PDB Chemical Component BGM
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 BGM
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
P |
OP1 |
1.477 |
1.480 |
P |
OP2 |
1.468 |
1.609 |
P |
O5' |
1.585 |
1.611 |
P |
OP3 |
|
1.609 |
OP2 |
HOP2 |
0.949 |
0.968 |
O5' |
C5' |
1.436 |
1.429 |
C5' |
C4' |
1.515 |
1.531 |
C5' |
H5' |
1.100 |
1.090 |
C5' |
H5'' |
1.100 |
1.089 |
C4' |
O4' |
1.437 |
1.443 |
C4' |
C3' |
1.526 |
1.550 |
C4' |
H4' |
1.100 |
1.089 |
O4' |
C1' |
1.439 |
1.437 |
C1' |
N9 |
1.450 |
1.465 |
C1' |
C2' |
1.513 |
1.542 |
C1' |
H1' |
1.100 |
1.090 |
N9 |
C8 |
1.380 |
1.365 |
N9 |
C4 |
1.369 |
1.369 |
C8 |
N7 |
1.304 |
1.302 |
C8 |
BR |
|
1.891 |
N7 |
C5 |
1.388 |
1.356 |
C5 |
C4 |
1.371 |
1.399 |
C5 |
C6 |
1.409 |
1.414 |
C4 |
N3 |
1.345 |
1.338 |
N3 |
C2 |
1.319 |
1.315 |
C2 |
N2 |
1.328 |
1.372 |
C2 |
N1 |
1.372 |
1.363 |
N2 |
H21 |
1.000 |
0.969 |
N2 |
H22 |
1.000 |
0.970 |
N1 |
C6 |
1.386 |
1.351 |
N1 |
H1 |
1.000 |
0.970 |
C6 |
O6 |
1.256 |
1.219 |
C2' |
C3' |
1.537 |
1.548 |
C2' |
H2' |
1.100 |
1.090 |
C2' |
H2'' |
1.100 |
1.090 |
C3' |
O3' |
1.431 |
1.429 |
C3' |
H3' |
1.100 |
1.090 |
O3' |
HO3' |
0.950 |
0.968 |
OP3 |
HOP3 |
|
0.967 |
Bond Angles for BGM
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
OP1 |
P |
OP2 |
117.5 |
109.5 |
OP1 |
P |
O5' |
107.1 |
109.4 |
OP1 |
P |
OP3 |
|
109.5 |
OP2 |
P |
O5' |
111.9 |
109.5 |
OP2 |
P |
OP3 |
|
109.5 |
P |
OP2 |
HOP2 |
109.5 |
114.0 |
O5' |
P |
OP3 |
|
109.5 |
P |
O5' |
C5' |
118.3 |
123.0 |
P |
OP3 |
HOP3 |
|
114.0 |
O5' |
C5' |
C4' |
105.4 |
109.4 |
O5' |
C5' |
H5' |
110.5 |
109.5 |
O5' |
C5' |
H5'' |
110.5 |
109.5 |
C4' |
C5' |
H5' |
110.5 |
109.4 |
C4' |
C5' |
H5'' |
110.5 |
109.5 |
C5' |
C4' |
O4' |
109.2 |
110.6 |
C5' |
C4' |
C3' |
117.6 |
110.6 |
C5' |
C4' |
H4' |
107.8 |
110.6 |
H5' |
C5' |
H5'' |
109.5 |
109.5 |
O4' |
C4' |
C3' |
105.7 |
103.5 |
O4' |
C4' |
H4' |
108.7 |
110.7 |
C4' |
O4' |
C1' |
110.1 |
107.0 |
C3' |
C4' |
H4' |
107.6 |
110.7 |
C4' |
C3' |
C2' |
103.2 |
102.1 |
C4' |
C3' |
O3' |
109.2 |
110.9 |
