PDB Chemical Component RYZ
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 RYZ
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C4 |
S |
1.667 |
1.763 |
| N3S |
S |
1.615 |
1.657 |
| O1S |
S |
1.475 |
1.421 |
| S |
O2S |
1.431 |
1.420 |
| C1' |
N' |
1.478 |
1.466 |
| N' |
C7 |
1.330 |
1.347 |
| N' |
HN' |
1.000 |
0.970 |
| O' |
C7 |
1.249 |
1.216 |
| C7 |
C1 |
1.476 |
1.479 |
| C1 |
C5 |
1.409 |
1.396 |
| C1 |
C3 |
1.406 |
1.395 |
| C3 |
C2 |
1.442 |
1.379 |
| C2 |
C4 |
1.414 |
1.384 |
| C2 |
H2 |
1.080 |
1.079 |
| C3 |
H3 |
1.080 |
1.080 |
| C6 |
C4 |
1.454 |
1.384 |
| C5 |
C6 |
1.427 |
1.380 |
| C5 |
H5 |
1.080 |
1.081 |
| C6 |
H6 |
1.080 |
1.080 |
| C2' |
F2'1 |
1.333 |
1.399 |
| F3'1 |
C3' |
1.336 |
1.399 |
| F4'1 |
C4' |
1.302 |
1.400 |
| C2' |
F2'2 |
1.297 |
1.399 |
| F3'2 |
C3' |
1.308 |
1.399 |
| C4' |
F4'2 |
1.309 |
1.398 |
| C4' |
F4'3 |
1.329 |
1.399 |
| C1' |
C2' |
1.557 |
1.530 |
| C1' |
H1' |
1.100 |
1.090 |
| C1' |
H1'A |
1.100 |
1.090 |
| C3' |
C2' |
1.491 |
1.529 |
| C3' |
C4' |
1.523 |
1.530 |
| N3S |
HN3S |
1.000 |
0.970 |
| N3S |
HN3A |
1.000 |
0.970 |
Bond Angles for RYZ
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C4 |
S |
O2S |
108.7 |
106.4 |
| O1S |
S |
O2S |
115.3 |
123.2 |
| C1' |
N' |
HN' |
118.7 |
120.0 |
| C7 |
N' |
HN' |
118.7 |
120.0 |
| N' |
C7 |
O' |
121.7 |
120.1 |
| N' |
C7 |
C1 |
120.5 |
120.0 |
| O' |
C7 |
C1 |
117.8 |
120.0 |
| C3 |
C1 |
C5 |
119.7 |
119.7 |
| C1 |
C5 |
C6 |
120.4 |
119.9 |
| C1 |
C5 |
H5 |
119.8 |
120.1 |
| C1 |
C3 |
C2 |
120.9 |
119.9 |
| C1 |
C3 |
H3 |
119.5 |
120.0 |
| C3 |
C2 |
C4 |
120.5 |
120.1 |
| C3 |
C2 |
H2 |
119.8 |
120.0 |
| C4 |
C2 |
H2 |
119.8 |
119.9 |
| C6 |
C5 |
H5 |
119.8 |
120.0 |
| C5 |
C6 |
H6 |
119.7 |
119.9 |
| F3'1 |
C3' |
F3'2 |
108.6 |
109.5 |
| F3'1 |
C3' |
C2' |
110.1 |
109.5 |
| F3'1 |
C3' |
C4' |
106.3 |
109.4 |
| F4'1 |
C4' |
F4'2 |
115.0 |
109.5 |
| F4'1 |
C4' |
F4'3 |
113.4 |
109.4 |
| F4'1 |
C4' |
C3' |
102.6 |
109.4 |
| F3'2 |
C3' |
C2' |
104.0 |
109.5 |
| F3'2 |
C3' |
C4' |
115.8 |
109.5 |
| C2' |
C1' |
H1' |
109.4 |
109.5 |
| C2' |
C1' |
H1'A |
109.4 |
109.4 |
| H1' |
C1' |
H1'A |
109.5 |
109.5 |
| HN3S |
N3S |
HN3A |
109.5 |
120.0 |
Torsion Angles for RYZ
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O1S |
S |
C4 |
O2S |
124.3 |
227.0 |
| C4 |
S |
O1S |
O2S |
239.9 |
122.9 |
| C7 |
N' |
C1' |
HN' |
180.0 |
179.9 |
| C1' |
N' |
C7 |
HN' |
180.0 |
180.1 |
| O' |
C7 |
N' |
C1 |
179.0 |
180.0 |
| HN' |
N' |
C7 |
O' |
178.7 |
180.0 |
| HN' |
N' |
C7 |
C1 |
359.6 |
359.9 |
| O' |
C7 |
N' |
HN' |
178.7 |
180.0 |
| N' |
C7 |
O' |
C1 |
180.9 |
180.0 |
| C1 |
C7 |
N' |
HN' |
359.6 |
359.9 |
| N' |
C7 |
C1 |
O' |
179.1 |
180.0 |
| C7 |
