PDB Chemical Component D5M
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 D5M
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
O5' |
C5' |
1.429 |
1.417 |
O5' |
P |
|
1.619 |
C5' |
C4' |
1.511 |
1.523 |
C5' |
H5'1 |
1.100 |
1.090 |
C5' |
H5'2 |
1.100 |
1.091 |
C4' |
O4' |
1.451 |
1.443 |
C4' |
C3' |
1.531 |
1.525 |
C4' |
H4' |
1.100 |
1.095 |
O4' |
C1' |
1.429 |
1.439 |
C3' |
O3' |
1.444 |
1.425 |
C3' |
C2' |
1.521 |
1.512 |
C3' |
H1 |
1.100 |
1.093 |
O3' |
H3' |
0.950 |
0.969 |
C2' |
C1' |
1.526 |
1.522 |
C2' |
H2'1 |
1.100 |
1.097 |
C2' |
H2'2 |
1.100 |
1.094 |
C1' |
N9 |
1.467 |
1.459 |
C1' |
H1' |
1.100 |
1.095 |
N9 |
C8 |
1.382 |
1.371 |
N9 |
C4 |
1.379 |
1.368 |
C8 |
N7 |
1.315 |
1.317 |
C8 |
H8 |
1.080 |
1.082 |
N7 |
C5 |
1.393 |
1.373 |
C5 |
C6 |
1.413 |
1.390 |
C5 |
C4 |
1.391 |
1.386 |
C6 |
N6 |
1.336 |
1.405 |
C6 |
N1 |
1.356 |
1.355 |
N6 |
HN61 |
1.000 |
1.002 |
N6 |
HN62 |
1.000 |
1.002 |
N1 |
C2 |
1.346 |
1.355 |
C2 |
N3 |
1.335 |
1.351 |
C2 |
H2 |
1.080 |
1.084 |
N3 |
C4 |
1.352 |
1.342 |
P |
O1P |
|
1.501 |
P |
O3P |
|
1.617 |
P |
O2P |
|
1.617 |
O3P |
H3P |
|
0.981 |
O2P |
H2P |
|
0.981 |
Bond Angles for D5M
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
C5' |
O5' |
P |
|
118.5 |
O5' |
C5' |
C4' |
111.4 |
108.7 |
O5' |
C5' |
H5'1 |
108.8 |
109.2 |
O5' |
C5' |
H5'2 |
108.4 |
109.2 |
O5' |
P |
O1P |
|
115.0 |
O5' |
P |
O3P |
|
103.7 |
O5' |
P |
O2P |
|
102.9 |
C4' |
C5' |
H5'1 |
108.8 |
110.1 |
C4' |
C5' |
H5'2 |
108.4 |
110.1 |
C5' |
C4' |
O4' |
109.0 |
108.0 |
C5' |
C4' |
C3' |
114.9 |
112.7 |
C5' |
C4' |
H4' |
105.0 |
109.4 |
H5'1 |
C5' |
H5'2 |
111.0 |
109.6 |
O4' |
C4' |
C3' |
105.7 |
106.8 |
O4' |
C4' |
H4' |
114.3 |
107.7 |
C4' |
O4' |
C1' |
109.9 |
108.7 |
C3' |
C4' |
H4' |
108.3 |
112.0 |
C4' |
C3' |
O3' |
110.2 |
109.6 |
C4' |
C3' |
C2' |
102.6 |
103.2 |
C4' |
C3' |
H1 |
112.7 |
114.0 |
O4' |
C1' |
C2' |
106.0 |
106.7 |
O4' |
C1' |
N9 |
107.9 |
110.0 |
O4' |
C1' |
H1' |
115.1 |
108.1 |
O3' |
C3' |
C2' |
107.3 |
