PDB Chemical Component 1VY
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 1VY
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O4 |
C4 |
1.236 |
1.217 |
| C4 |
N3 |
1.356 |
1.353 |
| C4 |
C4A |
1.405 |
1.472 |
| N5 |
C4A |
1.357 |
1.324 |
| N5 |
C6 |
1.350 |
1.317 |
| N3 |
C2 |
1.362 |
1.343 |
| C4A |
C8A |
1.401 |
1.417 |
| C9 |
C6 |
1.416 |
1.506 |
| C6 |
C7 |
1.393 |
1.393 |
| O4' |
C4' |
1.400 |
1.429 |
| C2 |
O2 |
1.234 |
1.219 |
| C2 |
N1 |
1.353 |
1.328 |
| C8A |
N1 |
1.350 |
1.327 |
| C8A |
N8 |
1.367 |
1.368 |
| O2' |
C2' |
1.449 |
1.429 |
| C7 |
N8 |
1.351 |
1.353 |
| C7 |
O7 |
1.367 |
1.348 |
| C3' |
C4' |
1.548 |
1.530 |
| C3' |
O3' |
1.465 |
1.429 |
| C3' |
C2' |
1.531 |
1.530 |
| C4' |
C5' |
1.520 |
1.530 |
| N8 |
C1' |
1.483 |
1.465 |
| C2' |
C1' |
1.516 |
1.530 |
| C5' |
O5' |
1.445 |
1.429 |
| C9 |
H1 |
1.100 |
1.090 |
| C9 |
H2 |
1.100 |
1.091 |
| C9 |
H3 |
1.101 |
1.089 |
| N3 |
H5 |
1.000 |
0.970 |
| C1' |
H6 |
1.100 |
1.090 |
| C1' |
H7 |
1.100 |
1.090 |
| C2' |
H8 |
1.100 |
1.090 |
| O2' |
H9 |
0.950 |
0.967 |
| C3' |
H10 |
1.100 |
1.089 |
| O3' |
H11 |
0.950 |
0.967 |
| C4' |
H12 |
1.100 |
1.090 |
| O4' |
H13 |
0.950 |
0.967 |
| C5' |
H14 |
1.100 |
1.091 |
| C5' |
H15 |
1.100 |
1.090 |
| O5' |
H16 |
0.950 |
0.967 |
| O7 |
H17 |
0.950 |
0.967 |
Bond Angles for 1VY
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O4 |
C4 |
N3 |
119.0 |
121.2 |
| C4 |
N3 |
C2 |
120.1 |
120.6 |
| C4 |
N3 |
H5 |
119.9 |
119.7 |
| C4 |
C4A |
C8A |
119.1 |
117.9 |
| N5 |
C4A |
C8A |
119.8 |
120.4 |
| N3 |
C2 |
O2 |
121.7 |
118.4 |
| N3 |
C2 |
N1 |
120.3 |
123.1 |
| C2 |
N3 |
H5 |
120.0 |
119.8 |
| C4A |
C8A |
N1 |
118.4 |
119.3 |
| C4A |
C8A |
N8 |
119.8 |
119.1 |
| C6 |
C7 |
N8 |
121.6 |
120.2 |
| O4' |
C4' |
C5' |
105.3 |
109.5 |
| O4' |
C4' |
H12 |
112.6 |
109.5 |
| O2 |
C2 |
N1 |
118.1 |
118.4 |
| C7 |
N8 |
C8A |
119.1 |
118.7 |
| C8A |
N8 |
C1' |
122.2 |
120.6 |
| O2' |
C2' |
H8 |
108.2 |
109.4 |
