PDB Chemical Component A5M
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 A5M
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| P |
OP1 |
1.486 |
1.502 |
| P |
OP2 |
1.485 |
1.617 |
| P |
O5' |
1.589 |
1.619 |
| P |
OP3 |
|
1.617 |
| OP2 |
HOP2 |
0.951 |
0.981 |
| O5' |
C5' |
1.420 |
1.416 |
| C5' |
C4' |
1.500 |
1.524 |
| C5' |
H5' |
1.114 |
1.091 |
| C5' |
H5'' |
1.115 |
1.091 |
| C4' |
O4' |
1.453 |
1.442 |
| C4' |
C3' |
1.514 |
1.524 |
| C4' |
H4' |
1.115 |
1.095 |
| O4' |
C1' |
1.417 |
1.439 |
| C1' |
N1 |
1.472 |
1.435 |
| C1' |
C2' |
1.533 |
1.524 |
| C1' |
H1' |
1.116 |
1.095 |
| N1 |
C6 |
1.366 |
1.387 |
| N1 |
C2 |
1.406 |
1.418 |
| C6 |
C5 |
1.342 |
1.332 |
| C6 |
H6 |
1.102 |
1.085 |
| C2 |
O2 |
1.243 |
1.232 |
| C2 |
N3 |
1.357 |
1.385 |
| N3 |
C4 |
1.337 |
1.308 |
| C4 |
N4 |
1.340 |
1.375 |
| C4 |
C5 |
1.431 |
1.486 |
| N4 |
H41 |
1.019 |
0.992 |
| N4 |
H42 |
1.021 |
0.991 |
| C5 |
H5 |
1.103 |
1.082 |
| C2' |
N2' |
1.472 |
1.453 |
| C2' |
C3' |
1.524 |
1.521 |
| C2' |
H2' |
1.115 |
1.097 |
| N2' |
H'1N |
1.019 |
1.001 |
| N2' |
H'2N |
1.021 |
1.001 |
| C3' |
O3' |
|
1.428 |
| C3' |
H3' |
1.114 |
1.094 |
| O3' |
HO3' |
|
0.969 |
| OP3 |
HOP3 |
|
0.981 |
Bond Angles for A5M
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP1 |
P |
OP2 |
119.5 |
115.3 |
| OP1 |
P |
O5' |
106.6 |
115.0 |
| OP1 |
P |
OP3 |
|
115.0 |
| OP2 |
P |
O5' |
108.6 |
103.7 |
| OP2 |
P |
OP3 |
|
103.3 |
| P |
OP2 |
HOP2 |
119.5 |
118.9 |
| O5' |
P |
OP3 |
|
102.9 |
| P |
O5' |
C5' |
119.9 |
118.5 |
| P |
OP3 |
HOP3 |
|
118.9 |
| O5' |
C5' |
C4' |
109.9 |
108.7 |
| O5' |
C5' |
H5' |
112.0 |
109.2 |
| O5' |
C5' |
H5'' |
112.0 |
109.2 |
| C4' |
C5' |
H5' |
112.0 |
110.0 |
| C4' |
C5' |
H5'' |
112.0 |
110.0 |
| C5' |
C4' |
O4' |
109.4 |
108.1 |
| C5' |
C4' |
C3' |
114.2 |
113.3 |
| C5' |
C4' |
H4' |
104.5 |
109.3 |
| H5' |
C5' |
H5'' |
98.4 |
109.6 |
| O4' |
C4' |
C3' |
103.2 |
106.0 |
| O4' |
C4' |
H4' |
115.2 |
107.7 |
| C4' |
O4' |
C1' |
109.6 |
109.4 |
| C3' |
C4' |
H4' |
110.6 |
112.1 |
| C4' |
C3' |
C2' |
101.4 |
102.3 |
| C4' |
C3' |
O3' |
|
