PDB Chemical Component ZP4
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 ZP4
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O5' |
PA |
1.574 |
1.610 |
| N3' |
N3A |
1.228 |
1.124 |
| N3A |
N3B |
1.137 |
1.124 |
| N1 |
C1' |
1.468 |
1.465 |
| C6 |
N1 |
1.371 |
1.368 |
| C6 |
H6 |
1.080 |
1.080 |
| C2 |
N1 |
1.364 |
1.346 |
| C2 |
O2 |
1.224 |
1.217 |
| N3 |
C2 |
1.370 |
1.345 |
| N3 |
HN3 |
0.999 |
0.970 |
| C4 |
N3 |
1.372 |
1.349 |
| C4 |
C5 |
1.437 |
1.416 |
| O4 |
C4 |
1.225 |
1.218 |
| C5 |
C6 |
1.329 |
1.350 |
| C5A |
C5 |
1.491 |
1.507 |
| C5A |
H5A |
1.100 |
1.090 |
| C5A |
H5AA |
1.100 |
1.090 |
| C5A |
H5AB |
1.100 |
1.090 |
| C2' |
C3' |
1.510 |
1.548 |
| C2' |
H2' |
1.100 |
1.090 |
| C2' |
H2'A |
1.100 |
1.090 |
| C5' |
O5' |
1.414 |
1.429 |
| C5' |
H5' |
1.100 |
1.090 |
| C5' |
H5'A |
1.100 |
1.090 |
| C4' |
C5' |
1.503 |
1.531 |
| C4' |
C3' |
1.508 |
1.541 |
| C4' |
H4' |
1.100 |
1.089 |
| O4' |
C4' |
1.426 |
1.438 |
| C1' |
C2' |
1.524 |
1.549 |
| C1' |
O4' |
1.416 |
1.444 |
| C1' |
H1' |
1.100 |
1.090 |
| C3' |
N3' |
1.452 |
1.465 |
| C3' |
H3' |
1.100 |
1.090 |
| PA |
O1A |
1.492 |
1.610 |
| PA |
O3A |
1.606 |
1.609 |
| O1A |
HO1A |
0.951 |
0.967 |
| O2A |
PA |
1.515 |
1.480 |
| O3A |
PB |
1.600 |
1.610 |
| PB |
O1B |
1.495 |
1.610 |
| PB |
O3B |
1.618 |
1.610 |
| O1B |
HO1B |
0.950 |
0.967 |
| O2B |
PB |
1.497 |
1.479 |
| PG |
O3B |
1.586 |
1.610 |
| PG |
O2G |
1.508 |
1.610 |
| O1G |
PG |
1.490 |
1.480 |
| O2G |
HO2G |
0.950 |
0.967 |
| O3G |
PG |
1.590 |
1.610 |
| O3G |
PD |
1.618 |
1.610 |
| PD |
O1D |
1.528 |
1.610 |
| O1D |
HO1D |
0.950 |
0.967 |
| O2D |
PD |
1.527 |
1.480 |
| O51 |
PD |
1.602 |
1.611 |
| C51 |
O51 |
1.395 |
1.429 |
| C51 |
H51 |
1.100 |
1.090 |
| C51 |
H51A |
1.100 |
1.090 |
| C41 |
C51 |
1.531 |
1.530 |
| C41 |
O41 |
1.434 |
1.437 |
| C41 |
H41 |
1.100 |
1.090 |
| C11 |
O41 |
1.457 |
1.444 |
| C11 |
H11 |
1.100 |
1.090 |
| C21 |
C11 |
1.554 |
1.550 |
| C21 |
C31 |
1.550 |
1.548 |
| C21 |
H21 |
1.100 |
1.090 |
| O21 |
C21 |
1.453 |
1.428 |
| O21 |
HO21 |
0.950 |
0.967 |
| C31 |
C41 |
1.525 |
1.541 |
| C31 |
H31 |
1.100 |
1.090 |
| O31 |
C31 |
1.455 |
1.429 |
| O31 |
HO31 |
0.950 |
0.966 |
| N9R |
C11 |
1.530 |
1.464 |
| N9R |
C8R |
1.370 |
1.362 |
| C8R |
H8R |
1.080 |
1.080 |
| N7R |
C8R |
1.356 |
1.302 |
| C5R |
N7R |
1.346 |
1.354 |
| C6R |
C5R |
1.497 |
1.405 |
