PDB Chemical Component DZ
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 DZ
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| OP2 |
P |
1.485 |
1.479 |
| ON1 |
N |
1.225 |
1.218 |
| OP1 |
P |
1.485 |
1.610 |
| P |
O5' |
1.597 |
1.610 |
| O5' |
C5' |
1.419 |
1.429 |
| N |
ON2 |
1.228 |
1.218 |
| N |
C5 |
1.488 |
1.480 |
| C3' |
C2' |
1.530 |
1.548 |
| C3' |
O3' |
1.426 |
1.429 |
| C3' |
C4' |
1.538 |
1.541 |
| C2' |
C1' |
1.524 |
1.550 |
| C5' |
C4' |
1.534 |
1.530 |
| C6 |
C5 |
1.412 |
1.394 |
| C6 |
C1 |
1.407 |
1.380 |
| C5 |
C4 |
1.407 |
1.379 |
| C4' |
O4' |
1.423 |
1.437 |
| C1' |
C1 |
1.515 |
1.507 |
| C1' |
O4' |
1.411 |
1.444 |
| C1 |
C2 |
1.411 |
1.399 |
| C4 |
N4 |
1.321 |
1.376 |
| C4 |
N3 |
1.322 |
1.363 |
| N3 |
C2 |
1.346 |
1.345 |
| C2 |
O2 |
1.231 |
1.222 |
| P |
OP3 |
1.617 |
1.610 |
| OP1 |
H1 |
0.950 |
0.968 |
| C5' |
H5'' |
1.099 |
1.090 |
| C5' |
H5' |
1.100 |
1.090 |
| C4' |
H4' |
1.100 |
1.090 |
| C1' |
H1' |
1.100 |
1.090 |
| N3 |
H3 |
1.000 |
0.970 |
| C6 |
H6 |
1.080 |
1.080 |
| N4 |
H42 |
1.000 |
0.969 |
| N4 |
H41 |
1.001 |
0.970 |
| C2' |
H2'' |
1.100 |
1.090 |
| C2' |
H2' |
1.100 |
1.089 |
| C3' |
H3' |
1.100 |
1.090 |
| O3' |
H2 |
0.950 |
0.967 |
| OP3 |
H4 |
0.950 |
0.967 |
Bond Angles for DZ
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP2 |
P |
O5' |
108.2 |
109.4 |
| OP2 |
P |
OP3 |
109.5 |
109.5 |
| ON1 |
N |
ON2 |
122.6 |
120.0 |
| OP1 |
P |
O5' |
108.2 |
109.4 |
| OP1 |
P |
OP3 |
108.2 |
109.5 |
| P |
O5' |
C5' |
119.4 |
123.0 |
| O5' |
P |
OP3 |
102.6 |
109.5 |
| O5' |
C5' |
C4' |
112.0 |
109.5 |
| O5' |
C5' |
H5'' |
108.8 |
109.5 |
| O5' |
C5' |
H5' |
108.8 |
109.5 |
| C3' |
C2' |
H2'' |
110.6 |
110.9 |
| C3' |
C2' |
H2' |
110.6 |
110.9 |
| O3' |
C3' |
H3' |
111.3 |
110.4 |
| C3' |
O3' |
H2 |
109.5 |
114.0 |
| C3' |
C4' |
H4' |
107.4 |
110.0 |
| C2' |
C1' |
H1' |
109.1 |
110.8 |
| C5' |
C4' |
O4' |
111.3 |
109.9 |
| C4' |
C5' |
H5'' |
108.8 |
109.5 |
| C4' |
C5' |
H5' |
108.8 |
109.5 |
| C5' |
C4' |
H4' |
107.4 |
109.9 |
| C5 |
C4 |
N4 |
122.4 |
119.8 |
| O4' |
C4' |
H4' |
108.8 |
109.9 |
| C1' |
C1 |
C2 |
120.1 |
120.3 |
| C1 |
C1' |
H1' |
109.2 |
110.6 |
| C1 |
C2 |
O2 |
124.1 |
119.8 |
| C4 |
N4 |
H42 |
109.5 |
120.0 |
| C4 |
N4 |
H41 |
109.4 |
120.0 |
| C4 |
N3 |
H3 |
117.6 |
119.5 |
| P |
OP3 |
H4 |
109.5 |
114.0 |
| H5'' |
C5' |
H5' |
109.5 |
109.4 |
| H42 |
N4 |
H41 |
109.4 |
120.0 |
| H2'' |
C2' |
H2' |
109.5 |
110.8 |
Torsion Angles for DZ
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP1 |
P |
OP2 |
O5' |
123.8 |
120.0 |
| OP1 |
P |
OP2 |
OP3 |
235.0 |
239.9 |
| OP2 |
P |
O5' |
C5' |
182.5 |
55.0 |
| O5' |
P |
OP2 |
OP3 |
111.2 |
120.0 |
| OP2 |
P |
OP3 |
H4 |
0.0 |
300.0 |
| OP2 |
P |
OP1 |
O5' |
236.2 |
240.0 |
| OP2 |
P |
OP1 |
OP3 |
125.7 |
120.0 |
| OP1 |
P |
O5' |
C5' |
52.5 |
295.0 |
| O5' |
P |
OP1 |
OP3 |
249.5 |
240.0 |
| OP1 |
P |
OP3 |
H4 |
131.0 |
60.0 |
| OP2 |
P |
O5' |
OP3 |
244.2 |
240.0 |
| OP1 |
P |
O5' |
OP3 |
114.2 |
