PDB Chemical Component DZ4
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 DZ4
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C2 |
N1 |
1.338 |
1.320 |
| N1 |
C6 |
1.358 |
1.329 |
| N3 |
C2 |
1.324 |
1.316 |
| C2 |
H2 |
1.080 |
1.080 |
| N3 |
C4 |
1.340 |
1.329 |
| N9 |
C4 |
1.335 |
1.373 |
| C4 |
C5 |
1.427 |
1.405 |
| C5 |
N7 |
1.354 |
1.356 |
| C5 |
C6 |
1.406 |
1.405 |
| C6 |
N6 |
1.383 |
1.385 |
| N6 |
HN6 |
1.000 |
0.970 |
| N6 |
HN6A |
1.000 |
0.970 |
| C8 |
N7 |
1.300 |
1.301 |
| N9 |
C8 |
1.385 |
1.363 |
| C8 |
H8 |
1.080 |
1.080 |
| C1' |
N9 |
1.440 |
1.465 |
| O5' |
PA |
1.527 |
1.610 |
| O1A |
PA |
1.276 |
1.481 |
| PA |
O2A |
1.397 |
1.610 |
| PA |
N3A |
1.593 |
1.683 |
| O1B |
PB |
1.274 |
1.480 |
| N3A |
PB |
1.663 |
1.683 |
| PB |
O2B |
1.276 |
1.611 |
| PB |
O3B |
1.534 |
1.610 |
| O1G |
PG |
1.325 |
1.480 |
| PG |
O3B |
1.530 |
1.611 |
| PG |
O2G |
1.334 |
1.610 |
| PG |
O3G |
1.360 |
1.610 |
| O4' |
C1' |
1.335 |
1.438 |
| C1' |
C2' |
1.539 |
1.541 |
| C1' |
H1' |
1.100 |
1.090 |
| C3' |
C2' |
1.505 |
1.548 |
| C2' |
H2' |
1.101 |
1.090 |
| C2' |
H2'A |
1.100 |
1.090 |
| O2A |
HO2A |
0.950 |
0.967 |
| O2B |
HO2B |
0.950 |
0.966 |
| O2G |
HO2G |
0.950 |
0.968 |
| C4' |
C3' |
1.534 |
1.550 |
| C3' |
O3' |
1.338 |
1.429 |
| C3' |
H3' |
1.100 |
1.090 |
| O3' |
HO3' |
0.950 |
0.967 |
| N3A |
HN3A |
1.000 |
1.010 |
| O3G |
HO3G |
0.950 |
0.967 |
| O4' |
C4' |
1.373 |
1.443 |
| C4' |
C5' |
1.532 |
1.530 |
| C4' |
H4' |
1.101 |
1.090 |
| C5' |
O5' |
1.396 |
1.429 |
| C5' |
H5' |
1.100 |
1.090 |
| C5' |
H5'A |
1.100 |
1.089 |
Bond Angles for DZ4
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N1 |
C6 |
121.2 |
121.2 |
| N1 |
C6 |
C5 |
119.2 |
118.5 |
| N1 |
C6 |
N6 |
120.1 |
120.8 |
| N3 |
C2 |
H2 |
119.1 |
118.8 |
| N3 |
C4 |
C5 |
120.6 |
119.1 |
| C4 |
C5 |
N7 |
107.0 |
107.1 |
| C4 |
C5 |
C6 |
116.6 |
118.2 |
| C6 |
C5 |
N7 |
136.4 |
134.7 |
| C5 |
C6 |
N6 |
120.6 |
120.7 |
| C6 |
N6 |
HN6 |
109.5 |
119.9 |
| C6 |
N6 |
HN6A |
109.5 |
120.0 |
| HN6 |
N6 |
HN6A |
109.5 |
120.1 |
| N9 |
C8 |
H8 |
124.9 |
125.0 |
| O1A |
PA |
O2A |
118.4 |
109.5 |
| O1A |
PA |
N3A |
109.4 |
109.5 |
| O2A |
PA |
N3A |
107.7 |
109.4 |
| PA |
O2A |
HO2A |
109.5 |
114.0 |
| PA |
N3A |
PB |
132.2 |
111.0 |
| PA |
N3A |
HN3A |
102.5 |
111.0 |
| O1B |
PB |
O2B |
111.7 |
109.4 |
| O1B |
