PDB Chemical Component 5PC
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 5PC
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
OP3 |
P |
|
1.618 |
OP3 |
HOP3 |
|
0.981 |
P |
OP1 |
1.476 |
1.501 |
P |
OP2 |
1.482 |
1.616 |
P |
O5' |
1.628 |
1.619 |
OP2 |
HOP2 |
0.949 |
0.981 |
C5' |
O5' |
1.432 |
1.418 |
C5' |
C4' |
1.538 |
1.523 |
C5' |
H5' |
1.090 |
1.092 |
C5' |
H5'' |
1.090 |
1.093 |
C4' |
O4' |
1.415 |
1.441 |
C4' |
C3' |
1.531 |
1.522 |
C4' |
H4' |
1.091 |
1.094 |
O4' |
C1' |
1.403 |
1.434 |
C3' |
O3' |
1.411 |
1.426 |
C3' |
C2' |
1.530 |
1.511 |
C3' |
H3' |
1.090 |
1.094 |
O3' |
HO3' |
0.949 |
0.973 |
C2' |
C1' |
1.514 |
1.520 |
C2' |
H2' |
1.090 |
1.097 |
C2' |
H2'' |
1.089 |
1.095 |
C1' |
N1 |
1.437 |
1.434 |
C1' |
H1' |
1.091 |
1.095 |
N1 |
C2 |
1.310 |
1.414 |
N1 |
C6 |
1.296 |
1.386 |
C2 |
O2 |
1.218 |
1.232 |
C2 |
N3 |
1.298 |
1.383 |
N3 |
C4 |
1.271 |
1.309 |
C4 |
N4 |
1.270 |
1.378 |
C4 |
C5 |
1.357 |
1.496 |
N4 |
H41 |
1.011 |
0.990 |
N4 |
H42 |
1.010 |
0.990 |
C5 |
C6 |
1.327 |
1.336 |
C5 |
C7 |
1.461 |
1.420 |
C6 |
H6 |
1.080 |
1.086 |
C7 |
C8 |
1.203 |
1.200 |
C8 |
C9 |
1.455 |
1.462 |
C9 |
H91 |
1.089 |
1.094 |
C9 |
H92 |
1.090 |
1.094 |
C9 |
H93 |
1.090 |
1.095 |
Bond Angles for 5PC
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
P |
OP3 |
HOP3 |
|
118.9 |
OP3 |
P |
OP1 |
|
115.3 |
OP3 |
P |
OP2 |
|
103.3 |
OP3 |
P |
O5' |
|
103.7 |
OP1 |
P |
OP2 |
119.5 |
115.0 |
OP1 |
P |
O5' |
109.2 |
115.0 |
OP2 |
P |
O5' |
108.4 |
102.9 |
P |
OP2 |
HOP2 |
149.7 |
118.9 |
P |
O5' |
C5' |
122.6 |
118.5 |
O5' |
C5' |
C4' |
112.5 |
108.9 |
O5' |
C5' |
H5' |
108.5 |
109.0 |
O5' |
C5' |
H5'' |
108.9 |
108.9 |
C4' |
C5' |
H5' |
109.4 |
110.3 |
C4' |
C5' |
H5'' |
108.7 |
110.3 |
C5' |
C4' |
O4' |
114.4 |
107.9 |
C5' |
C4' |
C3' |
116.0 |
112.9 |
C5' |
C4' |
H4' |
105.9 |
109.5 |
H5' |
C5' |
H5'' |
108.8 |
109.3 |
O4' |
C4' |
C3' |
107.4 |
106.2 |
O4' |
C4' |
H4' |
106.0 |
107.9 |
C4' |
O4' |
C1' |
105.1 |
109.3 |
C3' |
C4' |
H4' |
106.4 |
112.2 |
C4' |
C3' |
O3' |
110.4 |
109.9 |
C4' |
C3' |