120.0 |
| P |
O5' |
C5' |
C4' |
162.5 |
180.0 |
| P |
O5' |
C5' |
H5'' |
282.9 |
300.0 |
| P |
O5' |
C5' |
H5' |
42.1 |
60.0 |
| O5' |
P |
OP3 |
H4 |
245.2 |
180.0 |
| C5' |
O5' |
P |
OP3 |
298.3 |
175.0 |
| O5' |
C5' |
C4' |
O4' |
305.6 |
66.5 |
| C4' |
C5' |
O5' |
H5'' |
239.6 |
240.0 |
| C4' |
C5' |
O5' |
H5' |
120.4 |
120.0 |
| O5' |
C5' |
C4' |
H4' |
186.5 |
305.5 |
| H5'' |
C5' |
O5' |
H5' |
240.8 |
240.1 |
| N |
C5 |
C4 |
N4 |
359.6 |
360.0 |
| C2' |
C3' |
C4' |
H4' |
110.2 |
117.4 |
| C3' |
C2' |
C1' |
H1' |
271.6 |
278.5 |
| H2'' |
C2' |
C3' |
H2' |
238.6 |
123.6 |
| O3' |
C3' |
C2' |
H2'' |
223.8 |
339.6 |
| O3' |
C3' |
C2' |
H2' |
345.2 |
216.0 |
| O3' |
C3' |
C4' |
H4' |
349.2 |
358.7 |
| C3' |
C4' |
C5' |
H5'' |
307.6 |
64.2 |
| C3' |
C4' |
C5' |
H5' |
188.4 |
304.3 |
| C5' |
C4' |
C3' |
H4' |
118.6 |
121.1 |
| O4' |
C4' |
C3' |
H4' |
242.6 |
240.6 |
| C1 |
C1' |
C2' |
H1' |
237.0 |
237.0 |
| O5' |
C5' |
C4' |
H5'' |
120.4 |
120.1 |
| O5' |
C5' |
C4' |
H5' |
239.6 |
240.0 |
| C3' |
C4' |
C5' |
H4' |
241.5 |
238.8 |
| O4' |
C4' |
C5' |
H4' |
119.0 |
121.0 |
| H5'' |
C5' |
C4' |
H5' |
119.2 |
119.9 |
| C6 |
C5 |
C4 |
N4 |
180.0 |
179.6 |
| C6 |
C1 |
C1' |
H1' |
168.7 |
356.1 |
| C5 |
C4 |
N4 |
H42 |
180.0 |
174.4 |
| C5 |
C4 |
N4 |
H41 |
300.0 |
354.5 |
| C5 |
C4 |
N3 |
H3 |
180.7 |
180.0 |
| C3' |
C4' |
O4' |
H4' |
116.4 |
119.5 |
| O4' |
C4' |
C5' |
H5'' |
185.2 |
306.4 |
| O4' |
C4' |
C5' |
H5' |
65.9 |
186.5 |
| C5' |
C4' |
O4' |
H4' |
241.8 |
239.0 |
| C2' |
C1' |
C1 |
H1' |
122.9 |
123.1 |
| C1' |
C1 |
C2 |
O2 |
357.9 |
359.9 |
| C1' |
O4' |
C4' |
H4' |
270.8 |
267.0 |
| C2 |
C1 |
C1' |
H1' |
349.4 |
176.4 |
| N4 |
C4 |
N3 |
H3 |
0.8 |
0.1 |
| H42 |
N4 |
C4 |
H41 |
240.0 |
179.9 |
| OP2 |
P |
OP3 |
O5' |
114.8 |
120.0 |
| OP1 |
P |
OP3 |
O5' |
245.8 |
240.0 |
| OP3 |
P |
O5' |
C5' |
298.3 |
175.0 |
| H1 |
OP1 |
P |
O5' |
123.8 |
300.0 |
| H1 |
OP1 |
P |
OP3 |
234.3 |
59.9 |
| O5' |
C5' |
H5'' |
C4' |
237.7 |
239.9 |
| O5' |
C5' |
H5'' |
H5' |
118.8 |
120.0 |
| H5'' |
C5' |
C4' |
O4' |
185.2 |
306.4 |
| C4' |
C5' |
H5'' |
H5' |
241.1 |
240.1 |
| H5'' |
C5' |
C4' |
H4' |
66.1 |
185.4 |
| O5' |
C5' |
H5' |
C4' |
122.3 |
120.0 |
| O5' |
C5' |
H5' |
H5'' |
241.2 |
240.0 |
| H5' |
C5' |
C4' |
O4' |
65.9 |
186.5 |
| C4' |
C5' |
H5' |
H5'' |
118.8 |
120.0 |
| H5' |
C5' |
C4' |
H4' |
306.9 |
65.5 |
| C5' |
C4' |
H4' |
O4' |
120.6 |
121.0 |
| H4' |
C4' |
C5' |
H5'' |
66.1 |
185.4 |
| H4' |
C4' |
C5' |
H5' |
306.9 |
65.5 |
| H1' |
C1' |
C1 |
C2 |
349.4 |
176.4 |
| C4 |
N4 |
H42 |
H41 |
120.0 |
180.1 |
| C4 |
N4 |
H41 |
H42 |
240.0 |
179.9 |
| C3' |
C2' |
H2'' |
H2' |
122.0 |
236.3 |
| H2'' |
C2' |
C1' |
H1' |
152.3 |
36.6 |
| C3' |
C2' |
H2' |
H2'' |
238.0 |
123.6 |
| H2' |
C2' |
C1' |
H1' |
30.9 |
160.2 |
| H3' |
C3' |
C2' |
H2'' |
349.3 |
102.1 |
| H3' |
C3' |
C2' |
H2' |
110.7 |
338.5 |
| H3' |
C3' |
O3' |
H2 |
55.3 |
298.9 |
| H3' |
C3' |
C4' |
H4' |
226.8 |
236.2 |
| H2 |
O3' |
C3' |
H3' |
55.3 |
298.9 |