PB |
O3B |
112.7 |
109.5 |
| N3A |
PB |
O3B |
110.5 |
109.5 |
| O2B |
PB |
O3B |
108.2 |
109.5 |
| PB |
O2B |
HO2B |
109.5 |
114.0 |
| PB |
O3B |
PG |
128.6 |
134.0 |
| O1G |
PG |
O3B |
109.1 |
109.5 |
| O1G |
PG |
O2G |
114.2 |
109.5 |
| O1G |
PG |
O3G |
108.4 |
109.5 |
| O2G |
PG |
O3B |
109.8 |
109.4 |
| O3B |
PG |
O3G |
107.5 |
109.5 |
| O2G |
PG |
O3G |
107.7 |
109.5 |
| PG |
O2G |
HO2G |
109.5 |
114.0 |
| PG |
O3G |
HO3G |
109.5 |
114.0 |
| O4' |
C1' |
H1' |
109.2 |
110.0 |
| C2' |
C1' |
H1' |
112.5 |
109.9 |
| C1' |
C2' |
H2' |
110.5 |
110.5 |
| C1' |
C2' |
H2'A |
110.4 |
110.4 |
| C3' |
C2' |
H2' |
110.5 |
110.5 |
| C3' |
C2' |
H2'A |
110.5 |
110.6 |
| H2' |
C2' |
H2'A |
108.4 |
110.5 |
| C4' |
C3' |
H3' |
115.1 |
111.0 |
| O3' |
C3' |
H3' |
91.6 |
110.8 |
| C3' |
O3' |
HO3' |
109.5 |
114.0 |
| O4' |
C4' |
C5' |
115.5 |
110.6 |
| O4' |
C4' |
H4' |
103.9 |
110.8 |
| C5' |
C4' |
H4' |
106.2 |
110.6 |
| C4' |
C5' |
O5' |
119.9 |
109.4 |
| C4' |
C5' |
H5' |
106.2 |
109.4 |
| C4' |
C5' |
H5'A |
106.1 |
109.5 |
| O5' |
C5' |
H5' |
106.1 |
109.5 |
| O5' |
C5' |
H5'A |
106.2 |
109.5 |
| H5' |
C5' |
H5'A |
112.5 |
109.6 |
Torsion Angles for DZ4
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N1 |
C6 |
C5 |
0.9 |
359.9 |
| C2 |
N1 |
C6 |
N6 |
180.2 |
180.0 |
| C4 |
C5 |
C6 |
N1 |
358.5 |
0.1 |
| N1 |
C6 |
C5 |
N7 |
180.4 |
180.0 |
| C5 |
C6 |
N1 |
N6 |
180.7 |
179.9 |
| N1 |
C6 |
N6 |
HN6 |
360.0 |
359.9 |
| N1 |
C6 |
N6 |
HN6A |
120.0 |
179.9 |
| N3 |
C2 |
N1 |
C6 |
359.5 |
0.1 |
| H2 |
C2 |
N1 |
C6 |
179.5 |
180.0 |
| C4 |
N3 |
C2 |
H2 |
180.8 |
180.0 |
| N3 |
C4 |
C5 |
N7 |
180.4 |
180.0 |
| N3 |
C4 |
C5 |
C6 |
1.8 |
360.0 |
| N1 |
C6 |
C5 |
C4 |
358.5 |
0.1 |
| C6 |
C5 |
C4 |
N7 |
181.4 |
180.0 |
| C4 |
C5 |
C6 |
N6 |
179.2 |
180.0 |
| C4 |
C5 |
N7 |
C6 |
181.8 |
180.0 |
| N7 |
C5 |
C6 |
N6 |
1.1 |
359.9 |
| N1 |
C6 |
C5 |
N6 |
179.3 |
180.1 |
| C4 |
C5 |
C6 |
N7 |
178.1 |
180.0 |
| C5 |
C6 |
N6 |
HN6 |
179.3 |
180.0 |
| C5 |
C6 |
N6 |
HN6A |
299.3 |
0.0 |
| N1 |
C6 |
N6 |
C5 |
180.7 |
179.9 |
| N6 |
C6 |
C5 |
N7 |
1.1 |
359.9 |
| HN6 |
N6 |
C6 |
HN6A |
240.0 |
180.0 |
| C6 |
N6 |
HN6 |
HN6A |
120.0 |
180.0 |
| C6 |
N6 |
HN6A |
HN6 |
240.0 |
180.0 |
| C1' |
N9 |
C8 |
H8 |
1.3 |
0.0 |
| O5' |
PA |
O2A |
HO2A |
121.1 |
300.0 |
| O5' |
PA |
N3A |
HN3A |
38.9 |
304.0 |
| O2A |
PA |
O1A |
