PDB Chemical Component RY
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 RY
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| OP1 |
P |
1.481 |
1.480 |
| O2 |
C2 |
1.223 |
1.217 |
| O3' |
C3' |
1.428 |
1.429 |
| O2' |
C2' |
1.423 |
1.428 |
| P |
OP2 |
1.485 |
1.609 |
| P |
O5' |
1.626 |
1.610 |
| C2 |
N3 |
1.332 |
1.339 |
| C2 |
N1 |
1.400 |
1.348 |
| C3' |
C4' |
1.550 |
1.541 |
| C3' |
C2' |
1.547 |
1.548 |
| C4' |
O4' |
1.425 |
1.438 |
| C4' |
C5' |
1.539 |
1.530 |
| C1' |
C2' |
1.522 |
1.550 |
| C1' |
O4' |
1.415 |
1.443 |
| C1' |
N1 |
1.488 |
1.465 |
| N3 |
C4 |
1.295 |
1.386 |
| N1 |
C6 |
1.374 |
1.472 |
| C5' |
O5' |
1.432 |
1.429 |
| C4 |
N4 |
1.305 |
1.391 |
| C4 |
C5 |
1.421 |
1.332 |
| C6 |
C5 |
1.361 |
1.514 |
| P |
OP3 |
1.613 |
1.610 |
| C5' |
H5'' |
1.100 |
1.091 |
| C5' |
H5' |
1.100 |
1.090 |
| C4' |
H4' |
1.100 |
1.090 |
| C3' |
H3' |
1.100 |
1.090 |
| O3' |
H1 |
0.950 |
0.967 |
| C2' |
H2' |
1.100 |
1.091 |
| O2' |
HO2' |
0.950 |
0.967 |
| C1' |
H1' |
1.100 |
1.090 |
| N3 |
H3 |
1.000 |
0.970 |
| N4 |
H41 |
1.000 |
0.971 |
| N4 |
H42 |
1.000 |
0.970 |
| C5 |
H5 |
1.080 |
1.081 |
| C6 |
H6 |
1.100 |
1.090 |
| C6 |
H2 |
1.100 |
1.091 |
| OP2 |
H4 |
0.950 |
0.967 |
| OP3 |
H7 |
0.950 |
0.967 |
Bond Angles for RY
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP1 |
P |
OP2 |
116.5 |
109.5 |
| OP1 |
P |
OP3 |
107.2 |
109.5 |
| O2 |
C2 |
N3 |
116.5 |
119.0 |
| O3' |
C3' |
C2' |
110.1 |
110.5 |
| O3' |
C3' |
H3' |
111.0 |
110.5 |
| O2' |
C2' |
H2' |
110.5 |
110.8 |
| O5' |
P |
OP2 |
108.4 |
109.5 |
| OP2 |
P |
OP3 |
108.2 |
109.5 |
| P |
OP2 |
H4 |
109.5 |
114.0 |
| P |
O5' |
C5' |
124.4 |
123.0 |
| O5' |
P |
OP3 |
107.3 |
109.4 |
| C2 |
N3 |
C4 |
122.3 |
123.4 |
| C2 |
N3 |
H3 |
118.8 |
118.3 |
| C2 |
N1 |
C6 |
119.1 |
118.5 |
| C3' |
C4' |
H4' |
108.3 |
110.0 |
| C2' |
C3' |
H3' |
109.3 |
110.5 |
| C3' |
C2' |
H2' |
108.7 |
110.9 |
| O4' |
C4' |
H4' |
109.9 |
109.9 |
| C4' |
C5' |
H5'' |
108.1 |
109.5 |
| C4' |
C5' |
H5' |
108.1 |
109.4 |
| C1' |
C2' |
H2' |
109.1 |
110.9 |
| C1' |
N1 |
C6 |
121.4 |
120.8 |
| N1 |
C1' |
H1' |
108.8 |
110.7 |
| N3 |
C4 |
N4 |
119.2 |
119.5 |
| N3 |
C4 |
C5 |
121.1 |
121.1 |
| C4 |
N3 |
H3 |
118.9 |
118.3 |
| N1 |
C6 |
C5 |
120.2 |
117.2 |
| N1 |
C6 |
H6 |
106.7 |
107.9 |
| N1 |
C6 |
H2 |
106.7 |
107.9 |
| O5' |
C5' |
H5'' |
108.1 |
109.5 |
| O5' |
C5' |
H5' |
108.1 |
109.5 |
| N4 |
C4 |
C5 |
119.7 |
119.4 |
| C4 |
N4 |
H41 |
109.5 |
119.9 |
| C4 |