C1 |
C5 |
H5 |
359.2 |
0.2 |
| C7 |
C1 |
C3 |
H3 |
1.5 |
359.7 |
| N' |
C7 |
C1 |
C5 |
184.9 |
180.1 |
| O' |
C7 |
C1 |
C5 |
5.8 |
0.0 |
| C5 |
C1 |
C3 |
C2 |
359.7 |
359.9 |
| C5 |
C1 |
C3 |
H3 |
179.7 |
180.0 |
| C6 |
C5 |
C1 |
H5 |
180.0 |
180.1 |
| C1 |
C5 |
C6 |
H6 |
177.0 |
180.0 |
| N' |
C7 |
C1 |
C3 |
3.1 |
0.3 |
| O' |
C7 |
C1 |
C3 |
184.0 |
180.2 |
| C3 |
C1 |
C5 |
C6 |
1.0 |
0.1 |
| C3 |
C1 |
C5 |
H5 |
181.0 |
180.0 |
| C1 |
C3 |
C2 |
C4 |
1.6 |
0.0 |
| C1 |
C3 |
C2 |
H2 |
181.7 |
180.0 |
| C2 |
C3 |
C1 |
C5 |
359.7 |
359.9 |
| C1 |
C3 |
C2 |
H3 |
180.0 |
180.0 |
| C4 |
C2 |
C3 |
H2 |
180.0 |
180.0 |
| C2 |
C4 |
S |
O2S |
64.2 |
336.5 |
| C3 |
C2 |
C4 |
H2 |
180.0 |
180.0 |
| C3 |
C2 |
H2 |
C4 |
180.0 |
180.0 |
| H3 |
C3 |
C1 |
C5 |
179.7 |
180.0 |
| C1 |
C3 |
H3 |
C2 |
180.0 |
180.0 |
| H3 |
C3 |
C2 |
C4 |
181.7 |
180.0 |
| H3 |
C3 |
C2 |
H2 |
1.7 |
360.0 |
| C6 |
C4 |
S |
O2S |
247.9 |
156.5 |
| C1 |
C5 |
C6 |
C4 |
357.0 |
359.9 |
| C6 |
C4 |
C2 |
H2 |
176.5 |
180.0 |
| C1 |
C5 |
C6 |
H5 |
180.0 |
179.9 |
| C1 |
C5 |
H5 |
C6 |
180.0 |
180.1 |
| H5 |
C5 |
C6 |
H6 |
357.0 |
0.1 |
| H6 |
C6 |
C5 |
H5 |
357.0 |
0.1 |
| F4'1 |
C4' |
C3' |
F3'1 |
283.9 |
60.0 |
| F3'2 |
C3' |
F3'1 |
C2' |
113.3 |
240.0 |
| F3'2 |
C3' |
F3'1 |
C4' |
234.8 |
120.0 |
| F3'1 |
C3' |
C4' |
F4'1 |
283.9 |
60.0 |
| F3'2 |
C3' |
C4' |
F4'1 |
44.7 |
300.0 |
| F3'1 |
C3' |
C2' |
F2'2 |
292.8 |
60.0 |
| F3'1 |
C3' |
F3'2 |
C2' |
242.8 |
120.0 |
| F3'1 |
C3' |
F3'2 |
C4' |
119.5 |
240.0 |
| F4'1 |
C4' |
C3' |
F3'2 |
44.7 |
300.0 |
| F3'1 |
C3' |
C4' |
F4'2 |
159.1 |
300.0 |
| F4'1 |
C4' |
F4'2 |
F4'3 |
123.9 |
120.0 |
| F4'1 |
C4' |
F4'2 |
C3' |
242.1 |
240.0 |
| F3'2 |
C3' |
C4' |
F4'2 |
279.8 |
180.0 |
| F3'1 |
C3' |
C4' |
F4'3 |
44.6 |
179.9 |
| F4'1 |
C4' |
F4'3 |
F4'2 |
235.1 |
240.0 |
| F4'1 |
C4' |
F4'3 |
C3' |
113.8 |
119.9 |
| F3'2 |
C3' |
C4' |
F4'3 |
165.4 |
60.0 |
| C2' |
C1' |
N' |
HN' |
269.8 |
0.0 |
| F3'1 |
C3' |
C2' |
C1' |
55.7 |
300.0 |
| F3'2 |
C3' |
C2' |
C1' |
299.5 |
60.0 |
| H1' |
C1' |
C2' |
H1'A |
120.0 |
120.0 |
| H1' |
C1' |
N' |
HN' |
29.8 |
120.0 |
| C2' |
C1' |
H1' |
H1'A |
240.0 |
240.0 |
| H1'A |
C1' |
N' |
HN' |
149.7 |
240.0 |
| C2' |
C1' |
H1'A |
H1' |
120.0 |
120.0 |
| F3'1 |
C3' |
C2' |
F3'2 |
116.2 |
240.0 |
| F3'1 |
C3' |
C2' |
C4' |
242.0 |
120.0 |
| F4'1 |
C4' |
C3' |
C2' |
163.7 |
180.0 |
| F3'2 |
C3' |
C2' |
C4' |
125.7 |
240.0 |
| C3' |
C2' |
C1' |
H1' |
63.2 |
60.0 |
| C3' |
C2' |
C1' |
H1'A |
303.2 |
300.0 |
| F3'1 |
C3' |
C4' |
F3'2 |
239.3 |
120.0 |
| F3'1 |
C3' |
C4' |
C2' |
120.3 |
240.0 |
| F4'1 |
C4' |
C3' |
F4'2 |
124.9 |
120.0 |
| F4'1 |
C4' |
C3' |
F4'3 |
239.3 |
240.1 |
| F3'2 |
C3' |
C4' |
C2' |
241.0 |
120.0 |