108.4 |
O3' |
C3' |
H1 |
108.4 |
107.8 |
C3' |
O3' |
H3' |
109.5 |
106.6 |
C2' |
C3' |
H1 |
115.4 |
113.7 |
C3' |
C2' |
C1' |
101.7 |
101.6 |
C3' |
C2' |
H2'1 |
112.2 |
110.0 |
C3' |
C2' |
H2'2 |
113.8 |
114.2 |
C1' |
C2' |
H2'1 |
112.2 |
110.5 |
C1' |
C2' |
H2'2 |
113.8 |
111.7 |
C2' |
C1' |
N9 |
115.8 |
114.3 |
C2' |
C1' |
H1' |
107.1 |
111.7 |
H2'1 |
C2' |
H2'2 |
103.6 |
108.7 |
N9 |
C1' |
H1' |
105.2 |
105.9 |
C1' |
N9 |
C8 |
128.5 |
126.2 |
C1' |
N9 |
C4 |
125.8 |
126.9 |
C8 |
N9 |
C4 |
105.7 |
106.9 |
N9 |
C8 |
N7 |
113.8 |
112.3 |
N9 |
C8 |
H8 |
123.1 |
122.2 |
N9 |
C4 |
C5 |
105.9 |
105.3 |
N9 |
C4 |
N3 |
127.3 |
127.5 |
N7 |
C8 |
H8 |
123.1 |
125.6 |
C8 |
N7 |
C5 |
103.9 |
104.9 |
N7 |
C5 |
C6 |
132.3 |
132.4 |
N7 |
C5 |
C4 |
110.7 |
110.7 |
C6 |
C5 |
C4 |
117.0 |
116.9 |
C5 |
C6 |
N6 |
123.6 |
120.7 |
C5 |
C6 |
N1 |
117.6 |
119.1 |
C5 |
C4 |
N3 |
126.8 |
127.2 |
N6 |
C6 |
N1 |
118.8 |
120.2 |
C6 |
N6 |
HN61 |
109.5 |
119.5 |
C6 |
N6 |
HN62 |
109.5 |
119.4 |
C6 |
N1 |
C2 |
118.7 |
117.5 |
HN61 |
N6 |
HN62 |
109.5 |
120.8 |
N1 |
C2 |
N3 |
129.3 |
128.8 |
N1 |
C2 |
H2 |
115.4 |
115.5 |
N3 |
C2 |
H2 |
115.3 |
115.7 |
C2 |
N3 |
C4 |
110.6 |
110.5 |
O1P |
P |
O3P |
|
115.3 |
O1P |
P |
O2P |
|
115.0 |
O3P |
P |
O2P |
|
103.3 |
P |
O3P |
H3P |
|
118.9 |
P |
O2P |
H2P |
|
118.9 |
Torsion Angles for D5M
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
C5' |
O5' |
P |
O1P |
|
180.0 |
C5' |
O5' |
P |
O3P |
|
53.2 |
C5' |
O5' |
P |
O2P |
|
305.8 |
C4' |
C5' |
O5' |
H5'1 |
240.0 |
239.9 |
C4' |
C5' |
O5' |
H5'2 |
119.2 |
120.1 |
O5' |
C5' |
C4' |
O4' |
57.8 |
61.8 |
O5' |
C5' |
C4' |
C3' |
176.2 |
179.5 |
O5' |
C5' |
C4' |
H4' |
295.0 |
304.8 |
H5'1 |
C5' |
O5' |
H5'2 |
239.2 |
240.2 |
P |
O5' |
C5' |
C4' |
|
180.0 |
P |
O5' |
C5' |
H5'1 |
|
300.1 |
P |
O5' |
C5' |
H5'2 |
|
59.9 |
O1P |
P |
O5' |
O3P |
|
126.8 |
O1P |
P |
O5' |
O2P |
|
234.2 |
O3P |
P |
O5' |
O2P |
|
107.4 |
O5' |
P |
O3P |
H3P |
|
175.4 |
O5' |
P |
O2P |
H2P |
|
186.1 |
C4' |
C5' |