C4' |
C3' |
H3' |
109.8 |
110.9 |
O4' |
C1' |
N9 |
106.0 |
109.9 |
O4' |
C1' |
C2' |
104.5 |
107.3 |
O4' |
C1' |
H1' |
110.4 |
109.9 |
N9 |
C1' |
C2' |
116.0 |
109.9 |
N9 |
C1' |
H1' |
110.2 |
109.9 |
C1' |
N9 |
C8 |
131.2 |
126.2 |
C1' |
N9 |
C4 |
124.0 |
126.3 |
C2' |
C1' |
H1' |
109.4 |
110.0 |
C1' |
C2' |
C3' |
100.6 |
104.2 |
C1' |
C2' |
H2' |
111.6 |
110.5 |
C1' |
C2' |
H2'' |
111.6 |
110.5 |
C8 |
N9 |
C4 |
104.8 |
107.5 |
N9 |
C8 |
N7 |
114.8 |
109.8 |
N9 |
C8 |
BR |
|
125.1 |
N9 |
C4 |
C5 |
106.2 |
106.1 |
N9 |
C4 |
N3 |
125.8 |
134.2 |
N7 |
C8 |
BR |
|
125.1 |
C8 |
N7 |
C5 |
102.7 |
109.3 |
N7 |
C5 |
C4 |
111.5 |
107.3 |
N7 |
C5 |
C6 |
130.0 |
134.1 |
C4 |
C5 |
C6 |
118.5 |
118.6 |
C5 |
C4 |
N3 |
128.0 |
119.7 |
C5 |
C6 |
N1 |
113.3 |
118.3 |
C5 |
C6 |
O6 |
127.5 |
120.9 |
C4 |
N3 |
C2 |
112.5 |
121.1 |
N3 |
C2 |
N2 |
118.4 |
119.0 |
N3 |
C2 |
N1 |
124.4 |
121.9 |
N2 |
C2 |
N1 |
117.2 |
119.1 |
C2 |
N2 |
H21 |
120.0 |
120.0 |
C2 |
N2 |
H22 |
120.0 |
120.0 |
C2 |
N1 |
C6 |
123.3 |
120.3 |
C2 |
N1 |
H1 |
118.3 |
119.8 |
H21 |
N2 |
H22 |
120.0 |
120.0 |
C6 |
N1 |
H1 |
118.3 |
119.9 |
N1 |
C6 |
O6 |
119.3 |
120.8 |
C3' |
C2' |
H2' |
111.6 |
110.5 |
C3' |
C2' |
H2'' |
111.7 |
110.5 |
C2' |
C3' |
O3' |
113.6 |
110.9 |
C2' |
C3' |
H3' |
109.6 |
110.9 |
H2' |
C2' |
H2'' |
109.5 |
110.5 |
O3' |
C3' |
H3' |
111.1 |
110.8 |
C3' |
O3' |
HO3' |
109.5 |
114.0 |
Torsion Angles for BGM
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
OP2 |
P |
OP1 |
O5' |
233.1 |
240.0 |
OP2 |
P |
OP1 |
OP3 |
|
120.1 |
OP1 |
P |
OP2 |
HOP2 |
360.0 |
179.9 |
O5' |
P |
OP1 |
OP3 |
|
240.0 |
OP1 |
P |
O5' |
C5' |
167.2 |
305.0 |
OP1 |
P |
OP3 |
HOP3 |
|
60.1 |
OP1 |
P |
OP2 |
O5' |
124.6 |
119.9 |
OP1 |
P |
OP2 |
OP3 |
|
240.0 |
O5' |
P |
OP2 |
OP3 |
|
120.0 |
OP2 |
P |
O5' |
C5' |
297.4 |
64.9 |
OP2 |
P |
OP3 |
HOP3 |
|
300.0 |
OP1 |
P |
O5' |
OP2 |
229.8 |
240.0 |
OP1 |
P |
O5' |
OP3 |
|
120.0 |
OP2 |
P |
O5' |
OP3 |
|
239.9 |
O5' |
P |
OP2 |
HOP2 |
235.4 |
60.0 |
O5' |
P |
OP3 |
HOP3 |
|
180.0 |
P |
O5' |
C5' |
