PDB Chemical Component Z
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 Z
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
P |
OP1 |
1.487 |
1.501 |
P |
OP2 |
1.493 |
1.618 |
P |
O5' |
1.588 |
1.619 |
P |
OP3 |
|
1.616 |
OP2 |
HOP2 |
0.950 |
0.981 |
O5' |
C5' |
1.446 |
1.418 |
C5' |
C4' |
1.510 |
1.523 |
C5' |
H5' |
1.116 |
1.092 |
C5' |
H5'' |
1.114 |
1.093 |
C4' |
O4' |
1.439 |
1.441 |
C4' |
C3' |
1.519 |
1.522 |
C4' |
H4' |
1.114 |
1.094 |
O4' |
C1' |
1.422 |
1.434 |
C3' |
O3' |
1.424 |
1.426 |
C3' |
C2' |
1.518 |
1.511 |
C3' |
H3' |
1.115 |
1.094 |
O3' |
HO3' |
0.950 |
0.973 |
C2' |
C1' |
1.528 |
1.520 |
C2' |
H2' |
1.115 |
1.097 |
C2' |
H2'' |
1.115 |
1.095 |
C1' |
N1 |
1.477 |
1.434 |
C1' |
H1' |
1.115 |
1.095 |
N1 |
C2 |
1.388 |
1.421 |
N1 |
C6 |
1.398 |
1.389 |
C2 |
O2 |
1.245 |
1.232 |
C2 |
N3 |
1.352 |
1.387 |
N3 |
C4 |
1.335 |
1.292 |
C4 |
C5 |
1.421 |
1.467 |
C4 |
H4 |
1.104 |
1.102 |
C5 |
C6 |
1.368 |
1.333 |
C5 |
H5 |
1.104 |
1.080 |
C6 |
H6 |
1.102 |
1.084 |
OP3 |
HOP3 |
|
0.981 |
Bond Angles for Z
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
OP1 |
P |
OP2 |
119.8 |
115.3 |
OP1 |
P |
O5' |
106.3 |
115.0 |
OP1 |
P |
OP3 |
|
115.0 |
OP2 |
P |
O5' |
109.7 |
103.7 |
OP2 |
P |
OP3 |
|
103.3 |
P |
OP2 |
HOP2 |
119.9 |
118.9 |
O5' |
P |
OP3 |
|
102.9 |
P |
O5' |
C5' |
119.8 |
118.5 |
P |
OP3 |
HOP3 |
|
118.9 |
O5' |
C5' |
C4' |
110.5 |
108.9 |
O5' |
C5' |
H5' |
111.9 |
109.0 |
O5' |
C5' |
H5'' |
111.9 |
108.9 |
C4' |
C5' |
H5' |
111.8 |
110.3 |
C4' |
C5' |
H5'' |
111.8 |
110.3 |
C5' |
C4' |
O4' |
111.7 |
107.9 |
C5' |
C4' |
C3' |
112.8 |
112.9 |
C5' |
C4' |
H4' |
104.1 |
109.5 |
H5' |
C5' |
H5'' |
98.5 |
109.3 |
O4' |
C4' |
C3' |
104.4 |
106.2 |
O4' |
C4' |
H4' |
112.5 |
107.9 |
C4' |
O4' |
C1' |
108.4 |
109.3 |
C3' |
C4' |
H4' |
111.5 |
112.2 |
C4' |
C3' |
O3' |
106.5 |
109.9 |
C4' |
C3' |
C2' |
103.0 |
103.1 |
C4' |
C3' |
H3' |
115.7 |
113.5 |
O4' |
C1' |
C2' |
107.6 |
107.4 |
O4' |
C1' |
N1 |
108.9 |
109.3 |
O4' |
C1' |
H1' |
114.5 |
108.0 |
O3' |
C3' |
C2' |
110.5 |
109.7 |
O3' |
C3' |
H3' |
108.9 |
107.4 |
C3' |
O3' |
HO3' |
106.5 |
107.3 |
C2' |
C3' |
H3' |
112.0 |
113.2 |