O5' |
P |
|
180.0 |
O5' |
C5' |
C4' |
H5'1 |
120.0 |
119.6 |
O5' |
C5' |
C4' |
H5'2 |
240.8 |
240.5 |
H5'1 |
C5' |
C4' |
H5'2 |
120.8 |
120.9 |
O4' |
C4' |
C5' |
C3' |
241.7 |
242.3 |
O4' |
C4' |
C5' |
H4' |
122.8 |
117.0 |
C5' |
C4' |
O4' |
C1' |
116.5 |
116.0 |
C3' |
C4' |
C5' |
H4' |
241.1 |
234.7 |
C5' |
C4' |
C3' |
O3' |
153.8 |
152.1 |
C5' |
C4' |
C3' |
C2' |
267.9 |
267.4 |
C5' |
C4' |
C3' |
H1 |
32.6 |
31.2 |
H5'1 |
C5' |
O5' |
P |
|
300.1 |
O5' |
C5' |
H5'1 |
C4' |
238.4 |
240.8 |
O5' |
C5' |
H5'1 |
H5'2 |
119.2 |
119.6 |
C4' |
C5' |
H5'1 |
H5'2 |
240.8 |
238.8 |
H5'1 |
C5' |
C4' |
O4' |
297.8 |
302.2 |
H5'1 |
C5' |
C4' |
C3' |
56.1 |
60.0 |
H5'1 |
C5' |
C4' |
H4' |
175.0 |
185.3 |
H5'2 |
C5' |
O5' |
P |
|
59.9 |
O5' |
C5' |
H5'2 |
C4' |
121.1 |
119.2 |
O5' |
C5' |
H5'2 |
H5'1 |
240.5 |
240.4 |
C4' |
C5' |
H5'2 |
H5'1 |
119.5 |
121.2 |
H5'2 |
C5' |
C4' |
O4' |
177.0 |
181.3 |
H5'2 |
C5' |
C4' |
C3' |
295.3 |
299.1 |
H5'2 |
C5' |
C4' |
H4' |
54.2 |
64.3 |
O4' |
C4' |
C5' |
H5'1 |
297.8 |
302.2 |
O4' |
C4' |
C5' |
H5'2 |
177.0 |
181.3 |
C5' |
C4' |
O4' |
C3' |
123.9 |
121.5 |
C5' |
C4' |
O4' |
H4' |
242.9 |
242.0 |
C3' |
C4' |
O4' |
H4' |
119.0 |
120.5 |
O4' |
C4' |
C3' |
O3' |
274.0 |
270.6 |
O4' |
C4' |
C3' |
C2' |
28.0 |
25.9 |
O4' |
C4' |
C3' |
H1 |
152.7 |
149.7 |
C4' |
O4' |
C1' |
C2' |
343.6 |
342.7 |
C4' |
O4' |
C1' |
N9 |
218.9 |
218.2 |
C4' |
O4' |
C1' |
H1' |
101.8 |
103.1 |
C3' |
C4' |
C5' |
H5'1 |
56.1 |
60.0 |
C3' |
C4' |
C5' |
H5'2 |
295.3 |
299.1 |
C5' |
C4' |
C3' |
O4' |
239.8 |
241.5 |
C5' |
C4' |
C3' |
H4' |
117.0 |
123.8 |
O4' |
C4' |
C3' |
H4' |
237.1 |
242.3 |
C3' |
C4' |
O4' |
C1' |
352.6 |
354.5 |
O3' |
C3' |
C4' |
C2' |
246.0 |
244.7 |
O3' |
C3' |
C4' |
H1 |
121.2 |
120.9 |
C4' |
C3' |
O3' |
H3' |
159.3 |
46.6 |
C2' |
C3' |
C4' |
H1 |
235.3 |
236.3 |
C4' |
C3' |
C2' |
C1' |
323.3 |
325.2 |
C4' |
C3' |
C2' |
H2'1 |
83.3 |
82.2 |
C4' |
C3' |
C2' |
H2'2 |
200.5 |
204.8 |
H4' |
C4' |
C5' |
H5'1 |
175.0 |
185.3 |
H4' |
C4' |
