PDB Chemical Component YKI
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 YKI
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C3 |
C1 |
1.415 |
1.366 |
| C1 |
N1 |
1.394 |
1.322 |
| C1 |
H1 |
1.080 |
1.079 |
| N1 |
C2 |
1.391 |
1.319 |
| C6 |
C2 |
1.409 |
1.385 |
| C2 |
H2 |
1.080 |
1.080 |
| C4 |
N2 |
1.344 |
1.369 |
| C6 |
N2 |
1.372 |
1.379 |
| C3 |
C5 |
1.406 |
1.401 |
| C3 |
H3 |
1.080 |
1.079 |
| N3 |
C5 |
1.368 |
1.345 |
| N3 |
C4 |
1.358 |
1.313 |
| C7 |
C4 |
1.447 |
1.477 |
| C11 |
N4 |
1.349 |
1.348 |
| C16 |
N4 |
1.156 |
1.465 |
| N4 |
HN4 |
1.000 |
0.970 |
| C5 |
C6 |
1.452 |
1.411 |
| C26 |
N5 |
1.399 |
1.323 |
| N5 |
C15 |
1.392 |
1.316 |
| C27 |
N6 |
1.384 |
1.367 |
| N6 |
C26 |
1.376 |
1.376 |
| C18 |
C7 |
1.530 |
1.409 |
| C7 |
C10 |
1.418 |
1.394 |
| C17 |
C8 |
1.443 |
1.380 |
| C8 |
C9 |
1.427 |
1.384 |
| C8 |
H8 |
1.080 |
1.080 |
| C9 |
C10 |
1.435 |
1.380 |
| C9 |
H9 |
1.080 |
1.080 |
| C10 |
H10 |
1.081 |
1.079 |
| O13 |
C11 |
1.240 |
1.215 |
| C11 |
C12 |
1.508 |
1.477 |
| C25 |
C12 |
1.494 |
1.409 |
| C12 |
C14 |
1.442 |
1.397 |
| C14 |
C15 |
1.438 |
1.383 |
| C14 |
H14 |
1.081 |
1.079 |
| C15 |
H15 |
1.080 |
1.080 |
| C19 |
C16 |
1.558 |
1.509 |
| C16 |
C17 |
1.477 |
1.509 |
| C16 |
H16 |
1.100 |
1.089 |
| C17 |
C18 |
1.405 |
1.391 |
| C20 |
C18 |
1.480 |
1.482 |
| C24 |
C19 |
1.446 |
1.378 |
| C19 |
C20 |
1.440 |
1.393 |
| C21 |
C20 |
1.463 |
1.397 |
| C22 |
C21 |
1.434 |
1.380 |
| C21 |
H21 |
1.080 |
1.080 |
| C23 |
C22 |
1.455 |
1.384 |
| C22 |
H22 |
1.080 |
1.079 |
| C23 |
C24 |
1.434 |
1.384 |
| C23 |
H23 |
1.080 |
1.080 |
| C24 |
H24 |
1.080 |
1.080 |
| C28 |
C25 |
1.439 |
1.459 |
| C25 |
C26 |
1.379 |
1.410 |
| C28 |
C27 |
1.410 |
1.345 |
| C27 |
H27 |
1.080 |
1.081 |
| C28 |
H28 |
1.080 |
1.080 |
| N2 |
HN2 |
1.001 |
0.970 |
| N6 |
HN6 |
1.000 |
0.970 |
Bond Angles for YKI
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C3 |
C1 |
H1 |
119.2 |
119.2 |
| N1 |
C1 |
H1 |
119.1 |
119.3 |
| C1 |
N1 |
C2 |
121.4 |
122.3 |
| N1 |
C2 |
H2 |
120.5 |
119.9 |
| C6 |
C2 |
H2 |
120.5 |
119.9 |
| C4 |
N2 |
HN2 |
125.8 |
126.4 |
| C6 |
N2 |
HN2 |
125.8 |
126.4 |
| C5 |
C3 |
H3 |
121.2 |
120.6 |
| C3 |
C5 |
N3 |
133.6 |
134.6 |
| C3 |
C5 |
C6 |
120.6 |
118.1 |
| C4 |
N3 |
C5 |
108.8 |
109.7 |
| N3 |
C5 |
C6 |
105.8 |
107.3 |
| C11 |
N4 |
HN4 |
112.3 |
120.0 |
| C16 |
N4 |
HN4 |
112.3 |
120.0 |
| N5 |
C15 |
C14 |