108.8 |
| C4' |
C3' |
H3' |
120.0 |
113.5 |
| O4' |
C1' |
N1 |
108.1 |
109.0 |
| O4' |
C1' |
C2' |
106.9 |
106.8 |
| O4' |
C1' |
H1' |
113.8 |
107.5 |
| N1 |
C1' |
C2' |
114.2 |
112.9 |
| N1 |
C1' |
H1' |
106.4 |
107.7 |
| C1' |
N1 |
C6 |
120.9 |
118.7 |
| C1' |
N1 |
C2 |
118.9 |
122.0 |
| C2' |
C1' |
H1' |
107.6 |
112.8 |
| C1' |
C2' |
N2' |
108.6 |
113.1 |
| C1' |
C2' |
C3' |
101.1 |
102.2 |
| C1' |
C2' |
H2' |
116.1 |
109.8 |
| C6 |
N1 |
C2 |
120.3 |
119.2 |
| N1 |
C6 |
C5 |
121.0 |
122.8 |
| N1 |
C6 |
H6 |
120.4 |
116.0 |
| N1 |
C2 |
O2 |
118.8 |
120.9 |
| N1 |
C2 |
N3 |
119.4 |
118.9 |
| C5 |
C6 |
H6 |
118.6 |
121.2 |
| C6 |
C5 |
C4 |
117.7 |
116.4 |
| C6 |
C5 |
H5 |
118.1 |
123.1 |
| O2 |
C2 |
N3 |
121.9 |
120.1 |
| C2 |
N3 |
C4 |
119.8 |
121.0 |
| N3 |
C4 |
N4 |
118.0 |
120.1 |
| N3 |
C4 |
C5 |
121.8 |
121.7 |
| N4 |
C4 |
C5 |
120.1 |
118.2 |
| C4 |
N4 |
H41 |
118.1 |
118.1 |
| C4 |
N4 |
H42 |
109.1 |
118.0 |
| C4 |
C5 |
H5 |
124.2 |
120.5 |
| H41 |
N4 |
H42 |
109.1 |
123.9 |
| N2' |
C2' |
C3' |
111.7 |
114.1 |
| N2' |
C2' |
H2' |
106.3 |
108.6 |
| C2' |
N2' |
H'1N |
108.6 |
118.4 |
| C2' |
N2' |
H'2N |
112.5 |
118.5 |
| C3' |
C2' |
H2' |
113.2 |
108.8 |
| C2' |
C3' |
O3' |
|
111.4 |
| C2' |
C3' |
H3' |
138.5 |
113.4 |
| H'1N |
N2' |
H'2N |
112.5 |
121.7 |
| O3' |
C3' |
H3' |
|
107.5 |
| C3' |
O3' |
HO3' |
|
106.4 |
Torsion Angles for A5M
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP2 |
P |
OP1 |
O5' |
236.5 |
120.6 |
| OP2 |
P |
OP1 |
OP3 |
|
239.9 |
| OP1 |
P |
OP2 |
HOP2 |
180.0 |
48.9 |
| O5' |
P |
OP1 |
OP3 |
|
119.3 |
| OP1 |
P |
O5' |
C5' |
56.6 |
180.0 |
| OP1 |
P |
OP3 |
HOP3 |
|
312.0 |
| OP1 |
P |
OP2 |
O5' |
122.5 |
233.4 |
| OP1 |
P |
OP2 |
OP3 |
|
126.3 |
| O5' |
P |
OP2 |
OP3 |
|
252.9 |
| OP2 |
P |
O5' |
C5' |
186.6 |
53.2 |
| OP2 |
P |
OP3 |
HOP3 |
|
78.5 |
| OP1 |
P |
O5' |
OP2 |
230.0 |
126.8 |
| OP1 |
P |
O5' |
OP3 |
|
234.2 |
| OP2 |
P |
O5' |
OP3 |
|
107.4 |
| O5' |
P |
OP2 |
HOP2 |
57.5 |
175.4 |
| O5' |
P |
OP3 |
HOP3 |
|
186.2 |
| P |
O5' |
C5' |
C4' |
161.8 |
180.0 |
| P |
O5' |
C5' |
H5' |
287.0 |
300.1 |