C3' |
C2' |
C1' |
104.2 |
102.5 |
C3' |
C2' |
H2' |
114.2 |
109.7 |
C3' |
C2' |
H2'' |
114.2 |
114.1 |
C1' |
C2' |
H2' |
114.2 |
110.6 |
C1' |
C2' |
H2'' |
114.2 |
111.7 |
C2' |
C1' |
N1 |
117.8 |
112.8 |
C2' |
C1' |
H1' |
104.9 |
111.5 |
H2' |
C2' |
H2'' |
96.3 |
108.3 |
N1 |
C1' |
H1' |
103.4 |
107.8 |
C1' |
N1 |
C2 |
118.3 |
120.2 |
C1' |
N1 |
C6 |
121.4 |
120.1 |
C2 |
N1 |
C6 |
117.9 |
119.7 |
N1 |
C2 |
O2 |
118.7 |
121.1 |
N1 |
C2 |
N3 |
119.3 |
118.6 |
N1 |
C6 |
C5 |
117.1 |
122.7 |
N1 |
C6 |
H6 |
122.5 |
116.1 |
O2 |
C2 |
N3 |
122.1 |
120.3 |
C2 |
N3 |
C4 |
120.2 |
118.9 |
N3 |
C4 |
C5 |
121.5 |
125.6 |
N3 |
C4 |
H4 |
116.1 |
119.0 |
C5 |
C4 |
H4 |
122.4 |
115.4 |
C4 |
C5 |
C6 |
116.4 |
114.4 |
C4 |
C5 |
H5 |
123.5 |
121.2 |
C6 |
C5 |
H5 |
120.1 |
124.4 |
C5 |
C6 |
H6 |
120.4 |
121.2 |
Torsion Angles for Z
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
OP2 |
P |
OP1 |
O5' |
235.1 |
120.6 |
OP2 |
P |
OP1 |
OP3 |
|
239.9 |
OP1 |
P |
OP2 |
HOP2 |
180.0 |
48.8 |
O5' |
P |
OP1 |
OP3 |
|
119.3 |
OP1 |
P |
O5' |
C5' |
23.5 |
179.9 |
OP1 |
P |
OP3 |
HOP3 |
|
312.0 |
OP1 |
P |
OP2 |
O5' |
123.3 |
233.4 |
OP1 |
P |
OP2 |
OP3 |
|
126.3 |
O5' |
P |
OP2 |
OP3 |
|
252.9 |
OP2 |
P |
O5' |
C5' |
154.4 |
53.2 |
OP2 |
P |
OP3 |
HOP3 |
|
78.5 |
OP1 |
P |
O5' |
OP2 |
229.1 |
126.8 |
OP1 |
P |
O5' |
OP3 |
|
234.2 |
OP2 |
P |
O5' |
OP3 |
|
107.4 |
O5' |
P |
OP2 |
HOP2 |
56.7 |
175.4 |
O5' |
P |
OP3 |
HOP3 |
|
186.2 |
P |
O5' |
C5' |
C4' |
197.3 |
180.0 |
P |
O5' |
C5' |
H5' |
322.5 |
300.4 |
P |
O5' |
C5' |
H5'' |
72.0 |
59.6 |
OP1 |
P |
OP3 |
OP2 |
|
233.5 |
OP1 |
P |
OP3 |
O5' |
|
125.8 |
OP2 |
P |
OP3 |
O5' |
|
252.3 |
OP3 |
P |
OP2 |
HOP2 |
|
282.5 |
OP3 |
P |
O5' |
C5' |
|
305.8 |
HOP2 |
OP2 |
P |
O5' |
56.7 |
175.4 |
HOP2 |
OP2 |
P |
OP3 |
|
282.5 |
C5' |
O5' |
P |
OP3 |
|
305.8 |
C4' |
C5' |
O5' |
H5' |
234.8 |
239.6 |
C4' |
C5' |
O5' |
H5'' |
125.3 |
120.4 |
O5' |
C5' |
C4' |
O4' |
72.7 |
62.4 |
O5' |
C5' |
C4' |
C3' |
189.9 |
179.5 |
O5' |
C5' |
C4' |
H4' |
311.0 |
305.3 |
H5' |
C5' |
O5' |
H5'' |
250.5 |
240.8 |
O5' |
C5' |
C4' |
H5' |
125.3 |
119.6 |
O5' |
C5' |
C4' |
H5'' |
234.7 |
240.5 |
H5' |
C5' |
C4' |