N4 |
H42 |
109.5 |
120.0 |
| C4 |
C5 |
H5 |
121.1 |
121.0 |
| C6 |
C5 |
H5 |
121.2 |
121.0 |
| P |
OP3 |
H7 |
109.5 |
114.0 |
| H5'' |
C5' |
H5' |
109.5 |
109.5 |
| H41 |
N4 |
H42 |
109.5 |
120.0 |
| H6 |
C6 |
H2 |
109.5 |
107.7 |
Torsion Angles for RY
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O5' |
P |
OP1 |
OP2 |
122.9 |
120.0 |
| OP2 |
P |
OP1 |
OP3 |
121.3 |
120.1 |
| OP1 |
P |
OP2 |
H4 |
360.0 |
300.0 |
| O5' |
P |
OP1 |
OP3 |
244.2 |
240.0 |
| OP1 |
P |
OP3 |
H7 |
360.0 |
180.0 |
| O2 |
C2 |
N3 |
C4 |
183.6 |
180.0 |
| O2 |
C2 |
N3 |
H3 |
3.6 |
360.0 |
| O2 |
C2 |
N1 |
C6 |
174.2 |
180.3 |
| O3' |
C3' |
C4' |
H4' |
345.4 |
358.8 |
| C2' |
C3' |
O3' |
H3' |
121.1 |
122.6 |
| O3' |
C3' |
C2' |
H2' |
220.9 |
216.0 |
| O2' |
C2' |
C3' |
H3' |
107.8 |
102.2 |
| C3' |
C2' |
O2' |
H2' |
236.2 |
236.4 |
| C1' |
C2' |
O2' |
H2' |
121.0 |
123.6 |
| OP1 |
P |
OP2 |
OP3 |
239.3 |
239.9 |
| OP2 |
P |
O5' |
C5' |
132.9 |
175.0 |
| O5' |
P |
OP2 |
OP3 |
116.1 |
120.0 |
| OP2 |
P |
OP3 |
H7 |
233.7 |
60.0 |
| OP1 |
P |
O5' |
OP2 |
232.4 |
240.0 |
| OP1 |
P |
O5' |
OP3 |
115.7 |
120.0 |
| OP2 |
P |
O5' |
OP3 |
243.4 |
240.0 |
| O5' |
P |
OP2 |
H4 |
236.8 |
180.0 |
| P |
O5' |
C5' |
H5'' |
316.2 |
300.0 |
| P |
O5' |
C5' |
H5' |
197.8 |
60.0 |
| O5' |
P |
OP3 |
H7 |
116.9 |
300.0 |
| N3 |
C2 |
N1 |
C6 |
356.9 |
0.3 |
| C2 |
N3 |
C4 |
N4 |
180.7 |
180.0 |
| C2 |
N3 |
C4 |
C5 |
2.0 |
0.0 |
| C4 |
N3 |
C2 |
H3 |
180.0 |
180.0 |
| C1' |
N1 |
C2 |
C6 |
181.5 |
179.8 |
| C2 |
N1 |
C1' |
H1' |
346.4 |
172.3 |
| C2 |
N1 |
C6 |
C5 |
2.0 |
359.5 |
| C2 |
N1 |
C6 |
H6 |
123.6 |
121.7 |
| C2 |
N1 |
C6 |
H2 |
240.5 |
237.8 |
| O4' |
C4' |
C3' |
H4' |
242.8 |
240.5 |
| C3' |
C4' |
C5' |
H5'' |
299.8 |
64.3 |
| C3' |
C4' |
C5' |
H5' |
58.2 |
304.3 |
| O3' |
C3' |
C2' |
H3' |
237.9 |
237.3 |
| O2' |
C2' |
C3' |
H2' |
124.7 |
123.6 |
| C2' |
C3' |
C4' |
H4' |
104.7 |
117.5 |
| C1' |
C2' |
C3' |
H2' |
244.9 |
241.9 |
| C3' |
C4' |
O4' |
H4' |
116.0 |
119.6 |
| O4' |
C4' |
C5' |
H5'' |
181.6 |
306.4 |
| O4' |
C4' |
C5' |
H5' |
300.0 |
186.4 |
| O5' |
C5' |
C4' |
H5'' |
239.2 |
120.0 |
| O5' |
C5' |
C4' |
H5' |
120.8 |
240.0 |
| H5'' |
C5' |
C4' |
H5' |
241.6 |
120.0 |
| O2' |
C2' |
C1' |
H2' |
238.1 |
236.4 |
| C1' |
C2' |
C3' |
H3' |
227.9 |
220.5 |
| C3' |
C2' |
C1' |
H2' |
114.9 |
118.2 |
| C1' |
O4' |
C4' |
H4' |
283.1 |
266.9 |
| C2 |
N1 |
C1' |
C6 |
178.5 |
180.2 |
| N1 |
C1' |
C2' |
H2' |
47.5 |
37.4 |
| C1' |
N1 |
C6 |
C5 |
