PDB Chemical Component A9Z
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 A9Z
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
O3' |
C3' |
1.419 |
1.429 |
C3' |
C4' |
1.535 |
1.541 |
C3' |
C2' |
1.552 |
1.549 |
C4' |
C5' |
1.510 |
1.530 |
C4' |
O4' |
1.466 |
1.438 |
C5' |
O5' |
1.406 |
1.429 |
C6T |
C4T |
1.551 |
1.506 |
C6T |
C7T |
1.499 |
1.530 |
C4T |
C5T |
1.445 |
1.353 |
C4T |
N3T |
1.368 |
1.338 |
C5T |
N1T |
1.355 |
1.353 |
OP1 |
P |
1.569 |
1.480 |
N3T |
N2T |
1.374 |
1.286 |
N1T |
C2' |
1.378 |
1.465 |
N1T |
N2T |
1.413 |
1.287 |
C2' |
C1' |
1.551 |
1.549 |
O4' |
C1' |
1.469 |
1.444 |
O5' |
P |
1.754 |
1.610 |
C1' |
N9 |
1.431 |
1.466 |
P |
OP3 |
1.726 |
1.610 |
P |
OP2 |
1.500 |
1.610 |
N3 |
C4 |
1.341 |
1.329 |
N3 |
C2 |
1.360 |
1.316 |
N9 |
C4 |
1.355 |
1.372 |
N9 |
C8 |
1.371 |
1.363 |
C4 |
C5 |
1.454 |
1.405 |
C2 |
N1 |
1.325 |
1.321 |
C8 |
N7 |
1.338 |
1.301 |
C5 |
N7 |
1.397 |
1.355 |
C5 |
C6 |
1.456 |
1.405 |
N1 |
C6 |
1.408 |
1.329 |
C6 |
N6 |
1.317 |
1.383 |
OP2 |
H1 |
0.950 |
0.967 |
C5' |
H2 |
1.100 |
1.090 |
C5' |
H3 |
1.100 |
1.091 |
C4' |
H4 |
1.100 |
1.090 |
C3' |
H5 |
1.100 |
1.090 |
O3' |
H6 |
0.950 |
0.968 |
C2' |
H7 |
1.100 |
1.090 |
C5T |
H8 |
1.080 |
1.080 |
C6T |
H9 |
1.100 |
1.089 |
C6T |
H10 |
1.100 |
1.091 |
C7T |
H11 |
1.100 |
1.091 |
C7T |
H12 |
1.100 |
1.091 |
C7T |
H13 |
1.100 |
1.090 |
C1' |
H14 |
1.101 |
1.090 |
C8 |
H15 |
1.080 |
1.080 |
C2 |
H16 |
1.081 |
1.079 |
N6 |
H17 |
1.000 |
0.971 |
N6 |
H18 |
1.000 |
0.970 |
OP3 |
H19 |
0.950 |
0.967 |
Bond Angles for A9Z
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
O3' |
C3' |
C2' |
113.1 |
110.5 |
O3' |
C3' |
H5 |
112.5 |
110.5 |
C3' |
C4' |
O4' |
106.0 |
107.3 |
C3' |
C4' |
H4 |
107.4 |
110.0 |
C3' |
C2' |
C1' |
97.8 |
102.1 |
C2' |
C3' |
H5 |
110.4 |
110.5 |
C3' |
C2' |
H7 |
109.9 |
110.9 |
C4' |
C5' |
H2 |
111.2 |
109.5 |
C4' |
C5' |
H3 |
111.2 |
109.4 |
C4' |
O4' |
C1' |
105.4 |
107.0 |
O4' |
C4' |
H4 |
108.3 |
109.9 |
C6T |
C4T |
N3T |
126.0 |
126.8 |
C7T |
C6T |
H9 |
112.2 |
109.5 |
