PDB Chemical Component RPC
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 RPC
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
OP2 |
P |
1.486 |
1.480 |
OP5 |
P2 |
1.599 |
1.480 |
OP6 |
P2 |
1.485 |
1.609 |
OP1 |
P |
1.489 |
1.610 |
P |
O5' |
1.581 |
1.610 |
C5' |
O5' |
1.413 |
1.428 |
C5' |
C4' |
1.498 |
1.531 |
P2 |
O3' |
1.598 |
1.610 |
P2 |
OP4 |
1.486 |
1.610 |
C3' |
C4' |
1.521 |
1.541 |
C3' |
O3' |
1.422 |
1.429 |
C3' |
C2' |
1.524 |
1.549 |
C4' |
O4' |
1.456 |
1.437 |
C2' |
O2' |
1.414 |
1.430 |
C2' |
C1' |
1.526 |
1.550 |
O4' |
C1' |
1.416 |
1.444 |
C1' |
N1 |
1.469 |
1.465 |
C6 |
N1 |
1.365 |
1.362 |
C6 |
C5 |
1.344 |
1.354 |
N1 |
C2 |
1.396 |
1.346 |
C5 |
C4 |
1.425 |
1.410 |
C2 |
O2 |
1.242 |
1.219 |
C2 |
N3 |
1.361 |
1.333 |
C4 |
N3 |
1.334 |
1.326 |
C4 |
N4 |
1.339 |
1.376 |
OP1 |
H1 |
0.950 |
0.967 |
C5' |
H2 |
1.100 |
1.090 |
C5' |
H3 |
1.100 |
1.090 |
C4' |
H4 |
1.100 |
1.090 |
C3' |
H5 |
1.100 |
1.090 |
C2' |
H6 |
1.100 |
1.089 |
O2' |
H7 |
0.951 |
0.968 |
C1' |
H8 |
1.100 |
1.090 |
C6 |
H9 |
1.079 |
1.081 |
C5 |
H10 |
1.080 |
1.079 |
N4 |
H11 |
1.000 |
0.970 |
N4 |
H12 |
1.000 |
0.969 |
OP4 |
H14 |
0.950 |
0.967 |
OP6 |
H15 |
0.950 |
0.967 |
P |
OP3 |
|
1.610 |
OP3 |
H17 |
|
0.967 |
Bond Angles for RPC
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
OP2 |
P |
OP3 |
|
109.5 |
OP1 |
P |
O5' |
108.2 |
109.5 |
OP1 |
P |
OP3 |
|
109.5 |
O5' |
P |
OP3 |
|
109.5 |
C5' |
C4' |
O4' |
109.0 |
109.9 |
C4' |
C5' |
H2 |
109.1 |
109.4 |
C4' |
C5' |
H3 |
109.1 |
109.5 |
C5' |
C4' |
H4 |
109.2 |
109.8 |
P2 |
OP4 |
H14 |
109.5 |
114.0 |
C3' |
C4' |
O4' |
106.2 |
107.3 |
C3' |
C4' |
H4 |
108.9 |
110.0 |
O3' |
C3' |
C2' |
110.0 |
110.5 |
O3' |
C3' |
H5 |
112.9 |
110.5 |
C3' |
C2' |
O2' |
115.0 |
110.8 |
C3' |
C2' |
C1' |
101.1 |
102.1 |
C2' |
C3' |
H5 |
111.3 |
110.6 |
C3' |
C2' |
H6 |
108.9 |
110.9 |
C4' |
O4' |
C1' |
109.4 |
107.0 |
O4' |
C4' |
H4 |
109.8 |
109.9 |
O2' |
C2' |
C1' |
112.2 |
110.9 |
O2' |
C2' |
H6 |
110.4 |
110.8 |
C2' |
O2' |
H7 |
109.5 |