C5' |
H5'2 |
54.2 |
64.3 |
C5' |
C4' |
H4' |
O4' |
119.3 |
117.2 |
C5' |
C4' |
H4' |
C3' |
236.8 |
234.3 |
O4' |
C4' |
H4' |
C3' |
117.5 |
117.2 |
H4' |
C4' |
O4' |
C1' |
233.6 |
234.0 |
H4' |
C4' |
C3' |
O3' |
36.8 |
28.3 |
H4' |
C4' |
C3' |
C2' |
150.9 |
143.6 |
H4' |
C4' |
C3' |
H1 |
275.6 |
267.4 |
C1' |
O4' |
C4' |
C3' |
352.6 |
354.5 |
C1' |
O4' |
C4' |
H4' |
233.6 |
234.0 |
C3' |
C2' |
C1' |
O4' |
33.4 |
32.7 |
O4' |
C1' |
C2' |
H2'1 |
273.3 |
276.0 |
O4' |
C1' |
C2' |
H2'2 |
156.1 |
154.9 |
C2' |
C1' |
O4' |
N9 |
124.7 |
124.5 |
C2' |
C1' |
O4' |
H1' |
241.8 |
239.7 |
N9 |
C1' |
O4' |
H1' |
117.1 |
115.2 |
O4' |
C1' |
N9 |
C8 |
85.9 |
33.5 |
O4' |
C1' |
N9 |
C4 |
267.4 |
213.5 |
O3' |
C3' |
C4' |
H4' |
36.8 |
28.3 |
C4' |
C3' |
O3' |
C2' |
111.0 |
111.9 |
C4' |
C3' |
O3' |
H1 |
236.2 |
235.4 |
C2' |
C3' |
O3' |
H1 |
125.2 |
123.5 |
O3' |
C3' |
C2' |
C1' |
79.4 |
81.3 |
O3' |
C3' |
C2' |
H2'1 |
199.4 |
198.4 |
O3' |
C3' |
C2' |
H2'2 |
316.7 |
320.9 |
C2' |
C3' |
C4' |
H4' |
150.9 |
143.6 |
C4' |
C3' |
C2' |
O3' |
243.9 |
243.8 |
C4' |
C3' |
C2' |
H1 |
123.0 |
123.9 |
O4' |
C1' |
C2' |
C3' |
33.4 |
32.7 |
O3' |
C3' |
C2' |
H1 |
239.1 |
240.1 |
C2' |
C3' |
O3' |
H3' |
48.3 |
294.7 |
C1' |
C2' |
C3' |
H2'1 |
240.0 |
243.0 |
C1' |
C2' |
C3' |
H2'2 |
122.8 |
120.4 |
C3' |
C2' |
C1' |
N9 |
153.0 |
154.5 |
C3' |
C2' |
C1' |
H1' |
269.9 |
274.8 |
H2'1 |
C2' |
C3' |
H2'2 |
242.8 |
237.5 |
H1 |
C3' |
C4' |
H4' |
275.6 |
267.4 |
C4' |
C3' |
H1 |
O3' |
122.3 |
121.9 |
C4' |
C3' |
H1 |
C2' |
242.6 |
242.1 |
O3' |
C3' |
H1 |
C2' |
120.3 |
120.2 |
H1 |
C3' |
O3' |
H3' |
283.1 |
171.2 |
H1 |
C3' |
C2' |
C1' |
200.4 |
201.2 |
H1 |
C3' |
C2' |
H2'1 |
320.4 |
318.3 |
H1 |
C3' |
C2' |
H2'2 |
77.6 |
80.8 |
H3' |
O3' |
C3' |
C2' |
48.3 |
294.7 |
H3' |
O3' |
C3' |
H1 |
283.1 |
171.2 |
O4' |
C1' |
C2' |
N9 |
240.3 |
238.2 |
O4' |
C1' |
C2' |
H1' |
123.4 |
117.9 |
C1' |
C2' |
C3' |
H1 |
200.4 |
201.2 |
C3' |
C2' |
C1' |
H2'1 |
120.0 |
116.7 |
C3' |
C2' |
C1' |
H2'2 |
237.2 |