C2' |
102.6 |
103.1 |
C4' |
C3' |
H3' |
107.8 |
113.5 |
O4' |
C1' |
C2' |
106.7 |
107.4 |
O4' |
C1' |
N1 |
106.6 |
109.3 |
O4' |
C1' |
H1' |
109.9 |
108.0 |
O3' |
C3' |
C2' |
114.9 |
109.7 |
O3' |
C3' |
H3' |
110.8 |
107.4 |
C3' |
O3' |
HO3' |
110.4 |
107.3 |
C2' |
C3' |
H3' |
109.8 |
113.2 |
C3' |
C2' |
C1' |
104.2 |
102.5 |
C3' |
C2' |
H2' |
112.3 |
109.7 |
C3' |
C2' |
H2'' |
108.6 |
114.1 |
C1' |
C2' |
H2' |
108.9 |
110.6 |
C1' |
C2' |
H2'' |
112.3 |
111.7 |
C2' |
C1' |
N1 |
110.6 |
112.8 |
C2' |
C1' |
H1' |
110.4 |
111.5 |
H2' |
C2' |
H2'' |
110.5 |
108.3 |
N1 |
C1' |
H1' |
112.4 |
107.8 |
C1' |
N1 |
C2 |
121.3 |
121.9 |
C1' |
N1 |
C6 |
120.6 |
118.5 |
C2 |
N1 |
C6 |
118.0 |
119.6 |
N1 |
C2 |
O2 |
120.8 |
121.1 |
N1 |
C2 |
N3 |
121.0 |
118.7 |
N1 |
C6 |
C5 |
124.9 |
123.0 |
N1 |
C6 |
H6 |
118.6 |
115.3 |
O2 |
C2 |
N3 |
118.1 |
120.2 |
C2 |
N3 |
C4 |
118.2 |
121.4 |
N3 |
C4 |
N4 |
119.9 |
118.8 |
N3 |
C4 |
C5 |
125.5 |
121.4 |
N4 |
C4 |
C5 |
114.3 |
119.8 |
C4 |
N4 |
H41 |
115.5 |
117.9 |
C4 |
N4 |
H42 |
115.2 |
117.9 |
C4 |
C5 |
C6 |
111.5 |
115.9 |
C4 |
C5 |
C7 |
124.0 |
122.5 |
H41 |
N4 |
H42 |
129.3 |
124.2 |
C6 |
C5 |
C7 |
124.3 |
121.6 |
C5 |
C6 |
H6 |
116.6 |
121.7 |
C5 |
C7 |
C8 |
172.4 |
180.0 |
C7 |
C8 |
C9 |
176.9 |
179.9 |
C8 |
C9 |
H91 |
108.2 |
110.9 |
C8 |
C9 |
H92 |
109.1 |
110.9 |
C8 |
C9 |
H93 |
109.8 |
110.9 |
H91 |
C9 |
H92 |
107.8 |
108.0 |
H91 |
C9 |
H93 |
110.2 |
108.1 |
H92 |
C9 |
H93 |
111.6 |
108.0 |
Torsion Angles for 5PC
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
OP1 |
P |
OP3 |
OP2 |
|
126.3 |
OP1 |
P |
OP3 |
O5' |
|
233.4 |
OP2 |
P |
OP3 |
O5' |
|
107.1 |
OP3 |
P |
OP2 |
HOP2 |
|
78.5 |
OP3 |
P |
O5' |
C5' |
|
53.2 |
HOP3 |
OP3 |
P |
OP1 |
|
48.8 |
HOP3 |
OP3 |
P |
OP2 |
|
282.5 |
HOP3 |
OP3 |
P |
O5' |
|
175.4 |
OP1 |
P |
OP3 |
HOP3 |
|
48.8 |
OP3 |
P |
OP1 |
OP2 |
|
239.9 |
OP3 |
P |
OP1 |
O5' |
|
120.6 |
OP2 |
P |
OP1 |
O5' |
125.4 |
240.7 |
OP1 |
P |
OP2 |
HOP2 |
352.9 |
312.0 |
OP1 |
P |
O5' |
C5' |
174.0 |
179.9 |
OP2 |
P |
OP3 |
HOP3 |
|
282.5 |
OP3 |
P |
OP2 |
