PDB Chemical Component CL9
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 CL9
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C2 |
CL |
1.765 |
1.736 |
| C2 |
N3 |
1.322 |
1.317 |
| C2 |
N1 |
1.353 |
1.321 |
| C4 |
C5 |
1.385 |
1.404 |
| C4 |
N3 |
1.323 |
1.329 |
| C4 |
N9 |
1.307 |
1.371 |
| C5 |
C6 |
1.366 |
1.405 |
| C5 |
N7 |
1.322 |
1.355 |
| C6 |
N6 |
1.345 |
1.384 |
| C6 |
N1 |
1.338 |
1.329 |
| C8 |
N9 |
1.335 |
1.364 |
| C8 |
N7 |
1.351 |
1.301 |
| N9 |
C1' |
1.463 |
1.465 |
| C1' |
C2' |
1.496 |
1.541 |
| C1' |
O4' |
1.416 |
1.438 |
| C2' |
C3' |
1.509 |
1.549 |
| C3' |
O3' |
1.430 |
1.429 |
| C3' |
C4' |
1.514 |
1.550 |
| C4' |
O4' |
1.400 |
1.445 |
| C4' |
C5' |
1.499 |
1.530 |
| C5' |
O5' |
1.413 |
1.428 |
| C8 |
H8 |
1.080 |
1.080 |
| N6 |
HN6 |
1.000 |
0.970 |
| N6 |
HN6A |
1.000 |
0.969 |
| C1' |
H1' |
1.100 |
1.090 |
| C2' |
H2' |
1.100 |
1.090 |
| C2' |
H2'A |
1.101 |
1.090 |
| C3' |
H3' |
1.100 |
1.091 |
| O3' |
HO3' |
0.950 |
0.967 |
| C4' |
H4' |
1.100 |
1.090 |
| C5' |
H5' |
1.099 |
1.090 |
| C5' |
H5'A |
1.100 |
1.090 |
| O5' |
HO5' |
0.950 |
0.967 |
Bond Angles for CL9
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| CL |
C2 |
N3 |
116.1 |
118.8 |
| CL |
C2 |
N1 |
119.1 |
118.8 |
| N3 |
C2 |
N1 |
124.8 |
122.4 |
| C2 |
N3 |
C4 |
116.5 |
120.7 |
| C2 |
N1 |
C6 |
119.5 |
121.2 |
| C5 |
C4 |
N3 |
121.3 |
119.0 |
| C5 |
C4 |
N9 |
108.2 |
106.1 |
| C4 |
C5 |
C6 |
120.5 |
118.2 |
| C4 |
C5 |
N7 |
108.0 |
107.2 |
| N3 |
C4 |
N9 |
130.4 |
134.9 |
| C4 |
N9 |
C8 |
107.4 |
107.4 |
| C4 |
N9 |
C1' |
126.1 |
126.3 |
| C6 |
C5 |
N7 |
131.5 |
134.6 |
| C5 |
C6 |
N6 |
121.0 |
120.8 |
| C5 |
C6 |
N1 |
117.4 |
118.5 |
| C5 |
N7 |
C8 |
106.3 |
109.4 |
| N6 |
C6 |
N1 |
121.6 |
120.7 |
| C6 |
N6 |
HN6 |
109.5 |
119.9 |
| C6 |
N6 |
HN6A |
109.5 |
120.1 |
| N9 |
C8 |
N7 |
110.1 |
110.0 |
| C8 |
N9 |
C1' |
126.4 |
126.3 |
| N9 |
C8 |
H8 |
125.0 |
125.0 |
| N7 |
C8 |
H8 |
124.9 |