C7T |
C6T |
H10 |
112.2 |
109.4 |
C6T |
C7T |
H11 |
109.5 |
109.4 |
C6T |
C7T |
H12 |
109.4 |
109.5 |
C6T |
C7T |
H13 |
109.5 |
109.5 |
C4T |
C5T |
H8 |
125.9 |
126.9 |
C4T |
N3T |
N2T |
112.5 |
108.9 |
C5T |
N1T |
N2T |
109.4 |
108.2 |
OP1 |
P |
OP3 |
101.0 |
109.5 |
OP1 |
P |
OP2 |
109.7 |
109.5 |
N1T |
N2T |
N3T |
105.2 |
110.2 |
N1T |
C2' |
C1' |
112.0 |
110.9 |
N1T |
C2' |
H7 |
112.5 |
110.8 |
C2' |
C1' |
N9 |
109.3 |
110.6 |
C1' |
C2' |
H7 |
109.9 |
110.9 |
C2' |
C1' |
H14 |
111.5 |
110.6 |
O4' |
C1' |
N9 |
105.8 |
110.6 |
O4' |
C1' |
H14 |
112.7 |
110.7 |
O5' |
P |
OP3 |
96.0 |
109.5 |
C1' |
N9 |
C4 |
127.2 |
126.3 |
C1' |
N9 |
C8 |
124.4 |
126.3 |
N9 |
C1' |
H14 |
113.4 |
110.5 |
OP2 |
P |
OP3 |
121.3 |
109.4 |
P |
OP3 |
H19 |
109.5 |
114.0 |
P |
OP2 |
H1 |
109.5 |
114.0 |
N3 |
C2 |
N1 |
126.8 |
122.4 |
N3 |
C2 |
H16 |
116.6 |
118.8 |
C4 |
N9 |
C8 |
108.3 |
107.5 |
N9 |
C4 |
C5 |
107.2 |
106.0 |
N9 |
C8 |
N7 |
110.6 |
110.0 |
N9 |
C8 |
H15 |
124.7 |
125.0 |
C4 |
C5 |
N7 |
105.4 |
107.1 |
C4 |
C5 |
C6 |
116.5 |
118.2 |
C2 |
N1 |
C6 |
118.5 |
121.2 |
N1 |
C2 |
H16 |
116.6 |
118.8 |
N7 |
C5 |
C6 |
138.1 |
134.7 |
C5 |
C6 |
N1 |
118.6 |
118.4 |
C5 |
C6 |
N6 |
118.8 |
120.8 |
N1 |
C6 |
N6 |
122.5 |
120.8 |
C6 |
N6 |
H17 |
109.5 |
120.0 |
C6 |
N6 |
H18 |
109.5 |
120.0 |
H2 |
C5' |
H3 |
109.5 |
109.5 |
H9 |
C6T |
H10 |
109.5 |
109.5 |
H11 |
C7T |
H12 |
109.4 |
109.5 |
H11 |
C7T |
H13 |
109.5 |
109.5 |
H12 |
C7T |
H13 |
109.5 |
109.4 |
H17 |
N6 |
H18 |
109.5 |
120.0 |
Torsion Angles for A9Z
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
O3' |
C3' |
C4' |
O4' |
249.4 |
239.3 |
O3' |
C3' |
C4' |
H4 |
5.0 |
358.8 |
O3' |
C3' |
C2' |
C1' |
81.1 |
97.8 |
C2' |
C3' |
O3' |
H5 |
125.9 |
122.6 |
O3' |
C3' |
C2' |
H7 |
195.6 |
216.0 |
C3' |
C4' |
C5' |
H2 |
194.4 |
64.2 |
C3' |
C4' |
C5' |
H3 |
316.7 |
304.3 |
C3' |
C4' |
O4' |
C1' |
20.5 |
26.5 |
O4' |
C4' |
C3' |
H4 |
244.4 |
240.5 |
O3' |
C3' |
C2' |
H5 |
233.0 |
237.4 |
C2' |
C3' |
C4' |
O4' |
8.8 |
358.0 |
C2' |
C3' |
C4' |
H4 |
124.3 |
117.4 |
