PDB Chemical Component PYO
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 PYO
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| OP3 |
P |
1.602 |
1.610 |
| OP3 |
HOP3 |
0.950 |
0.967 |
| P |
OP1 |
1.487 |
1.608 |
| P |
OP2 |
1.485 |
1.479 |
| P |
O5' |
1.589 |
1.610 |
| OP1 |
HOP1 |
0.949 |
0.966 |
| O5' |
C5' |
1.413 |
1.429 |
| C5' |
C4' |
1.504 |
1.530 |
| C5' |
H5'' |
1.115 |
1.090 |
| C5' |
H5' |
1.114 |
1.090 |
| C4' |
O4' |
1.455 |
1.446 |
| C4' |
C3' |
1.519 |
1.544 |
| C4' |
H4' |
1.115 |
1.090 |
| O4' |
C1' |
1.419 |
1.444 |
| C3' |
O3' |
1.415 |
1.429 |
| C3' |
C2' |
1.525 |
1.545 |
| C3' |
H3' |
1.114 |
1.090 |
| C1' |
C2' |
1.531 |
1.545 |
| C1' |
N1 |
1.478 |
1.464 |
| C1' |
H1' |
1.116 |
1.090 |
| O3' |
HO3 |
0.950 |
0.966 |
| C2' |
O2' |
1.415 |
1.428 |
| C2' |
H2' |
1.115 |
1.090 |
| O2' |
HO2 |
0.951 |
0.966 |
| N1 |
C6 |
1.330 |
1.358 |
| N1 |
C2 |
1.403 |
1.346 |
| C6 |
C5 |
1.344 |
1.360 |
| C6 |
HC6 |
1.102 |
1.080 |
| C2 |
O2 |
1.266 |
1.220 |
| C2 |
N3 |
1.365 |
1.335 |
| C5 |
C4 |
1.373 |
1.397 |
| C5 |
HC5 |
1.103 |
1.081 |
| N3 |
C4 |
1.321 |
1.319 |
| C4 |
HC4 |
1.103 |
1.081 |
Bond Angles for PYO
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| P |
OP3 |
HOP3 |
107.5 |
106.8 |
| OP3 |
P |
OP1 |
107.5 |
109.4 |
| OP3 |
P |
OP2 |
109.0 |
109.4 |
| OP3 |
P |
O5' |
105.1 |
109.4 |
| OP1 |
P |
OP2 |
119.4 |
109.5 |
| OP1 |
P |
O5' |
107.3 |
109.5 |
| P |
OP1 |
HOP1 |
107.4 |
106.9 |
| OP2 |
P |
O5' |
107.6 |
109.5 |
| P |
O5' |
C5' |
118.7 |
106.8 |
| O5' |
C5' |
C4' |
111.6 |
109.5 |
| O5' |
C5' |
H5'' |
111.4 |
109.5 |
| O5' |
C5' |
H5' |
111.4 |
109.4 |
| C4' |
C5' |
H5'' |
111.4 |
109.5 |
| C4' |
C5' |
H5' |
111.4 |
109.5 |
| C5' |
C4' |
O4' |
111.5 |
110.4 |
| C5' |
C4' |
C3' |
110.5 |
110.7 |
| C5' |
C4' |
H4' |
106.4 |
110.3 |
| H5'' |
C5' |
H5' |
99.0 |
109.5 |
| O4' |
C4' |
C3' |
106.0 |
104.7 |
| O4' |
C4' |
H4' |
110.8 |
110.4 |
| C4' |
O4' |
C1' |
109.6 |
105.4 |
| C3' |
C4' |
H4' |