125.0 |
| N9 |
C1' |
C2' |
115.0 |
109.9 |
| N9 |
C1' |
O4' |
105.3 |
109.9 |
| N9 |
C1' |
H1' |
107.5 |
109.9 |
| C2' |
C1' |
O4' |
105.5 |
107.3 |
| C1' |
C2' |
C3' |
100.7 |
104.2 |
| C2' |
C1' |
H1' |
107.3 |
109.9 |
| C1' |
C2' |
H2' |
112.5 |
110.5 |
| C1' |
C2' |
H2'A |
114.3 |
110.5 |
| C1' |
O4' |
C4' |
110.2 |
106.9 |
| O4' |
C1' |
H1' |
116.7 |
110.0 |
| C2' |
C3' |
O3' |
106.2 |
110.9 |
| C2' |
C3' |
C4' |
105.9 |
102.1 |
| C3' |
C2' |
H2' |
112.5 |
110.5 |
| C3' |
C2' |
H2'A |
114.3 |
110.5 |
| C2' |
C3' |
H3' |
113.0 |
110.9 |
| O3' |
C3' |
C4' |
107.2 |
110.9 |
| O3' |
C3' |
H3' |
111.8 |
110.8 |
| C3' |
O3' |
HO3' |
109.5 |
114.0 |
| C3' |
C4' |
O4' |
105.5 |
103.5 |
| C3' |
C4' |
C5' |
115.5 |
110.6 |
| C4' |
C3' |
H3' |
112.1 |
110.9 |
| C3' |
C4' |
H4' |
106.5 |
110.6 |
| O4' |
C4' |
C5' |
103.4 |
110.6 |
| O4' |
C4' |
H4' |
118.0 |
110.6 |
| C4' |
C5' |
O5' |
102.5 |
109.5 |
| C5' |
C4' |
H4' |
108.4 |
110.7 |
| C4' |
C5' |
H5' |
111.9 |
109.5 |
| C4' |
C5' |
H5'A |
113.3 |
109.5 |
| O5' |
C5' |
H5' |
111.9 |
109.4 |
| O5' |
C5' |
H5'A |
113.4 |
109.5 |
| C5' |
O5' |
HO5' |
109.5 |
114.1 |
| HN6 |
N6 |
HN6A |
109.5 |
120.0 |
| H2' |
C2' |
H2'A |
103.0 |
110.5 |
| H5' |
C5' |
H5'A |
104.2 |
109.4 |
Torsion Angles for CL9
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| N3 |
C2 |
CL |
N1 |
177.7 |
180.3 |
| CL |
C2 |
N3 |
C4 |
181.5 |
180.0 |
| CL |
C2 |
N1 |
C6 |
178.4 |
180.0 |
| CL |
C2 |
N3 |
N1 |
182.4 |
179.7 |
| N3 |
C2 |
N1 |
C6 |
0.9 |
359.7 |
| C5 |
C4 |
N3 |
C2 |
0.3 |
359.9 |
| C2 |
N3 |
C4 |
N9 |
181.5 |
179.7 |
| CL |
C2 |
N1 |
N3 |
177.5 |
180.3 |
| N1 |
C2 |
N3 |
C4 |
359.1 |
0.3 |
| C5 |
C6 |
N1 |
C2 |
359.8 |
360.0 |
| N6 |
C6 |
N1 |
C2 |
179.2 |
180.3 |
| C2 |
N3 |
C4 |
C5 |
0.3 |
359.9 |
| N3 |
C4 |
C5 |
N9 |
180.9 |
179.8 |
| C5 |
C4 |
N9 |
C8 |
1.4 |
360.0 |
| C5 |
C4 |
N9 |
C1' |
177.3 |
180.0 |
| C6 |
C5 |
C4 |
N7 |
180.1 |
179.7 |
| C4 |
C5 |