| P |
O5' |
C5' |
H5'' |
36.6 |
60.0 |
| OP1 |
P |
OP3 |
OP2 |
|
233.5 |
| OP1 |
P |
OP3 |
O5' |
|
125.8 |
| OP2 |
P |
OP3 |
O5' |
|
252.3 |
| OP3 |
P |
OP2 |
HOP2 |
|
282.6 |
| OP3 |
P |
O5' |
C5' |
|
305.8 |
| HOP2 |
OP2 |
P |
O5' |
57.5 |
175.4 |
| HOP2 |
OP2 |
P |
OP3 |
|
282.6 |
| C5' |
O5' |
P |
OP3 |
|
305.8 |
| C4' |
C5' |
O5' |
H5' |
234.8 |
240.0 |
| C4' |
C5' |
O5' |
H5'' |
125.2 |
120.0 |
| O5' |
C5' |
C4' |
O4' |
296.1 |
62.4 |
| O5' |
C5' |
C4' |
C3' |
51.1 |
179.5 |
| O5' |
C5' |
C4' |
H4' |
172.1 |
305.4 |
| H5' |
C5' |
O5' |
H5'' |
250.4 |
240.1 |
| O5' |
C5' |
C4' |
H5' |
125.3 |
119.5 |
| O5' |
C5' |
C4' |
H5'' |
234.8 |
240.5 |
| H5' |
C5' |
C4' |
H5'' |
109.5 |
120.9 |
| O4' |
C4' |
C5' |
C3' |
244.9 |
242.8 |
| O4' |
C4' |
C5' |
H4' |
123.9 |
117.0 |
| C5' |
C4' |
O4' |
C1' |
147.2 |
107.5 |
| C3' |
C4' |
C5' |
H4' |
239.0 |
234.1 |
| C5' |
C4' |
C3' |
C2' |
201.1 |
273.2 |
| C5' |
C4' |
C3' |
O3' |
|
155.2 |
| C5' |
C4' |
C3' |
H3' |
19.1 |
35.6 |
| O5' |
C5' |
H5' |
C4' |
235.9 |
240.8 |
| O5' |
C5' |
H5' |
H5'' |
118.0 |
119.6 |
| C4' |
C5' |
H5' |
H5'' |
242.1 |
238.8 |
| H5' |
C5' |
C4' |
O4' |
170.8 |
302.8 |
| H5' |
C5' |
C4' |
C3' |
285.9 |
60.0 |
| H5' |
C5' |
C4' |
H4' |
46.9 |
185.9 |
| O5' |
C5' |
H5'' |
C4' |
124.1 |
119.2 |
| O5' |
C5' |
H5'' |
H5' |
242.0 |
240.4 |
| C4' |
C5' |
H5'' |
H5' |
117.9 |
121.2 |
| H5'' |
C5' |
C4' |
O4' |
61.3 |
181.9 |
| H5'' |
C5' |
C4' |
C3' |
176.4 |
299.1 |
| H5'' |
C5' |
C4' |
H4' |
297.4 |
64.9 |
| O4' |
C4' |
C5' |
H5' |
170.8 |
302.8 |
| O4' |
C4' |
C5' |
H5'' |
61.3 |
181.9 |
| C5' |
C4' |
O4' |
C3' |
122.0 |
121.8 |
| C5' |
C4' |
O4' |
H4' |
242.6 |
242.0 |
| C3' |
C4' |
O4' |
H4' |
120.6 |
120.2 |
| O4' |
C4' |
C3' |
C2' |
319.8 |
31.6 |
| O4' |
C4' |
C3' |
O3' |
|
273.6 |
| O4' |
C4' |
C3' |
H3' |
137.8 |
154.1 |
| C4' |
O4' |
C1' |
N1 |
236.8 |
228.8 |
| C4' |
O4' |
C1' |
C2' |
0.2 |
351.0 |
| C4' |
O4' |
C1' |
H1' |
118.9 |
112.3 |
| C3' |
C4' |
C5' |
H5' |
285.9 |
60.0 |
| C3' |
C4' |
C5' |
H5'' |
176.4 |
299.1 |
| C5' |
C4' |
C3' |
O4' |
241.3 |
241.6 |
| C5' |