113.9 |
C2' |
C1' |
N1 |
114.6 |
110.6 |
C1' |
C2' |
H6 |
108.9 |
111.0 |
C2' |
C1' |
H8 |
108.5 |
110.6 |
O4' |
C1' |
N1 |
108.8 |
110.6 |
O4' |
C1' |
H8 |
110.0 |
110.7 |
C1' |
N1 |
C2 |
117.7 |
119.8 |
N1 |
C1' |
H8 |
109.2 |
110.6 |
C6 |
N1 |
C2 |
119.9 |
120.4 |
C6 |
C5 |
C4 |
118.0 |
118.9 |
C5 |
C6 |
H9 |
119.5 |
120.3 |
C6 |
C5 |
H10 |
121.0 |
120.6 |
N1 |
C2 |
O2 |
117.6 |
119.5 |
N1 |
C2 |
N3 |
119.8 |
121.0 |
C5 |
C4 |
N3 |
121.5 |
119.6 |
C5 |
C4 |
N4 |
120.2 |
120.2 |
C4 |
C5 |
H10 |
121.0 |
120.5 |
N4 |
C4 |
N3 |
118.3 |
120.2 |
C4 |
N4 |
H11 |
120.0 |
119.9 |
C4 |
N4 |
H12 |
120.0 |
120.0 |
H2 |
C5' |
H3 |
109.5 |
109.4 |
H11 |
N4 |
H12 |
120.0 |
120.0 |
P |
OP3 |
H17 |
|
114.1 |
Torsion Angles for RPC
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
OP1 |
P |
OP2 |
OP3 |
|
120.0 |
O5' |
P |
OP2 |
OP3 |
|
240.0 |
OP2 |
P |
OP3 |
H17 |
|
60.0 |
OP5 |
P2 |
OP4 |
H14 |
0.0 |
180.0 |
OP6 |
P2 |
OP4 |
H14 |
126.8 |
60.0 |
OP2 |
P |
OP1 |
OP3 |
|
240.0 |
O5' |
P |
OP1 |
OP3 |
|
120.0 |
OP1 |
P |
OP3 |
H17 |
|
300.0 |
OP2 |
P |
O5' |
OP3 |
|
120.0 |
OP1 |
P |
O5' |
OP3 |
|
240.0 |
O5' |
P |
OP3 |
H17 |
|
180.0 |
C5' |
O5' |
P |
OP3 |
|
185.0 |
C3' |
C4' |
C5' |
O4' |
118.2 |
117.9 |
C3' |
C4' |
C5' |
H4 |
238.1 |
238.9 |
C5' |
C4' |
O4' |
C1' |
119.4 |
146.0 |
O4' |
C4' |
C5' |
H4 |
119.9 |
121.1 |
H2 |
C5' |
C4' |
H3 |
119.6 |
119.9 |
P2 |
O3' |
C3' |
H5 |
330.3 |
2.5 |
C5' |
C4' |
C3' |
O4' |
240.2 |
240.6 |
C3' |
C4' |
C5' |
H2 |
17.4 |
64.3 |
C3' |
C4' |
C5' |
H3 |
257.8 |
304.3 |
C5' |
C4' |
C3' |
H4 |
122.1 |
121.0 |
C3' |
C4' |
O4' |
C1' |
356.5 |
26.5 |
O4' |
C4' |
C3' |
H4 |
241.9 |
240.5 |
O3' |
C3' |
C4' |
O4' |
270.0 |
239.3 |
O3' |
C3' |
C4' |
H4 |
28.1 |
358.8 |
O3' |
C3' |
C2' |
O2' |
316.8 |
339.6 |
O3' |
C3' |
C2' |
C1' |
77.9 |
97.8 |
C2' |
C3' |
O3' |
H5 |
124.9 |
122.7 |
O3' |
C3' |
C2' |
H6 |
192.4 |
216.1 |
C2' |
C3' |
C4' |
O4' |
26.2 |
358.0 |
C2' |
C3' |
C4' |
H4 |
144.3 |
117.5 |
O3' |
C3' |
C2' |
H5 |
234.2 |
237.4 |
O2' |
C2' |
C3' |
