PDB Chemical Component CGY
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 CGY
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O3' |
C3' |
1.465 |
1.429 |
| C3' |
C2' |
1.525 |
1.545 |
| C3' |
C4' |
1.525 |
1.545 |
| OP1 |
P |
1.479 |
1.480 |
| C2' |
C1' |
1.505 |
1.544 |
| C5' |
O5' |
1.447 |
1.429 |
| C5' |
C4' |
1.507 |
1.530 |
| O5' |
P |
1.597 |
1.611 |
| C4' |
O4' |
1.452 |
1.444 |
| P |
OP2 |
1.491 |
1.610 |
| C1' |
O4' |
1.428 |
1.444 |
| C1' |
C1 |
1.498 |
1.507 |
| C1 |
C6 |
1.394 |
1.387 |
| C1 |
C2 |
1.385 |
1.388 |
| C6 |
C5 |
1.393 |
1.390 |
| ON1 |
N5 |
1.308 |
1.463 |
| N1 |
C2 |
1.265 |
1.393 |
| C2 |
N3 |
1.346 |
1.325 |
| C5 |
N5 |
1.248 |
1.404 |
| C5 |
C4 |
1.385 |
1.395 |
| N5 |
ON2 |
1.310 |
1.463 |
| N3 |
C4 |
1.347 |
1.323 |
| C4 |
N4 |
1.267 |
1.393 |
| C1' |
H1'1 |
1.101 |
1.091 |
| C2' |
H2'1 |
1.100 |
1.090 |
| C2' |
H2'2 |
1.100 |
1.090 |
| C3' |
H3'1 |
1.100 |
1.090 |
| C4' |
H4'1 |
1.100 |
1.091 |
| C5' |
H5'2 |
1.100 |
1.090 |
| C5' |
H5'1 |
1.100 |
1.090 |
| C6 |
H61 |
1.080 |
1.080 |
| N1 |
H12 |
1.001 |
0.970 |
| N1 |
H11 |
1.000 |
0.970 |
| N4 |
H41 |
1.000 |
0.969 |
| N4 |
H42 |
1.000 |
0.970 |
| O3' |
H3'2 |
0.950 |
0.966 |
| ON1 |
HN11 |
0.951 |
0.968 |
| ON2 |
HN21 |
0.951 |
0.967 |
| OP2 |
H1 |
0.950 |
0.967 |
| P |
OP3 |
1.589 |
1.609 |
| OP3 |
HO3' |
0.950 |
0.968 |
Bond Angles for CGY
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O3' |
C3' |
H3'1 |
107.8 |
110.6 |
| C3' |
C2' |
H2'1 |
110.2 |
110.5 |
| C3' |
C2' |
H2'2 |
110.3 |
110.6 |
| C3' |
C4' |
O4' |
103.6 |
104.8 |
| C4' |
C3' |
H3'1 |
107.0 |
110.5 |
| C3' |
C4' |
H4'1 |
108.5 |
110.4 |
| O5' |
P |
OP1 |
106.5 |
109.5 |
| OP1 |
P |
OP2 |
118.1 |
109.5 |
| OP1 |
P |
OP3 |
112.7 |
109.5 |
| C2' |
C1' |
O4' |
106.4 |
104.8 |
| C2' |
C1' |
H1'1 |
107.9 |
110.5 |
| C5' |
O5' |
P |
122.6 |
123.0 |
| O5' |
C5' |
H5'2 |
109.3 |
109.4 |
| O5' |
C5' |
H5'1 |
109.2 |
109.4 |
| C5' |
C4' |
O4' |
112.2 |
110.4 |
| C5' |
C4' |
H4'1 |
108.7 |
110.4 |