111.8 |
110.3 |
| C4' |
C3' |
O3' |
109.1 |
110.6 |
| C4' |
C3' |
C2' |
102.2 |
104.2 |
| C4' |
C3' |
H3' |
115.1 |
110.5 |
| O4' |
C1' |
C2' |
105.2 |
104.8 |
| O4' |
C1' |
N1 |
108.8 |
110.5 |
| O4' |
C1' |
H1' |
115.1 |
110.3 |
| O3' |
C3' |
C2' |
111.7 |
110.5 |
| O3' |
C3' |
H3' |
106.2 |
110.5 |
| C3' |
O3' |
HO3 |
109.2 |
106.8 |
| C2' |
C3' |
H3' |
112.6 |
110.5 |
| C3' |
C2' |
C1' |
100.9 |
104.1 |
| C3' |
C2' |
O2' |
113.0 |
110.5 |
| C3' |
C2' |
H2' |
114.1 |
110.5 |
| C2' |
C1' |
N1 |
115.8 |
110.3 |
| C2' |
C1' |
H1' |
108.0 |
110.3 |
| C1' |
C2' |
O2' |
112.9 |
110.7 |
| C1' |
C2' |
H2' |
114.1 |
110.5 |
| N1 |
C1' |
H1' |
104.4 |
110.3 |
| C1' |
N1 |
C6 |
120.5 |
120.0 |
| C1' |
N1 |
C2 |
117.8 |
119.9 |
| O2' |
C2' |
H2' |
102.3 |
110.4 |
| C2' |
O2' |
HO2 |
113.1 |
106.9 |
| C6 |
N1 |
C2 |
121.7 |
120.1 |
| N1 |
C6 |
C5 |
119.3 |
119.2 |
| N1 |
C6 |
HC6 |
119.9 |
120.4 |
| N1 |
C2 |
O2 |
121.8 |
119.5 |
| N1 |
C2 |
N3 |
118.1 |
121.0 |
| C5 |
C6 |
HC6 |
120.8 |
120.4 |
| C6 |
C5 |
C4 |
119.1 |
119.1 |
| C6 |
C5 |
HC5 |
119.4 |
120.5 |
| O2 |
C2 |
N3 |
120.1 |
119.5 |
| C2 |
N3 |
C4 |
118.7 |
120.8 |
| C4 |
C5 |
HC5 |
121.5 |
120.4 |
| C5 |
C4 |
N3 |
123.0 |
119.8 |
| C5 |
C4 |
HC4 |
120.6 |
120.2 |
| N3 |
C4 |
HC4 |
116.4 |
120.0 |
Torsion Angles for PYO
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP1 |
P |
OP3 |
OP2 |
130.8 |
120.0 |
| OP1 |
P |
OP3 |
O5' |
245.9 |
240.0 |
| OP3 |
P |
OP1 |
HOP1 |
180.0 |
60.0 |
| OP2 |
P |
OP3 |
O5' |
115.1 |
120.0 |
| OP3 |
P |
O5' |
C5' |
170.3 |
180.0 |
| HOP3 |
OP3 |
P |
OP1 |
180.0 |
60.0 |
| HOP3 |
OP3 |
P |
OP2 |
49.3 |
299.9 |
| HOP3 |
OP3 |
P |
O5' |
294.1 |
180.0 |
| OP1 |
P |
OP3 |
HOP3 |
180.0 |
60.0 |
| OP3 |
P |
OP1 |
OP2 |
235.3 |
240.0 |
| OP3 |
P |
OP1 |
O5' |
112.6 |
120.0 |
| OP2 |
P |
OP1 |
O5' |
237.3 |
239.9 |
| OP1 |
P |
O5' |
C5' |
284.5 |
299.9 |
| OP2 |
P |
OP3 |
HOP3 |
49.3 |
299.9 |
| OP3 |
P |
OP2 |
OP1 |
124.0 |
120.0 |
| OP3 |
P |
OP2 |
O5' |