180.5 |
179.7 |
| C1' |
N1 |
C6 |
H6 |
302.1 |
301.9 |
| C1' |
N1 |
C6 |
H2 |
59.0 |
58.0 |
| C2 |
N3 |
C4 |
H3 |
180.0 |
180.0 |
| N4 |
C4 |
N3 |
C5 |
178.7 |
180.0 |
| N3 |
C4 |
N4 |
H41 |
180.0 |
0.1 |
| N3 |
C4 |
N4 |
H42 |
300.0 |
180.0 |
| N3 |
C4 |
C5 |
H5 |
177.0 |
180.0 |
| C6 |
N1 |
C1' |
H1' |
167.9 |
352.1 |
| N1 |
C6 |
C5 |
H5 |
180.9 |
180.3 |
| H6 |
C6 |
N1 |
H2 |
243.0 |
243.9 |
| C5' |
O5' |
P |
OP2 |
132.9 |
175.0 |
| C5' |
O5' |
P |
OP3 |
249.5 |
295.0 |
| C4' |
C5' |
O5' |
H5'' |
120.8 |
240.0 |
| C4' |
C5' |
O5' |
H5' |
239.2 |
120.0 |
| H5'' |
C5' |
O5' |
H5' |
118.4 |
240.0 |
| N3 |
C4 |
N4 |
C5 |
181.3 |
180.0 |
| N4 |
C4 |
N3 |
H3 |
0.6 |
0.0 |
| N4 |
C4 |
C5 |
H5 |
358.3 |
360.0 |
| H41 |
N4 |
C4 |
H42 |
240.0 |
180.0 |
| N3 |
C4 |
C5 |
N4 |
178.7 |
180.0 |
| C5 |
C4 |
N3 |
H3 |
181.9 |
180.0 |
| N1 |
C6 |
C5 |
C4 |
0.9 |
0.5 |
| C5 |
C4 |
N4 |
H41 |
358.7 |
180.0 |
| C5 |
C4 |
N4 |
H42 |
118.7 |
0.0 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
179.7 |
| N1 |
C6 |
C5 |
H6 |
121.5 |
122.1 |
| N1 |
C6 |
C5 |
H2 |
238.5 |
238.2 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
180.3 |
| OP1 |
P |
OP3 |
OP2 |
126.3 |
120.1 |
| O5' |
P |
OP3 |
OP2 |
243.3 |
240.0 |
| OP3 |
P |
OP2 |
H4 |
120.7 |
60.0 |
| OP3 |
P |
O5' |
C5' |
249.5 |
295.0 |
| C4' |
C5' |
H5'' |
H5' |
117.5 |
240.0 |
| O5' |
C5' |
H5'' |
H5' |
242.5 |
120.0 |
| C4' |
C5' |
H5' |
H5'' |
242.5 |
120.0 |
| O5' |
C5' |
H5' |
H5'' |
117.5 |
240.0 |
| H4' |
C4' |
C5' |
H5'' |
60.3 |
185.4 |
| H4' |
C4' |
C5' |
H5' |
178.8 |
65.5 |
| O3' |
C3' |
H3' |
C2' |
121.6 |
122.6 |
| H3' |
C3' |
C4' |
H4' |
220.8 |
236.2 |
| H3' |
C3' |
C2' |
H2' |
343.1 |
338.6 |
| H1 |
O3' |
C3' |
C2' |
64.9 |
65.3 |
| H1 |
O3' |
C3' |
H3' |
303.8 |
302.6 |
| H2' |
C2' |
C3' |
H3' |
343.1 |
338.6 |
| HO2' |
O2' |
C2' |
H2' |
303.8 |
62.2 |
| H1' |
C1' |
C2' |
H2' |
169.0 |
160.3 |
| H1' |
C1' |
N1 |
C6 |
167.9 |
352.1 |
| C2 |
N3 |
H3 |
C4 |
180.0 |
180.0 |
| H3 |
N3 |
C4 |
N4 |
0.6 |
0.0 |
| H3 |
N3 |
C4 |
C5 |
181.9 |
180.0 |
| H41 |
N4 |
C4 |
C5 |
358.7 |
180.0 |
| C4 |
N4 |
H41 |
H42 |
120.0 |
180.0 |
| H42 |
N4 |
C4 |
C5 |
118.7 |
0.0 |
| C4 |
N4 |
H42 |
H41 |
240.0 |
180.0 |
| N1 |
C6 |
H6 |
C5 |
230.3 |
232.4 |
| N1 |
C6 |
H6 |
H2 |
115.1 |
116.2 |
| H6 |
C6 |
C5 |
H5 |
59.4 |
58.2 |
| N1 |
C6 |
H2 |
C5 |
129.7 |
127.4 |
| N1 |
C6 |
H2 |
H6 |
244.9 |
243.8 |
| H2 |
C6 |
C5 |
H5 |
302.4 |
302.1 |
| H4 |
OP2 |
P |
OP3 |
120.7 |
60.0 |