| O5' |
P |
OP2 |
111.0 |
109.5 |
| O5' |
P |
OP3 |
103.6 |
109.4 |
| C1' |
O4' |
C4' |
106.6 |
105.3 |
| O4' |
C4' |
H4'1 |
109.4 |
110.3 |
| P |
OP2 |
H1 |
109.5 |
114.0 |
| O4' |
C1' |
H1'1 |
108.9 |
110.3 |
| C1' |
C1 |
C6 |
117.5 |
120.3 |
| C1' |
C1 |
C2 |
124.5 |
120.4 |
| C2 |
C1 |
C6 |
118.0 |
119.3 |
| C1 |
C6 |
C5 |
119.4 |
118.5 |
| C1 |
C6 |
H61 |
120.3 |
120.8 |
| C1 |
C2 |
N3 |
123.7 |
120.8 |
| C6 |
C5 |
N5 |
121.5 |
120.4 |
| ON1 |
N5 |
ON2 |
119.8 |
111.0 |
| N1 |
C2 |
N3 |
117.3 |
119.6 |
| C2 |
N3 |
C4 |
117.2 |
121.6 |
| C5 |
N5 |
ON2 |
120.0 |
111.0 |
| C5 |
C4 |
N4 |
118.3 |
119.7 |
| N5 |
ON2 |
HN21 |
109.5 |
114.0 |
| N3 |
C4 |
N4 |
118.2 |
119.7 |
| C4 |
N4 |
H41 |
109.5 |
120.0 |
| C4 |
N4 |
H42 |
109.5 |
120.0 |
| H2'1 |
C2' |
H2'2 |
109.5 |
110.4 |
| H5'2 |
C5' |
H5'1 |
109.5 |
109.5 |
| H12 |
N1 |
H11 |
109.5 |
119.9 |
| H41 |
N4 |
H42 |
109.4 |
120.0 |
| P |
OP3 |
HO3' |
109.5 |
114.0 |
Torsion Angles for CGY
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O3' |
C3' |
C2' |
H2'1 |
269.7 |
360.0 |
| O3' |
C3' |
C2' |
H2'2 |
30.7 |
237.3 |
| O3' |
C3' |
C4' |
O4' |
194.6 |
217.4 |
| C4' |
C3' |
O3' |
H3'1 |
239.7 |
237.3 |
| O3' |
C3' |
C4' |
H4'1 |
310.8 |
336.2 |
| C3' |
C2' |
C1' |
O4' |
0.3 |
23.9 |
| C3' |
C2' |
C1' |
H1'1 |
243.6 |
265.1 |
| H2'1 |
C2' |
C3' |
H2'2 |
239.0 |
122.6 |
| O3' |
C3' |
C4' |
H3'1 |
120.7 |
122.7 |
| C4' |
C3' |
C2' |
H2'1 |
142.3 |
241.3 |
| C4' |
C3' |
C2' |
H2'2 |
263.3 |
118.7 |
| C5' |
C4' |
C3' |
O4' |
237.7 |
241.1 |
| C5' |
C4' |
C3' |
H4'1 |
121.4 |
122.3 |
| C1' |
O4' |
C4' |
C3' |
40.3 |
40.5 |
| O4' |
C4' |
C3' |
H4'1 |
243.8 |
241.2 |
| C5' |
O5' |
P |
OP1 |
55.8 |
305.0 |
| O5' |
P |
OP1 |
OP2 |
125.6 |
120.0 |
| O5' |
P |
OP1 |
OP3 |
247.1 |
240.0 |
| OP1 |
P |
OP2 |
H1 |
360.0 |
180.0 |
| OP1 |
P |
OP3 |
HO3' |
0.0 |
60.0 |
| C2' |
C1' |
O4' |
C4' |
334.9 |
319.6 |
| O4' |
C1' |
C2' |
H1'1 |
116.7 |
118.8 |
| C2' |
C1' |
C1 |
C6 |
289.2 |
268.2 |
| O5' |
C5' |
C4' |
O4' |