237.8 |
H2'1 |
C2' |
C1' |
H2'2 |
117.2 |
121.1 |
N9 |
C1' |
C2' |
H1' |
243.1 |
239.7 |
C2' |
C1' |
N9 |
C8 |
327.3 |
273.4 |
C2' |
C1' |
N9 |
C4 |
148.8 |
93.5 |
H2'1 |
C2' |
C3' |
H1 |
320.4 |
318.3 |
C3' |
C2' |
H2'1 |
C1' |
246.3 |
248.6 |
C3' |
C2' |
H2'1 |
H2'2 |
123.2 |
125.7 |
C1' |
C2' |
H2'1 |
H2'2 |
236.9 |
237.1 |
H2'1 |
C2' |
C1' |
N9 |
33.0 |
37.8 |
H2'1 |
C2' |
C1' |
H1' |
149.9 |
158.1 |
H2'2 |
C2' |
C3' |
H1 |
77.6 |
80.8 |
C3' |
C2' |
H2'2 |
C1' |
115.9 |
114.6 |
C3' |
C2' |
H2'2 |
H2'1 |
237.9 |
236.7 |
C1' |
C2' |
H2'2 |
H2'1 |
122.1 |
122.1 |
H2'2 |
C2' |
C1' |
N9 |
275.8 |
276.7 |
H2'2 |
C2' |
C1' |
H1' |
32.7 |
37.0 |
O4' |
C1' |
N9 |
C2' |
118.6 |
120.0 |
O4' |
C1' |
N9 |
H1' |
236.6 |
243.5 |
N9 |
C1' |
C2' |
H2'1 |
33.0 |
37.8 |
N9 |
C1' |
C2' |
H2'2 |
275.8 |
276.7 |
C2' |
C1' |
N9 |
H1' |
118.0 |
123.5 |
C8 |
N9 |
C1' |
C4 |
178.5 |
179.9 |
C1' |
N9 |
C8 |
N7 |
182.5 |
180.0 |
C1' |
N9 |
C8 |
H8 |
2.5 |
0.0 |
C1' |
N9 |
C4 |
C5 |
177.4 |
180.0 |
C1' |
N9 |
C4 |
N3 |
358.2 |
359.9 |
O4' |
C1' |
H1' |
C2' |
242.4 |
242.9 |
O4' |
C1' |
H1' |
N9 |
118.7 |
117.8 |
H1' |
C1' |
C2' |
H2'1 |
149.9 |
158.1 |
H1' |
C1' |
C2' |
H2'2 |
32.7 |
37.0 |
C2' |
C1' |
H1' |
N9 |
236.3 |
234.9 |
H1' |
C1' |
N9 |
C8 |
209.3 |
150.0 |
H1' |
C1' |
N9 |
C4 |
30.8 |
330.1 |
C8 |
N9 |
C1' |
H1' |
209.3 |
150.0 |
C1' |
N9 |
C8 |
C4 |
181.3 |
180.1 |
C8 |
N9 |
C4 |
C5 |
358.6 |
0.0 |
C8 |
N9 |
C4 |
N3 |
179.4 |
180.0 |
N7 |
C8 |
N9 |
H8 |
180.0 |
180.0 |
N9 |
C8 |
N7 |
C5 |
359.5 |
0.0 |
C4 |
N9 |
C1' |
H1' |
30.8 |
330.1 |
C1' |
N9 |
C4 |
C8 |
178.8 |
179.9 |
C4 |
N9 |
C8 |
N7 |
1.2 |
360.0 |
C4 |
N9 |
C8 |
H8 |
181.2 |
180.0 |
N7 |
C5 |
C4 |
N9 |
1.2 |
360.0 |
C6 |
C5 |
C4 |
N9 |
181.5 |
180.0 |
C5 |
C4 |
N9 |
N3 |
179.2 |
180.1 |
C2 |
N3 |
C4 |
N9 |
178.9 |
180.0 |
N7 |
C8 |
N9 |
C4 |
1.2 |
360.0 |
N9 |
C8 |
N7 |
H8 |
180.0 |
180.0 |
C8 |
N7 |
C5 |
C6 |
179.2 |
180.0 |
C8 |
N7 |
C5 |
C4 |
359.6 |
0.0 |
H8 |
C8 |
N9 |
C4 |
181.2 |
180.0 |
N9 |
C8 |