| C6R |
N6R |
1.358 |
1.383 |
| N6R |
HN6R |
1.000 |
0.970 |
| N6R |
HN6A |
1.000 |
0.970 |
| N1R |
C6R |
1.386 |
1.330 |
| C2R |
N1R |
1.375 |
1.321 |
| C2R |
N3R |
1.368 |
1.317 |
| C2R |
H2R |
1.079 |
1.080 |
| N3R |
C4R |
1.397 |
1.329 |
| C4R |
N9R |
1.353 |
1.373 |
| C4R |
C5R |
1.495 |
1.405 |
Bond Angles for ZP4
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C5' |
O5' |
PA |
120.5 |
123.0 |
| O5' |
PA |
O1A |
109.1 |
109.4 |
| O5' |
PA |
O3A |
100.8 |
109.5 |
| N3' |
N3A |
N3B |
172.5 |
179.9 |
| C6 |
N1 |
C1' |
120.8 |
119.7 |
| C2 |
N1 |
C1' |
117.9 |
119.7 |
| N1 |
C1' |
C2' |
115.6 |
110.6 |
| N1 |
C1' |
O4' |
107.0 |
110.6 |
| N1 |
C1' |
H1' |
106.1 |
110.6 |
| C5 |
C6 |
H6 |
118.2 |
120.2 |
| C4 |
N3 |
HN3 |
116.4 |
119.8 |
| O4 |
C4 |
C5 |
125.2 |
120.3 |
| H5A |
C5A |
H5AA |
109.5 |
109.4 |
| H5A |
C5A |
H5AB |
109.4 |
109.4 |
| H5AA |
C5A |
H5AB |
109.6 |
109.4 |
| C3' |
C2' |
H2' |
111.9 |
110.9 |
| C3' |
C2' |
H2'A |
113.4 |
110.9 |
| C2' |
C3' |
C4' |
102.2 |
104.2 |
| C1' |
C2' |
C3' |
102.4 |
102.1 |
| C2' |
C3' |
H3' |
115.4 |
110.5 |
| H2' |
C2' |
H2'A |
104.1 |
110.8 |
| C1' |
C2' |
H2' |
111.9 |
110.9 |
| C1' |
C2' |
H2'A |
113.4 |
111.0 |
| H5' |
C5' |
H5'A |
109.0 |
109.5 |
| C4' |
C5' |
H5' |
109.7 |
109.5 |
| C4' |
C5' |
H5'A |
109.8 |
109.5 |
| C3' |
C4' |
H4' |
108.2 |
109.9 |
| O4' |
C4' |
C3' |
105.1 |
107.3 |
| C4' |
C3' |
H3' |
111.7 |
110.5 |
| O4' |
C4' |
H4' |
115.6 |
110.1 |
| O1A |
PA |
O3A |
110.9 |
109.5 |
| PA |
O1A |
HO1A |
109.5 |
114.0 |
| O2A |
PA |
O3A |
107.5 |
109.5 |
| PA |
O3A |
PB |
127.1 |
134.0 |
| O3A |
PB |
O1B |
103.6 |
109.5 |
| O3A |
PB |
O3B |
109.0 |
109.5 |
| O1B |
PB |
O3B |
103.9 |
109.5 |
| PB |
O1B |
HO1B |
109.5 |
114.0 |
| O2B |
PB |
O3B |
109.6 |
109.5 |
| O1G |
PG |
O2G |
116.8 |
109.4 |
| PG |
O2G |
HO2G |
109.5 |
114.0 |
| O3G |
PD |
O1D |
113.5 |
109.5 |
| PD |
O1D |
HO1D |
109.5 |
114.0 |
| H51 |
C51 |
H51A |
107.9 |
109.5 |
| C41 |
C51 |
H51 |
110.2 |
109.5 |
| C41 |
C51 |
H51A |
110.6 |
109.5 |
| O41 |
C41 |
H41 |
108.6 |
109.9 |
| C31 |
C41 |
H41 |
111.3 |
110.0 |
| C21 |
C11 |
H11 |
108.4 |
110.6 |
| N9R |
C11 |
H11 |
105.6 |
110.6 |
| C31 |
C21 |
H21 |
112.0 |
110.8 |
| O21 |
C21 |
C31 |
115.2 |
110.9 |
| C21 |
C31 |
H31 |
111.6 |
110.5 |
| O21 |
C21 |
H21 |
97.3 |
110.9 |
| O31 |
C31 |
H31 |
109.9 |
110.5 |
| N9R |
C8R |
H8R |