N3A |
236.1 |
240.0 |
| O1A |
PA |
O2A |
HO2A |
360.0 |
180.0 |
| O1A |
PA |
N3A |
PB |
38.0 |
300.0 |
| O1A |
PA |
N3A |
HN3A |
158.0 |
64.0 |
| O1A |
PA |
O2A |
N3A |
124.8 |
120.0 |
| O2A |
PA |
N3A |
PB |
168.0 |
60.0 |
| O2A |
PA |
N3A |
HN3A |
288.0 |
184.0 |
| O1A |
PA |
N3A |
O2A |
230.0 |
240.0 |
| N3A |
PA |
O2A |
HO2A |
235.2 |
60.0 |
| PA |
N3A |
PB |
O3B |
237.4 |
180.0 |
| PA |
N3A |
PB |
O1B |
359.8 |
300.0 |
| N3A |
PB |
O1B |
O3B |
239.1 |
240.0 |
| O2B |
PB |
O1B |
O3B |
122.1 |
120.0 |
| O1B |
PB |
O2B |
HO2B |
360.0 |
180.0 |
| O1B |
PB |
O3B |
PG |
305.4 |
60.0 |
| PA |
N3A |
PB |
HN3A |
120.0 |
123.9 |
| O1B |
PB |
N3A |
O3B |
122.3 |
120.0 |
| O2B |
PB |
N3A |
O3B |
242.0 |
240.0 |
| N3A |
PB |
O2B |
HO2B |
244.0 |
60.0 |
| N3A |
PB |
O3B |
PG |
63.7 |
180.0 |
| PA |
N3A |
PB |
O2B |
119.4 |
60.0 |
| O1B |
PB |
O2B |
O3B |
235.4 |
240.0 |
| N3A |
PB |
O2B |
O3B |
119.5 |
120.0 |
| O2B |
PB |
O3B |
PG |
181.4 |
300.0 |
| O1B |
PB |
O3B |
O2B |
124.0 |
120.0 |
| O3B |
PB |
O2B |
HO2B |
124.6 |
299.9 |
| O1G |
PG |
O3B |
PB |
1.6 |
45.0 |
| O2G |
PG |
O3B |
PB |
127.4 |
165.0 |
| PB |
O3B |
PG |
O3G |
244.2 |
285.0 |
| PB |
O3B |
PG |
O1G |
1.6 |
45.0 |
| O2G |
PG |
O1G |
O3B |
236.8 |
240.1 |
| O3B |
PG |
O1G |
O3G |
243.2 |
240.0 |
| O2G |
PG |
O1G |
O3G |
120.0 |
120.1 |
| O1G |
PG |
O2G |
HO2G |
0.0 |
299.9 |
| O1G |
PG |
O3G |
HO3G |
0.0 |
180.0 |
| O1G |
PG |
O3B |
O2G |
234.2 |
240.0 |
| O1G |
PG |
O3B |
O3G |
117.4 |
120.0 |
| O2G |
PG |
O3B |
O3G |
243.2 |
240.0 |
| O3B |
PG |
O2G |
HO2G |
237.2 |
180.0 |
| O3B |
PG |
O3G |
HO3G |
117.8 |
300.0 |
| PB |
O3B |
PG |
O2G |
127.4 |
165.0 |
| O1G |
PG |
O2G |
O3B |
122.8 |
120.0 |
| O1G |
PG |
O2G |
O3G |
239.6 |
239.9 |
| O3B |
PG |
O2G |
O3G |
116.7 |
120.0 |
| O2G |
PG |
O3G |
HO3G |
236.0 |
60.0 |
| O1G |
PG |
O3G |
O3B |
242.2 |
240.0 |
| O1G |
PG |
O3G |
O2G |
124.0 |
120.0 |
| O2G |
PG |
O3G |
O3B |
118.2 |
120.0 |
| O3G |
PG |
O2G |
HO2G |
120.4 |
60.0 |
| C2' |
C1' |
O4' |
H1' |
238.0 |
240.5 |
| O4' |
C1' |
C2' |
H2' |
103.2 |
120.7 |
| O4' |
C1' |
C2' |
H2'A |
223.2 |
243.2 |
| O4' |
C1' |
C2' |
H1' |
119.9 |
119.5 |
| C3' |
C2' |
C1' |
H2' |
240.0 |
241.3 |
| C3' |
C2' |
C1' |
H2'A |
120.0 |
118.8 |
| H2' |
C2' |
C1' |
H2'A |
240.0 |
237.5 |
| H1' |
C1' |
C2' |
H2' |
343.3 |
1.1 |
| H1' |
C1' |
C2' |
H2'A |