OP1 |
|
126.5 |
OP3 |
P |
OP2 |
O5' |
|
252.3 |
OP1 |
P |
OP2 |
O5' |
234.2 |
125.8 |
OP2 |
P |
O5' |
C5' |
42.4 |
305.8 |
O5' |
P |
OP3 |
HOP3 |
|
175.4 |
OP3 |
P |
O5' |
OP1 |
|
233.2 |
OP3 |
P |
O5' |
OP2 |
|
107.4 |
OP1 |
P |
O5' |
OP2 |
131.7 |
234.2 |
O5' |
P |
OP2 |
HOP2 |
118.7 |
186.2 |
P |
O5' |
C5' |
C4' |
170.4 |
180.0 |
P |
O5' |
C5' |
H5' |
291.5 |
300.4 |
P |
O5' |
C5' |
H5'' |
49.8 |
59.6 |
HOP2 |
OP2 |
P |
O5' |
118.7 |
186.2 |
C4' |
C5' |
O5' |
H5' |
238.8 |
239.6 |
C4' |
C5' |
O5' |
H5'' |
120.6 |
120.4 |
O5' |
C5' |
C4' |
O4' |
294.9 |
62.4 |
O5' |
C5' |
C4' |
C3' |
60.8 |
179.5 |
O5' |
C5' |
C4' |
H4' |
178.6 |
305.3 |
H5' |
C5' |
O5' |
H5'' |
241.7 |
240.8 |
O5' |
C5' |
C4' |
H5' |
120.7 |
119.6 |
O5' |
C5' |
C4' |
H5'' |
239.3 |
240.5 |
H5' |
C5' |
C4' |
H5'' |
118.7 |
120.9 |
O4' |
C4' |
C5' |
C3' |
234.1 |
242.9 |
O4' |
C4' |
C5' |
H4' |
116.3 |
117.1 |
C5' |
C4' |
O4' |
C1' |
166.2 |
108.6 |
C3' |
C4' |
C5' |
H4' |
242.2 |
234.2 |
C5' |
C4' |
C3' |
O3' |
88.3 |
154.2 |
C5' |
C4' |
C3' |
C2' |
211.3 |
271.2 |
C5' |
C4' |
C3' |
H3' |
327.2 |
34.0 |
O5' |
C5' |
H5' |
C4' |
237.0 |
240.5 |
O5' |
C5' |
H5' |
H5'' |
118.4 |
119.0 |
C4' |
C5' |
H5' |
H5'' |
241.4 |
238.5 |
H5' |
C5' |
C4' |
O4' |
174.3 |
302.9 |
H5' |
C5' |
C4' |
C3' |
300.1 |
60.0 |
H5' |
C5' |
C4' |
H4' |
58.0 |
185.7 |
O5' |
C5' |
H5'' |
C4' |
122.9 |
119.4 |
O5' |
C5' |
H5'' |
H5' |
241.9 |
241.0 |
C4' |
C5' |
H5'' |
H5' |
119.0 |
121.5 |
H5'' |
C5' |
C4' |
O4' |
55.6 |
181.9 |
H5'' |
C5' |
C4' |
C3' |
181.5 |
299.0 |
H5'' |
C5' |
C4' |
H4' |
299.3 |
64.8 |
O4' |
C4' |
C5' |
H5' |
174.3 |
302.9 |
O4' |
C4' |
C5' |
H5'' |
55.6 |
181.9 |
C5' |
C4' |
O4' |
C3' |
130.3 |
121.4 |
C5' |
C4' |
O4' |
H4' |
243.7 |
241.8 |
C3' |
C4' |
O4' |
H4' |
113.4 |
120.5 |
O4' |
C4' |
C3' |
O3' |
217.7 |
272.3 |
O4' |
C4' |
C3' |
C2' |
340.6 |
29.2 |
O4' |
C4' |
C3' |
H3' |
96.5 |
152.1 |
C4' |
O4' |
C1' |
C2' |
322.2 |
351.0 |
C4' |
O4' |
C1' |
N1 |
204.0 |
228.3 |
C4' |
O4' |
C1' |
H1' |
81.9 |
111.3 |
C3' |
C4' |
C5' |
H5' |
300.1 |
