PDB Chemical Component P5P
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 P5P
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N1 |
C2 |
1.337 |
1.320 |
| N1 |
C6 |
1.353 |
1.322 |
| C2 |
N3 |
1.337 |
1.317 |
| C2 |
H2 |
1.103 |
1.080 |
| N3 |
C4 |
1.362 |
1.325 |
| C4 |
C5 |
1.373 |
1.410 |
| C4 |
N9 |
1.314 |
1.372 |
| C5 |
C6 |
1.402 |
1.395 |
| C5 |
N7 |
1.409 |
1.355 |
| C6 |
H6 |
1.104 |
1.080 |
| N7 |
C8 |
1.305 |
1.301 |
| C8 |
N9 |
1.315 |
1.363 |
| C8 |
H8 |
1.102 |
1.080 |
| N9 |
C1' |
1.326 |
1.465 |
| C1' |
C2' |
1.553 |
1.544 |
| C1' |
O4' |
1.447 |
1.443 |
| C1' |
H1' |
1.115 |
1.091 |
| C2' |
O2' |
1.449 |
1.428 |
| C2' |
C3' |
1.528 |
1.544 |
| C2' |
H2' |
1.115 |
1.090 |
| O2' |
HO2' |
0.949 |
0.967 |
| C3' |
O3' |
1.436 |
1.429 |
| C3' |
C4' |
1.551 |
1.544 |
| C3' |
H3' |
1.115 |
1.090 |
| O3' |
HO3' |
0.950 |
0.967 |
| C4' |
O4' |
1.474 |
1.446 |
| C4' |
C5' |
1.565 |
1.530 |
| C4' |
H4' |
1.115 |
1.089 |
| C5' |
O5' |
1.467 |
1.428 |
| C5' |
H5'1 |
1.116 |
1.090 |
| C5' |
H5'2 |
1.115 |
1.090 |
| O5' |
P |
1.661 |
1.610 |
| P |
OP1 |
1.502 |
1.480 |
| P |
OP2 |
1.497 |
1.610 |
| P |
OP3 |
1.632 |
1.609 |
| OP2 |
HOP2 |
0.950 |
0.967 |
| OP3 |
HOP3 |
0.950 |
0.967 |
Bond Angles for P5P
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N1 |
C6 |
119.4 |
121.4 |
| N1 |
C2 |
N3 |
128.8 |
122.4 |
| N1 |
C2 |
H2 |
115.6 |
118.8 |
| N1 |
C6 |
C5 |
118.0 |
118.6 |
| N1 |
C6 |
H6 |
119.3 |
120.7 |
| N3 |
C2 |
H2 |
115.6 |
118.8 |
| C2 |
N3 |
C4 |
109.2 |
120.5 |
| N3 |
C4 |
C5 |
128.9 |
119.0 |
| N3 |
C4 |
N9 |
128.1 |
135.1 |
| C5 |
C4 |
N9 |
103.0 |
105.9 |
| C4 |
C5 |
C6 |
115.7 |
118.2 |
| C4 |
C5 |
N7 |
111.2 |
107.0 |
| C4 |
N9 |
C8 |
111.5 |
107.5 |
| C4 |
N9 |
C1' |
124.6 |
126.3 |
| C6 |
C5 |
N7 |
133.1 |
134.8 |
| C5 |
C6 |
H6 |
122.7 |
120.7 |
| C5 |
N7 |
C8 |
101.9 |
109.5 |
| N7 |
C8 |
N9 |
112.4 |
110.1 |
| N7 |
C8 |
H8 |
123.5 |
125.0 |
| N9 |
C8 |
H8 |
124.1 |
124.9 |
| C8 |
N9 |
C1' |
123.7 |
126.2 |
| N9 |
C1' |
C2' |
119.2 |
110.4 |
| N9 |
C1' |
O4' |
120.8 |
110.5 |
| N9 |
C1' |