246.5 |
240.1 |
| OP1 |
P |
OP2 |
O5' |
122.6 |
120.1 |
| OP2 |
P |
OP1 |
HOP1 |
304.7 |
180.0 |
| OP2 |
P |
O5' |
C5' |
54.2 |
60.0 |
| O5' |
P |
OP3 |
HOP3 |
294.1 |
180.0 |
| OP3 |
P |
O5' |
OP1 |
245.8 |
240.0 |
| OP3 |
P |
O5' |
OP2 |
116.1 |
119.9 |
| OP1 |
P |
O5' |
OP2 |
230.3 |
239.9 |
| O5' |
P |
OP1 |
HOP1 |
67.4 |
300.1 |
| P |
O5' |
C5' |
C4' |
187.3 |
180.0 |
| P |
O5' |
C5' |
H5'' |
312.5 |
300.0 |
| P |
O5' |
C5' |
H5' |
62.1 |
60.0 |
| HOP1 |
OP1 |
P |
OP2 |
304.7 |
180.0 |
| HOP1 |
OP1 |
P |
O5' |
67.4 |
300.1 |
| C4' |
C5' |
O5' |
H5'' |
234.8 |
240.0 |
| C4' |
C5' |
O5' |
H5' |
125.2 |
120.0 |
| O5' |
C5' |
C4' |
O4' |
45.3 |
61.4 |
| O5' |
C5' |
C4' |
C3' |
163.0 |
176.9 |
| O5' |
C5' |
C4' |
H4' |
284.5 |
299.2 |
| H5'' |
C5' |
O5' |
H5' |
250.5 |
240.0 |
| O5' |
C5' |
C4' |
H5'' |
125.3 |
120.0 |
| O5' |
C5' |
C4' |
H5' |
234.7 |
240.1 |
| H5'' |
C5' |
C4' |
H5' |
109.5 |
120.1 |
| O4' |
C4' |
C5' |
C3' |
242.3 |
244.5 |
| O4' |
C4' |
C5' |
H4' |
120.8 |
122.2 |
| C5' |
C4' |
O4' |
C1' |
116.3 |
159.5 |
| C3' |
C4' |
C5' |
H4' |
238.5 |
237.7 |
| C5' |
C4' |
C3' |
O3' |
147.7 |
98.5 |
| C5' |
C4' |
C3' |
C2' |
266.1 |
217.2 |
| C5' |
C4' |
C3' |
H3' |
28.5 |
335.9 |
| O5' |
C5' |
H5'' |
C4' |
234.6 |
240.0 |
| O5' |
C5' |
H5'' |
H5' |
117.4 |
120.0 |
| C4' |
C5' |
H5'' |
H5' |
242.7 |
240.0 |
| H5'' |
C5' |
C4' |
O4' |
280.0 |
301.5 |
| H5'' |
C5' |
C4' |
C3' |
37.7 |
56.9 |
| H5'' |
C5' |
C4' |
H4' |
159.2 |
179.2 |
| O5' |
C5' |
H5' |
C4' |
125.4 |
120.0 |
| O5' |
C5' |
H5' |
H5'' |
242.7 |
240.0 |
| C4' |
C5' |
H5' |
H5'' |
117.3 |
120.0 |
| H5' |
C5' |
C4' |
O4' |
170.6 |
181.4 |
| H5' |
C5' |
C4' |
C3' |
288.2 |
296.9 |
| H5' |
C5' |
C4' |
H4' |
49.7 |
59.2 |
| O4' |
C4' |
C5' |
H5'' |
280.0 |
301.5 |
| O4' |
C4' |
C5' |
H5' |
170.6 |
181.4 |
| C5' |
C4' |
O4' |
C3' |
120.3 |
119.1 |
| C5' |
C4' |
O4' |
H4' |
241.8 |
237.8 |
| C3' |
C4' |
O4' |
H4' |
121.4 |
118.7 |
| O4' |
C4' |
C3' |
O3' |
268.7 |
217.5 |