H5'' |
109.4 |
120.9 |
O4' |
C4' |
C5' |
C3' |
242.8 |
242.9 |
O4' |
C4' |
C5' |
H4' |
121.7 |
117.1 |
C5' |
C4' |
O4' |
C1' |
154.9 |
108.6 |
C3' |
C4' |
C5' |
H4' |
238.9 |
234.2 |
C5' |
C4' |
C3' |
O3' |
87.2 |
154.2 |
C5' |
C4' |
C3' |
C2' |
203.5 |
271.2 |
C5' |
C4' |
C3' |
H3' |
326.0 |
34.0 |
O5' |
C5' |
H5' |
C4' |
235.5 |
240.5 |
O5' |
C5' |
H5' |
H5'' |
117.8 |
119.0 |
C4' |
C5' |
H5' |
H5'' |
242.3 |
238.5 |
H5' |
C5' |
C4' |
O4' |
307.4 |
302.9 |
H5' |
C5' |
C4' |
C3' |
64.7 |
60.0 |
H5' |
C5' |
C4' |
H4' |
185.7 |
185.7 |
O5' |
C5' |
H5'' |
C4' |
124.5 |
119.4 |
O5' |
C5' |
H5'' |
H5' |
242.2 |
241.0 |
C4' |
C5' |
H5'' |
H5' |
117.7 |
121.5 |
H5'' |
C5' |
C4' |
O4' |
198.0 |
181.9 |
H5'' |
C5' |
C4' |
C3' |
315.2 |
299.0 |
H5'' |
C5' |
C4' |
H4' |
76.3 |
64.8 |
O4' |
C4' |
C5' |
H5' |
307.4 |
302.9 |
O4' |
C4' |
C5' |
H5'' |
198.0 |
181.9 |
C5' |
C4' |
O4' |
C3' |
122.2 |
121.4 |
C5' |
C4' |
O4' |
H4' |
243.3 |
241.8 |
C3' |
C4' |
O4' |
H4' |
121.1 |
120.5 |
O4' |
C4' |
C3' |
O3' |
208.7 |
272.3 |
O4' |
C4' |
C3' |
C2' |
325.0 |
29.2 |
O4' |
C4' |
C3' |
H3' |
87.5 |
152.1 |
C4' |
O4' |
C1' |
C2' |
343.1 |
351.0 |
C4' |
O4' |
C1' |
N1 |
214.4 |
228.3 |
C4' |
O4' |
C1' |
H1' |
99.2 |
111.3 |
C3' |
C4' |
C5' |
H5' |
64.7 |
60.0 |
C3' |
C4' |
C5' |
H5'' |
315.2 |
299.0 |
C5' |
C4' |
C3' |
O4' |
238.5 |
241.9 |
C5' |
C4' |
C3' |
H4' |
116.8 |
124.3 |
O4' |
C4' |
C3' |
H4' |
238.2 |
242.4 |
C3' |
C4' |
O4' |
C1' |
32.7 |
347.3 |
O3' |
C3' |
C4' |
C2' |
243.7 |
243.1 |
O3' |
C3' |
C4' |
H3' |
121.2 |
120.2 |
C4' |
C3' |
O3' |
HO3' |
180.0 |
232.5 |
C2' |
C3' |
C4' |
H3' |
237.5 |
237.2 |
C4' |
C3' |
C2' |
C1' |
24.5 |
326.6 |
C4' |
C3' |
C2' |
H2' |
149.7 |
84.1 |
C4' |
C3' |
C2' |
H2'' |
259.2 |
205.7 |
H4' |
C4' |
C5' |
H5' |
185.7 |
185.7 |
H4' |
C4' |
C5' |
H5'' |
76.3 |
64.8 |
C5' |
C4' |
H4' |
O4' |
121.2 |
117.1 |
C5' |
C4' |
H4' |
C3' |
238.1 |
233.8 |
O4' |
C4' |
H4' |
C3' |
116.9 |
116.7 |
H4' |
C4' |
O4' |
C1' |
271.7 |
226.8 |
H4' |
C4' |
C3' |
O3' |
330.4 |
29.9 |
H4' |
C4' |
C3' |
C2' |
86.8 |
146.9 |
H4' |
C4' |
C3' |
H3' |
209.3 |
269.7 |
C1' |
O4' |
C4' |
C3' |
32.7 |
347.3 |
C1' |
O4' |