N1T |
C2' |
C3' |
C1' |
241.7 |
241.8 |
N1T |
C2' |
C3' |
H7 |
127.2 |
123.5 |
C3' |
C2' |
C1' |
N9 |
157.7 |
155.5 |
C1' |
C2' |
C3' |
H7 |
245.5 |
241.8 |
C3' |
C2' |
C1' |
H14 |
283.8 |
278.4 |
H2 |
C5' |
C4' |
H3 |
237.7 |
120.0 |
C3' |
C4' |
O4' |
H4 |
115.0 |
119.6 |
O4' |
C4' |
C5' |
H2 |
73.2 |
306.4 |
O4' |
C4' |
C5' |
H3 |
195.5 |
186.5 |
C4' |
O4' |
C1' |
N9 |
202.8 |
201.4 |
C4' |
O4' |
C1' |
H14 |
78.3 |
78.5 |
C5' |
O5' |
P |
OP3 |
138.3 |
185.0 |
C6T |
C4T |
C5T |
H8 |
2.9 |
0.1 |
C6T |
C4T |
N3T |
N2T |
177.4 |
179.7 |
C7T |
C6T |
C4T |
N3T |
285.1 |
305.0 |
H9 |
C6T |
C7T |
H10 |
123.8 |
120.0 |
H11 |
C7T |
C6T |
H12 |
240.0 |
240.0 |
H11 |
C7T |
C6T |
H13 |
120.0 |
120.0 |
H12 |
C7T |
C6T |
H13 |
240.0 |
240.0 |
C4T |
C5T |
N1T |
N2T |
359.3 |
0.3 |
N3T |
C4T |
C5T |
H8 |
180.8 |
180.0 |
N1T |
N2T |
N3T |
C4T |
0.2 |
0.4 |
C5T |
N1T |
N2T |
N3T |
0.3 |
359.6 |
C5T |
N1T |
C2' |
C1' |
333.9 |
331.5 |
C5T |
N1T |
C2' |
H7 |
209.5 |
207.8 |
O5' |
P |
OP1 |
OP3 |
99.2 |
240.0 |
OP2 |
P |
OP1 |
OP3 |
230.8 |
119.9 |
OP1 |
P |
OP3 |
H19 |
360.0 |
60.0 |
OP1 |
P |
OP2 |
H1 |
0.0 |
180.0 |
C3' |
C2' |
N1T |
C1' |
109.8 |
112.7 |
N1T |
C2' |
C3' |
H5 |
89.8 |
102.2 |
C3' |
C2' |
N1T |
H7 |
234.2 |
236.4 |
N1T |
C2' |
C1' |
N9 |
277.3 |
273.7 |
C1' |
C2' |
N1T |
H7 |
124.4 |
123.7 |
N1T |
C2' |
C1' |
H14 |
43.4 |
36.6 |
C4T |
N3T |
N2T |
N1T |
0.2 |
0.4 |
N2T |
N1T |
C2' |
C1' |
159.2 |
151.2 |
N2T |
N1T |
C2' |
H7 |
34.8 |
27.5 |
C1' |
C2' |
C3' |
H5 |
208.1 |
220.4 |
C3' |
C2' |
C1' |
H7 |
114.5 |
118.2 |
C4' |
O4' |
C1' |
C2' |
317.7 |
319.9 |
N1T |
C2' |
C1' |
H7 |
234.1 |
236.4 |
O4' |
C1' |
C2' |
N9 |
247.6 |
241.5 |
O4' |
C1' |
C2' |
H14 |
121.5 |
118.7 |
C2' |
C1' |
N9 |
C4 |
110.8 |
85.0 |
C2' |
C1' |
N9 |
C8 |
285.9 |
264.7 |
N9 |
C1' |
C2' |
H14 |
233.9 |
237.1 |
C1' |
O4' |
C4' |
H4 |
265.5 |
267.0 |
C2' |
C1' |
O4' |
N9 |
114.9 |
118.5 |
O4' |
C1' |
C2' |
H7 |
290.7 |
278.9 |
C2' |
C1' |
O4' |
H14 |
239.4 |
241.4 |
O4' |
C1' |
N9 |
C4 |
221.8 |
199.1 |
O4' |
C1' |
N9 |
