PDB Chemical Component RYY
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 RYY
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C1' |
N |
1.473 |
1.465 |
| N |
C7 |
1.356 |
1.348 |
| N |
HN |
1.000 |
0.970 |
| C4 |
S |
1.670 |
1.763 |
| N3S |
S |
1.468 |
1.655 |
| S |
O2S |
1.476 |
1.421 |
| S |
O1S |
1.664 |
1.421 |
| C7 |
C1 |
1.473 |
1.478 |
| C1 |
C6 |
1.372 |
1.396 |
| C1 |
C2 |
1.372 |
1.396 |
| C2 |
C3 |
1.404 |
1.380 |
| C2 |
H2 |
1.080 |
1.080 |
| C3 |
C4 |
1.397 |
1.383 |
| C3 |
H3 |
1.080 |
1.080 |
| C5 |
C4 |
1.431 |
1.383 |
| C6 |
C5 |
1.365 |
1.379 |
| C5 |
H5 |
1.080 |
1.080 |
| C6 |
H6 |
1.080 |
1.080 |
| O7 |
C7 |
1.201 |
1.215 |
| C2' |
C1' |
1.555 |
1.530 |
| C1' |
H1' |
1.100 |
1.090 |
| C1' |
H1'A |
1.100 |
1.091 |
| C16 |
C2' |
1.527 |
1.530 |
| C16 |
H16 |
1.100 |
1.089 |
| C16 |
H16A |
1.100 |
1.090 |
| C16 |
H16B |
1.100 |
1.091 |
| C2' |
H2' |
1.100 |
1.090 |
| C2' |
H2'A |
1.099 |
1.090 |
| N3S |
HN3S |
1.000 |
0.970 |
| N3S |
HN3A |
1.000 |
0.970 |
Bond Angles for RYY
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C1' |
N |
HN |
117.2 |
120.0 |
| C7 |
N |
HN |
117.1 |
119.9 |
| N |
C7 |
C1 |
123.1 |
120.0 |
| C4 |
S |
O2S |
104.1 |
106.4 |
| C4 |
S |
O1S |
115.3 |
106.4 |
| O1S |
S |
O2S |
108.1 |
123.1 |
| C2 |
C1 |
C6 |
116.1 |
119.7 |
| C1 |
C6 |
C5 |
124.5 |
119.8 |
| C1 |
C6 |
H6 |
117.7 |
120.0 |
| C1 |
C2 |
C3 |
120.9 |
119.8 |
| C1 |
C2 |
H2 |
119.6 |
120.1 |
| C3 |
C2 |
H2 |
119.5 |
120.1 |
| C2 |
C3 |
C4 |
123.5 |
120.2 |
| C2 |
C3 |
H3 |
118.3 |
119.9 |
| C4 |
C3 |
H3 |
118.3 |
119.9 |
| C6 |
C5 |
H5 |
119.5 |
119.9 |
| C2' |
C1' |
H1' |
111.1 |
109.5 |
| C2' |
C1' |
H1'A |
111.1 |
109.4 |
| H1' |
C1' |
H1'A |
107.8 |
109.4 |
| C2' |
C16 |
H16 |
109.5 |
109.5 |
| C2' |
C16 |
H16A |
109.4 |
109.4 |
| C2' |
C16 |
H16B |
109.5 |
109.4 |
| C16 |
C2' |
H2' |
107.9 |
109.5 |
| C16 |
C2' |
H2'A |
107.9 |
109.5 |
| H16 |
C16 |
H16A |
109.5 |
109.5 |
| H16 |
C16 |
H16B |
109.4 |
109.5 |
| H16A |
C16 |
H16B |
109.5 |
109.5 |
| H2' |
C2' |
H2'A |
111.0 |
109.5 |
| HN3S |
N3S |
HN3A |
109.5 |
120.1 |
Torsion Angles for RYY
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C7 |
N |
C1' |
HN |
180.0 |
179.8 |
| C1' |
N |
C7 |
HN |
180.0 |
180.2 |
| HN |
N |
C7 |
C1 |
4.2 |
0.1 |
| O1S |
S |
C4 |
O2S |
118.3 |
227.2 |
| C4 |
S |
O2S |
O1S |
123.1 |
237.1 |
| C4 |
S |
O1S |
O2S |
244.0 |
122.9 |
| C1 |
C7 |
N |
HN |
4.2 |
0.1 |
| C7 |
C1 |
C6 |
H6 |
356.0 |
0.3 |
| C7 |
C1 |
C2 |
H2 |
0.1 |
359.7 |
| N |
C7 |
C1 |
C6 |
0.3 |
179.9 |
| C6 |
C1 |
C2 |
C3 |
355.7 |
0.0 |
| C6 |
C1 |
C2 |
H2 |
175.7 |
180.0 |
| C1 |
C6 |
C5 |
H5 |
181.9 |
180.0 |
| N |
C7 |
C1 |
