PDB Chemical Component DI
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 DI
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
OP3 |
P |
|
1.617 |
OP3 |
HOP3 |
|
0.981 |
P |
OP1 |
1.459 |
1.501 |
P |
OP2 |
1.523 |
1.617 |
P |
O5' |
1.536 |
1.619 |
OP2 |
HOP2 |
0.950 |
0.981 |
O5' |
C5' |
1.403 |
1.417 |
C5' |
C4' |
1.506 |
1.523 |
C5' |
H5' |
1.100 |
1.090 |
C5' |
H5'' |
1.100 |
1.091 |
C4' |
O4' |
1.458 |
1.443 |
C4' |
C3' |
1.534 |
1.525 |
C4' |
H4' |
1.101 |
1.095 |
O4' |
C1' |
1.452 |
1.439 |
C3' |
O3' |
1.405 |
1.425 |
C3' |
C2' |
1.522 |
1.512 |
C3' |
H3' |
1.100 |
1.093 |
O3' |
HO3' |
0.950 |
0.969 |
C2' |
C1' |
1.531 |
1.522 |
C2' |
H2' |
1.100 |
1.097 |
C2' |
H2'' |
1.100 |
1.094 |
C1' |
N9 |
1.439 |
1.459 |
C1' |
H1' |
1.100 |
1.095 |
N9 |
C8 |
1.395 |
1.376 |
N9 |
C4 |
1.386 |
1.366 |
C8 |
N7 |
1.329 |
1.318 |
C8 |
H8 |
1.080 |
1.082 |
N7 |
C5 |
1.399 |
1.365 |
C5 |
C6 |
1.405 |
1.440 |
C5 |
C4 |
1.401 |
1.377 |
C6 |
O6 |
1.263 |
1.224 |
C6 |
N1 |
1.388 |
1.402 |
N1 |
C2 |
1.424 |
1.400 |
N1 |
H1 |
1.000 |
1.016 |
C2 |
N3 |
1.385 |
1.302 |
C2 |
H2 |
1.079 |
1.101 |
N3 |
C4 |
1.345 |
1.352 |
Bond Angles for DI
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 |
120.0 |
115.0 |
OP1 |
P |
O5' |
108.3 |
115.0 |
OP2 |
P |
O5' |
106.5 |
102.9 |
P |
OP2 |
HOP2 |
109.5 |
118.9 |
P |
O5' |
C5' |
120.6 |
118.5 |
O5' |
C5' |
C4' |
107.0 |
108.7 |
O5' |
C5' |
H5' |
110.9 |
109.2 |
O5' |
C5' |
H5'' |
110.3 |
109.2 |
C4' |
C5' |
H5' |
110.9 |
110.1 |
C4' |
C5' |
H5'' |
110.3 |
110.1 |
C5' |
C4' |
O4' |
113.7 |
108.0 |
C5' |
C4' |
C3' |
120.0 |
112.7 |
C5' |
C4' |
H4' |
97.4 |
109.4 |
H5' |
C5' |
H5'' |
107.6 |
109.6 |
O4' |
C4' |
C3' |
107.9 |
106.8 |
O4' |
C4' |
H4' |
112.4 |
107.7 |
C4' |
O4' |
C1' |
106.8 |
108.7 |
C3' |
C4' |
H4' |
104.7 |
112.0 |
C4' |
C3' |
O3' |
107.0 |
109.6 |
C4' |
C3' |
C2' |
99.9 |
103.2 |
C4' |
C3' |
H3' |
117.3 |
114.0 |
O4' |
C1' |