123.9 |
125.0 |
| N7R |
C8R |
H8R |
124.0 |
125.0 |
| C6R |
N6R |
HN6R |
109.5 |
120.0 |
| C6R |
N6R |
HN6A |
109.5 |
120.1 |
| HN6R |
N6R |
HN6A |
109.5 |
119.9 |
| N3R |
C2R |
H2R |
119.1 |
118.7 |
| C2R |
N3R |
C4R |
121.6 |
120.6 |
Torsion Angles for ZP4
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O1A |
PA |
O5' |
O3A |
243.2 |
240.0 |
| O5' |
PA |
O1A |
HO1A |
290.0 |
60.1 |
| O2A |
PA |
O5' |
O3A |
113.1 |
120.0 |
| O5' |
PA |
O3A |
PB |
294.8 |
165.0 |
| N1 |
C1' |
C2' |
C3' |
95.6 |
155.5 |
| N1 |
C1' |
C2' |
H2' |
335.6 |
273.7 |
| N1 |
C1' |
C2' |
H2'A |
218.1 |
37.4 |
| C2 |
N1 |
C6 |
C1' |
181.7 |
180.3 |
| C6 |
N1 |
C1' |
C2' |
256.8 |
115.0 |
| C6 |
N1 |
C1' |
O4' |
15.5 |
229.1 |
| C6 |
N1 |
C1' |
H1' |
139.0 |
352.2 |
| H6 |
C6 |
N1 |
C1' |
353.6 |
359.9 |
| C6 |
N1 |
C2 |
C1' |
178.4 |
179.7 |
| C2 |
N1 |
C1' |
C2' |
75.2 |
294.7 |
| C2 |
N1 |
C1' |
O4' |
193.9 |
48.8 |
| C2 |
N1 |
C1' |
H1' |
317.4 |
171.8 |
| O2 |
C2 |
N1 |
C1' |
7.0 |
360.0 |
| N3 |
C2 |
N1 |
C1' |
187.0 |
180.0 |
| C4 |
C5 |
C6 |
H6 |
179.4 |
180.0 |
| C5 |
C4 |
N3 |
HN3 |
176.1 |
180.2 |
| O4 |
C4 |
N3 |
HN3 |
354.8 |
0.0 |
| C5 |
C6 |
N1 |
C1' |
173.6 |
180.0 |
| C5A |
C5 |
C6 |
H6 |
359.4 |
359.8 |
| H5AA |
C5A |
H5A |
H5AB |
120.1 |
119.9 |
| H5A |
C5A |
H5AA |
H5AB |
240.0 |
240.1 |
| H5A |
C5A |
H5AB |
H5AA |
120.0 |
119.9 |
| H2' |
C2' |
C3' |
H2'A |
242.6 |
123.5 |
| C1' |
C2' |
C3' |
H2' |
240.0 |
118.2 |
| C1' |
C2' |
C3' |
H2'A |
122.5 |
241.8 |
| C2' |
C3' |
C4' |
H4' |
89.3 |
117.6 |
| O4' |
C4' |
C3' |
C2' |
325.3 |
357.9 |
| C4' |
C3' |
C2' |
H3' |
121.5 |
118.7 |
| C3' |
C2' |
H2' |
H2'A |
122.9 |
236.4 |
| H2' |
C2' |
C3' |
C4' |
154.7 |
220.9 |
| C1' |
C2' |
H2' |
C3' |
114.3 |
247.3 |
| H2' |
C2' |
C3' |
H3' |
33.2 |
102.2 |
| C1' |
C2' |
H2' |
H2'A |
237.2 |
123.7 |
| C3' |
C2' |
H2'A |
H2' |
238.1 |
123.6 |
| H2'A |
C2' |
C3' |
C4' |
272.1 |
97.4 |
| C1' |
C2' |
H2'A |
C3' |
243.8 |
112.7 |
| H2'A |
C2' |
C3' |
H3' |
150.7 |
338.7 |
| C1' |
C2' |
H2'A |
H2' |
121.9 |
236.3 |
| C5' |
O5' |
PA |
O1A |
350.7 |
64.9 |
| C5' |
O5' |
PA |
O3A |
107.4 |
185.0 |
| H5' |
C5' |
O5' |
PA |
314.3 |
300.0 |
| C4' |
C5' |
H5' |
H5'A |
239.8 |
240.0 |
| H5'A |
C5' |
O5' |
PA |
74.1 |
60.0 |
| C4' |
C5' |
H5'A |
H5' |
120.2 |
120.0 |
| C4' |
C5' |
O5' |
PA |
194.3 |
180.0 |
| C2' |
C3' |
C4' |
C5' |
207.3 |
238.6 |