H1' |
89.9 |
110.2 |
| C2' |
C1' |
O4' |
103.2 |
104.8 |
| C2' |
C1' |
H1' |
112.6 |
110.4 |
| C1' |
C2' |
O2' |
114.5 |
110.7 |
| C1' |
C2' |
C3' |
98.6 |
104.1 |
| C1' |
C2' |
H2' |
113.7 |
110.5 |
| O4' |
C1' |
H1' |
110.7 |
110.4 |
| C1' |
O4' |
C4' |
103.9 |
105.4 |
| O2' |
C2' |
C3' |
110.4 |
110.5 |
| O2' |
C2' |
H2' |
102.6 |
110.5 |
| C2' |
O2' |
HO2' |
114.5 |
106.8 |
| C3' |
C2' |
H2' |
117.6 |
110.5 |
| C2' |
C3' |
O3' |
109.6 |
110.5 |
| C2' |
C3' |
C4' |
103.6 |
104.2 |
| C2' |
C3' |
H3' |
114.5 |
110.5 |
| O3' |
C3' |
C4' |
113.3 |
110.5 |
| O3' |
C3' |
H3' |
105.1 |
110.5 |
| C3' |
O3' |
HO3' |
109.5 |
106.7 |
| C4' |
C3' |
H3' |
111.0 |
110.5 |
| C3' |
C4' |
O4' |
106.9 |
104.7 |
| C3' |
C4' |
C5' |
110.1 |
110.7 |
| C3' |
C4' |
H4' |
113.3 |
110.2 |
| O4' |
C4' |
C5' |
115.8 |
110.4 |
| O4' |
C4' |
H4' |
107.1 |
110.4 |
| C5' |
C4' |
H4' |
103.8 |
110.3 |
| C4' |
C5' |
O5' |
115.5 |
109.5 |
| C4' |
C5' |
H5'1 |
110.0 |
109.4 |
| C4' |
C5' |
H5'2 |
110.0 |
109.4 |
| O5' |
C5' |
H5'1 |
110.1 |
109.5 |
| O5' |
C5' |
H5'2 |
110.1 |
109.5 |
| C5' |
O5' |
P |
123.0 |
106.8 |
| H5'1 |
C5' |
H5'2 |
100.1 |
109.5 |
| O5' |
P |
OP1 |
113.8 |
109.5 |
| O5' |
P |
OP2 |
106.7 |
109.5 |
| O5' |
P |
OP3 |
102.0 |
109.5 |
| OP1 |
P |
OP2 |
115.5 |
109.4 |
| OP1 |
P |
OP3 |
109.1 |
109.5 |
| OP2 |
P |
OP3 |
108.8 |
109.5 |
| P |
OP2 |
HOP2 |
106.7 |
106.9 |
| P |
OP3 |
HOP3 |
102.0 |
106.8 |
Torsion Angles for P5P
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N1 |
C6 |
C5 |
359.5 |
0.1 |
| C2 |
N1 |
C6 |
H6 |
179.5 |
180.0 |
| N3 |
C2 |
N1 |
H2 |
180.0 |
180.0 |
| N1 |
C2 |
N3 |
C4 |
359.2 |
359.7 |
| C6 |
N1 |
C2 |
N3 |
0.3 |
359.9 |
| C6 |
N1 |
C2 |
H2 |
180.3 |
179.9 |
| C4 |
C5 |
C6 |
N1 |
1.2 |
0.2 |
| N1 |
C6 |
C5 |
N7 |
177.8 |
179.9 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
180.1 |
| N3 |
C2 |
N1 |
C6 |
0.3 |
359.9 |
| N1 |
C2 |
N3 |
H2 |
180.0 |
180.0 |
| C2 |
N3 |
C4 |
C5 |
1.7 |
0.6 |
| C2 |
N3 |
C4 |
N9 |
179.8 |
179.6 |
| H2 |
C2 |
N1 |
C6 |
180.3 |
179.9 |
| N1 |
C2 |
H2 |
N3 |
180.0 |
180.0 |
| H2 |