C4' |
H4' |
271.7 |
226.8 |
C3' |
C2' |
C1' |
O4' |
354.2 |
26.9 |
O4' |
C1' |
C2' |
H2' |
229.0 |
270.0 |
O4' |
C1' |
C2' |
H2'' |
119.6 |
149.4 |
C2' |
C1' |
O4' |
N1 |
128.7 |
122.7 |
C2' |
C1' |
O4' |
H1' |
243.9 |
239.7 |
N1 |
C1' |
O4' |
H1' |
115.2 |
117.0 |
O4' |
C1' |
N1 |
C2 |
300.0 |
212.9 |
O4' |
C1' |
N1 |
C6 |
102.3 |
32.9 |
O3' |
C3' |
C4' |
H4' |
330.4 |
29.9 |
C4' |
C3' |
O3' |
C2' |
111.1 |
112.7 |
C4' |
C3' |
O3' |
H3' |
234.6 |
236.1 |
C2' |
C3' |
O3' |
H3' |
123.4 |
123.4 |
O3' |
C3' |
C2' |
C1' |
137.9 |
83.6 |
O3' |
C3' |
C2' |
H2' |
263.1 |
201.1 |
O3' |
C3' |
C2' |
H2'' |
12.6 |
322.8 |
C2' |
C3' |
C4' |
H4' |
86.8 |
146.9 |
C4' |
C3' |
C2' |
O3' |
246.6 |
242.9 |
C4' |
C3' |
C2' |
H3' |
125.0 |
123.0 |
O4' |
C1' |
C2' |
C3' |
354.2 |
26.9 |
O3' |
C3' |
C2' |
H3' |
238.4 |
240.1 |
C2' |
C3' |
O3' |
HO3' |
68.9 |
119.8 |
C1' |
C2' |
C3' |
H2' |
234.7 |
242.5 |
C1' |
C2' |
C3' |
H2'' |
125.3 |
120.8 |
C3' |
C2' |
C1' |
N1 |
117.7 |
147.4 |
C3' |
C2' |
C1' |
H1' |
231.9 |
268.8 |
H2' |
C2' |
C3' |
H2'' |
250.6 |
238.3 |
H3' |
C3' |
C4' |
H4' |
209.3 |
269.7 |
C4' |
C3' |
H3' |
O3' |
119.9 |
121.7 |
C4' |
C3' |
H3' |
C2' |
242.4 |
242.9 |
O3' |
C3' |
H3' |
C2' |
122.5 |
121.3 |
H3' |
C3' |
O3' |
HO3' |
305.4 |
356.3 |
H3' |
C3' |
C2' |
C1' |
259.5 |
203.6 |
H3' |
C3' |
C2' |
H2' |
24.7 |
321.1 |
H3' |
C3' |
C2' |
H2'' |
134.2 |
82.7 |
HO3' |
O3' |
C3' |
C2' |
68.9 |
119.8 |
HO3' |
O3' |
C3' |
H3' |
305.4 |
356.3 |
O4' |
C1' |
C2' |
N1 |
236.6 |
239.5 |
O4' |
C1' |
C2' |
H1' |
122.3 |
118.1 |
C1' |
C2' |
C3' |
H3' |
259.5 |
203.6 |
C3' |
C2' |
C1' |
H2' |
125.3 |
116.9 |
C3' |
C2' |
C1' |
H2'' |
234.7 |
237.5 |
H2' |
C2' |
C1' |
H2'' |
109.4 |
120.7 |
N1 |
C1' |
C2' |
H1' |
245.7 |
238.6 |
C2' |
C1' |
N1 |
C2 |
177.3 |
93.5 |
C2' |
C1' |
N1 |
C6 |
339.5 |
273.5 |
H2' |
C2' |
C3' |
H3' |
24.7 |
321.1 |
C3' |
C2' |
H2' |
C1' |
240.2 |
247.7 |
C3' |
C2' |
H2' |
H2'' |
120.1 |
125.1 |
C1' |
C2' |
H2' |
H2'' |
239.9 |
237.3 |
H2' |
C2' |
C1' |
N1 |
352.4 |
30.6 |
H2' |
C2' |
C1' |
H1' |
106.7 |
151.9 |
H2'' |
C2' |
C3' |
H3' |
134.2 |
82.7 |
C3' |
C2' |
H2'' |
C1' |
119.9 |
115.6 |
C3' |
C2' |