H8 |
N7 |
180.0 |
180.0 |
H8 |
C8 |
N7 |
C5 |
179.5 |
180.0 |
N9 |
C4 |
C5 |
N7 |
1.2 |
360.0 |
C5 |
N7 |
C8 |
H8 |
179.5 |
180.0 |
C6 |
C5 |
N7 |
C4 |
179.6 |
180.0 |
N7 |
C5 |
C6 |
N6 |
359.2 |
360.0 |
N7 |
C5 |
C6 |
N1 |
179.6 |
180.0 |
N7 |
C5 |
C4 |
N3 |
180.4 |
180.0 |
N9 |
C4 |
C5 |
C6 |
181.5 |
180.0 |
N7 |
C5 |
C6 |
C4 |
180.4 |
180.0 |
C6 |
C5 |
C4 |
N3 |
0.7 |
0.1 |
N6 |
C6 |
C5 |
N1 |
179.6 |
180.0 |
C5 |
C6 |
N6 |
HN61 |
62.6 |
85.4 |
C5 |
C6 |
N6 |
HN62 |
182.6 |
271.6 |
C5 |
C6 |
N1 |
C2 |
0.4 |
0.0 |
N9 |
C4 |
C5 |
N3 |
180.8 |
179.9 |
N7 |
C5 |
C4 |
C6 |
179.7 |
180.0 |
C4 |
C5 |
C6 |
N6 |
178.9 |
180.0 |
C4 |
C5 |
C6 |
N1 |
359.2 |
359.9 |
C2 |
N3 |
C4 |
C5 |
359.9 |
359.9 |
N6 |
C6 |
C5 |
C4 |
178.9 |
180.0 |
C5 |
C6 |
N6 |
N1 |
180.4 |
180.0 |
N6 |
C6 |
N1 |
C2 |
180.7 |
180.0 |
HN61 |
N6 |
C6 |
HN62 |
240.0 |
173.8 |
N1 |
C6 |
C5 |
C4 |
359.2 |
359.9 |
C5 |
C6 |
N1 |
N6 |
179.6 |
180.0 |
N1 |
C6 |
N6 |
HN61 |
242.2 |
265.4 |
N1 |
C6 |
N6 |
HN62 |
2.3 |
91.6 |
C6 |
N1 |
C2 |
N3 |
0.2 |
360.0 |
C6 |
N1 |
C2 |
H2 |
180.2 |
180.0 |
HN61 |
N6 |
C6 |
N1 |
242.2 |
265.4 |
C6 |
N6 |
HN61 |
HN62 |
120.0 |
186.3 |
HN62 |
N6 |
C6 |
N1 |
2.3 |
91.6 |
C6 |
N6 |
HN62 |
HN61 |
240.0 |
173.7 |
N3 |
C2 |
N1 |
H2 |
180.0 |
180.0 |
N1 |
C2 |
N3 |
C4 |
359.7 |
0.0 |
N9 |
C4 |
N3 |
C2 |
178.9 |
180.0 |
C5 |
C4 |
N3 |
C2 |
359.9 |
359.9 |
N1 |
C2 |
N3 |
H2 |
180.0 |
180.0 |
N1 |
C2 |
H2 |
N3 |
180.0 |
180.0 |
H2 |
C2 |
N3 |
C4 |
179.7 |
180.0 |
N9 |
C4 |
N3 |
C5 |
179.0 |
180.1 |
C4 |
N3 |
C2 |
H2 |
179.7 |
180.0 |
O5' |
P |
O1P |
O3P |
|
239.4 |
O5' |
P |
O1P |
O2P |
|
119.3 |
O3P |
P |
O1P |
O2P |
|
239.9 |
O1P |
P |
O3P |
H3P |
|
48.8 |
O1P |
P |
O2P |
H2P |
|
312.0 |
O5' |
P |
O3P |
O1P |
|
126.6 |
O5' |
P |
O3P |
O2P |
|
252.9 |
O1P |
P |
O3P |
O2P |
|
126.3 |
O3P |
P |
O2P |
H2P |
|
78.5 |
O5' |
P |
O2P |
O1P |
|
234.2 |
O5' |
P |
O2P |
O3P |
|
107.7 |
O1P |
P |
O2P |
O3P |
|
233.5 |
O2P |
P |
O3P |
H3P |
|
282.5 |
H3P |
O3P |
P |
O2P |
|
282.5 |