| C7 |
N8 |
C1' |
118.1 |
120.7 |
| C7 |
O7 |
H17 |
109.5 |
116.9 |
| O3' |
C3' |
C4' |
112.8 |
109.5 |
| C3' |
C4' |
C5' |
112.3 |
109.4 |
| C4' |
C3' |
H10 |
106.5 |
109.5 |
| C3' |
C4' |
H12 |
110.3 |
109.5 |
| O3' |
C3' |
H10 |
107.5 |
109.5 |
| C3' |
O3' |
H11 |
109.5 |
114.0 |
| C3' |
C2' |
H8 |
107.2 |
109.5 |
| C4' |
C5' |
O5' |
115.4 |
109.5 |
| C5' |
C4' |
H12 |
110.7 |
109.5 |
| C4' |
C5' |
H14 |
108.0 |
109.5 |
| C4' |
C5' |
H15 |
108.0 |
109.5 |
| N8 |
C1' |
H6 |
106.9 |
109.5 |
| N8 |
C1' |
H7 |
107.0 |
109.5 |
| C2' |
C1' |
H6 |
107.0 |
109.5 |
| C2' |
C1' |
H7 |
107.0 |
109.5 |
| O5' |
C5' |
H14 |
108.0 |
109.4 |
| O5' |
C5' |
H15 |
108.0 |
109.5 |
| C5' |
O5' |
H16 |
109.5 |
114.0 |
| H1 |
C9 |
H2 |
109.4 |
109.4 |
| H1 |
C9 |
H3 |
109.5 |
109.5 |
| H2 |
C9 |
H3 |
109.5 |
109.5 |
| H6 |
C1' |
H7 |
109.5 |
109.5 |
| H14 |
C5' |
H15 |
109.5 |
109.5 |
Torsion Angles for 1VY
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O4 |
C4 |
N3 |
C2 |
185.1 |
180.0 |
| O4 |
C4 |
N3 |
H5 |
5.1 |
360.0 |
| O4 |
C4 |
C4A |
C8A |
171.7 |
180.0 |
| N3 |
C4 |
C4A |
C8A |
0.7 |
360.0 |
| C4 |
N3 |
C2 |
O2 |
185.7 |
180.0 |
| C4 |
N3 |
C2 |
N1 |
4.3 |
0.0 |
| C2 |
N3 |
C4 |
H5 |
180.0 |
180.0 |
| N5 |
C4A |
C4 |
C8A |
185.1 |
180.0 |
| C4 |
C4A |
C8A |
N1 |
1.8 |
0.0 |
| C4 |
C4A |
C8A |
N8 |
184.3 |
180.0 |
| C4 |
C4A |
N5 |
C8A |
174.9 |
180.0 |
| N5 |
C4A |
C8A |
N1 |
176.7 |
180.0 |
| N5 |
C4A |
C8A |
N8 |
359.3 |
360.0 |
| N5 |
C6 |
C7 |
N8 |
1.3 |
359.9 |
| C4 |
N3 |
C2 |
H5 |
180.0 |
180.0 |
| O2 |
C2 |
N3 |
N1 |
181.3 |
180.0 |
| C7 |
N8 |
C8A |
C4A |
1.4 |
0.0 |
| C4A |
C8A |
N8 |
C1' |
172.1 |
180.4 |
| C9 |
C6 |
C7 |
N8 |
181.6 |
180.0 |
| C6 |
C7 |
N8 |
C8A |
358.3 |
0.0 |
| C6 |
C7 |
N8 |
C1' |
187.2 |
179.7 |
| C6 |
C7 |
O7 |
H17 |
180.0 |
0.2 |
| C3' |
C4' |
O4' |
C5' |
241.0 |
240.1 |
| O4' |
C4' |
C3' |
H10 |
304.8 |
60.0 |
| C3' |
C4' |
O4' |
H12 |
120.3 |
120.0 |
| O4' |
C4' |
C5' |
O5' |
109.2 |