C4' |
179.3 |
180.0 |
P |
O5' |
C5' |
H5' |
298.6 |
300.0 |
P |
O5' |
C5' |
H5'' |
59.9 |
60.1 |
OP1 |
P |
OP3 |
OP2 |
|
120.0 |
OP1 |
P |
OP3 |
O5' |
|
240.1 |
OP2 |
P |
OP3 |
O5' |
|
120.1 |
OP3 |
P |
OP2 |
HOP2 |
|
300.0 |
OP3 |
P |
O5' |
C5' |
|
185.0 |
HOP2 |
OP2 |
P |
O5' |
235.4 |
60.0 |
HOP2 |
OP2 |
P |
OP3 |
|
300.0 |
C5' |
O5' |
P |
OP3 |
|
185.0 |
C4' |
C5' |
O5' |
H5' |
240.7 |
240.1 |
C4' |
C5' |
O5' |
H5'' |
119.4 |
120.0 |
O5' |
C5' |
C4' |
O4' |
159.8 |
66.5 |
O5' |
C5' |
C4' |
C3' |
280.2 |
180.5 |
O5' |
C5' |
C4' |
H4' |
41.9 |
303.5 |
H5' |
C5' |
O5' |
H5'' |
238.7 |
239.9 |
O5' |
C5' |
C4' |
H5' |
119.3 |
120.0 |
O5' |
C5' |
C4' |
H5'' |
240.6 |
240.0 |
H5' |
C5' |
C4' |
H5'' |
121.3 |
120.0 |
O4' |
C4' |
C5' |
C3' |
239.6 |
246.0 |
O4' |
C4' |
C5' |
H4' |
117.9 |
123.0 |
C5' |
C4' |
O4' |
C1' |
129.5 |
158.5 |
C3' |
C4' |
C5' |
H4' |
238.3 |
237.0 |
C5' |
C4' |
C3' |
C2' |
260.1 |
204.5 |
C5' |
C4' |
C3' |
O3' |
139.0 |
86.3 |
C5' |
C4' |
C3' |
H3' |
16.9 |
322.7 |
O5' |
C5' |
H5' |
C4' |
243.8 |
240.1 |
O5' |
C5' |
H5' |
H5'' |
121.9 |
120.1 |
C4' |
C5' |
H5' |
H5'' |
238.1 |
240.0 |
H5' |
C5' |
C4' |
O4' |
40.5 |
306.5 |
H5' |
C5' |
C4' |
C3' |
160.8 |
60.5 |
H5' |
C5' |
C4' |
H4' |
282.5 |
183.5 |
O5' |
C5' |
H5'' |
C4' |
116.2 |
119.9 |
O5' |
C5' |
H5'' |
H5' |
238.1 |
239.9 |
C4' |
C5' |
H5'' |
H5' |
121.9 |
120.0 |
H5'' |
C5' |
C4' |
O4' |
279.2 |
186.5 |
H5'' |
C5' |
C4' |
C3' |
39.6 |
300.5 |
H5'' |
C5' |
C4' |
H4' |
161.3 |
63.5 |
O4' |
C4' |
C5' |
H5' |
40.5 |
306.5 |
O4' |
C4' |
C5' |
H5'' |
279.2 |
186.5 |
C5' |
C4' |
O4' |
C3' |
127.4 |
118.5 |
C5' |
C4' |
O4' |
H4' |
242.7 |
237.1 |
C3' |
C4' |
O4' |
H4' |
115.2 |
118.6 |
O4' |
C4' |
C3' |
C2' |
22.2 |
323.0 |
O4' |
C4' |
C3' |
O3' |
261.2 |
204.7 |
O4' |
C4' |
C3' |
H3' |
139.1 |
81.2 |
C4' |
O4' |
C1' |
N9 |
210.8 |
214.1 |
C4' |
O4' |
C1' |
C2' |
333.9 |
333.5 |
C4' |
O4' |
C1' |
H1' |
91.4 |
93.0 |
C3' |
C4' |
C5' |
H5' |
160.8 |
60.5 |
C3' |
C4' |
C5' |
H5'' |
39.6 |
300.5 |
C5' |
C4' |
C3' |
O4' |