60.0 |
C3' |
C4' |
C5' |
H5'' |
181.5 |
299.0 |
C5' |
C4' |
C3' |
O4' |
230.7 |
241.9 |
C5' |
C4' |
C3' |
H4' |
117.5 |
124.3 |
O4' |
C4' |
C3' |
H4' |
246.8 |
242.4 |
C3' |
C4' |
O4' |
C1' |
35.9 |
347.3 |
O3' |
C3' |
C4' |
C2' |
237.1 |
243.1 |
O3' |
C3' |
C4' |
H3' |
121.2 |
120.2 |
C4' |
C3' |
O3' |
HO3' |
180.0 |
232.0 |
C2' |
C3' |
C4' |
H3' |
244.1 |
237.2 |
C4' |
C3' |
C2' |
C1' |
357.0 |
326.6 |
C4' |
C3' |
C2' |
H2' |
239.3 |
84.1 |
C4' |
C3' |
C2' |
H2'' |
116.9 |
205.7 |
H4' |
C4' |
C5' |
H5' |
58.0 |
185.7 |
H4' |
C4' |
C5' |
H5'' |
299.3 |
64.8 |
C5' |
C4' |
H4' |
O4' |
121.9 |
117.1 |
C5' |
C4' |
H4' |
C3' |
235.9 |
233.8 |
O4' |
C4' |
H4' |
C3' |
114.1 |
116.7 |
H4' |
C4' |
O4' |
C1' |
282.5 |
226.8 |
H4' |
C4' |
C3' |
O3' |
330.8 |
29.9 |
H4' |
C4' |
C3' |
C2' |
93.8 |
146.9 |
H4' |
C4' |
C3' |
H3' |
209.7 |
269.7 |
C1' |
O4' |
C4' |
C3' |
35.9 |
347.3 |
C1' |
O4' |
C4' |
H4' |
282.5 |
226.8 |
C3' |
C2' |
C1' |
O4' |
24.7 |
26.9 |
O4' |
C1' |
C2' |
H2' |
144.7 |
270.0 |
O4' |
C1' |
C2' |
H2'' |
267.4 |
149.4 |
C2' |
C1' |
O4' |
N1 |
118.1 |
122.7 |
C2' |
C1' |
O4' |
H1' |
240.3 |
239.7 |
N1 |
C1' |
O4' |
H1' |
122.1 |
117.0 |
O4' |
C1' |
N1 |
C2 |
210.3 |
212.8 |
O4' |
C1' |
N1 |
C6 |
35.0 |
32.9 |
O3' |
C3' |
C4' |
H4' |
330.8 |
29.9 |
C4' |
C3' |
O3' |
C2' |
115.4 |
112.7 |
C4' |
C3' |
O3' |
H3' |
240.6 |
236.1 |
C2' |
C3' |
O3' |
H3' |
125.2 |
123.4 |
O3' |
C3' |
C2' |
C1' |
116.8 |
83.6 |
O3' |
C3' |
C2' |
H2' |
359.2 |
201.1 |
O3' |
C3' |
C2' |
H2'' |
236.7 |
322.8 |
C2' |
C3' |
C4' |
H4' |
93.8 |
146.9 |
C4' |
C3' |
C2' |
O3' |
240.2 |
242.9 |
C4' |
C3' |
C2' |
H3' |
114.5 |
123.0 |
O4' |
C1' |
C2' |
C3' |
24.7 |
26.9 |
O3' |
C3' |
C2' |
H3' |
234.3 |
240.1 |
C2' |
C3' |
O3' |
HO3' |
64.6 |
119.3 |
C1' |
C2' |
C3' |
H2' |
117.7 |
242.5 |
C1' |
C2' |
C3' |
H2'' |
240.1 |
120.8 |
C3' |
C2' |
C1' |
N1 |
140.2 |
147.4 |
C3' |
C2' |
C1' |
H1' |
265.3 |
268.8 |
H2' |
C2' |
C3' |
H2'' |
122.4 |
238.3 |
H3' |
C3' |
C4' |
H4' |
209.7 |
269.7 |
C4' |
C3' |
H3' |
O3' |
120.9 |
121.7 |
C4' |
C3' |