65.1 |
| C5' |
C4' |
O4' |
H12 |
239.3 |
240.0 |
| O4' |
C4' |
C5' |
H14 |
230.0 |
185.0 |
| O4' |
C4' |
C5' |
H15 |
348.3 |
305.0 |
| N3 |
C2 |
O2 |
N1 |
178.7 |
180.0 |
| O2 |
C2 |
N3 |
H5 |
5.7 |
360.0 |
| N3 |
C2 |
N1 |
O2 |
181.3 |
180.0 |
| N1 |
C2 |
N3 |
H5 |
184.4 |
180.0 |
| C4A |
C8A |
N1 |
C2 |
358.8 |
0.0 |
| C4A |
C8A |
N1 |
N8 |
182.6 |
180.0 |
| C7 |
N8 |
C8A |
N1 |
184.0 |
180.0 |
| C4A |
C8A |
N8 |
N1 |
177.4 |
180.0 |
| C7 |
N8 |
C8A |
C1' |
189.3 |
179.7 |
| C8A |
N8 |
C1' |
H6 |
221.1 |
29.7 |
| C8A |
N8 |
C1' |
H7 |
338.3 |
149.7 |
| C3' |
C2' |
O2' |
H8 |
241.7 |
240.0 |
| O2' |
C2' |
C1' |
H6 |
283.1 |
180.1 |
| O2' |
C2' |
C1' |
H7 |
165.8 |
60.1 |
| C4A |
C8A |
N8 |
C7 |
1.4 |
0.0 |
| C8A |
N8 |
C7 |
C1' |
171.1 |
180.3 |
| N8 |
C7 |
O7 |
H17 |
356.3 |
180.0 |
| C7 |
N8 |
C1' |
H6 |
31.9 |
210.0 |
| C7 |
N8 |
C1' |
H7 |
149.1 |
330.0 |
| O4' |
C4' |
C3' |
C5' |
114.2 |
120.0 |
| O4' |
C4' |
C3' |
H12 |
238.2 |
239.9 |
| O3' |
C3' |
C4' |
H10 |
117.7 |
120.0 |
| C4' |
C3' |
O3' |
H11 |
180.0 |
60.0 |
| C4' |
C3' |
C2' |
H8 |
317.6 |
300.1 |
| C3' |
C4' |
C5' |
O5' |
223.5 |
185.0 |
| C5' |
C4' |
C3' |
H12 |
124.0 |
120.0 |
| C3' |
C4' |
C5' |
H14 |
344.3 |
305.0 |
| C3' |
C4' |
C5' |
H15 |
102.6 |
65.0 |
| O3' |
C3' |
C4' |
C5' |
308.3 |
60.0 |
| C4' |
C3' |
O3' |
H10 |
242.9 |
239.9 |
| O3' |
C3' |
C4' |
H12 |
184.3 |
300.0 |
| O3' |
C3' |
C2' |
H8 |
84.7 |
60.1 |
| O2' |
C2' |
C3' |
H8 |
118.9 |
119.9 |
| C3' |
C2' |
C1' |
H6 |
157.6 |
60.0 |
| C3' |
C2' |
C1' |
H7 |
40.4 |
300.0 |
| O4' |
C4' |
C5' |
H12 |
121.9 |
120.1 |
| C5' |
C4' |
C3' |
H10 |
190.6 |
300.0 |
| C3' |
C4' |
C5' |
H12 |
236.2 |
240.0 |
| O5' |
C5' |
C4' |
H14 |
239.1 |
240.0 |
| O5' |
C5' |
C4' |
H15 |
120.9 |
120.0 |
| C4' |
C5' |
O5' |
H16 |
180.0 |
180.0 |
| H14 |
C5' |
C4' |
H15 |
241.7 |
240.0 |
| C7 |
N8 |
C1' |
C8A |
170.8 |
180.3 |
| C2' |
C1' |
N8 |
H6 |
238.6 |
240.0 |
| C2' |
C1' |
N8 |
H7 |
121.4 |
120.0 |