| H5' |
C5' |
C4' |
H5'A |
119.7 |
120.0 |
| C4' |
C3' |
C2' |
H2' |
154.7 |
220.9 |
| C4' |
C3' |
C2' |
H2'A |
272.1 |
97.4 |
| C1' |
C2' |
C3' |
C4' |
34.7 |
339.1 |
| C2' |
C3' |
C4' |
H3' |
236.0 |
241.3 |
| C3' |
C4' |
C5' |
H5' |
279.8 |
65.0 |
| C3' |
C4' |
C5' |
H5'A |
160.0 |
304.9 |
| O4' |
C4' |
C3' |
H4' |
236.0 |
240.4 |
| H4' |
C4' |
C5' |
H5' |
39.1 |
186.0 |
| H4' |
C4' |
C5' |
H5'A |
279.4 |
66.0 |
| O4' |
C4' |
H4' |
C3' |
117.5 |
117.9 |
| H4' |
C4' |
C3' |
H3' |
213.3 |
236.2 |
| N1 |
C1' |
O4' |
C4' |
237.3 |
201.4 |
| C2' |
C3' |
C4' |
O4' |
325.3 |
357.9 |
| O4' |
C4' |
C5' |
H5' |
163.1 |
307.2 |
| O4' |
C4' |
C5' |
H5'A |
43.4 |
187.2 |
| C3' |
C4' |
O4' |
H4' |
119.2 |
119.5 |
| O4' |
C4' |
C3' |
H3' |
89.3 |
116.6 |
| N1 |
C1' |
C2' |
O4' |
118.9 |
118.5 |
| N1 |
C1' |
C2' |
H1' |
242.4 |
237.2 |
| C3' |
C2' |
C1' |
H2' |
120.0 |
241.8 |
| C3' |
C2' |
C1' |
H2'A |
237.4 |
118.2 |
| C1' |
C2' |
C3' |
H3' |
273.2 |
220.4 |
| H2' |
C2' |
C1' |
H2'A |
117.4 |
236.4 |
| N1 |
C1' |
O4' |
C2' |
235.6 |
241.5 |
| N1 |
C1' |
O4' |
H1' |
117.7 |
122.9 |
| O4' |
C1' |
C2' |
C3' |
336.7 |
37.0 |
| O4' |
C1' |
C2' |
H2' |
216.7 |
155.2 |
| O4' |
C1' |
C2' |
H2'A |
99.3 |
278.9 |
| C1' |
O4' |
C4' |
C3' |
20.9 |
26.6 |
| C1' |
O4' |
C4' |
H4' |
261.7 |
267.0 |
| N1 |
C1' |
H1' |
C2' |
123.7 |
122.9 |
| N1 |
C1' |
H1' |
O4' |
241.8 |
237.0 |
| H1' |
C1' |
C2' |
C3' |
213.2 |
278.4 |
| H1' |
C1' |
C2' |
H2' |
93.2 |
36.6 |
| H1' |
C1' |
C2' |
H2'A |
335.8 |
160.2 |
| H3' |
C3' |
C2' |
H2' |
33.2 |
102.2 |
| H3' |
C3' |
C2' |
H2'A |
150.7 |
338.7 |
| C2' |
C3' |
H3' |
C4' |
116.2 |
114.8 |
| H3' |
C3' |
C4' |
H4' |
213.3 |
236.2 |
| O5' |
PA |
O1A |
O3A |
110.1 |
120.0 |
| O2A |
PA |
O1A |
O3A |
235.8 |
240.0 |
| O1A |
PA |
O3A |
PB |
50.2 |
285.0 |
| O5' |
PA |
O3A |
O1A |
244.6 |
240.0 |
| O3A |
PA |
O1A |
HO1A |
179.9 |
300.0 |
| PA |
O3A |
PB |
O1B |
120.5 |
80.0 |
| PA |
O3A |
PB |
O3B |
230.7 |
200.0 |
| HO1A |
O1A |
PA |
O3A |
179.9 |
300.0 |
| O5' |
PA |
O2A |
O3A |
251.3 |
240.0 |
| O1A |
PA |
O2A |
O3A |
125.9 |
120.0 |
| O2A |
PA |
O1A |
HO1A |
55.7 |
180.0 |
| O2A |
PA |
O3A |
PB |
180.0 |
45.0 |
| O1B |
PB |
O3A |
O3B |
249.8 |
240.0 |
| O3A |
PB |
O1B |
HO1B |
136.3 |
60.0 |
| O2B |
PB |
O3A |
O3B |
121.5 |
120.0 |
| O3A |
PB |
O1B |
O3B |
113.9 |
120.0 |
| O2B |
PB |
O1B |
O3B |
238.5 |