286.2 |
69.6 |
| O5' |
C5' |
C4' |
H4'1 |
165.1 |
307.3 |
| C5' |
O5' |
P |
OP2 |
185.6 |
65.0 |
| C5' |
O5' |
P |
OP3 |
296.8 |
185.0 |
| H5'2 |
C5' |
O5' |
H5'1 |
240.3 |
120.0 |
| C3' |
C4' |
C5' |
O4' |
117.5 |
115.4 |
| C5' |
C4' |
C3' |
H3'1 |
311.5 |
335.8 |
| C3' |
C4' |
C5' |
H4'1 |
238.7 |
237.7 |
| C1' |
O4' |
C4' |
C5' |
164.0 |
159.3 |
| O4' |
C4' |
C5' |
H4'1 |
121.2 |
122.2 |
| OP1 |
P |
O5' |
OP2 |
230.2 |
240.0 |
| OP1 |
P |
O5' |
OP3 |
119.0 |
120.0 |
| P |
O5' |
C5' |
H5'2 |
283.2 |
60.0 |
| P |
O5' |
C5' |
H5'1 |
42.9 |
300.0 |
| O5' |
P |
OP2 |
H1 |
236.7 |
60.0 |
| O5' |
P |
OP3 |
HO3' |
114.6 |
180.0 |
| O4' |
C4' |
C3' |
H3'1 |
73.9 |
94.7 |
| C3' |
C4' |
O4' |
H4'1 |
115.6 |
118.9 |
| C5' |
C4' |
O4' |
H4'1 |
239.3 |
237.7 |
| C4' |
O4' |
C1' |
H1'1 |
90.9 |
78.5 |
| O5' |
P |
OP2 |
OP1 |
236.7 |
240.0 |
| OP1 |
P |
OP2 |
OP3 |
234.2 |
240.0 |
| O5' |
P |
OP2 |
OP3 |
110.8 |
120.0 |
| C3' |
C4' |
O4' |
C1' |
40.3 |
40.5 |
| C2' |
C1' |
O4' |
H1'1 |
244.0 |
241.1 |
| C5' |
C4' |
O4' |
C1' |
164.0 |
159.3 |
| C1' |
O4' |
C4' |
H4'1 |
284.7 |
281.6 |
| O4' |
C1' |
C1 |
C6 |
49.7 |
23.6 |
| O4' |
C1' |
C1 |
C2 |
228.4 |
203.8 |
| C2 |
C1 |
C1' |
C6 |
178.8 |
180.2 |
| C1' |
C1 |
C6 |
C5 |
179.3 |
180.2 |
| C1' |
C1 |
C6 |
H61 |
359.3 |
0.3 |
| C1' |
C1 |
C2 |
N3 |
180.6 |
179.8 |
| C1' |
C1 |
C6 |
C2 |
178.8 |
180.2 |
| C6 |
C1 |
C2 |
N3 |
359.4 |
360.0 |
| C1 |
C6 |
C5 |
N5 |
179.5 |
180.0 |
| C1' |
C1 |
C2 |
C6 |
181.2 |
179.8 |
| C2 |
C1 |
C6 |
C5 |
0.5 |
0.0 |
| C2 |
C1 |
C6 |
H61 |
180.5 |
180.0 |
| N1 |
C2 |
C1 |
N3 |
180.4 |
180.0 |
| C1 |
C2 |
N3 |
C4 |
0.5 |
360.0 |
| C1 |
C6 |
C5 |
H61 |
180.0 |
180.0 |
| C6 |
C5 |
N5 |
ON2 |
173.4 |
84.5 |
| C6 |
C5 |
C4 |
N4 |
179.8 |
180.0 |
| C5 |
N5 |
ON1 |
ON2 |
180.7 |
124.0 |
| ON1 |
N5 |
ON2 |
HN21 |
180.0 |
304.0 |
| C1 |
C2 |
N1 |
N3 |
179.7 |
180.0 |
| N1 |
C2 |
N3 |
C4 |
180.1 |
180.0 |
| N3 |
C2 |
C1 |
C6 |
359.4 |
360.0 |
| C2 |
N3 |
C4 |
N4 |
180.1 |
180.0 |
| ON1 |
N5 |