| H6 |
C1' |
N8 |
H7 |
242.8 |
240.0 |
| N8 |
C1' |
C2' |
H6 |
121.4 |
120.0 |
| N8 |
C1' |
C2' |
H7 |
238.6 |
240.0 |
| H6 |
C1' |
C2' |
H7 |
117.2 |
120.0 |
| O5' |
C5' |
C4' |
H12 |
347.2 |
305.0 |
| C4' |
C5' |
O5' |
H14 |
120.8 |
120.0 |
| C4' |
C5' |
O5' |
H15 |
239.1 |
240.0 |
| H14 |
C5' |
O5' |
H15 |
118.3 |
120.0 |
| H2 |
C9 |
H1 |
H3 |
120.0 |
120.0 |
| H1 |
C9 |
H2 |
H3 |
240.0 |
239.9 |
| H1 |
C9 |
H3 |
H2 |
120.0 |
120.0 |
| C4 |
N3 |
H5 |
C2 |
180.0 |
180.0 |
| H5 |
N3 |
C2 |
O2 |
5.7 |
360.0 |
| H5 |
N3 |
C2 |
N1 |
184.4 |
180.0 |
| N8 |
C1' |
H6 |
H7 |
115.5 |
120.0 |
| C2' |
C1' |
H6 |
H7 |
244.4 |
240.0 |
| N8 |
C1' |
H7 |
H6 |
244.5 |
240.0 |
| C2' |
C1' |
H7 |
H6 |
115.6 |
120.0 |
| H8 |
C2' |
C1' |
H6 |
41.1 |
300.0 |
| H8 |
C2' |
C1' |
H7 |
283.8 |
180.0 |
| H9 |
O2' |
C2' |
H8 |
298.3 |
179.9 |
| O3' |
C3' |
H10 |
C4' |
238.8 |
240.0 |
| H10 |
C3' |
C4' |
C5' |
190.6 |
300.0 |
| H10 |
C3' |
C4' |
H12 |
66.6 |
180.0 |
| H10 |
C3' |
O3' |
H11 |
297.1 |
180.1 |
| H10 |
C3' |
C2' |
H8 |
201.8 |
180.0 |
| H11 |
O3' |
C3' |
C4' |
180.0 |
60.0 |
| H11 |
O3' |
C3' |
H10 |
297.1 |
180.1 |
| O4' |
C4' |
H12 |
C5' |
242.4 |
240.0 |
| C3' |
C4' |
H12 |
C5' |
124.9 |
120.0 |
| H12 |
C4' |
C3' |
H10 |
66.6 |
180.0 |
| H12 |
C4' |
C5' |
O5' |
347.2 |
305.0 |
| H12 |
C4' |
C5' |
H14 |
108.1 |
64.9 |
| H12 |
C4' |
C5' |
H15 |
226.4 |
185.0 |
| H13 |
O4' |
C4' |
C5' |
299.0 |
60.0 |
| H13 |
O4' |
C4' |
H12 |
59.7 |
180.0 |
| C4' |
C5' |
H14 |
O5' |
234.6 |
240.0 |
| H14 |
C5' |
C4' |
H12 |
108.1 |
64.9 |
| C4' |
C5' |
H14 |
H15 |
117.3 |
120.0 |
| O5' |
C5' |
H14 |
H15 |
242.7 |
240.0 |
| H14 |
C5' |
O5' |
H16 |
59.2 |
60.0 |
| C4' |
C5' |
H15 |
O5' |
125.4 |
120.0 |
| H15 |
C5' |
C4' |
H12 |
226.4 |
185.0 |
| C4' |
C5' |
H15 |
H14 |
242.7 |
240.0 |
| O5' |
C5' |
H15 |
H14 |
117.3 |
120.0 |
| H15 |
C5' |
O5' |
H16 |
300.9 |
300.0 |
| H16 |
O5' |
C5' |
H14 |
59.2 |
60.0 |
| H16 |
O5' |
C5' |
H15 |
300.9 |
300.0 |