C2 |
175.6 |
0.2 |
| C2 |
C1 |
C6 |
C5 |
0.5 |
359.9 |
| C2 |
C1 |
C6 |
H6 |
180.5 |
180.0 |
| C3 |
C2 |
C1 |
H2 |
180.0 |
180.0 |
| C1 |
C2 |
C3 |
C4 |
6.0 |
0.0 |
| C1 |
C2 |
C3 |
H3 |
186.0 |
180.0 |
| C3 |
C2 |
C1 |
C6 |
355.7 |
0.0 |
| C1 |
C2 |
C3 |
H2 |
180.0 |
180.0 |
| C4 |
C3 |
C2 |
H3 |
180.0 |
180.1 |
| H2 |
C2 |
C1 |
C6 |
175.7 |
180.0 |
| C1 |
C2 |
H2 |
C3 |
180.0 |
180.0 |
| H2 |
C2 |
C3 |
C4 |
186.0 |
180.0 |
| H2 |
C2 |
C3 |
H3 |
6.0 |
359.9 |
| C3 |
C4 |
S |
O2S |
331.3 |
336.4 |
| C3 |
C4 |
S |
O1S |
89.6 |
203.6 |
| C4 |
C3 |
C2 |
H2 |
186.0 |
180.0 |
| C2 |
C3 |
C4 |
H3 |
180.0 |
179.9 |
| H3 |
C3 |
C2 |
H2 |
6.0 |
359.9 |
| C2 |
C3 |
H3 |
C4 |
180.0 |
180.1 |
| C5 |
C4 |
S |
O2S |
151.0 |
156.4 |
| C5 |
C4 |
S |
O1S |
269.3 |
23.6 |
| C1 |
C6 |
C5 |
C4 |
1.9 |
0.0 |
| C5 |
C4 |
C3 |
H3 |
176.7 |
180.0 |
| C1 |
C6 |
C5 |
H6 |
180.0 |
180.1 |
| C1 |
C6 |
H6 |
C5 |
180.0 |
179.9 |
| H6 |
C6 |
C5 |
H5 |
1.9 |
360.0 |
| O7 |
C7 |
N |
HN |
181.7 |
180.0 |
| C2' |
C1' |
N |
HN |
288.6 |
0.2 |
| H1' |
C1' |
C2' |
H1'A |
120.0 |
119.9 |
| H1' |
C1' |
N |
HN |
48.6 |
120.3 |
| C2' |
C1' |
H1' |
H1'A |
238.1 |
240.1 |
| H1'A |
C1' |
N |
HN |
168.6 |
240.2 |
| C2' |
C1' |
H1'A |
H1' |
121.9 |
120.0 |
| C16 |
C2' |
C1' |
H1' |
177.9 |
59.9 |
| C16 |
C2' |
C1' |
H1'A |
57.9 |
300.0 |
| H16 |
C16 |
C2' |
H16A |
240.0 |
240.0 |
| H16 |
C16 |
C2' |
H16B |
120.0 |
120.0 |
| H16A |
C16 |
C2' |
H16B |
240.0 |
240.0 |
| H2' |
C2' |
C16 |
H2'A |
120.0 |
120.1 |
| C2' |
C16 |
H16 |
H16A |
120.0 |
120.0 |
| C2' |
C16 |
H16 |
H16B |
240.0 |
240.0 |
| H16 |
C16 |
C2' |
H2' |
60.0 |
180.0 |
| H16 |
C16 |
C2' |
H2'A |
300.0 |
60.0 |
| H16A |
C16 |
H16 |
H16B |
120.0 |
120.1 |
| C2' |
C16 |
H16A |
H16 |
240.0 |
240.0 |
| C2' |
C16 |
H16A |
H16B |
120.0 |
119.9 |
| H16A |
C16 |
C2' |
H2' |
180.0 |
300.1 |
| H16A |
C16 |
C2' |
H2'A |
60.0 |
180.0 |
| H16 |
C16 |
H16A |
H16B |
240.0 |
239.9 |
| C2' |
C16 |
H16B |
H16 |
120.0 |
120.0 |
| C2' |
C16 |
H16B |
H16A |
240.0 |
240.1 |
| H16B |
C16 |
C2' |
H2' |
300.0 |
60.0 |
| H16B |
C16 |
C2' |
H2'A |
180.0 |
300.0 |
| H16 |
C16 |
H16B |
H16A |
120.0 |
120.1 |
| H2' |
C2' |
C1' |
H1' |
297.8 |
180.0 |
| H2' |
C2' |
C1' |
H1'A |
177.8 |
60.1 |
| H2' |
C2' |
C16 |
H16 |
60.0 |
180.0 |
| H2' |
C2' |
C16 |
H16A |
180.0 |
300.1 |
| H2' |
C2' |
C16 |
H16B |
300.0 |
60.0 |
| C16 |
C2' |
H2' |
H2'A |
241.9 |
239.9 |
| H2'A |
C2' |
C1' |
H1' |
57.8 |
299.9 |
| H2'A |
C2' |
C1' |
H1'A |
297.9 |
180.0 |
| H2'A |
C2' |
C16 |
H16 |
300.0 |
60.0 |
| H2'A |
C2' |
C16 |
H16A |
60.0 |
180.0 |
| H2'A |
C2' |
C16 |
H16B |
180.0 |
300.0 |
| C16 |
C2' |
H2'A |
H2' |
118.0 |
120.1 |