C6 |
N6 |
180.3 |
180.0 |
| C4 |
C5 |
C6 |
N1 |
359.7 |
0.3 |
| C4 |
C5 |
N7 |
C8 |
359.9 |
359.6 |
| C4 |
N3 |
C2 |
N1 |
359.1 |
0.3 |
| C5 |
C4 |
N3 |
N9 |
178.8 |
180.3 |
| N3 |
C4 |
C5 |
C6 |
0.2 |
359.7 |
| N3 |
C4 |
C5 |
N7 |
180.1 |
180.0 |
| N3 |
C4 |
N9 |
C8 |
180.3 |
180.3 |
| N3 |
C4 |
N9 |
C1' |
356.2 |
0.2 |
| C5 |
C4 |
N9 |
N3 |
181.1 |
179.7 |
| N9 |
C4 |
C5 |
C6 |
179.3 |
179.9 |
| N9 |
C4 |
C5 |
N7 |
359.2 |
0.3 |
| C4 |
N9 |
C8 |
N7 |
358.5 |
359.7 |
| C8 |
N9 |
C4 |
C1' |
184.1 |
180.0 |
| C4 |
N9 |
C8 |
H8 |
178.5 |
180.0 |
| C4 |
N9 |
C1' |
C2' |
83.3 |
85.0 |
| C4 |
N9 |
C1' |
O4' |
198.9 |
202.9 |
| C4 |
N9 |
C1' |
H1' |
323.9 |
324.0 |
| C2 |
N1 |
C6 |
C5 |
359.8 |
360.0 |
| C6 |
C5 |
C4 |
N3 |
0.2 |
359.7 |
| C6 |
C5 |
C4 |
N9 |
179.3 |
179.9 |
| C4 |
C5 |
C6 |
N7 |
179.8 |
180.4 |
| C6 |
C5 |
N7 |
C8 |
179.8 |
180.0 |
| N6 |
C6 |
C5 |
N1 |
180.5 |
179.7 |
| C5 |
C6 |
N6 |
HN6 |
119.7 |
360.0 |
| C5 |
C6 |
N6 |
HN6A |
239.7 |
180.1 |
| N7 |
C5 |
C4 |
N3 |
180.1 |
180.0 |
| N7 |
C5 |
C4 |
N9 |
359.2 |
0.3 |
| C4 |
C5 |
N7 |
C6 |
180.2 |
179.6 |
| N7 |
C5 |
C6 |
N6 |
0.5 |
359.6 |
| N7 |
C5 |
C6 |
N1 |
179.9 |
179.9 |
| N9 |
C8 |
N7 |
C5 |
0.9 |
0.4 |
| C5 |
N7 |
C8 |
H8 |
180.9 |
180.2 |
| C2 |
N1 |
C6 |
N6 |
179.2 |
180.3 |
| N6 |
C6 |
C5 |
N7 |
0.5 |
359.6 |
| C5 |
C6 |
N6 |
N1 |
179.4 |
180.3 |
| HN6 |
N6 |
C6 |
HN6A |
240.0 |
179.9 |
| N1 |
C6 |
C5 |
N7 |
179.9 |
179.9 |
| C5 |
C6 |
N1 |
N6 |
180.6 |
179.7 |
| N1 |
C6 |
N6 |
HN6 |
300.2 |
179.7 |
| N1 |
C6 |
N6 |
HN6A |
60.3 |
359.8 |
| C4 |
N9 |
C8 |
C1' |
175.8 |
180.0 |
| C5 |
N7 |
C8 |
N9 |
0.9 |
0.4 |
| N7 |
C8 |
N9 |
H8 |
180.0 |
179.8 |
| C8 |
N9 |
C1' |
C2' |
258.4 |
265.0 |
| C8 |
N9 |
C1' |
O4' |
14.0 |
22.8 |
| C8 |
N9 |
C1' |
H1' |
139.0 |
144.0 |
| N7 |
C8 |
N9 |
C1' |
182.7 |
179.8 |
| N9 |
C8 |
N7 |
H8 |
180.0 |
180.2 |
| C4 |
N9 |
C1' |
C8 |
184.9 |
180.0 |
| C1' |
N9 |
C8 |
N7 |
182.7 |
179.8 |
| C1' |