C2' |
106.9 |
106.7 |
O4' |
C1' |
N9 |
103.0 |
110.0 |
O4' |
C1' |
H1' |
118.8 |
108.1 |
O3' |
C3' |
C2' |
110.5 |
108.4 |
O3' |
C3' |
H3' |
107.8 |
107.8 |
C3' |
O3' |
HO3' |
109.5 |
106.6 |
C2' |
C3' |
H3' |
114.1 |
113.7 |
C3' |
C2' |
C1' |
102.1 |
101.6 |
C3' |
C2' |
H2' |
113.6 |
110.0 |
C3' |
C2' |
H2'' |
112.0 |
114.2 |
C1' |
C2' |
H2' |
113.6 |
110.5 |
C1' |
C2' |
H2'' |
112.0 |
111.7 |
C2' |
C1' |
N9 |
118.6 |
114.3 |
C2' |
C1' |
H1' |
103.3 |
111.7 |
H2' |
C2' |
H2'' |
103.9 |
108.7 |
N9 |
C1' |
H1' |
107.2 |
105.9 |
C1' |
N9 |
C8 |
123.3 |
126.2 |
C1' |
N9 |
C4 |
128.3 |
127.3 |
C8 |
N9 |
C4 |
108.4 |
106.6 |
N9 |
C8 |
N7 |
111.4 |
112.6 |
N9 |
C8 |
H8 |
124.3 |
121.9 |
N9 |
C4 |
C5 |
103.8 |
105.0 |
N9 |
C4 |
N3 |
127.7 |
126.2 |
N7 |
C8 |
H8 |
124.3 |
125.5 |
C8 |
N7 |
C5 |
104.7 |
103.9 |
N7 |
C5 |
C6 |
128.9 |
128.6 |
N7 |
C5 |
C4 |
111.7 |
112.0 |
C6 |
C5 |
C4 |
119.4 |
119.4 |
C5 |
C6 |
O6 |
124.8 |
123.8 |
C5 |
C6 |
N1 |
113.3 |
110.9 |
C5 |
C4 |
N3 |
128.4 |
128.8 |
O6 |
C6 |
N1 |
121.9 |
125.4 |
C6 |
N1 |
C2 |
125.1 |
123.6 |
C6 |
N1 |
H1 |
117.5 |
118.2 |
C2 |
N1 |
H1 |
117.4 |
118.2 |
N1 |
C2 |
N3 |
120.8 |
125.8 |
N1 |
C2 |
H2 |
119.6 |
112.7 |
N3 |
C2 |
H2 |
119.6 |
121.5 |
C2 |
N3 |
C4 |
113.1 |
111.5 |
Torsion Angles for DI
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' |
122.3 |
240.7 |
OP1 |
P |
OP2 |
HOP2 |
121.3 |
312.0 |
OP1 |
P |
O5' |
C5' |
288.6 |
180.0 |
OP2 |
P |
OP3 |
HOP3 |
|
282.5 |
OP3 |
P |
OP2 |
OP1 |
|
126.5 |
OP3 |
P |
OP2 |
O5' |
|
252.3 |
OP1 |
P |
OP2 |
O5' |
236.8 |
125.8 |
OP2 |
P |
O5' |
C5' |
158.4 |
305.8 |
O5' |
P |
OP3 |
HOP3 |
|
175.4 |
OP3 |
P |
O5' |
OP1 |
|
233.2 |
OP3 |
P |
O5' |
OP2 |
|
107.4 |
OP1 |
P |
O5' |
OP2 |
130.2 |
234.2 |
O5' |
P |
OP2 |
HOP2 |
244.5 |
186.1 |
P |
O5' |
C5' |
C4' |
144.8 |
180.0 |
P |
O5' |
C5' |
H5' |
23.8 |
300.1 |
P |
O5' |
C5' |
H5'' |
264.8 |
59.9 |
HOP2 |
OP2 |
P |
O5' |
244.5 |