240.0 |
| O3A |
PB |
O3B |
O1B |
250.0 |
240.0 |
| O3B |
PB |
O1B |
HO1B |
22.4 |
300.0 |
| HO1B |
O1B |
PB |
O3B |
22.4 |
300.0 |
| O3A |
PB |
O2B |
O3B |
238.8 |
240.0 |
| O1B |
PB |
O2B |
O3B |
118.6 |
120.0 |
| O2B |
PB |
O1B |
HO1B |
260.9 |
180.0 |
| O1G |
PG |
O2G |
HO2G |
323.3 |
180.0 |
| O3G |
PG |
O2G |
HO2G |
82.2 |
300.0 |
| O3G |
PD |
O1D |
HO1D |
238.6 |
300.0 |
| O2D |
PD |
O1D |
HO1D |
112.1 |
180.0 |
| O51 |
PD |
O1D |
HO1D |
348.5 |
60.0 |
| C41 |
C51 |
H51 |
H51A |
239.1 |
240.0 |
| C41 |
C51 |
H51A |
H51 |
120.6 |
120.0 |
| H51 |
C51 |
C41 |
H51A |
119.2 |
120.0 |
| O41 |
C41 |
C51 |
H51 |
329.4 |
306.5 |
| O41 |
C41 |
C51 |
H51A |
210.2 |
186.5 |
| C31 |
C41 |
O41 |
H41 |
120.2 |
119.6 |
| H41 |
C41 |
C51 |
H51 |
211.6 |
185.4 |
| H41 |
C41 |
C51 |
H51A |
92.4 |
65.4 |
| C11 |
O41 |
C41 |
H41 |
260.1 |
267.0 |
| N9R |
C11 |
C21 |
H11 |
242.3 |
237.0 |
| C21 |
C31 |
C41 |
H41 |
91.4 |
117.5 |
| C31 |
C21 |
C11 |
H11 |
223.9 |
278.5 |
| O21 |
C21 |
C31 |
H21 |
110.0 |
123.6 |
| O31 |
C31 |
C21 |
H31 |
237.5 |
237.4 |
| H21 |
C21 |
C11 |
H11 |
103.6 |
160.4 |
| O21 |
C21 |
H21 |
C31 |
239.0 |
236.3 |
| H21 |
C21 |
C31 |
H31 |
16.4 |
338.5 |
| O21 |
C21 |
C11 |
H11 |
354.2 |
36.8 |
| C31 |
C21 |
O21 |
H21 |
241.5 |
236.4 |
| O21 |
C21 |
C31 |
H31 |
126.3 |
102.2 |
| HO21 |
O21 |
C21 |
C31 |
43.9 |
292.7 |
| HO21 |
O21 |
C21 |
H21 |
162.4 |
56.4 |
| C31 |
C41 |
C51 |
H51 |
91.9 |
64.3 |
| C31 |
C41 |
C51 |
H51A |
332.7 |
304.3 |
| O41 |
C41 |
C31 |
H41 |
241.5 |
240.4 |
| H31 |
C31 |
C41 |
H41 |
214.0 |
236.2 |
| H31 |
C31 |
C21 |
H21 |
16.4 |
338.5 |
| O31 |
C31 |
C41 |
H41 |
335.8 |
358.8 |
| O31 |
C31 |
C21 |
H21 |
253.9 |
216.0 |
| C21 |
C31 |
O31 |
H31 |
123.5 |
122.6 |
| HO31 |
O31 |
C31 |
H31 |
105.0 |
298.9 |
| C21 |
C11 |
N9R |
H11 |
119.2 |
123.0 |
| C8R |
N9R |
C11 |
H11 |
170.8 |
146.5 |
| N7R |
C8R |
N9R |
H8R |
180.0 |
180.0 |
| N9R |
C8R |
N7R |
H8R |
180.0 |
180.0 |
| C5R |
N7R |
C8R |
H8R |
180.1 |
180.0 |
| HN6R |
N6R |
C6R |
HN6A |
240.0 |
180.0 |
| C6R |
N6R |
HN6R |
HN6A |
120.0 |
180.0 |
| C6R |
N6R |
HN6A |
HN6R |
240.0 |
180.0 |
| N1R |
C6R |
N6R |
HN6R |
292.2 |
180.0 |
| N1R |
C6R |
N6R |
HN6A |
52.3 |
0.1 |
| H2R |
C2R |
N3R |
C4R |
179.4 |
179.7 |
| C4R |
N3R |
C2R |
H2R |
179.4 |
179.7 |
| C4R |
N9R |
C11 |
H11 |
351.8 |
326.1 |
| C4R |
N9R |
C8R |
H8R |
180.3 |
180.2 |