| O4' |
C4' |
C3' |
C2' |
27.0 |
336.2 |
| O4' |
C4' |
C3' |
H3' |
149.5 |
94.9 |
| C4' |
O4' |
C1' |
C2' |
339.1 |
319.6 |
| C4' |
O4' |
C1' |
N1 |
214.5 |
200.7 |
| C4' |
O4' |
C1' |
H1' |
97.8 |
78.4 |
| C3' |
C4' |
C5' |
H5'' |
37.7 |
56.9 |
| C3' |
C4' |
C5' |
H5' |
288.2 |
296.9 |
| C5' |
C4' |
C3' |
O4' |
239.0 |
241.0 |
| C5' |
C4' |
C3' |
H4' |
118.3 |
122.3 |
| O4' |
C4' |
C3' |
H4' |
239.2 |
241.3 |
| C3' |
C4' |
O4' |
C1' |
356.0 |
40.3 |
| O3' |
C3' |
C4' |
C2' |
241.7 |
241.3 |
| O3' |
C3' |
C4' |
H3' |
119.2 |
122.6 |
| C4' |
C3' |
O3' |
HO3 |
180.0 |
178.1 |
| C2' |
C3' |
C4' |
H3' |
237.6 |
241.3 |
| C4' |
C3' |
C2' |
C1' |
321.9 |
359.9 |
| C4' |
C3' |
C2' |
O2' |
201.0 |
241.1 |
| C4' |
C3' |
C2' |
H2' |
84.7 |
118.5 |
| H4' |
C4' |
C5' |
H5'' |
159.2 |
179.2 |
| H4' |
C4' |
C5' |
H5' |
49.7 |
59.2 |
| C5' |
C4' |
H4' |
O4' |
121.3 |
122.3 |
| C5' |
C4' |
H4' |
C3' |
239.3 |
237.5 |
| O4' |
C4' |
H4' |
C3' |
118.0 |
115.2 |
| H4' |
C4' |
O4' |
C1' |
234.6 |
281.7 |
| H4' |
C4' |
C3' |
O3' |
29.5 |
336.2 |
| H4' |
C4' |
C3' |
C2' |
147.8 |
94.9 |
| H4' |
C4' |
C3' |
H3' |
270.2 |
213.6 |
| C1' |
O4' |
C4' |
C3' |
356.0 |
40.3 |
| C1' |
O4' |
C4' |
H4' |
234.6 |
281.7 |
| C3' |
C2' |
C1' |
O4' |
36.9 |
23.9 |
| C2' |
C1' |
O4' |
N1 |
124.6 |
118.9 |
| C2' |
C1' |
O4' |
H1' |
241.3 |
241.2 |
| O4' |
C1' |
C2' |
O2' |
157.9 |
142.7 |
| O4' |
C1' |
C2' |
H2' |
274.1 |
265.4 |
| N1 |
C1' |
O4' |
H1' |
116.6 |
122.3 |
| O4' |
C1' |
N1 |
C6 |
6.7 |
235.5 |
| O4' |
C1' |
N1 |
C2 |
187.2 |
55.1 |
| O3' |
C3' |
C4' |
H4' |
29.5 |
336.2 |
| C4' |
C3' |
O3' |
C2' |
112.3 |
114.8 |
| C4' |
C3' |
O3' |
H3' |
235.4 |
237.4 |
| C2' |
C3' |
O3' |
H3' |
123.1 |
122.6 |
| O3' |
C3' |
C2' |
C1' |
78.4 |
118.7 |
| O3' |
C3' |
C2' |
O2' |
317.5 |
359.8 |
| O3' |
C3' |
C2' |
H2' |
201.2 |
237.3 |
| C2' |
C3' |
C4' |
H4' |
147.8 |
94.9 |
| C4' |
C3' |
C2' |
O3' |
243.5 |
241.2 |
| C4' |
C3' |
C2' |
H3' |
124.1 |
118.7 |
| O4' |
C1' |
C2' |