C2 |
N3 |
C4 |
179.2 |
179.7 |
| C4 |
N3 |
C2 |
H2 |
179.2 |
179.7 |
| C5 |
C4 |
N3 |
N9 |
181.8 |
181.0 |
| N3 |
C4 |
C5 |
C6 |
358.1 |
359.5 |
| N3 |
C4 |
C5 |
N7 |
180.7 |
179.7 |
| N3 |
C4 |
N9 |
C8 |
179.4 |
180.5 |
| N3 |
C4 |
N9 |
C1' |
354.6 |
0.8 |
| N1 |
C6 |
C5 |
C4 |
1.2 |
0.2 |
| N3 |
C4 |
C5 |
N9 |
178.5 |
179.3 |
| C5 |
C4 |
N9 |
C8 |
357.9 |
359.6 |
| C5 |
C4 |
N9 |
C1' |
173.2 |
179.9 |
| C6 |
C5 |
C4 |
N7 |
177.3 |
179.8 |
| C4 |
C5 |
C6 |
H6 |
181.2 |
180.3 |
| C4 |
C5 |
N7 |
C8 |
358.5 |
359.7 |
| N3 |
C4 |
N9 |
C5 |
181.5 |
180.9 |
| N9 |
C4 |
C5 |
C6 |
179.6 |
180.2 |
| N9 |
C4 |
C5 |
N7 |
2.2 |
0.4 |
| N7 |
C8 |
N9 |
C4 |
1.3 |
0.3 |
| C4 |
N9 |
C8 |
H8 |
181.3 |
180.2 |
| C8 |
N9 |
C4 |
C1' |
184.8 |
179.7 |
| C4 |
N9 |
C1' |
C2' |
204.4 |
89.6 |
| C4 |
N9 |
C1' |
O4' |
334.1 |
205.1 |
| C4 |
N9 |
C1' |
H1' |
88.3 |
327.4 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
179.9 |
| C6 |
C5 |
C4 |
N9 |
179.6 |
180.2 |
| C4 |
C5 |
C6 |
N7 |
183.4 |
180.3 |
| C6 |
C5 |
N7 |
C8 |
181.8 |
180.0 |
| N7 |
C5 |
C4 |
N9 |
2.2 |
0.4 |
| C4 |
C5 |
N7 |
C6 |
176.7 |
179.7 |
| N7 |
C5 |
C6 |
H6 |
357.8 |
360.0 |
| C5 |
N7 |
C8 |
N9 |
0.2 |
0.0 |
| C5 |
N7 |
C8 |
H8 |
180.1 |
180.1 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
180.1 |
| H6 |
C6 |
C5 |
N7 |
357.8 |
360.0 |
| C4 |
N9 |
C8 |
N7 |
1.3 |
0.3 |
| N9 |
C8 |
N7 |
H8 |
180.1 |
179.9 |
| N7 |
C8 |
N9 |
C1' |
186.0 |
179.9 |
| C4 |
N9 |
C8 |
C1' |
175.3 |
180.3 |
| N7 |
C8 |
N9 |
H8 |
179.9 |
180.1 |
| C8 |
N9 |
C1' |
C2' |
19.1 |
270.0 |
| C8 |
N9 |
C1' |
O4' |
148.8 |
25.5 |
| C8 |
N9 |
C1' |
H1' |
263.0 |
147.8 |
| N7 |
C8 |
H8 |
N9 |
180.1 |
179.9 |
| H8 |
C8 |
N9 |
C1' |
6.0 |
359.8 |
| C4 |
N9 |
C1' |
C8 |
185.3 |
179.6 |
| C1' |
N9 |
C8 |
H8 |
6.0 |
359.8 |
| C2' |
C1' |
N9 |
O4' |
230.4 |
244.5 |
| C2' |
C1' |
N9 |
H1' |
116.1 |
122.2 |
| N9 |
C1' |
C2' |
O2' |
205.9 |
261.7 |
| N9 |
C1' |
C2' |
C3' |
88.7 |
143.0 |
| N9 |
C1' |
C2' |
H2' |
323.4 |
24.4 |
| O4' |
C1' |
N9 |
H1' |
245.8 |
237.7 |
| N9 |
C1' |
O4' |
C4' |
267.5 |
200.6 |
| N9 |