C1' |
238.9 |
241.8 |
O2' |
C2' |
C3' |
H6 |
124.4 |
123.6 |
C3' |
C2' |
O2' |
H7 |
135.6 |
180.0 |
C3' |
C2' |
C1' |
N1 |
156.4 |
155.5 |
C1' |
C2' |
C3' |
H6 |
245.5 |
241.7 |
C3' |
C2' |
C1' |
H8 |
278.7 |
278.4 |
O4' |
C4' |
C5' |
H2 |
259.1 |
306.4 |
O4' |
C4' |
C5' |
H3 |
139.5 |
186.5 |
C5' |
C4' |
O4' |
H4 |
240.4 |
239.0 |
C3' |
C4' |
O4' |
H4 |
117.6 |
119.6 |
C4' |
O4' |
C1' |
N1 |
215.5 |
201.4 |
C4' |
O4' |
C1' |
H8 |
95.9 |
78.5 |
C3' |
C2' |
O2' |
C1' |
114.8 |
112.7 |
O2' |
C2' |
C3' |
H5 |
82.7 |
102.2 |
C3' |
C2' |
O2' |
H6 |
236.4 |
236.4 |
O2' |
C2' |
C1' |
N1 |
279.4 |
273.7 |
C1' |
C2' |
O2' |
H6 |
121.6 |
123.7 |
O2' |
C2' |
C1' |
H8 |
41.7 |
36.5 |
C3' |
C2' |
C1' |
O2' |
237.0 |
241.9 |
C1' |
C2' |
C3' |
H5 |
203.7 |
220.4 |
C3' |
C2' |
C1' |
H6 |
114.5 |
118.3 |
C4' |
O4' |
C1' |
C2' |
339.0 |
319.9 |
O2' |
C2' |
C1' |
H6 |
237.5 |
236.4 |
C1' |
C2' |
O2' |
H7 |
20.9 |
67.3 |
O4' |
C1' |
C2' |
N1 |
240.2 |
241.5 |
O4' |
C1' |
C2' |
H8 |
117.9 |
118.6 |
C2' |
C1' |
N1 |
C2 |
83.4 |
295.1 |
N1 |
C1' |
C2' |
H8 |
237.7 |
237.1 |
C1' |
O4' |
C4' |
H4 |
239.0 |
267.0 |
C2' |
C1' |
O4' |
N1 |
123.5 |
118.5 |
O4' |
C1' |
C2' |
H6 |
282.1 |
278.8 |
C2' |
C1' |
O4' |
H8 |
243.1 |
241.4 |
O4' |
C1' |
N1 |
C2 |
201.5 |
49.2 |
N1 |
C1' |
O4' |
H8 |
119.6 |
122.9 |
N1 |
C1' |
C2' |
H6 |
41.9 |
37.3 |
C2' |
C1' |
N1 |
H8 |
121.9 |
122.9 |
O4' |
C1' |
N1 |
H8 |
239.9 |
237.0 |
C6 |
N1 |
C1' |
C2 |
179.3 |
180.2 |
C1' |
N1 |
C2 |
O2 |
359.4 |
359.9 |
C1' |
N1 |
C2 |
N3 |
179.8 |
179.7 |
C1' |
N1 |
C6 |
C2 |
180.7 |
179.8 |
C6 |
N1 |
C1' |
H8 |
140.8 |
352.3 |
C6 |
N1 |
C2 |
O2 |
180.1 |
179.7 |
C6 |
N1 |
C2 |
N3 |
0.5 |
359.6 |
C5 |
C6 |
N1 |
C2 |
359.6 |
0.2 |
C6 |
C5 |
C4 |
N3 |
359.4 |
0.1 |
C6 |
C5 |
C4 |
N4 |
179.6 |
180.0 |
C4 |
C5 |
C6 |
H10 |
180.0 |
180.0 |
C2 |
N1 |
C1' |
H8 |
321.6 |
172.2 |
C4 |
C5 |
C6 |
H9 |
180.4 |
180.0 |
C6 |
C5 |
C4 |
H10 |
180.0 |
180.0 |
N4 |
C4 |
C5 |
N3 |
180.2 |
179.9 |
C5 |
C4 |
N4 |
H11 |
179.8 |
0.0 |
C5 |
C4 |
N4 |
H12 |
359.8 |