N9 |
C8 |
H8 |
2.7 |
0.0 |
| C2' |
C1' |
N9 |
O4' |
244.4 |
242.1 |
| N9 |
C1' |
C2' |
C3' |
150.3 |
121.5 |
| C2' |
C1' |
N9 |
H1' |
119.4 |
121.0 |
| N9 |
C1' |
C2' |
H2' |
270.2 |
240.1 |
| N9 |
C1' |
C2' |
H2'A |
27.2 |
2.8 |
| N9 |
C1' |
O4' |
C4' |
207.7 |
214.1 |
| O4' |
C1' |
N9 |
H1' |
235.0 |
238.8 |
| N9 |
C1' |
C2' |
O4' |
115.5 |
119.4 |
| N9 |
C1' |
C2' |
H1' |
240.5 |
239.0 |
| C2' |
C1' |
O4' |
C4' |
329.6 |
333.5 |
| O4' |
C1' |
C2' |
H1' |
125.0 |
119.6 |
| C1' |
C2' |
C3' |
O3' |
86.4 |
139.1 |
| C1' |
C2' |
C3' |
C4' |
332.5 |
20.9 |
| C3' |
C2' |
C1' |
H2' |
240.0 |
241.3 |
| C3' |
C2' |
C1' |
H2'A |
123.0 |
118.7 |
| C1' |
C2' |
C3' |
H3' |
209.4 |
262.7 |
| H2' |
C2' |
C1' |
H2'A |
243.0 |
237.3 |
| N9 |
C1' |
O4' |
C2' |
238.0 |
240.6 |
| N9 |
C1' |
O4' |
H1' |
119.1 |
121.1 |
| O4' |
C1' |
C2' |
C3' |
34.8 |
2.1 |
| C2' |
C1' |
O4' |
H1' |
241.0 |
240.5 |
| O4' |
C1' |
C2' |
H2' |
154.8 |
120.7 |
| O4' |
C1' |
C2' |
H2'A |
271.7 |
243.4 |
| C3' |
C4' |
O4' |
C1' |
11.9 |
40.0 |
| C1' |
O4' |
C4' |
C5' |
133.5 |
158.6 |
| C1' |
O4' |
C4' |
H4' |
253.2 |
281.6 |
| C3' |
C2' |
C1' |
O4' |
34.8 |
2.1 |
| C3' |
C2' |
C1' |
H1' |
269.7 |
242.5 |
| C1' |
C2' |
C3' |
H2' |
120.0 |
118.7 |
| C1' |
C2' |
C3' |
H2'A |
237.0 |
241.3 |
| O3' |
C3' |
C2' |
C4' |
113.8 |
118.2 |
| O3' |
C3' |
C2' |
H3' |
237.0 |
236.4 |
| C2' |
C3' |
O3' |
HO3' |
248.2 |
61.4 |
| C2' |
C3' |
C4' |
O4' |
10.9 |
323.0 |
| C2' |
C3' |
C4' |
C5' |
257.4 |
204.5 |
| C4' |
C3' |
C2' |
H3' |
123.1 |
118.2 |
| C2' |
C3' |
C4' |
H4' |
137.0 |
81.5 |
| H2' |
C2' |
C3' |
H2'A |
117.0 |
122.6 |
| C2' |
C3' |
O3' |
C4' |
247.1 |
247.3 |
| O3' |
C3' |
C2' |
H2' |
326.4 |
20.4 |
| O3' |
C3' |
C2' |
H2'A |
209.4 |
257.8 |
| C2' |
C3' |
O3' |
H3' |
123.8 |
123.6 |
| O3' |
C3' |
C4' |
O4' |
257.8 |
204.8 |
| O3' |
C3' |
C4' |
C5' |
144.3 |
86.3 |
| C4' |
C3' |
O3' |
H3' |
236.7 |
236.4 |
| O3' |
C3' |
C4' |
H4' |