186.1 |
C4' |
C5' |
O5' |
H5' |
121.0 |
239.9 |
C4' |
C5' |
O5' |
H5'' |
240.0 |
120.1 |
O5' |
C5' |
C4' |
O4' |
169.2 |
61.8 |
O5' |
C5' |
C4' |
C3' |
299.0 |
179.5 |
O5' |
C5' |
C4' |
H4' |
50.7 |
304.8 |
H5' |
C5' |
O5' |
H5'' |
119.0 |
240.2 |
O5' |
C5' |
C4' |
H5' |
239.0 |
119.6 |
O5' |
C5' |
C4' |
H5'' |
120.0 |
240.5 |
H5' |
C5' |
C4' |
H5'' |
241.0 |
120.9 |
O4' |
C4' |
C5' |
C3' |
230.2 |
242.3 |
O4' |
C4' |
C5' |
H4' |
118.5 |
117.0 |
C5' |
C4' |
O4' |
C1' |
121.9 |
116.0 |
C3' |
C4' |
C5' |
H4' |
248.3 |
234.7 |
C5' |
C4' |
C3' |
O3' |
146.3 |
152.1 |
C5' |
C4' |
C3' |
C2' |
261.4 |
267.4 |
C5' |
C4' |
C3' |
H3' |
25.2 |
31.2 |
O5' |
C5' |
H5' |
C4' |
118.6 |
240.8 |
O5' |
C5' |
H5' |
H5'' |
239.3 |
119.6 |
C4' |
C5' |
H5' |
H5'' |
120.7 |
238.8 |
H5' |
C5' |
C4' |
O4' |
290.1 |
302.2 |
H5' |
C5' |
C4' |
C3' |
59.9 |
60.0 |
H5' |
C5' |
C4' |
H4' |
171.6 |
185.3 |
O5' |
C5' |
H5'' |
C4' |
242.1 |
119.2 |
O5' |
C5' |
H5'' |
H5' |
121.0 |
240.4 |
C4' |
C5' |
H5'' |
H5' |
239.0 |
121.2 |
H5'' |
C5' |
C4' |
O4' |
49.2 |
181.3 |
H5'' |
C5' |
C4' |
C3' |
179.0 |
299.1 |
H5'' |
C5' |
C4' |
H4' |
290.7 |
64.3 |
O4' |
C4' |
C5' |
H5' |
290.1 |
302.2 |
O4' |
C4' |
C5' |
H5'' |
49.2 |
181.3 |
C5' |
C4' |
O4' |
C3' |
135.6 |
121.5 |
C5' |
C4' |
O4' |
H4' |
250.5 |
242.0 |
C3' |
C4' |
O4' |
H4' |
114.9 |
120.5 |
O4' |
C4' |
C3' |
O3' |
278.6 |
270.6 |
O4' |
C4' |
C3' |
C2' |
33.8 |
25.9 |
O4' |
C4' |
C3' |
H3' |
157.6 |
149.7 |
C4' |
O4' |
C1' |
C2' |
347.7 |
342.7 |
C4' |
O4' |
C1' |
N9 |
222.0 |
218.2 |
C4' |
O4' |
C1' |
H1' |
103.9 |
103.1 |
C3' |
C4' |
C5' |
H5' |
59.9 |
60.0 |
C3' |
C4' |
C5' |
H5'' |
179.0 |
299.1 |
C5' |
C4' |
C3' |
O4' |
227.7 |
241.5 |
C5' |
C4' |
C3' |
H4' |
107.7 |
123.8 |
O4' |
C4' |
C3' |
H4' |
240.1 |
242.3 |
C3' |
C4' |
O4' |
C1' |
346.2 |
354.5 |
O3' |
C3' |
C4' |
C2' |
244.9 |
244.7 |
O3' |
C3' |
C4' |
H3' |
121.1 |
120.9 |
C4' |
C3' |
O3' |