C1' |
C2' |
O4' |
137.2 |
119.0 |
| N9 |
C1' |
C2' |
H1' |
256.6 |
237.9 |
| O4' |
C1' |
C2' |
H1' |
119.4 |
118.8 |
| C2' |
C1' |
O4' |
C4' |
43.8 |
319.6 |
| O2' |
C2' |
C1' |
C3' |
117.2 |
118.7 |
| O2' |
C2' |
C1' |
H2' |
242.5 |
237.4 |
| C1' |
C2' |
O2' |
HO2' |
180.0 |
183.8 |
| C3' |
C2' |
C1' |
H2' |
125.3 |
118.6 |
| C1' |
C2' |
C3' |
O3' |
154.7 |
118.7 |
| C1' |
C2' |
C3' |
C4' |
33.5 |
359.9 |
| C1' |
C2' |
C3' |
H3' |
272.5 |
241.3 |
| N9 |
C1' |
O4' |
C2' |
223.6 |
241.0 |
| N9 |
C1' |
O4' |
H1' |
102.9 |
122.2 |
| C2' |
C1' |
O4' |
H1' |
239.3 |
241.1 |
| O4' |
C1' |
C2' |
O2' |
68.7 |
142.7 |
| O4' |
C1' |
C2' |
C3' |
311.5 |
24.0 |
| O4' |
C1' |
C2' |
H2' |
186.2 |
265.3 |
| C3' |
C4' |
O4' |
C1' |
338.5 |
40.3 |
| C1' |
O4' |
C4' |
C5' |
101.6 |
159.5 |
| C1' |
O4' |
C4' |
H4' |
216.8 |
281.7 |
| N9 |
C1' |
H1' |
C2' |
121.9 |
122.2 |
| N9 |
C1' |
H1' |
O4' |
236.9 |
237.7 |
| C2' |
C1' |
H1' |
O4' |
114.9 |
115.4 |
| H1' |
C1' |
C2' |
O2' |
309.4 |
23.8 |
| H1' |
C1' |
C2' |
C3' |
192.1 |
265.1 |
| H1' |
C1' |
C2' |
H2' |
66.9 |
146.5 |
| H1' |
C1' |
O4' |
C4' |
164.6 |
78.4 |
| O2' |
C2' |
C1' |
O4' |
68.7 |
142.7 |
| O2' |
C2' |
C1' |
H1' |
309.4 |
23.8 |
| C1' |
C2' |
O2' |
C3' |
249.8 |
245.3 |
| C1' |
C2' |
O2' |
H2' |
123.7 |
122.6 |
| C3' |
C2' |
O2' |
H2' |
233.9 |
237.4 |
| O2' |
C2' |
C3' |
O3' |
34.4 |
359.9 |
| O2' |
C2' |
C3' |
C4' |
273.2 |
241.1 |
| O2' |
C2' |
C3' |
H3' |
152.2 |
122.5 |
| C3' |
C2' |
C1' |
O4' |
311.5 |
24.0 |
| C3' |
C2' |
C1' |
H1' |
192.1 |
265.1 |
| C1' |
C2' |
C3' |
O2' |
120.3 |
118.8 |
| C1' |
C2' |
C3' |
H2' |
237.5 |
241.4 |
| O2' |
C2' |
C3' |
H2' |
117.2 |
122.6 |
| C3' |
C2' |
O2' |
HO2' |
290.2 |
298.5 |
| O3' |
C3' |
C2' |
C4' |
121.2 |
118.7 |
| O3' |
C3' |
C2' |
H3' |
242.2 |
237.4 |
| C2' |
C3' |
O3' |
HO3' |
180.0 |
63.3 |
| C4' |
C3' |
C2' |
H3' |
121.0 |
118.7 |
| C2' |
C3' |
C4' |
O4' |
350.8 |
336.2 |
| C2' |
C3' |
C4' |
C5' |
224.2 |
217.3 |
| C2' |
C3' |
C4' |
H4' |
108.6 |
94.9 |
| H2' |
C2' |
C1' |
O4' |
186.2 |
265.3 |
| H2' |
C2' |
C1' |
H1' |