C4' |
C3' |
H4' |
117.6 |
124.4 |
| O4' |
C4' |
C3' |
H4' |
236.2 |
242.8 |
| C3' |
C4' |
O4' |
C1' |
25.3 |
345.7 |
| C1' |
C2' |
C3' |
C4' |
39.4 |
324.2 |
| N2' |
C2' |
C3' |
C4' |
284.1 |
201.7 |
| C4' |
C3' |
C2' |
H2' |
164.2 |
80.3 |
| C2' |
C3' |
C4' |
O3' |
|
118.0 |
| C2' |
C3' |
C4' |
H3' |
182.0 |
237.5 |
| O3' |
C3' |
C4' |
H3' |
|
119.6 |
| C4' |
C3' |
O3' |
HO3' |
|
190.5 |
| H4' |
C4' |
C5' |
H5' |
46.9 |
185.9 |
| H4' |
C4' |
C5' |
H5'' |
297.4 |
64.9 |
| C5' |
C4' |
H4' |
O4' |
120.1 |
117.3 |
| C5' |
C4' |
H4' |
C3' |
236.6 |
233.5 |
| O4' |
C4' |
H4' |
C3' |
116.5 |
116.2 |
| H4' |
C4' |
O4' |
C1' |
264.6 |
225.5 |
| H4' |
C4' |
C3' |
C2' |
83.6 |
148.8 |
| H4' |
C4' |
C3' |
O3' |
|
30.8 |
| H4' |
C4' |
C3' |
H3' |
261.6 |
271.3 |
| C1' |
O4' |
C4' |
C3' |
25.3 |
345.7 |
| C1' |
O4' |
C4' |
H4' |
264.6 |
225.5 |
| N1 |
C1' |
O4' |
C2' |
236.6 |
237.8 |
| N1 |
C1' |
O4' |
H1' |
117.9 |
116.5 |
| O4' |
C1' |
N1 |
C6 |
24.2 |
33.6 |
| O4' |
C1' |
N1 |
C2 |
204.1 |
213.6 |
| C2' |
C1' |
O4' |
H1' |
241.3 |
238.7 |
| O4' |
C1' |
C2' |
N2' |
92.3 |
151.5 |
| O4' |
C1' |
C2' |
C3' |
334.7 |
28.4 |
| O4' |
C1' |
C2' |
H2' |
211.9 |
273.1 |
| O4' |
C1' |
N1 |
C2' |
118.8 |
118.4 |
| O4' |
C1' |
N1 |
H1' |
237.4 |
243.6 |
| C2' |
C1' |
N1 |
H1' |
118.6 |
125.2 |
| N1 |
C1' |
C2' |
N2' |
211.8 |
271.2 |
| N1 |
C1' |
C2' |
C3' |
94.3 |
148.1 |
| N1 |
C1' |
C2' |
H2' |
331.4 |
32.8 |
| C6 |
N1 |
C1' |
C2 |
180.1 |
180.0 |
| C1' |
N1 |
C6 |
C5 |
179.4 |
179.9 |
| C1' |
N1 |
C6 |
H6 |
359.4 |
360.0 |
| C1' |
N1 |
C2 |
O2 |
1.2 |
0.0 |
| C1' |
N1 |
C2 |
N3 |
180.9 |
180.0 |
| C4' |
C3' |
C2' |
C1' |
39.4 |
324.2 |
| O4' |
C1' |
C2' |
N1 |
240.5 |
240.3 |
| O4' |
C1' |
C2' |
H1' |
122.6 |
117.9 |
| N1 |
C1' |
C2' |
H1' |
242.1 |
237.6 |
| C2' |
C1' |
N1 |
C6 |
265.3 |
275.2 |
| C2' |
C1' |
N1 |
C2 |
85.2 |
95.2 |
| N2' |
C2' |
C1' |
C3' |
117.6 |
123.1 |
| N2' |
C2' |
C1' |
H2' |
240.4 |
238.4 |
| C1' |
C2' |
N2' |
H'1N |
180.0 |
46.1 |
| C1' |
C2' |
N2' |
H'2N |
54.7 |
239.5 |
| C3' |
C2' |
C1' |
H2' |
122.9 |
115.3 |
| C1' |
C2' |
C3' |
O3' |