HO3' |
161.4 |
46.6 |
C2' |
C3' |
C4' |
H3' |
236.2 |
236.3 |
C4' |
C3' |
C2' |
C1' |
320.6 |
325.2 |
C4' |
C3' |
C2' |
H2' |
198.0 |
82.2 |
C4' |
C3' |
C2' |
H2'' |
80.7 |
204.8 |
H4' |
C4' |
C5' |
H5' |
171.6 |
185.3 |
H4' |
C4' |
C5' |
H5'' |
290.7 |
64.3 |
C5' |
C4' |
H4' |
O4' |
119.5 |
117.2 |
C5' |
C4' |
H4' |
C3' |
236.3 |
234.3 |
O4' |
C4' |
H4' |
C3' |
116.8 |
117.2 |
H4' |
C4' |
O4' |
C1' |
231.3 |
234.0 |
H4' |
C4' |
C3' |
O3' |
38.6 |
28.3 |
H4' |
C4' |
C3' |
C2' |
153.7 |
143.6 |
H4' |
C4' |
C3' |
H3' |
277.5 |
267.4 |
C1' |
O4' |
C4' |
C3' |
346.2 |
354.5 |
C1' |
O4' |
C4' |
H4' |
231.3 |
234.0 |
C3' |
C2' |
C1' |
O4' |
33.5 |
32.7 |
O4' |
C1' |
C2' |
H2' |
156.1 |
276.0 |
O4' |
C1' |
C2' |
H2'' |
273.4 |
154.9 |
C2' |
C1' |
O4' |
N9 |
125.6 |
124.5 |
C2' |
C1' |
O4' |
H1' |
243.8 |
239.7 |
N9 |
C1' |
O4' |
H1' |
118.2 |
115.2 |
O4' |
C1' |
N9 |
C8 |
250.6 |
33.5 |
O4' |
C1' |
N9 |
C4 |
67.5 |
213.5 |
O3' |
C3' |
C4' |
H4' |
38.6 |
28.3 |
C4' |
C3' |
O3' |
C2' |
107.8 |
111.9 |
C4' |
C3' |
O3' |
H3' |
233.1 |
235.4 |
C2' |
C3' |
O3' |
H3' |
125.3 |
123.5 |
O3' |
C3' |
C2' |
C1' |
73.1 |
81.3 |
O3' |
C3' |
C2' |
H2' |
310.4 |
198.4 |
O3' |
C3' |
C2' |
H2'' |
193.1 |
320.9 |
C2' |
C3' |
C4' |
H4' |
153.7 |
143.6 |
C4' |
C3' |
C2' |
O3' |
247.6 |
243.8 |
C4' |
C3' |
C2' |
H3' |
125.9 |
123.9 |
O4' |
C1' |
C2' |
C3' |
33.5 |
32.7 |
O3' |
C3' |
C2' |
H3' |
238.4 |
240.1 |
C2' |
C3' |
O3' |
HO3' |
53.6 |
294.7 |
C1' |
C2' |
C3' |
H2' |
122.7 |
243.0 |
C1' |
C2' |
C3' |
H2'' |
240.0 |
120.4 |
C3' |
C2' |
C1' |
N9 |
149.1 |
154.5 |
C3' |
C2' |
C1' |
H1' |
267.4 |
274.8 |
H2' |
C2' |
C3' |
H2'' |
117.3 |
237.5 |
H3' |
C3' |
C4' |
H4' |
277.5 |
267.4 |
C4' |
C3' |
H3' |
O3' |
120.7 |
121.9 |
C4' |
C3' |
H3' |
C2' |
243.8 |
242.1 |
O3' |
C3' |
H3' |
C2' |
123.1 |
120.2 |
H3' |
C3' |
O3' |
HO3' |
288.3 |
171.2 |
H3' |
C3' |
C2' |
C1' |
194.7 |
201.2 |
H3' |
C3' |
C2' |
H2' |