237.8 |
241.5 |
C5' |
C4' |
C3' |
H4' |
121.8 |
122.9 |
O4' |
C4' |
C3' |
H4' |
244.0 |
241.4 |
C3' |
C4' |
O4' |
C1' |
2.1 |
40.1 |
C1' |
C2' |
C3' |
C4' |
323.4 |
20.9 |
C4' |
C3' |
C2' |
H2' |
204.8 |
262.2 |
C4' |
C3' |
C2' |
H2'' |
81.9 |
139.6 |
C2' |
C3' |
C4' |
O3' |
121.1 |
118.2 |
C2' |
C3' |
C4' |
H3' |
243.2 |
241.8 |
O3' |
C3' |
C4' |
H3' |
122.1 |
123.6 |
C4' |
C3' |
O3' |
HO3' |
180.0 |
180.0 |
H4' |
C4' |
C5' |
H5' |
282.5 |
183.5 |
H4' |
C4' |
C5' |
H5'' |
161.3 |
63.5 |
C5' |
C4' |
H4' |
O4' |
118.2 |
123.0 |
C5' |
C4' |
H4' |
C3' |
232.3 |
237.1 |
O4' |
C4' |
H4' |
C3' |
114.0 |
114.1 |
H4' |
C4' |
O4' |
C1' |
246.8 |
281.5 |
H4' |
C4' |
C3' |
C2' |
138.3 |
81.6 |
H4' |
C4' |
C3' |
O3' |
17.2 |
323.3 |
H4' |
C4' |
C3' |
H3' |
255.1 |
199.8 |
C1' |
O4' |
C4' |
C3' |
2.1 |
40.1 |
C1' |
O4' |
C4' |
H4' |
246.8 |
281.5 |
N9 |
C1' |
O4' |
C2' |
236.9 |
240.6 |
N9 |
C1' |
O4' |
H1' |
119.4 |
121.1 |
O4' |
C1' |
N9 |
C8 |
60.6 |
43.5 |
O4' |
C1' |
N9 |
C4 |
243.9 |
223.3 |
C2' |
C1' |
O4' |
H1' |
242.5 |
240.5 |
O4' |
C1' |
C2' |
C3' |
38.4 |
2.0 |
O4' |
C1' |
C2' |
H2' |
157.0 |
120.7 |
O4' |
C1' |
C2' |
H2'' |
279.9 |
243.3 |
O4' |
C1' |
N9 |
C2' |
115.5 |
117.8 |
O4' |
C1' |
N9 |
H1' |
240.5 |
238.9 |
C2' |
C1' |
N9 |
H1' |
125.0 |
121.1 |
N9 |
C1' |
C2' |
C3' |
154.8 |
121.5 |
N9 |
C1' |
C2' |
H2' |
273.3 |
240.1 |
N9 |
C1' |
C2' |
H2'' |
36.2 |
2.8 |
C8 |
N9 |
C1' |
C4 |
176.7 |
180.2 |
C1' |
N9 |
C8 |
N7 |
182.6 |
180.0 |
C1' |
N9 |
C8 |
BR |
|
0.0 |
C1' |
N9 |
C4 |
C5 |
177.7 |
179.9 |
C1' |
N9 |
C4 |
N3 |
358.3 |
359.9 |
C4' |
C3' |
C2' |
C1' |
323.4 |
20.9 |
O4' |
C1' |
C2' |
N9 |
243.7 |
240.6 |
O4' |
C1' |
C2' |
H1' |
118.3 |
119.5 |
N9 |
C1' |
C2' |
H1' |
234.6 |
239.0 |
C2' |
C1' |
N9 |
C8 |
305.1 |
285.7 |
C2' |
C1' |
N9 |
C4 |
128.3 |
105.5 |
C3' |
C2' |
C1' |
H2' |
241.5 |
241.3 |
C3' |
C2' |
C1' |
H2'' |
118.6 |
118.7 |
C1' |
C2' |
C3' |
O3' |
81.5 |
139.1 |
C1' |
C2' |
C3' |
H3' |
206.4 |
262.7 |
H2' |
C2' |
C1' |
H2'' |
237.1 |
237.3 |
O4' |
C1' |
H1' |
N9 |
116.8 |