103.3 |
123.7 |
| C3' |
C2' |
C1' |
H1' |
223.3 |
242.5 |
| C1' |
C2' |
C3' |
H2' |
120.0 |
118.7 |
| C1' |
C2' |
C3' |
H2'A |
240.0 |
241.3 |
| H2' |
C2' |
C3' |
H2'A |
120.0 |
122.7 |
| H2' |
C2' |
C1' |
H1' |
343.3 |
1.1 |
| C1' |
C2' |
H2' |
H2'A |
121.2 |
122.5 |
| C3' |
C2' |
H2' |
H2'A |
238.8 |
237.2 |
| H2'A |
C2' |
C1' |
H1' |
103.3 |
123.7 |
| C1' |
C2' |
H2'A |
H2' |
238.8 |
237.5 |
| C3' |
C2' |
H2'A |
H2' |
121.2 |
122.7 |
| HO2A |
O2A |
PA |
N3A |
235.2 |
60.0 |
| HO2B |
O2B |
PB |
O3B |
124.6 |
299.9 |
| HO2G |
O2G |
PG |
O3B |
237.2 |
180.0 |
| HO2G |
O2G |
PG |
O3G |
120.4 |
60.0 |
| C4' |
C3' |
C2' |
H2' |
258.3 |
262.3 |
| C4' |
C3' |
C2' |
H2'A |
138.3 |
139.6 |
| O3' |
C3' |
C4' |
H3' |
106.7 |
123.6 |
| C4' |
C3' |
O3' |
HO3' |
302.1 |
174.2 |
| O3' |
C3' |
C2' |
H2' |
29.2 |
20.4 |
| O3' |
C3' |
C2' |
H2'A |
269.2 |
257.8 |
| C4' |
C3' |
O3' |
H3' |
240.2 |
236.3 |
| H3' |
C3' |
C2' |
H2' |
135.6 |
144.0 |
| H3' |
C3' |
C2' |
H2'A |
15.6 |
21.3 |
| H3' |
C3' |
O3' |
HO3' |
61.9 |
297.8 |
| HO3' |
O3' |
C3' |
H3' |
61.9 |
297.8 |
| PA |
N3A |
HN3A |
PB |
221.1 |
236.0 |
| HN3A |
N3A |
PB |
O3B |
117.4 |
56.1 |
| C4' |
O4' |
C1' |
H1' |
128.8 |
93.0 |
| O4' |
C4' |
C3' |
H3' |
105.9 |
81.2 |
| C5' |
C4' |
O4' |
H4' |
244.1 |
237.0 |
| O4' |
C4' |
C5' |
O5' |
310.6 |
71.0 |
| O4' |
C4' |
C5' |
H5' |
70.7 |
190.9 |
| O4' |
C4' |
C5' |
H5'A |
190.6 |
311.0 |
| C5' |
C4' |
C3' |
H3' |
337.7 |
322.7 |
| O4' |
C4' |
C5' |
H4' |
114.6 |
123.1 |
| O5' |
C5' |
C4' |
H5' |
240.0 |
240.1 |
| O5' |
C5' |
C4' |
H5'A |
120.0 |
120.0 |
| H5' |
C5' |
C4' |
H5'A |
240.0 |
239.9 |
| H4' |
C4' |
C3' |
H3' |
221.0 |
199.8 |
| O4' |
C4' |
H4' |
C5' |
237.7 |
237.0 |
| H4' |
C4' |
C5' |
O5' |
196.1 |
307.9 |
| H4' |
C4' |
C5' |
H5' |
316.1 |
67.8 |
| H4' |
C4' |
C5' |
H5'A |
76.0 |
187.9 |
| O5' |
C5' |
C4' |
H4' |
196.1 |
307.9 |
| C4' |
C5' |
O5' |
H5' |
120.0 |
119.9 |
| C4' |
C5' |
O5' |
H5'A |
240.0 |
240.0 |
| H5' |
C5' |
O5' |
H5'A |
120.0 |
120.1 |
| H5' |
C5' |
C4' |
H4' |
316.1 |
67.8 |
| C4' |
C5' |
H5' |
O5' |
231.4 |
240.1 |
| C4' |
C5' |
H5' |
H5'A |
115.7 |
120.0 |
| O5' |
C5' |
H5' |
H5'A |
244.3 |
239.9 |
| H5'A |
C5' |
C4' |
H4' |
76.0 |
187.9 |
| C4' |
C5' |
H5'A |
O5' |
128.6 |
119.9 |
| C4' |
C5' |
H5'A |
H5' |
244.3 |
240.0 |
| O5' |
C5' |
H5'A |
H5' |
115.7 |
120.1 |