|
80.3 |
| C1' |
C2' |
C3' |
H3' |
222.0 |
201.7 |
| O4' |
C1' |
H1' |
N1 |
118.9 |
117.3 |
| O4' |
C1' |
H1' |
C2' |
241.8 |
242.6 |
| N1 |
C1' |
H1' |
C2' |
122.8 |
125.2 |
| H1' |
C1' |
N1 |
C6 |
146.8 |
149.9 |
| H1' |
C1' |
N1 |
C2 |
326.7 |
329.9 |
| H1' |
C1' |
C2' |
N2' |
329.7 |
33.7 |
| H1' |
C1' |
C2' |
C3' |
212.1 |
270.6 |
| H1' |
C1' |
C2' |
H2' |
89.2 |
155.2 |
| C6 |
N1 |
C1' |
C2' |
265.3 |
275.2 |
| C6 |
N1 |
C1' |
H1' |
146.8 |
149.9 |
| C1' |
N1 |
C6 |
C2 |
179.9 |
180.0 |
| C6 |
N1 |
C2 |
O2 |
181.0 |
180.0 |
| C6 |
N1 |
C2 |
N3 |
0.7 |
360.0 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
180.0 |
| N1 |
C6 |
C5 |
C4 |
360.0 |
0.1 |
| N1 |
C6 |
C5 |
H5 |
179.9 |
180.0 |
| C2 |
N1 |
C1' |
C2' |
85.2 |
95.2 |
| C2 |
N1 |
C1' |
H1' |
326.7 |
329.9 |
| C1' |
N1 |
C2 |
C6 |
180.1 |
180.0 |
| C2 |
N1 |
C6 |
C5 |
359.6 |
360.0 |
| C2 |
N1 |
C6 |
H6 |
179.5 |
180.0 |
| O2 |
C2 |
N1 |
N3 |
180.3 |
180.0 |
| N1 |
C2 |
N3 |
C4 |
359.5 |
0.1 |
| C5 |
C6 |
N1 |
C2 |
359.6 |
360.0 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.0 |
| N3 |
C4 |
C5 |
C6 |
0.2 |
360.0 |
| N4 |
C4 |
C5 |
C6 |
180.1 |
180.0 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
180.0 |
| H6 |
C6 |
N1 |
C2 |
179.5 |
180.0 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
180.0 |
| H6 |
C6 |
C5 |
C4 |
180.0 |
180.0 |
| H6 |
C6 |
C5 |
H5 |
359.9 |
360.0 |
| N1 |
C2 |
O2 |
N3 |
179.7 |
180.0 |
| O2 |
C2 |
N3 |
C4 |
179.1 |
180.0 |
| N1 |
C2 |
N3 |
O2 |
180.3 |
180.0 |
| C2 |
N3 |
C4 |
N4 |
180.2 |
180.0 |
| C2 |
N3 |
C4 |
C5 |
0.1 |
360.0 |
| C6 |
C5 |
C4 |
N3 |
0.2 |
360.0 |
| N4 |
C4 |
N3 |
C5 |
180.1 |
180.0 |
| N3 |
C4 |
N4 |
H41 |
180.0 |
353.3 |
| N3 |
C4 |
N4 |
H42 |
54.7 |
173.3 |
| N3 |
C4 |
C5 |
H5 |
180.3 |
180.0 |
| C6 |
C5 |
C4 |
N4 |
180.1 |
180.0 |
| N3 |
C4 |
N4 |
C5 |
179.9 |
180.0 |
| N4 |
C4 |
C5 |
H5 |
0.1 |
0.0 |
| H41 |
N4 |
C4 |
H42 |
125.3 |
180.0 |
| C4 |
C5 |
C6 |
H6 |
180.0 |
180.0 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
180.0 |
| N3 |
C4 |
C5 |
N4 |
180.1 |
180.0 |
| C5 |
C4 |
N4 |
H41 |
0.1 |
173.3 |
| C5 |