C8 |
36.8 |
18.8 |
N9 |
C1' |
O4' |
H14 |
124.5 |
122.9 |
OP1 |
P |
O5' |
OP3 |
257.0 |
120.0 |
OP2 |
P |
O5' |
OP3 |
132.7 |
240.0 |
O5' |
P |
OP3 |
H19 |
254.3 |
180.1 |
O5' |
P |
OP2 |
H1 |
121.7 |
60.0 |
N9 |
C1' |
C2' |
H7 |
43.2 |
37.3 |
C2' |
C1' |
N9 |
H14 |
125.0 |
122.9 |
O4' |
C1' |
N9 |
H14 |
235.9 |
237.0 |
C4 |
N9 |
C1' |
C8 |
185.0 |
180.3 |
C1' |
N9 |
C4 |
C5 |
177.9 |
180.0 |
C1' |
N9 |
C8 |
N7 |
182.3 |
179.8 |
C1' |
N9 |
C8 |
H15 |
2.3 |
359.9 |
OP1 |
P |
OP3 |
OP2 |
238.6 |
120.0 |
OP3 |
P |
OP2 |
H1 |
242.9 |
300.0 |
OP1 |
P |
OP2 |
OP3 |
117.1 |
240.0 |
O5' |
P |
OP2 |
OP3 |
238.8 |
120.0 |
OP2 |
P |
OP3 |
H19 |
121.3 |
300.0 |
N3 |
C4 |
C5 |
C6 |
358.8 |
0.1 |
N3 |
C2 |
N1 |
C6 |
2.0 |
0.0 |
N1 |
C2 |
N3 |
H16 |
180.0 |
180.0 |
C1' |
N9 |
C4 |
C8 |
175.7 |
179.7 |
C4 |
N9 |
C1' |
H14 |
345.8 |
322.1 |
C4 |
N9 |
C8 |
N7 |
358.1 |
359.6 |
C4 |
N9 |
C8 |
H15 |
178.1 |
179.7 |
N9 |
C4 |
C5 |
N7 |
358.1 |
359.9 |
N9 |
C4 |
C5 |
C6 |
179.4 |
180.0 |
C1' |
N9 |
C8 |
C4 |
184.2 |
180.3 |
C8 |
N9 |
C1' |
H14 |
160.9 |
141.8 |
C8 |
N9 |
C4 |
C5 |
2.3 |
0.3 |
C5 |
C4 |
N9 |
C8 |
2.3 |
0.3 |
N7 |
C5 |
C4 |
C6 |
178.7 |
179.9 |
C4 |
C5 |
C6 |
N1 |
358.6 |
359.9 |
C4 |
C5 |
C6 |
N6 |
179.7 |
180.0 |
N3 |
C2 |
N1 |
H16 |
180.0 |
180.0 |
C5 |
C6 |
N1 |
C2 |
1.1 |
0.1 |
C2 |
N1 |
C6 |
N6 |
179.9 |
180.0 |
N9 |
C8 |
N7 |
H15 |
180.0 |
180.1 |
C8 |
N7 |
C5 |
C6 |
179.1 |
179.7 |
N9 |
C8 |
N7 |
C5 |
0.6 |
0.4 |
C4 |
C5 |
N7 |
C6 |
181.7 |
180.1 |
N7 |
C5 |
C6 |
N1 |
180.4 |
180.0 |
N7 |
C5 |
C6 |
N6 |
1.5 |
0.1 |
C4 |
C5 |
C6 |
N7 |
178.2 |
179.9 |
C2 |
N1 |
C6 |
C5 |
1.1 |
0.1 |
N1 |
C6 |
C5 |
N6 |
178.8 |
179.9 |
C5 |
C6 |
N6 |
H17 |
178.8 |
359.8 |
C5 |
C6 |
N6 |
H18 |
298.8 |
180.0 |
C6 |
N1 |
C2 |
H16 |
182.0 |
180.0 |
C5 |
C6 |
N1 |
N6 |
181.2 |
180.1 |
N1 |
C6 |
N6 |
H17 |
360.0 |
179.9 |
N1 |
C6 |
N6 |
H18 |
120.0 |
0.1 |
C5 |
C6 |
N6 |
N1 |
178.8 |
179.9 |
H17 |
N6 |
C6 |
H18 |
240.0 |
179.9 |
H1 |
OP2 |
P |
OP3 |
242.9 |
300.0 |
C4' |
C5' |
H2 |
H3 |
123.3 |
240.1 |
C4' |
C5' |
H3 |
