H1' |
C1' |
C2' |
H2' |
33.0 |
151.9 |
H1' |
C1' |
C2' |
H2'' |
150.4 |
31.3 |
C2' |
C1' |
H1' |
N1 |
236.6 |
235.7 |
H1' |
C1' |
N1 |
C2 |
5.2 |
330.0 |
H1' |
C1' |
N1 |
C6 |
184.8 |
150.0 |
C2 |
N1 |
C1' |
H1' |
5.2 |
330.0 |
C1' |
N1 |
C2 |
C6 |
179.5 |
180.0 |
C2 |
N1 |
C6 |
C5 |
0.2 |
360.0 |
C2 |
N1 |
C6 |
H6 |
180.2 |
180.0 |
O2 |
C2 |
N1 |
N3 |
179.8 |
180.0 |
N1 |
C2 |
N3 |
C4 |
0.5 |
0.0 |
N1 |
C2 |
N3 |
H3 |
180.5 |
180.0 |
C6 |
N1 |
C1' |
H1' |
184.8 |
150.0 |
C1' |
N1 |
C6 |
C2 |
180.5 |
180.0 |
C6 |
N1 |
C2 |
O2 |
179.5 |
180.0 |
C6 |
N1 |
C2 |
N3 |
359.6 |
360.0 |
C4 |
C5 |
C6 |
N1 |
359.9 |
0.0 |
N1 |
C6 |
C5 |
H5 |
179.9 |
180.0 |
C5 |
C6 |
N1 |
H6 |
180.0 |
180.0 |
O2 |
C2 |
N1 |
C6 |
179.5 |
180.0 |
N1 |
C2 |
O2 |
N3 |
180.2 |
180.0 |
O2 |
C2 |
N3 |
C4 |
180.7 |
180.0 |
O2 |
C2 |
N3 |
H3 |
0.7 |
360.0 |
N3 |
C2 |
N1 |
C6 |
359.6 |
360.0 |
N1 |
C2 |
N3 |
O2 |
179.8 |
180.0 |
C4 |
N3 |
C2 |
H3 |
180.0 |
180.0 |
C2 |
N3 |
C4 |
O4 |
178.5 |
179.9 |
C2 |
N3 |
C4 |
C5 |
359.6 |
360.0 |
C2 |
N3 |
C4 |
H3 |
180.0 |
180.0 |
O4 |
C4 |
N3 |
C5 |
178.9 |
180.0 |
N3 |
C4 |
C5 |
C6 |
0.2 |
360.0 |
N3 |
C4 |
C5 |
H5 |
180.2 |
180.0 |
C2 |
N3 |
H3 |
C4 |
180.0 |
180.0 |
H3 |
N3 |
C4 |
O4 |
358.5 |
360.0 |
H3 |
N3 |
C4 |
C5 |
179.6 |
180.0 |
O4 |
C4 |
N3 |
H3 |
358.5 |
360.0 |
N3 |
C4 |
O4 |
C5 |
181.2 |
180.0 |
O4 |
C4 |
C5 |
C6 |
181.3 |
180.0 |
O4 |
C4 |
C5 |
H5 |
1.4 |
0.0 |
N1 |
C6 |
C5 |
C4 |
359.9 |
0.0 |
C5 |
C4 |
N3 |
H3 |
179.6 |
180.0 |
N3 |
C4 |
C5 |
O4 |
178.9 |
180.0 |
C6 |
C5 |
C4 |
H5 |
180.0 |
180.0 |
C4 |
C5 |
C6 |
H6 |
179.9 |
180.0 |
N1 |
C6 |
C5 |
H6 |
180.0 |
180.0 |
C4 |
C5 |
C6 |
H5 |
180.0 |
180.0 |
C4 |
C5 |
H5 |
C6 |
180.0 |
180.0 |
H5 |
C5 |
C6 |
H6 |
359.9 |
0.0 |
N1 |
C6 |
H6 |
C5 |
180.0 |
180.0 |
H6 |
C6 |
C5 |
H5 |
359.9 |
0.0 |