121.1 |
O4' |
C1' |
H1' |
C2' |
245.5 |
242.1 |
N9 |
C1' |
H1' |
C2' |
128.7 |
121.0 |
H1' |
C1' |
N9 |
C8 |
180.1 |
164.6 |
H1' |
C1' |
N9 |
C4 |
3.4 |
344.4 |
H1' |
C1' |
C2' |
C3' |
280.2 |
242.5 |
H1' |
C1' |
C2' |
H2' |
38.7 |
1.2 |
H1' |
C1' |
C2' |
H2'' |
161.6 |
123.8 |
C8 |
N9 |
C1' |
C2' |
305.1 |
285.7 |
C8 |
N9 |
C1' |
H1' |
180.1 |
164.6 |
C1' |
N9 |
C8 |
C4 |
182.8 |
179.8 |
C8 |
N9 |
C4 |
C5 |
0.3 |
359.7 |
C8 |
N9 |
C4 |
N3 |
180.8 |
179.7 |
N7 |
C8 |
N9 |
BR |
|
180.0 |
N9 |
C8 |
N7 |
C5 |
360.0 |
0.0 |
C4 |
N9 |
C1' |
C2' |
128.3 |
105.5 |
C4 |
N9 |
C1' |
H1' |
3.4 |
344.4 |
C1' |
N9 |
C4 |
C8 |
177.5 |
180.2 |
C4 |
N9 |
C8 |
N7 |
359.8 |
0.2 |
C4 |
N9 |
C8 |
BR |
|
180.2 |
N7 |
C5 |
C4 |
N9 |
359.7 |
0.3 |
N9 |
C4 |
C5 |
C6 |
180.5 |
180.2 |
C5 |
C4 |
N9 |
N3 |
179.4 |
179.9 |
N9 |
C4 |
N3 |
C2 |
179.8 |
180.0 |
N7 |
C8 |
N9 |
C4 |
359.8 |
0.2 |
N9 |
C8 |
N7 |
BR |
|
180.0 |
C8 |
N7 |
C5 |
C4 |
0.2 |
359.8 |
C8 |
N7 |
C5 |
C6 |
179.3 |
180.0 |
BR |
C8 |
N9 |
C4 |
|
180.2 |
N9 |
C8 |
BR |
N7 |
|
180.0 |
BR |
C8 |
N7 |
C5 |
|
180.0 |
N9 |
C4 |
C5 |
N7 |
359.7 |
0.3 |
C5 |
N7 |
C8 |
BR |
|
180.0 |
C4 |
C5 |
N7 |
C6 |
180.9 |
179.8 |
N7 |
C5 |
C4 |
N3 |
179.1 |
180.3 |
N7 |
C5 |
C6 |
N1 |
180.7 |
179.3 |
N7 |
C5 |
C6 |
O6 |
0.9 |
360.0 |
N9 |
C4 |
C5 |
N3 |
180.6 |
180.1 |
N7 |
C5 |
C4 |
C6 |
179.2 |
180.2 |
C4 |
C5 |
C6 |
N1 |
359.7 |
359.5 |
C4 |
C5 |
C6 |
O6 |
180.0 |
180.2 |
C5 |
C4 |
N3 |
C2 |
0.5 |
0.1 |
N7 |
C5 |
C6 |
C4 |
180.9 |
179.8 |
C6 |
C5 |
C4 |
N3 |
359.9 |
0.1 |
C2 |
N1 |
C6 |
C5 |
0.3 |
0.6 |
C5 |
C6 |
N1 |
H1 |
180.3 |
180.2 |
N1 |
C6 |
C5 |
O6 |
179.7 |
179.3 |
N9 |
C4 |
N3 |
C5 |
179.3 |
179.9 |
N3 |
C4 |
C5 |
C6 |
359.9 |
0.1 |
C4 |
N3 |
C2 |
N2 |
181.1 |
180.0 |
C4 |
N3 |
C2 |
N1 |
359.5 |
360.0 |
N2 |
C2 |
N3 |
N1 |
181.6 |
180.1 |
N3 |
C2 |
N2 |
H21 |
0.0 |
359.9 |
N3 |
C2 |
N2 |
H22 |
180.0 |
180.0 |
N3 |
C2 |
N1 |
C6 |
0.1 |
359.7 |
N3 |
C2 |
N1 |
H1 |
180.1 |
180.0 |
N3 |
C2 |
N2 |
N1 |
178.6 |
179.9 |
N2 |
C2 |
N1 |
C6 |
178.6 |
179.6 |
N2 |
C2 |
N1 |