H2 |
236.7 |
120.0 |
C3' |
C4' |
H4 |
O4' |
245.9 |
242.1 |
H4 |
C4' |
C5' |
H2 |
314.9 |
185.4 |
H4 |
C4' |
C5' |
H3 |
77.2 |
65.5 |
H4 |
C4' |
O4' |
C1' |
265.5 |
267.0 |
O3' |
C3' |
H5 |
C2' |
127.3 |
122.6 |
H5 |
C3' |
C4' |
O4' |
128.3 |
116.7 |
H5 |
C3' |
C4' |
H4 |
243.9 |
236.1 |
H5 |
C3' |
C2' |
C1' |
208.1 |
220.4 |
H5 |
C3' |
C2' |
H7 |
322.6 |
338.7 |
H6 |
O3' |
C3' |
C2' |
65.8 |
183.8 |
H6 |
O3' |
C3' |
H5 |
299.8 |
61.2 |
C3' |
C2' |
H7 |
C1' |
253.4 |
247.3 |
H7 |
C2' |
C3' |
H5 |
322.6 |
338.7 |
N1T |
C2' |
H7 |
C1' |
125.6 |
123.7 |
H7 |
C2' |
C1' |
N9 |
43.2 |
37.3 |
H7 |
C2' |
C1' |
H14 |
169.3 |
160.2 |
H8 |
C5T |
N1T |
N2T |
179.3 |
180.2 |
H9 |
C6T |
C4T |
N3T |
43.2 |
65.1 |
C7T |
C6T |
H9 |
H10 |
234.7 |
240.0 |
H9 |
C6T |
C7T |
H11 |
61.9 |
300.0 |
H9 |
C6T |
C7T |
H12 |
181.9 |
60.0 |
H9 |
C6T |
C7T |
H13 |
301.9 |
180.0 |
H10 |
C6T |
C4T |
N3T |
167.0 |
185.1 |
C7T |
C6T |
H10 |
H9 |
125.3 |
120.0 |
H10 |
C6T |
C7T |
H11 |
298.2 |
180.0 |
H10 |
C6T |
C7T |
H12 |
58.1 |
300.0 |
H10 |
C6T |
C7T |
H13 |
178.1 |
60.0 |
H11 |
C7T |
C6T |
H9 |
61.9 |
300.0 |
H11 |
C7T |
C6T |
H10 |
298.2 |
180.0 |
C6T |
C7T |
H11 |
H12 |
120.0 |
120.0 |
C6T |
C7T |
H11 |
H13 |
240.0 |
240.0 |
H12 |
C7T |
H11 |
H13 |
120.0 |
120.0 |
H12 |
C7T |
C6T |
H9 |
181.9 |
60.0 |
H12 |
C7T |
C6T |
H10 |
58.1 |
300.0 |
C6T |
C7T |
H12 |
H11 |
240.0 |
240.0 |
C6T |
C7T |
H12 |
H13 |
120.0 |
120.0 |
H11 |
C7T |
H12 |
H13 |
240.0 |
240.0 |
H13 |
C7T |
C6T |
H9 |
301.9 |
180.0 |
H13 |
C7T |
C6T |
H10 |
178.1 |
60.0 |
C6T |
C7T |
H13 |
H11 |
120.1 |
120.0 |
C6T |
C7T |
H13 |
H12 |
240.0 |
240.0 |
H11 |
C7T |
H13 |
H12 |
120.0 |
120.0 |
C2' |
C1' |
H14 |
N9 |
236.2 |
237.1 |
H14 |
C1' |
C2' |
H7 |
169.3 |
160.2 |
O4' |
C1' |
H14 |
N9 |
120.2 |
122.9 |
H14 |
C1' |
N9 |
C4 |
345.8 |
322.1 |
H14 |
C1' |
N9 |
C8 |
160.9 |
141.8 |
N9 |
C8 |
H15 |
N7 |
180.0 |
179.9 |
N3 |
C2 |
H16 |
N1 |
180.0 |
180.0 |
H16 |
C2 |
N1 |
C6 |
182.0 |
180.0 |
C6 |
N6 |
H17 |
H18 |
120.0 |
180.1 |
C6 |
N6 |
H18 |
H17 |
239.9 |
179.9 |