C4 |
N4 |
H42 |
234.8 |
353.3 |
| H41 |
N4 |
C4 |
C5 |
0.1 |
173.3 |
| C4 |
N4 |
H41 |
H42 |
234.7 |
180.0 |
| H42 |
N4 |
C4 |
C5 |
234.8 |
353.3 |
| C4 |
N4 |
H42 |
H41 |
130.4 |
180.0 |
| H5 |
C5 |
C6 |
H6 |
359.9 |
360.0 |
| C6 |
C5 |
H5 |
C4 |
180.0 |
180.0 |
| C4' |
C3' |
C2' |
N2' |
284.1 |
201.7 |
| N2' |
C2' |
C1' |
H1' |
329.7 |
33.7 |
| C1' |
C2' |
N2' |
C3' |
249.4 |
243.8 |
| C1' |
C2' |
N2' |
H2' |
125.5 |
122.2 |
| C3' |
C2' |
N2' |
H2' |
236.1 |
238.5 |
| N2' |
C2' |
C3' |
O3' |
|
317.8 |
| N2' |
C2' |
C3' |
H3' |
106.7 |
79.2 |
| H'1N |
N2' |
C2' |
H'2N |
125.2 |
166.6 |
| C2' |
C3' |
C4' |
H4' |
83.6 |
148.8 |
| C4' |
C3' |
C2' |
O3' |
|
243.9 |
| C4' |
C3' |
C2' |
H3' |
177.4 |
122.5 |
| C3' |
C2' |
C1' |
H1' |
212.1 |
270.6 |
| C1' |
C2' |
C3' |
N2' |
115.3 |
122.5 |
| C1' |
C2' |
C3' |
H2' |
235.2 |
243.9 |
| N2' |
C2' |
C3' |
H2' |
119.9 |
121.4 |
| C3' |
C2' |
N2' |
H'1N |
290.5 |
162.4 |
| C3' |
C2' |
N2' |
H'2N |
165.3 |
355.8 |
| O3' |
C3' |
C2' |
H3' |
|
238.6 |
| C2' |
C3' |
O3' |
HO3' |
|
78.4 |
| H2' |
C2' |
C1' |
H1' |
89.2 |
155.2 |
| C1' |
C2' |
H2' |
N2' |
239.2 |
235.8 |
| C1' |
C2' |
H2' |
C3' |
116.3 |
111.1 |
| N2' |
C2' |
H2' |
C3' |
237.0 |
235.3 |
| H2' |
C2' |
N2' |
H'1N |
54.5 |
283.9 |
| H2' |
C2' |
N2' |
H'2N |
289.2 |
117.3 |
| H2' |
C2' |
C3' |
O3' |
|
196.4 |
| H2' |
C2' |
C3' |
H3' |
346.8 |
317.8 |
| H'1N |
N2' |
C2' |
C3' |
290.5 |
162.4 |
| H'1N |
N2' |
C2' |
H2' |
54.5 |
283.9 |
| C2' |
N2' |
H'1N |
H'2N |
234.7 |
193.9 |
| H'2N |
N2' |
C2' |
C3' |
165.3 |
355.8 |
| H'2N |
N2' |
C2' |
H2' |
289.2 |
117.3 |
| C2' |
N2' |
H'2N |
H'1N |
123.1 |
166.1 |
| O3' |
C3' |
C4' |
H4' |
|
30.8 |
| C4' |
C3' |
O3' |
C2' |
|
112.0 |
| C4' |
C3' |
O3' |
H3' |
|
236.8 |
| O3' |
C3' |
C2' |
H2' |
|
196.4 |
| C2' |
C3' |
O3' |
H3' |
|
124.7 |
| H3' |
C3' |
C4' |
H4' |
261.6 |
271.3 |
| C4' |
C3' |
H3' |
C2' |
182.9 |
243.9 |
| C4' |
C3' |
H3' |
O3' |
|
120.3 |
| H3' |
C3' |
C2' |
H2' |
346.8 |
317.8 |
| C2' |
C3' |
H3' |
O3' |
|
236.4 |
| H3' |
C3' |
O3' |
HO3' |
|
313.7 |
| HO3' |
O3' |
C3' |
H3' |
|
313.7 |