C3' |
36.9 |
23.9 |
| O3' |
C3' |
C2' |
H3' |
240.6 |
237.4 |
| C2' |
C3' |
O3' |
HO3 |
67.7 |
63.3 |
| C3' |
C2' |
C1' |
N1 |
157.0 |
143.0 |
| C3' |
C2' |
C1' |
H1' |
273.5 |
265.2 |
| C1' |
C2' |
C3' |
O2' |
120.9 |
118.9 |
| C1' |
C2' |
C3' |
H2' |
237.2 |
241.4 |
| O2' |
C2' |
C3' |
H2' |
116.3 |
122.5 |
| C3' |
C2' |
O2' |
HO2 |
180.0 |
298.6 |
| H3' |
C3' |
C4' |
H4' |
270.2 |
213.6 |
| C4' |
C3' |
H3' |
O3' |
120.8 |
122.7 |
| C4' |
C3' |
H3' |
C2' |
243.4 |
245.3 |
| O3' |
C3' |
H3' |
C2' |
122.5 |
122.6 |
| H3' |
C3' |
O3' |
HO3 |
304.6 |
300.7 |
| H3' |
C3' |
C2' |
C1' |
197.8 |
241.3 |
| H3' |
C3' |
C2' |
O2' |
76.9 |
122.4 |
| H3' |
C3' |
C2' |
H2' |
320.6 |
359.9 |
| O4' |
C1' |
C2' |
N1 |
239.9 |
241.0 |
| O4' |
C1' |
C2' |
H1' |
123.4 |
118.8 |
| C1' |
C2' |
C3' |
H3' |
197.8 |
241.3 |
| C3' |
C2' |
C1' |
O2' |
239.0 |
241.3 |
| C3' |
C2' |
C1' |
H2' |
122.8 |
118.6 |
| N1 |
C1' |
C2' |
H1' |
243.5 |
237.8 |
| C2' |
C1' |
N1 |
C6 |
248.5 |
120.0 |
| C2' |
C1' |
N1 |
C2 |
69.0 |
299.6 |
| O2' |
C2' |
C1' |
H2' |
243.8 |
237.3 |
| C1' |
C2' |
O2' |
HO2 |
66.2 |
183.9 |
| O4' |
C1' |
N1 |
C2' |
118.2 |
115.5 |
| O4' |
C1' |
N1 |
H1' |
236.7 |
237.7 |
| C2' |
C1' |
N1 |
H1' |
118.5 |
122.2 |
| N1 |
C1' |
C2' |
O2' |
278.0 |
261.7 |
| N1 |
C1' |
C2' |
H2' |
34.2 |
24.4 |
| C6 |
N1 |
C1' |
C2 |
179.5 |
180.4 |
| C1' |
N1 |
C6 |
C5 |
181.2 |
180.0 |
| C1' |
N1 |
C6 |
HC6 |
1.1 |
359.9 |
| C1' |
N1 |
C2 |
O2 |
358.7 |
0.4 |
| C1' |
N1 |
C2 |
N3 |
178.7 |
179.8 |
| O4' |
C1' |
H1' |
C2' |
242.8 |
244.6 |
| O4' |
C1' |
H1' |
N1 |
119.1 |
122.4 |
| C2' |
C1' |
H1' |
N1 |
236.3 |
237.8 |
| H1' |
C1' |
C2' |
O2' |
34.5 |
23.9 |
| H1' |
C1' |
C2' |
H2' |
150.7 |
146.6 |
| H1' |
C1' |
N1 |
C6 |
130.0 |
357.8 |
| H1' |
C1' |
N1 |
C2 |
310.5 |
177.4 |
| HO3 |
O3' |
C3' |
C2' |
67.7 |
63.3 |
| HO3 |
O3' |
C3' |
H3' |
304.6 |
300.7 |
| O2' |
C2' |
C3' |
H3' |
76.9 |
122.4 |
| C3' |
C2' |
O2' |
C1' |
113.8 |
114.8 |
| C3' |
C2' |
O2' |