72.0 |
318.3 |
H3' |
C3' |
C2' |
H2'' |
314.7 |
80.8 |
HO3' |
O3' |
C3' |
C2' |
53.6 |
294.7 |
HO3' |
O3' |
C3' |
H3' |
288.3 |
171.2 |
O4' |
C1' |
C2' |
N9 |
244.4 |
238.2 |
O4' |
C1' |
C2' |
H1' |
126.1 |
117.9 |
C1' |
C2' |
C3' |
H3' |
194.7 |
201.2 |
C3' |
C2' |
C1' |
H2' |
237.3 |
116.7 |
C3' |
C2' |
C1' |
H2'' |
120.0 |
237.8 |
H2' |
C2' |
C1' |
H2'' |
242.7 |
121.1 |
N9 |
C1' |
C2' |
H1' |
241.7 |
239.7 |
C2' |
C1' |
N9 |
C8 |
132.9 |
273.4 |
C2' |
C1' |
N9 |
C4 |
309.8 |
93.5 |
H2' |
C2' |
C3' |
H3' |
72.0 |
318.3 |
C3' |
C2' |
H2' |
C1' |
116.1 |
248.6 |
C3' |
C2' |
H2' |
H2'' |
238.0 |
125.7 |
C1' |
C2' |
H2' |
H2'' |
121.9 |
237.1 |
H2' |
C2' |
C1' |
N9 |
271.7 |
37.8 |
H2' |
C2' |
C1' |
H1' |
30.1 |
158.1 |
H2'' |
C2' |
C3' |
H3' |
314.7 |
80.8 |
C3' |
C2' |
H2'' |
C1' |
246.0 |
114.6 |
C3' |
C2' |
H2'' |
H2' |
123.0 |
236.7 |
C1' |
C2' |
H2'' |
H2' |
237.0 |
122.1 |
H2'' |
C2' |
C1' |
N9 |
29.1 |
276.7 |
H2'' |
C2' |
C1' |
H1' |
147.4 |
37.0 |
O4' |
C1' |
N9 |
C2' |
117.7 |
120.0 |
O4' |
C1' |
N9 |
H1' |
233.9 |
243.5 |
N9 |
C1' |
C2' |
H2' |
271.7 |
37.8 |
N9 |
C1' |
C2' |
H2'' |
29.1 |
276.7 |
C2' |
C1' |
N9 |
H1' |
116.3 |
123.5 |
C8 |
N9 |
C1' |
C4 |
183.1 |
180.0 |
C1' |
N9 |
C8 |
N7 |
177.7 |
180.1 |
C1' |
N9 |
C8 |
H8 |
357.8 |
0.1 |
C1' |
N9 |
C4 |
C5 |
183.0 |
179.9 |
C1' |
N9 |
C4 |
N3 |
2.1 |
0.0 |
O4' |
C1' |
H1' |
C2' |
242.0 |
242.9 |
O4' |
C1' |
H1' |
N9 |
116.0 |
117.8 |
H1' |
C1' |
C2' |
H2' |
30.1 |
158.1 |
H1' |
C1' |
C2' |
H2'' |
147.4 |
37.0 |
C2' |
C1' |
H1' |
N9 |
234.0 |
234.9 |
H1' |
C1' |
N9 |
C8 |
16.6 |
150.0 |
H1' |
C1' |
N9 |
C4 |
193.5 |
330.0 |
C8 |
N9 |
C1' |
H1' |
16.6 |
150.0 |
C1' |
N9 |
C8 |
C4 |
177.4 |
180.0 |
C8 |
N9 |
C4 |
C5 |
0.3 |
359.9 |
C8 |
N9 |
C4 |
N3 |
179.4 |
180.1 |
N7 |
C8 |
N9 |
H8 |
180.0 |
180.0 |
N9 |
C8 |
N7 |
C5 |
359.3 |
0.0 |
C4 |
N9 |
C1' |
H1' |
193.5 |
330.0 |
C1' |
N9 |
C4 |
C8 |
182.7 |
180.0 |
C4 |