H1 |
358.6 |
360.0 |
H21 |
N2 |
C2 |
H22 |
180.0 |
179.9 |
C5 |
C6 |
N1 |
C2 |
0.3 |
0.6 |
N3 |
C2 |
N1 |
N2 |
181.5 |
180.1 |
N1 |
C2 |
N2 |
H21 |
181.5 |
179.9 |
N1 |
C2 |
N2 |
H22 |
1.5 |
0.1 |
C6 |
N1 |
C2 |
H1 |
180.0 |
179.6 |
C2 |
N1 |
C6 |
O6 |
180.0 |
179.9 |
H21 |
N2 |
C2 |
N1 |
181.5 |
179.9 |
C2 |
N2 |
H21 |
H22 |
180.0 |
180.1 |
H22 |
N2 |
C2 |
N1 |
1.5 |
0.1 |
C2 |
N2 |
H22 |
H21 |
180.0 |
179.9 |
C5 |
C6 |
N1 |
O6 |
180.2 |
180.7 |
C2 |
N1 |
C6 |
H1 |
180.0 |
180.4 |
C2 |
N1 |
H1 |
C6 |
180.0 |
179.6 |
H1 |
N1 |
C6 |
O6 |
0.0 |
359.5 |
C5 |
C6 |
O6 |
N1 |
179.7 |
179.3 |
O6 |
C6 |
N1 |
H1 |
0.0 |
359.5 |
C2' |
C3' |
C4' |
H4' |
138.3 |
81.6 |
C4' |
C3' |
C2' |
O3' |
241.9 |
241.8 |
C4' |
C3' |
C2' |
H3' |
116.9 |
118.2 |
C3' |
C2' |
C1' |
H1' |
280.2 |
242.5 |
C1' |
C2' |
C3' |
H2' |
118.5 |
118.7 |
C1' |
C2' |
C3' |
H2'' |
241.4 |
241.3 |
H2' |
C2' |
C3' |
H2'' |
122.9 |
122.7 |
O3' |
C3' |
C2' |
H3' |
235.0 |
236.4 |
C2' |
C3' |
O3' |
HO3' |
65.5 |
67.3 |
H2' |
C2' |
C1' |
H1' |
38.7 |
1.2 |
C1' |
C2' |
H2' |
C3' |
248.2 |
245.3 |
C1' |
C2' |
H2' |
H2'' |
124.1 |
122.6 |
C3' |
C2' |
H2' |
H2'' |
235.9 |
237.4 |
H2' |
C2' |
C3' |
O3' |
322.9 |
20.4 |
H2' |
C2' |
C3' |
H3' |
87.9 |
144.0 |
H2'' |
C2' |
C1' |
H1' |
161.6 |
123.8 |
C1' |
C2' |
H2'' |
C3' |
111.8 |
114.8 |
C1' |
C2' |
H2'' |
H2' |
235.9 |
237.4 |
C3' |
C2' |
H2'' |
H2' |
124.1 |
122.6 |
H2'' |
C2' |
C3' |
O3' |
200.0 |
257.8 |
H2'' |
C2' |
C3' |
H3' |
325.0 |
21.4 |
O3' |
C3' |
C4' |
H4' |
17.2 |
323.3 |
C4' |
C3' |
O3' |
C2' |
114.5 |
112.7 |
C4' |
C3' |
O3' |
H3' |
238.7 |
236.4 |
O3' |
C3' |
C2' |
H2' |
322.9 |
20.4 |
O3' |
C3' |
C2' |
H2'' |
200.0 |
257.8 |
C2' |
C3' |
O3' |
H3' |
124.2 |
123.6 |
H3' |
C3' |
C4' |
H4' |
255.1 |
199.8 |
C4' |
C3' |
H3' |
C2' |
247.3 |
247.3 |
C4' |
C3' |
H3' |
O3' |
121.0 |
123.6 |
H3' |
C3' |
C2' |
H2' |
87.9 |
144.0 |
H3' |
C3' |
C2' |
H2'' |
325.0 |
21.4 |
C2' |
C3' |
H3' |
O3' |
233.6 |
236.3 |
H3' |
C3' |
O3' |
HO3' |
301.3 |
303.6 |
HO3' |
O3' |
C3' |
H3' |
301.3 |
303.6 |