66.9 |
146.5 |
| C1' |
C2' |
H2' |
O2' |
235.8 |
237.2 |
| C1' |
C2' |
H2' |
C3' |
114.5 |
114.6 |
| O2' |
C2' |
H2' |
C3' |
238.7 |
237.4 |
| H2' |
C2' |
O2' |
HO2' |
56.3 |
61.2 |
| H2' |
C2' |
C3' |
O3' |
277.2 |
237.3 |
| H2' |
C2' |
C3' |
C4' |
156.0 |
118.5 |
| H2' |
C2' |
C3' |
H3' |
35.0 |
359.9 |
| HO2' |
O2' |
C2' |
C3' |
290.2 |
298.5 |
| HO2' |
O2' |
C2' |
H2' |
56.3 |
61.2 |
| O3' |
C3' |
C2' |
H2' |
277.2 |
237.3 |
| C2' |
C3' |
O3' |
C4' |
244.9 |
245.2 |
| C2' |
C3' |
O3' |
H3' |
123.6 |
122.6 |
| C4' |
C3' |
O3' |
H3' |
238.7 |
237.4 |
| O3' |
C3' |
C4' |
O4' |
232.2 |
217.4 |
| O3' |
C3' |
C4' |
C5' |
105.6 |
98.5 |
| O3' |
C3' |
C4' |
H4' |
349.9 |
336.2 |
| C1' |
O4' |
C4' |
C3' |
338.5 |
40.3 |
| C4' |
C3' |
C2' |
H2' |
156.0 |
118.5 |
| C2' |
C3' |
C4' |
O3' |
118.6 |
118.7 |
| C2' |
C3' |
C4' |
H3' |
236.6 |
241.3 |
| O3' |
C3' |
C4' |
H3' |
118.0 |
122.6 |
| C4' |
C3' |
O3' |
HO3' |
295.1 |
178.2 |
| O4' |
C4' |
C3' |
C5' |
126.6 |
118.9 |
| O4' |
C4' |
C3' |
H4' |
242.3 |
241.3 |
| C5' |
C4' |
C3' |
H4' |
115.7 |
122.4 |
| C3' |
C4' |
C5' |
O5' |
287.5 |
176.9 |
| C3' |
C4' |
C5' |
H5'1 |
52.8 |
296.9 |
| C3' |
C4' |
C5' |
H5'2 |
162.1 |
56.9 |
| H3' |
C3' |
C2' |
H2' |
35.0 |
359.9 |
| C2' |
C3' |
H3' |
O3' |
239.7 |
237.4 |
| C2' |
C3' |
H3' |
C4' |
116.8 |
114.8 |
| O3' |
C3' |
H3' |
C4' |
237.2 |
237.4 |
| H3' |
C3' |
O3' |
HO3' |
56.4 |
300.7 |
| H3' |
C3' |
C4' |
O4' |
114.2 |
94.9 |
| H3' |
C3' |
C4' |
C5' |
347.6 |
336.0 |
| H3' |
C3' |
C4' |
H4' |
231.9 |
213.6 |
| HO3' |
O3' |
C3' |
C4' |
295.1 |
178.2 |
| HO3' |
O3' |
C3' |
H3' |
56.4 |
300.7 |
| C4' |
O4' |
C1' |
H1' |
164.6 |
78.4 |
| O4' |
C4' |
C3' |
H3' |
114.2 |
94.9 |
| C3' |
C4' |
O4' |
C5' |
236.9 |
240.8 |
| C3' |
C4' |
O4' |
H4' |
121.7 |
118.6 |
| C5' |
C4' |
O4' |
H4' |
244.8 |
237.8 |
| O4' |
C4' |
C5' |
O5' |
166.1 |
61.5 |
| O4' |
C4' |
C5' |
H5'1 |
291.4 |
181.5 |
| O4' |
C4' |
C5' |
H5'2 |
40.7 |
301.5 |
| C5' |
C4' |
C3' |
H3' |
347.6 |
336.0 |
| C3' |
C4' |
C5' |
O4' |
121.4 |
115.4 |
| C3' |
C4' |
C5' |
H4' |
238.5 |
237.7 |