N9 |
C8 |
N7 |
0.3 |
0.0 |
C4 |
N9 |
C8 |
H8 |
180.3 |
180.0 |
N7 |
C5 |
C4 |
N9 |
359.3 |
0.1 |
C6 |
C5 |
C4 |
N9 |
178.9 |
180.1 |
C5 |
C4 |
N9 |
N3 |
180.9 |
179.9 |
C2 |
N3 |
C4 |
N9 |
180.7 |
179.9 |
N7 |
C8 |
N9 |
C4 |
0.3 |
0.0 |
N9 |
C8 |
N7 |
H8 |
180.0 |
180.0 |
C8 |
N7 |
C5 |
C6 |
181.4 |
179.9 |
C8 |
N7 |
C5 |
C4 |
0.9 |
359.9 |
H8 |
C8 |
N9 |
C4 |
180.3 |
180.0 |
N9 |
C8 |
H8 |
N7 |
180.0 |
180.0 |
H8 |
C8 |
N7 |
C5 |
179.3 |
180.0 |
N9 |
C4 |
C5 |
N7 |
359.3 |
0.1 |
C5 |
N7 |
C8 |
H8 |
179.3 |
180.0 |
C6 |
C5 |
N7 |
C4 |
180.5 |
180.0 |
N7 |
C5 |
C6 |
O6 |
0.7 |
360.0 |
N7 |
C5 |
C6 |
N1 |
180.1 |
180.0 |
N7 |
C5 |
C4 |
N3 |
180.2 |
180.0 |
N9 |
C4 |
C5 |
C6 |
178.9 |
180.1 |
N7 |
C5 |
C6 |
C4 |
179.5 |
180.0 |
C6 |
C5 |
C4 |
N3 |
359.8 |
359.9 |
O6 |
C6 |
C5 |
N1 |
180.6 |
180.0 |
C5 |
C6 |
N1 |
C2 |
359.5 |
0.0 |
C5 |
C6 |
N1 |
H1 |
179.5 |
180.1 |
N9 |
C4 |
C5 |
N3 |
179.1 |
180.1 |
N7 |
C5 |
C4 |
C6 |
180.4 |
180.0 |
C4 |
C5 |
C6 |
O6 |
181.2 |
180.0 |
C4 |
C5 |
C6 |
N1 |
0.6 |
360.0 |
C2 |
N3 |
C4 |
C5 |
359.6 |
0.1 |
O6 |
C6 |
C5 |
C4 |
181.2 |
180.0 |
C5 |
C6 |
O6 |
N1 |
179.4 |
180.0 |
O6 |
C6 |
N1 |
C2 |
178.9 |
180.0 |
O6 |
C6 |
N1 |
H1 |
358.9 |
0.1 |
N1 |
C6 |
C5 |
C4 |
0.6 |
360.0 |
C5 |
C6 |
N1 |
O6 |
180.6 |
180.0 |
C2 |
N1 |
C6 |
H1 |
180.0 |
180.0 |
C6 |
N1 |
C2 |
N3 |
359.9 |
360.0 |
C6 |
N1 |
C2 |
H2 |
179.9 |
179.9 |
C6 |
N1 |
C2 |
H1 |
180.0 |
180.0 |
N3 |
C2 |
N1 |
H2 |
180.0 |
180.0 |
N1 |
C2 |
N3 |
C4 |
0.5 |
360.0 |
C6 |
N1 |
H1 |
C2 |
180.0 |
180.0 |
H1 |
N1 |
C2 |
N3 |
179.9 |
179.9 |
H1 |
N1 |
C2 |
H2 |
359.9 |
359.9 |
N9 |
C4 |
N3 |
C2 |
180.7 |
179.9 |
C5 |
C4 |
N3 |
C2 |
359.6 |
0.1 |
N3 |
C2 |
N1 |
H1 |
179.9 |
179.9 |
N1 |
C2 |
N3 |
H2 |
180.0 |
180.0 |
H2 |
C2 |
N1 |
H1 |
359.9 |
359.9 |
N1 |
C2 |
H2 |
N3 |
180.0 |
180.0 |
H2 |
C2 |
N3 |
C4 |
180.6 |
180.0 |
N9 |
C4 |
N3 |
C5 |
181.1 |
179.8 |
C4 |
N3 |
C2 |
H2 |
180.6 |
180.0 |