23.9 |
323.3 |
| C1' |
O4' |
C4' |
C3' |
11.9 |
40.0 |
| C2' |
C3' |
C4' |
O3' |
113.2 |
118.2 |
| C4' |
C3' |
C2' |
H2' |
212.5 |
262.2 |
| C4' |
C3' |
C2' |
H2'A |
95.6 |
139.6 |
| C2' |
C3' |
C4' |
H3' |
236.3 |
241.8 |
| O3' |
C3' |
C4' |
H3' |
123.1 |
123.6 |
| C4' |
C3' |
O3' |
HO3' |
1.2 |
174.2 |
| O4' |
C4' |
C3' |
C5' |
113.5 |
118.5 |
| O4' |
C4' |
C3' |
H4' |
233.9 |
241.5 |
| C3' |
C4' |
C5' |
O5' |
97.6 |
185.0 |
| C5' |
C4' |
C3' |
H4' |
120.4 |
123.0 |
| C3' |
C4' |
C5' |
H5' |
217.6 |
305.0 |
| C3' |
C4' |
C5' |
H5'A |
335.0 |
65.0 |
| C4' |
O4' |
C1' |
H1' |
88.6 |
93.0 |
| C3' |
C4' |
O4' |
C5' |
238.3 |
241.5 |
| O4' |
C4' |
C3' |
H3' |
134.6 |
81.2 |
| C3' |
C4' |
O4' |
H4' |
118.7 |
118.5 |
| O4' |
C4' |
C5' |
O5' |
342.9 |
70.9 |
| C5' |
C4' |
O4' |
H4' |
240.4 |
237.0 |
| O4' |
C4' |
C5' |
H5' |
102.9 |
190.9 |
| O4' |
C4' |
C5' |
H5'A |
220.4 |
310.9 |
| C3' |
C4' |
C5' |
O4' |
114.7 |
114.1 |
| C5' |
C4' |
C3' |
H3' |
21.2 |
322.7 |
| C3' |
C4' |
C5' |
H4' |
240.7 |
237.0 |
| O4' |
C4' |
C5' |
H4' |
126.0 |
122.9 |
| O5' |
C5' |
C4' |
H5' |
240.0 |
240.0 |
| O5' |
C5' |
C4' |
H5'A |
122.5 |
120.1 |
| C4' |
C5' |
O5' |
HO5' |
280.5 |
180.0 |
| H5' |
C5' |
C4' |
H5'A |
242.5 |
240.1 |
| O5' |
C5' |
C4' |
H4' |
216.9 |
308.0 |
| C4' |
C5' |
O5' |
H5' |
120.0 |
120.0 |
| C4' |
C5' |
O5' |
H5'A |
237.5 |
239.9 |
| H5' |
C5' |
O5' |
H5'A |
117.5 |
119.9 |
| N9 |
C8 |
H8 |
N7 |
180.0 |
179.7 |
| H8 |
C8 |
N9 |
C1' |
2.7 |
0.0 |
| HN6 |
N6 |
C6 |
N1 |
300.2 |
179.7 |
| C6 |
N6 |
HN6 |
HN6A |
120.0 |
180.1 |
| HN6A |
N6 |
C6 |
N1 |
60.3 |
359.8 |
| C6 |
N6 |
HN6A |
HN6 |
240.0 |
179.9 |
| N9 |
C1' |
H1' |
C2' |
124.2 |
121.0 |
| N9 |
C1' |
H1' |
O4' |
242.2 |
238.9 |
| C2' |
C1' |
H1' |
O4' |
118.0 |
117.9 |
| H1' |
C1' |
C2' |
C3' |
269.7 |
242.5 |
| H1' |
C1' |
C2' |
H2' |
29.7 |
1.2 |
| H1' |
C1' |
C2' |
H2'A |
146.7 |
123.8 |
| H1' |
C1' |
O4' |
C4' |
88.6 |
93.0 |
| H2' |