H3' |
C2' |
248.9 |
242.9 |
O3' |
C3' |
H3' |
C2' |
128.0 |
121.3 |
H3' |
C3' |
O3' |
HO3' |
299.4 |
355.9 |
H3' |
C3' |
C2' |
C1' |
242.6 |
203.6 |
H3' |
C3' |
C2' |
H2' |
124.9 |
321.1 |
H3' |
C3' |
C2' |
H2'' |
2.4 |
82.7 |
HO3' |
O3' |
C3' |
C2' |
64.6 |
119.3 |
HO3' |
O3' |
C3' |
H3' |
299.4 |
355.9 |
O4' |
C1' |
C2' |
N1 |
244.5 |
239.5 |
O4' |
C1' |
C2' |
H1' |
119.4 |
118.1 |
C1' |
C2' |
C3' |
H3' |
242.6 |
203.6 |
C3' |
C2' |
C1' |
H2' |
240.0 |
116.9 |
C3' |
C2' |
C1' |
H2'' |
117.3 |
237.5 |
H2' |
C2' |
C1' |
H2'' |
237.3 |
120.7 |
N1 |
C1' |
C2' |
H1' |
234.9 |
238.6 |
C2' |
C1' |
N1 |
C2 |
94.8 |
93.5 |
C2' |
C1' |
N1 |
C6 |
279.4 |
273.5 |
H2' |
C2' |
C3' |
H3' |
124.9 |
321.1 |
C3' |
C2' |
H2' |
C1' |
114.9 |
247.7 |
C3' |
C2' |
H2' |
H2'' |
238.6 |
125.1 |
C1' |
C2' |
H2' |
H2'' |
123.8 |
237.3 |
H2' |
C2' |
C1' |
N1 |
260.2 |
30.6 |
H2' |
C2' |
C1' |
H1' |
25.3 |
151.9 |
H2'' |
C2' |
C3' |
H3' |
2.4 |
82.7 |
C3' |
C2' |
H2'' |
C1' |
245.3 |
115.6 |
C3' |
C2' |
H2'' |
H2' |
123.6 |
237.5 |
C1' |
C2' |
H2'' |
H2' |
238.3 |
122.0 |
H2'' |
C2' |
C1' |
N1 |
22.9 |
269.9 |
H2'' |
C2' |
C1' |
H1' |
148.0 |
31.3 |
O4' |
C1' |
N1 |
C2' |
115.6 |
119.4 |
O4' |
C1' |
N1 |
H1' |
239.5 |
242.9 |
N1 |
C1' |
C2' |
H2' |
260.2 |
30.6 |
N1 |
C1' |
C2' |
H2'' |
22.9 |
269.9 |
C2' |
C1' |
N1 |
H1' |
123.9 |
123.5 |
C2 |
N1 |
C1' |
C6 |
175.4 |
180.0 |
C1' |
N1 |
C2 |
O2 |
356.9 |
359.9 |
C1' |
N1 |
C2 |
N3 |
179.7 |
180.0 |
C1' |
N1 |
C6 |
C5 |
185.6 |
180.0 |
C1' |
N1 |
C6 |
H6 |
6.3 |
360.0 |
O4' |
C1' |
H1' |
C2' |
242.6 |
242.3 |
O4' |
C1' |
H1' |
N1 |
118.6 |
118.0 |
H1' |
C1' |
C2' |
H2' |
25.3 |
151.9 |
H1' |
C1' |
C2' |
H2'' |
148.0 |
31.3 |
C2' |
C1' |
H1' |
N1 |
236.0 |
235.7 |
H1' |
C1' |
N1 |
C2 |
330.9 |
330.0 |
H1' |
C1' |
N1 |
C6 |
155.5 |
150.0 |
C2 |
N1 |
C1' |
H1' |
330.9 |
330.0 |
C1' |
N1 |
C2 |
C6 |
184.5 |
180.0 |
C2 |
N1 |
C6 |
C5 |
10.1 |
0.0 |
C2 |
N1 |
C6 |
H6 |
190.8 |
180.0 |
O2 |
C2 |
N1 |
N3 |
177.3 |
179.9 |
N1 |
C2 |
N3 |
C4 |
356.4 |
360.0 |
C6 |
N1 |
C1' |
H1' |
155.5 |
150.0 |