H2' |
236.9 |
237.5 |
| O2' |
C2' |
C1' |
N1 |
278.0 |
261.7 |
| O2' |
C2' |
C1' |
H1' |
34.5 |
23.9 |
| C1' |
C2' |
O2' |
H2' |
123.1 |
122.7 |
| H2' |
C2' |
C3' |
H3' |
320.6 |
359.9 |
| C3' |
C2' |
H2' |
C1' |
244.7 |
245.4 |
| C3' |
C2' |
H2' |
O2' |
122.4 |
122.5 |
| H2' |
C2' |
C1' |
N1 |
34.2 |
24.4 |
| H2' |
C2' |
C1' |
H1' |
150.7 |
146.6 |
| C1' |
C2' |
H2' |
O2' |
237.7 |
237.2 |
| H2' |
C2' |
O2' |
HO2 |
303.1 |
61.1 |
| HO2 |
O2' |
C2' |
H2' |
303.1 |
61.1 |
| C6 |
N1 |
C1' |
H1' |
130.0 |
357.8 |
| C1' |
N1 |
C6 |
C2 |
180.6 |
179.6 |
| C6 |
N1 |
C2 |
O2 |
179.2 |
180.0 |
| C6 |
N1 |
C2 |
N3 |
359.3 |
359.4 |
| C5 |
C6 |
N1 |
HC6 |
180.0 |
180.1 |
| N1 |
C6 |
C5 |
C4 |
359.9 |
359.9 |
| N1 |
C6 |
C5 |
HC5 |
179.9 |
180.0 |
| C2 |
N1 |
C1' |
H1' |
310.5 |
177.4 |
| C1' |
N1 |
C2 |
C6 |
179.5 |
180.4 |
| C2 |
N1 |
C6 |
C5 |
0.6 |
0.4 |
| C2 |
N1 |
C6 |
HC6 |
180.6 |
180.3 |
| O2 |
C2 |
N1 |
N3 |
180.0 |
180.6 |
| N1 |
C2 |
N3 |
C4 |
0.3 |
0.6 |
| C5 |
C6 |
N1 |
C2 |
0.6 |
0.4 |
| N1 |
C6 |
C5 |
HC6 |
180.0 |
179.9 |
| C4 |
C5 |
C6 |
HC5 |
180.1 |
179.9 |
| C6 |
C5 |
C4 |
N3 |
359.6 |
0.0 |
| C6 |
C5 |
C4 |
HC4 |
179.6 |
180.0 |
| HC6 |
C6 |
N1 |
C2 |
180.6 |
180.3 |
| N1 |
C6 |
HC6 |
C5 |
180.0 |
180.1 |
| HC6 |
C6 |
C5 |
C4 |
180.0 |
180.0 |
| HC6 |
C6 |
C5 |
HC5 |
359.9 |
0.1 |
| N1 |
C2 |
O2 |
N3 |
180.0 |
179.4 |
| O2 |
C2 |
N3 |
C4 |
180.3 |
180.0 |
| N1 |
C2 |
N3 |
O2 |
180.0 |
180.6 |
| C5 |
C4 |
N3 |
C2 |
0.3 |
359.7 |
| C2 |
N3 |
C4 |
HC4 |
180.3 |
179.7 |
| C4 |
C5 |
C6 |
HC6 |
180.0 |
180.0 |
| C6 |
C5 |
C4 |
HC5 |
179.9 |
180.1 |
| C2 |
N3 |
C4 |
C5 |
0.3 |
359.7 |
| N3 |
C4 |
C5 |
HC4 |
180.0 |
180.0 |
| HC5 |
C5 |
C6 |
HC6 |
359.9 |
0.1 |
| C6 |
C5 |
HC5 |
C4 |
180.1 |
179.9 |
| HC5 |
C5 |
C4 |
N3 |
179.7 |
180.0 |
| HC5 |
C5 |
C4 |
HC4 |
359.7 |
360.0 |
| N3 |
C4 |
C5 |
HC5 |
179.7 |
180.0 |
| C5 |
C4 |
N3 |
HC4 |
180.0 |
180.0 |
| HC4 |
C4 |
C5 |
HC5 |
359.7 |
360.0 |
| C5 |
C4 |
HC4 |
N3 |
180.0 |
180.0 |