C5 |
ON2 |
179.3 |
236.0 |
| N5 |
C5 |
C4 |
N4 |
0.0 |
360.0 |
| C5 |
N5 |
ON2 |
HN21 |
359.4 |
180.0 |
| C1 |
C6 |
C5 |
C4 |
359.7 |
0.0 |
| C2 |
N3 |
C4 |
C5 |
359.8 |
0.1 |
| N3 |
C4 |
C5 |
N4 |
180.3 |
180.0 |
| C5 |
C4 |
N4 |
H41 |
180.3 |
354.5 |
| C5 |
C4 |
N4 |
H42 |
300.3 |
174.5 |
| C5 |
C4 |
N3 |
N4 |
179.7 |
180.0 |
| N3 |
C4 |
N4 |
H41 |
0.0 |
174.5 |
| N3 |
C4 |
N4 |
H42 |
120.0 |
354.6 |
| H41 |
N4 |
C4 |
H42 |
240.0 |
180.0 |
| C2' |
C1' |
H1'1 |
O4' |
115.1 |
115.4 |
| H1'1 |
C1' |
O4' |
C4' |
90.9 |
78.5 |
| H1'1 |
C1' |
C1 |
C6 |
170.2 |
145.8 |
| H1'1 |
C1' |
C1 |
C2 |
349.0 |
326.0 |
| C3' |
C2' |
H2'1 |
H2'2 |
121.4 |
237.3 |
| H2'1 |
C2' |
C1' |
O4' |
240.8 |
142.7 |
| H2'1 |
C2' |
C1' |
H1'1 |
124.1 |
23.8 |
| C3' |
C2' |
H2'2 |
H2'1 |
238.6 |
122.7 |
| H2'2 |
C2' |
C1' |
O4' |
119.8 |
265.1 |
| H2'2 |
C2' |
C1' |
H1'1 |
3.1 |
146.3 |
| H3'1 |
C3' |
C2' |
H2'1 |
30.6 |
122.7 |
| H3'1 |
C3' |
C2' |
H2'2 |
151.6 |
0.1 |
| H3'1 |
C3' |
C4' |
O4' |
73.9 |
94.7 |
| H3'1 |
C3' |
C4' |
H4'1 |
190.1 |
213.5 |
| C3' |
C4' |
H4'1 |
O4' |
247.6 |
244.6 |
| H4'1 |
C4' |
C3' |
H3'1 |
190.1 |
213.5 |
| C5' |
C4' |
H4'1 |
O4' |
122.8 |
122.3 |
| H5'2 |
C5' |
O5' |
P |
283.2 |
60.0 |
| O5' |
C5' |
H5'2 |
H5'1 |
119.6 |
240.1 |
| H5'2 |
C5' |
C4' |
O4' |
166.1 |
189.6 |
| H5'2 |
C5' |
C4' |
H4'1 |
44.9 |
67.4 |
| H5'1 |
C5' |
O5' |
P |
42.9 |
300.0 |
| O5' |
C5' |
H5'1 |
H5'2 |
240.4 |
119.9 |
| H5'1 |
C5' |
C4' |
O4' |
46.4 |
309.6 |
| H5'1 |
C5' |
C4' |
H4'1 |
285.2 |
187.4 |
| C1 |
C6 |
H61 |
C5 |
180.0 |
180.0 |
| H61 |
C6 |
C5 |
N5 |
359.5 |
360.0 |
| H12 |
N1 |
C2 |
N3 |
360.0 |
180.0 |
| H11 |
N1 |
C2 |
N3 |
120.0 |
360.0 |
| C4 |
N4 |
H41 |
H42 |
120.0 |
180.0 |
| C4 |
N4 |
H42 |
H41 |
240.0 |
180.0 |
| H3'2 |
O3' |
C3' |
H3'1 |
59.5 |
298.8 |
| HN11 |
ON1 |
N5 |
ON2 |
359.4 |
56.0 |
| O5' |
P |
OP3 |
OP1 |
114.6 |
120.0 |
| OP1 |
P |
OP3 |
OP2 |
129.2 |
120.0 |
| O5' |
P |
OP3 |
OP2 |
243.8 |
240.0 |
| OP3 |
P |
OP2 |
H1 |
125.8 |
300.0 |