C2' |
C1' |
O4' |
154.8 |
120.7 |
| C1' |
C2' |
H2' |
C3' |
247.1 |
245.2 |
| H2' |
C2' |
C1' |
H1' |
29.7 |
1.2 |
| C1' |
C2' |
H2' |
H2'A |
123.5 |
122.7 |
| H2' |
C2' |
C3' |
O3' |
326.4 |
20.4 |
| H2' |
C2' |
C3' |
C4' |
212.5 |
262.2 |
| C3' |
C2' |
H2' |
H2'A |
236.4 |
237.5 |
| H2' |
C2' |
C3' |
H3' |
89.4 |
144.0 |
| H2'A |
C2' |
C1' |
O4' |
271.7 |
243.4 |
| C1' |
C2' |
H2'A |
C3' |
115.3 |
114.8 |
| H2'A |
C2' |
C1' |
H1' |
146.7 |
123.8 |
| C1' |
C2' |
H2'A |
H2' |
237.7 |
237.3 |
| H2'A |
C2' |
C3' |
O3' |
209.4 |
257.8 |
| H2'A |
C2' |
C3' |
C4' |
95.6 |
139.6 |
| C3' |
C2' |
H2'A |
H2' |
122.3 |
122.5 |
| H2'A |
C2' |
C3' |
H3' |
332.4 |
21.4 |
| C2' |
C3' |
H3' |
O3' |
240.1 |
236.4 |
| C2' |
C3' |
H3' |
C4' |
119.7 |
112.7 |
| H3' |
C3' |
C2' |
H2' |
89.4 |
144.0 |
| H3' |
C3' |
C2' |
H2'A |
332.4 |
21.4 |
| O3' |
C3' |
H3' |
C4' |
239.5 |
236.3 |
| H3' |
C3' |
O3' |
HO3' |
124.5 |
297.8 |
| H3' |
C3' |
C4' |
O4' |
134.6 |
81.2 |
| H3' |
C3' |
C4' |
C5' |
21.2 |
322.7 |
| H3' |
C3' |
C4' |
H4' |
260.8 |
199.7 |
| HO3' |
O3' |
C3' |
C4' |
1.2 |
174.2 |
| HO3' |
O3' |
C3' |
H3' |
124.5 |
297.8 |
| C3' |
C4' |
H4' |
O4' |
241.8 |
245.9 |
| C3' |
C4' |
H4' |
C5' |
124.9 |
123.0 |
| H4' |
C4' |
C3' |
H3' |
260.8 |
199.7 |
| O4' |
C4' |
H4' |
C5' |
243.0 |
237.1 |
| H4' |
C4' |
C5' |
O5' |
216.9 |
308.0 |
| H4' |
C4' |
C5' |
H5' |
336.9 |
68.0 |
| H4' |
C4' |
C5' |
H5'A |
94.4 |
187.9 |
| C4' |
C5' |
H5' |
O5' |
245.7 |
240.0 |
| H5' |
C5' |
C4' |
H4' |
336.9 |
68.0 |
| C4' |
C5' |
H5' |
H5'A |
122.8 |
120.0 |
| O5' |
C5' |
H5' |
H5'A |
237.1 |
240.0 |
| H5' |
C5' |
O5' |
HO5' |
160.5 |
60.0 |
| C4' |
C5' |
H5'A |
O5' |
116.3 |
120.1 |
| H5'A |
C5' |
C4' |
H4' |
94.4 |
187.9 |
| C4' |
C5' |
H5'A |
H5' |
238.2 |
240.0 |
| O5' |
C5' |
H5'A |
H5' |
121.9 |
120.0 |
| H5'A |
C5' |
O5' |
HO5' |
43.0 |
300.1 |
| HO5' |
O5' |
C5' |
H5' |
160.5 |
60.0 |
| HO5' |
O5' |
C5' |
H5'A |
43.0 |
300.1 |