H2'' |
H2' |
239.9 |
237.5 |
C1' |
C2' |
H2'' |
H2' |
120.1 |
122.0 |
H2'' |
C2' |
C1' |
N1 |
243.0 |
269.9 |
H2'' |
C2' |
C1' |
H1' |
357.3 |
31.3 |
O4' |
C1' |
N1 |
C2' |
122.8 |
119.4 |
O4' |
C1' |
N1 |
H1' |
237.8 |
242.9 |
N1 |
C1' |
C2' |
H2' |
352.4 |
30.6 |
N1 |
C1' |
C2' |
H2'' |
243.0 |
269.9 |
C2' |
C1' |
N1 |
H1' |
115.1 |
123.5 |
C2 |
N1 |
C1' |
C6 |
197.7 |
180.0 |
C1' |
N1 |
C2 |
O2 |
2.8 |
0.1 |
C1' |
N1 |
C2 |
N3 |
182.6 |
180.0 |
C1' |
N1 |
C6 |
C5 |
164.5 |
180.0 |
C1' |
N1 |
C6 |
H6 |
344.5 |
0.0 |
O4' |
C1' |
H1' |
C2' |
242.4 |
242.3 |
O4' |
C1' |
H1' |
N1 |
118.3 |
118.0 |
H1' |
C1' |
C2' |
H2' |
106.7 |
151.9 |
H1' |
C1' |
C2' |
H2'' |
357.3 |
31.3 |
C2' |
C1' |
H1' |
N1 |
236.0 |
235.7 |
H1' |
C1' |
N1 |
C2 |
62.2 |
330.0 |
H1' |
C1' |
N1 |
C6 |
224.5 |
150.0 |
C2 |
N1 |
C1' |
H1' |
62.2 |
330.0 |
C1' |
N1 |
C2 |
C6 |
162.9 |
180.0 |
C2 |
N1 |
C6 |
C5 |
326.8 |
0.0 |
C2 |
N1 |
C6 |
H6 |
146.8 |
180.0 |
O2 |
C2 |
N1 |
N3 |
180.2 |
180.0 |
N1 |
C2 |
N3 |
C4 |
359.1 |
359.9 |
C6 |
N1 |
C1' |
H1' |
224.5 |
150.0 |
C1' |
N1 |
C6 |
C2 |
197.7 |
180.0 |
C6 |
N1 |
C2 |
O2 |
200.0 |
180.1 |
C6 |
N1 |
C2 |
N3 |
19.8 |
0.0 |
C4 |
C5 |
C6 |
N1 |
27.2 |
360.0 |
N1 |
C6 |
C5 |
H5 |
207.2 |
180.0 |
C5 |
C6 |
N1 |
H6 |
180.0 |
180.0 |
O2 |
C2 |
N1 |
C6 |
200.0 |
180.1 |
N1 |
C2 |
O2 |
N3 |
179.8 |
180.0 |
O2 |
C2 |
N3 |
C4 |
178.9 |
179.9 |
N3 |
C2 |
N1 |
C6 |
19.8 |
0.0 |
N1 |
C2 |
N3 |
O2 |
180.2 |
180.0 |
C2 |
N3 |
C4 |
C5 |
355.4 |
0.1 |
C2 |
N3 |
C4 |
H4 |
175.4 |
180.0 |
C5 |
C4 |
N3 |
H4 |
180.0 |
180.1 |
N3 |
C4 |
C5 |
C6 |
351.1 |
360.0 |
N3 |
C4 |
C5 |
H5 |
171.2 |
180.0 |
N1 |
C6 |
C5 |
C4 |
27.2 |
360.0 |
N3 |
C4 |
C5 |
H4 |
180.0 |
179.9 |
C6 |
C5 |
C4 |
H5 |
180.0 |
180.0 |
C4 |
C5 |
C6 |
H6 |
207.2 |
180.0 |
N3 |
C4 |
H4 |
C5 |
180.0 |
180.1 |
H4 |
C4 |
C5 |
C6 |
171.2 |
180.1 |
H4 |
C4 |
C5 |
H5 |
351.2 |
0.1 |
N1 |
C6 |
C5 |
H6 |
180.0 |
180.0 |
C6 |
C5 |
C4 |
H4 |
171.2 |
180.1 |
C4 |
C5 |
C6 |
H5 |
180.0 |
180.0 |
H5 |
C5 |
C4 |
H4 |
351.2 |
0.1 |
C4 |
C5 |
H5 |
C6 |
180.0 |
180.0 |
H5 |
C5 |
C6 |
H6 |
27.2 |
360.0 |
N1 |
C6 |
H6 |
C5 |
180.0 |
180.0 |
H6 |
C6 |
C5 |
H5 |
27.2 |
360.0 |