C1' |
N1 |
C6 |
C2 |
175.5 |
180.0 |
C6 |
N1 |
C2 |
O2 |
172.4 |
179.9 |
C6 |
N1 |
C2 |
N3 |
355.2 |
0.0 |
C4 |
C5 |
C6 |
N1 |
354.0 |
360.0 |
N1 |
C6 |
C5 |
C7 |
180.1 |
180.0 |
C5 |
C6 |
N1 |
H6 |
179.3 |
180.0 |
O2 |
C2 |
N1 |
C6 |
172.4 |
179.9 |
N1 |
C2 |
O2 |
N3 |
182.6 |
180.1 |
O2 |
C2 |
N3 |
C4 |
179.0 |
180.1 |
N3 |
C2 |
N1 |
C6 |
355.2 |
0.0 |
N1 |
C2 |
N3 |
O2 |
177.4 |
179.9 |
C2 |
N3 |
C4 |
N4 |
181.1 |
180.1 |
C2 |
N3 |
C4 |
C5 |
8.0 |
0.0 |
N4 |
C4 |
N3 |
C5 |
173.1 |
180.1 |
N3 |
C4 |
N4 |
H41 |
2.0 |
304.3 |
N3 |
C4 |
N4 |
H42 |
183.2 |
124.3 |
N3 |
C4 |
C5 |
C6 |
356.7 |
360.0 |
N3 |
C4 |
C5 |
C7 |
170.6 |
180.0 |
N3 |
C4 |
N4 |
C5 |
186.1 |
179.9 |
N4 |
C4 |
C5 |
C6 |
183.2 |
179.9 |
N4 |
C4 |
C5 |
C7 |
357.1 |
360.0 |
H41 |
N4 |
C4 |
H42 |
178.8 |
179.9 |
N1 |
C6 |
C5 |
C4 |
354.0 |
360.0 |
N3 |
C4 |
C5 |
N4 |
173.5 |
180.1 |
C5 |
C4 |
N4 |
H41 |
175.9 |
124.3 |
C5 |
C4 |
N4 |
H42 |
357.1 |
304.4 |
C6 |
C5 |
C4 |
C7 |
186.1 |
180.0 |
C4 |
C5 |
C6 |
H6 |
173.3 |
180.0 |
C4 |
C5 |
C7 |
C8 |
269.3 |
126.7 |
H41 |
N4 |
C4 |
C5 |
175.9 |
124.3 |
C4 |
N4 |
H41 |
H42 |
181.4 |
180.1 |
H42 |
N4 |
C4 |
C5 |
357.1 |
304.4 |
C4 |
N4 |
H42 |
H41 |
178.6 |
179.9 |
N1 |
C6 |
C5 |
H6 |
180.7 |
180.0 |
C4 |
C5 |
C6 |
C7 |
173.9 |
180.0 |
C6 |
C5 |
C7 |
C8 |
82.5 |
306.7 |
C4 |
C5 |
C7 |
C6 |
186.8 |
180.0 |
C7 |
C5 |
C6 |
H6 |
359.4 |
360.0 |
C5 |
C7 |
C8 |
C9 |
335.0 |
190.7 |
N1 |
C6 |
H6 |
C5 |
179.3 |
180.0 |
H6 |
C6 |
C5 |
C7 |
359.4 |
360.0 |
C7 |
C8 |
C9 |
H91 |
228.3 |
218.5 |
C7 |
C8 |
C9 |
H92 |
345.4 |
338.4 |
C7 |
C8 |
C9 |
H93 |
108.0 |
98.4 |
H91 |
C9 |
C8 |
H92 |
242.9 |
240.0 |
H91 |
C9 |
C8 |
H93 |
120.3 |
120.0 |
H92 |
C9 |
C8 |
H93 |
237.4 |
240.0 |
C8 |
C9 |
H91 |
H92 |
117.9 |
121.7 |
C8 |
C9 |
H91 |
H93 |
239.9 |
238.3 |
H92 |
C9 |
H91 |
H93 |
122.0 |
116.7 |
C8 |
C9 |
H92 |
H91 |
242.7 |
238.4 |
C8 |
C9 |
H92 |
H93 |
121.5 |
121.7 |
H91 |
C9 |
H92 |
H93 |
238.9 |
243.3 |
C8 |
C9 |
H93 |
H91 |
119.1 |
121.7 |
C8 |
C9 |
H93 |
H92 |
238.9 |
238.3 |
H91 |
C9 |
H93 |
H92 |
119.7 |
116.6 |