180.1 |
N1 |
C2 |
O2 |
N3 |
180.4 |
179.9 |
N1 |
C2 |
N3 |
O2 |
179.6 |
180.1 |
N1 |
C2 |
N3 |
C4 |
359.4 |
0.5 |
C5 |
C4 |
N3 |
N4 |
180.2 |
179.9 |
N3 |
C4 |
C5 |
H10 |
179.4 |
180.0 |
N3 |
C4 |
N4 |
H11 |
360.0 |
180.0 |
N3 |
C4 |
N4 |
H12 |
180.0 |
0.0 |
C5 |
C4 |
N4 |
N3 |
179.8 |
180.1 |
N4 |
C4 |
C5 |
H10 |
359.6 |
360.0 |
H11 |
N4 |
C4 |
H12 |
180.0 |
179.9 |
H1 |
OP1 |
P |
O5' |
235.7 |
60.0 |
H1 |
OP1 |
P |
OP3 |
|
300.0 |
H2 |
C5' |
C4' |
O4' |
259.1 |
306.4 |
C4' |
C5' |
H2 |
H3 |
240.6 |
240.0 |
H2 |
C5' |
C4' |
H4 |
139.2 |
185.4 |
H3 |
C5' |
C4' |
O4' |
139.5 |
186.5 |
C4' |
C5' |
H3 |
H2 |
119.4 |
119.9 |
H3 |
C5' |
C4' |
H4 |
19.6 |
65.4 |
C5' |
C4' |
H4 |
O4' |
119.4 |
121.0 |
H4 |
C4' |
C5' |
H2 |
139.2 |
185.4 |
H4 |
C4' |
C5' |
H3 |
19.6 |
65.4 |
C3' |
C4' |
H4 |
O4' |
244.2 |
242.1 |
H4 |
C4' |
O4' |
C1' |
239.0 |
267.0 |
H5 |
C3' |
C4' |
O4' |
145.1 |
116.7 |
H5 |
C3' |
C4' |
H4 |
263.2 |
236.3 |
O3' |
C3' |
H5 |
C2' |
124.2 |
122.7 |
H5 |
C3' |
C2' |
O2' |
82.7 |
102.2 |
H5 |
C3' |
C2' |
C1' |
203.7 |
220.4 |
H5 |
C3' |
C2' |
H6 |
318.3 |
338.7 |
C3' |
C2' |
H6 |
O2' |
127.1 |
123.6 |
C3' |
C2' |
H6 |
C1' |
250.7 |
247.2 |
H6 |
C2' |
C3' |
H5 |
318.3 |
338.7 |
O2' |
C2' |
H6 |
C1' |
123.6 |
123.7 |
H6 |
C2' |
O2' |
H7 |
259.2 |
303.6 |
H6 |
C2' |
C1' |
N1 |
41.9 |
37.3 |
H6 |
C2' |
C1' |
H8 |
164.1 |
160.2 |
H7 |
O2' |
C2' |
C1' |
20.9 |
67.3 |
H7 |
O2' |
C2' |
H6 |
259.2 |
303.6 |
C2' |
C1' |
H8 |
N1 |
234.5 |
237.1 |
H8 |
C1' |
C2' |
H6 |
164.1 |
160.2 |
O4' |
C1' |
H8 |
N1 |
119.4 |
122.9 |
H8 |
C1' |
N1 |
C2 |
321.6 |
172.2 |
H9 |
C6 |
N1 |
C2 |
179.6 |
180.2 |
H9 |
C6 |
C5 |
C4 |
180.4 |
180.0 |
H9 |
C6 |
C5 |
H10 |
0.5 |
0.1 |
C6 |
C5 |
H10 |
C4 |
180.0 |
179.9 |
H10 |
C5 |
C6 |
H9 |
0.5 |
0.1 |
H10 |
C5 |
C4 |
N3 |
179.4 |
180.0 |
H10 |
C5 |
C4 |
N4 |
359.6 |
360.0 |
H11 |
N4 |
C4 |
N3 |
360.0 |
180.0 |
C4 |
N4 |
H11 |
H12 |
180.0 |
180.1 |
H12 |
N4 |
C4 |
N3 |
180.0 |
0.0 |
C4 |
N4 |
H12 |
H11 |
180.0 |
179.9 |
OP1 |
P |
OP3 |
O5' |
|
120.0 |