| O4' |
C4' |
C5' |
H4' |
117.1 |
122.3 |
| O5' |
C5' |
C4' |
H5'1 |
234.7 |
240.0 |
| O5' |
C5' |
C4' |
H5'2 |
125.3 |
120.0 |
| C4' |
C5' |
O5' |
P |
275.8 |
180.0 |
| H5'1 |
C5' |
C4' |
H5'2 |
250.6 |
240.0 |
| H4' |
C4' |
C3' |
H3' |
231.9 |
213.6 |
| C3' |
C4' |
H4' |
O4' |
242.4 |
244.9 |
| C3' |
C4' |
H4' |
C5' |
119.3 |
122.6 |
| O4' |
C4' |
H4' |
C5' |
237.0 |
237.7 |
| H4' |
C4' |
C5' |
O5' |
49.0 |
299.2 |
| H4' |
C4' |
C5' |
H5'1 |
174.3 |
59.2 |
| H4' |
C4' |
C5' |
H5'2 |
283.7 |
179.2 |
| O5' |
C5' |
C4' |
H4' |
49.0 |
299.2 |
| C4' |
C5' |
O5' |
H5'1 |
125.3 |
120.0 |
| C4' |
C5' |
O5' |
H5'2 |
234.7 |
240.0 |
| H5'1 |
C5' |
O5' |
H5'2 |
109.4 |
120.1 |
| C5' |
O5' |
P |
OP1 |
156.6 |
60.0 |
| C5' |
O5' |
P |
OP2 |
28.0 |
180.0 |
| C5' |
O5' |
P |
OP3 |
274.0 |
300.0 |
| H5'1 |
C5' |
C4' |
H4' |
174.3 |
59.2 |
| C4' |
C5' |
H5'1 |
O5' |
231.6 |
240.0 |
| C4' |
C5' |
H5'1 |
H5'2 |
115.8 |
119.9 |
| O5' |
C5' |
H5'1 |
H5'2 |
244.2 |
239.9 |
| H5'1 |
C5' |
O5' |
P |
150.5 |
60.0 |
| H5'2 |
C5' |
C4' |
H4' |
283.7 |
179.2 |
| C4' |
C5' |
H5'2 |
O5' |
128.4 |
120.0 |
| C4' |
C5' |
H5'2 |
H5'1 |
244.2 |
240.1 |
| O5' |
C5' |
H5'2 |
H5'1 |
115.9 |
120.1 |
| H5'2 |
C5' |
O5' |
P |
41.1 |
300.0 |
| P |
O5' |
C5' |
H5'1 |
150.5 |
60.0 |
| P |
O5' |
C5' |
H5'2 |
41.1 |
300.0 |
| OP1 |
P |
O5' |
OP2 |
128.6 |
240.1 |
| OP1 |
P |
O5' |
OP3 |
242.7 |
120.0 |
| OP2 |
P |
O5' |
OP3 |
114.1 |
240.0 |
| O5' |
P |
OP2 |
HOP2 |
180.0 |
180.0 |
| O5' |
P |
OP3 |
HOP3 |
180.0 |
300.0 |
| O5' |
P |
OP1 |
OP2 |
236.0 |
120.0 |
| O5' |
P |
OP1 |
OP3 |
113.1 |
239.9 |
| OP2 |
P |
OP1 |
OP3 |
237.1 |
120.0 |
| OP1 |
P |
OP2 |
HOP2 |
52.4 |
300.0 |
| OP1 |
P |
OP3 |
HOP3 |
300.6 |
180.0 |
| O5' |
P |
OP2 |
OP1 |
127.6 |
240.0 |
| O5' |
P |
OP2 |
OP3 |
250.6 |
120.1 |
| OP1 |
P |
OP2 |
OP3 |
123.0 |
240.0 |
| OP2 |
P |
OP3 |
HOP3 |
67.5 |
60.0 |
| O5' |
P |
OP3 |
OP1 |
239.4 |
120.0 |
| O5' |
P |
OP3 |
OP2 |
112.5 |
240.0 |
| OP1 |
P |
OP3 |
OP2 |
233.2 |
119.9 |
| OP3 |
P |
OP2 |
HOP2 |
289.4 |
59.9 |
| HOP2 |
OP2 |
P |
OP3 |
289.4 |
59.9 |