120.5 |
121.8 |
| N5 |
C15 |
H15 |
119.7 |
119.1 |
| C27 |
N6 |
HN6 |
126.7 |
125.0 |
| N6 |
C26 |
C25 |
111.9 |
106.9 |
| C26 |
N6 |
HN6 |
126.8 |
125.0 |
| C7 |
C10 |
C9 |
121.9 |
120.0 |
| C7 |
C10 |
H10 |
119.0 |
120.0 |
| C17 |
C8 |
H8 |
119.7 |
119.8 |
| C9 |
C8 |
H8 |
119.6 |
119.9 |
| C8 |
C9 |
C10 |
119.5 |
120.3 |
| C8 |
C9 |
H9 |
120.3 |
119.9 |
| C10 |
C9 |
H9 |
120.2 |
119.8 |
| C9 |
C10 |
H10 |
119.0 |
120.0 |
| C11 |
C12 |
C14 |
125.2 |
121.1 |
| C12 |
C14 |
C15 |
118.0 |
119.2 |
| C12 |
C14 |
H14 |
121.0 |
120.4 |
| C15 |
C14 |
H14 |
121.0 |
120.4 |
| C14 |
C15 |
H15 |
119.8 |
119.1 |
| C19 |
C16 |
H16 |
110.0 |
110.1 |
| C17 |
C16 |
H16 |
117.6 |
110.2 |
| C16 |
C17 |
C18 |
114.5 |
107.6 |
| C22 |
C21 |
H21 |
119.7 |
120.0 |
| C23 |
C22 |
H22 |
120.1 |
119.9 |
| C24 |
C23 |
H23 |
120.0 |
120.0 |
| C23 |
C24 |
H24 |
120.1 |
119.9 |
| C28 |
C27 |
H27 |
125.2 |
125.1 |
Torsion Angles for YKI
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| N1 |
C1 |
C3 |
H1 |
180.0 |
179.6 |
| C3 |
C1 |
N1 |
H1 |
180.0 |
180.4 |
| C1 |
N1 |
C2 |
H2 |
180.2 |
180.0 |
| H1 |
C1 |
N1 |
C2 |
179.7 |
179.9 |
| C2 |
N1 |
C1 |
H1 |
179.7 |
179.9 |
| C6 |
C2 |
N1 |
H2 |
180.0 |
180.0 |
| N1 |
C2 |
C6 |
H2 |
180.0 |
180.0 |
| C6 |
N2 |
C4 |
HN2 |
180.0 |
180.0 |
| N2 |
C6 |
C2 |
H2 |
0.4 |
0.5 |
| C4 |
N2 |
C6 |
HN2 |
180.0 |
180.0 |
| C5 |
C3 |
C1 |
H1 |
180.4 |
180.3 |
| C4 |
N3 |
C5 |
C3 |
179.9 |
180.1 |
| N3 |
C5 |
C3 |
C6 |
180.3 |
180.5 |
| H3 |
C3 |
C1 |
H1 |
0.4 |
0.3 |
| H3 |
C3 |
C5 |
N3 |
359.8 |
0.1 |
| H3 |
C3 |
C5 |
C6 |
179.5 |
179.6 |
| N3 |
C5 |
C3 |
H3 |
359.8 |
0.1 |
| C3 |
C5 |
N3 |
C6 |
179.7 |
179.5 |
| N3 |
C4 |
N2 |
HN2 |
179.9 |
180.4 |
| C3 |
C5 |
N3 |
C4 |
179.9 |
180.1 |
| C4 |
N3 |
C5 |
C6 |
0.3 |
0.6 |
| C7 |
C4 |
N2 |
HN2 |
0.6 |
359.8 |
| C16 |
N4 |
C11 |
HN4 |
180.0 |
180.0 |
| C11 |
N4 |
C16 |
HN4 |
180.0 |
180.0 |
| C5 |
C6 |
C2 |
H2 |
179.7 |
179.5 |
| C5 |
C6 |
N2 |
HN2 |
180.2 |
180.0 |
| C6 |
C5 |
C3 |
H3 |
179.5 |
179.6 |
| C3 |
C5 |
C6 |
N3 |
180.3 |
180.4 |
| C26 |
N5 |
C15 |
H15 |
179.5 |
180.0 |
| C12 |
C14 |
C15 |
N5 |
0.4 |
360.0 |
| N5 |
C15 |
C14 |
H14 |
180.4 |
180.0 |
| C14 |
C15 |
N5 |
H15 |
180.0 |
180.0 |
| C26 |
N6 |
C27 |
HN6 |
180.0 |
179.9 |
| C27 |
N6 |
C26 |
HN6 |
180.0 |
180.1 |
| C18 |
C7 |
C10 |
H10 |
179.6 |
180.3 |
| C8 |
C9 |
C10 |
C7 |
0.1 |
360.0 |
| C7 |
C10 |
C9 |
H9 |
180.1 |
179.8 |
| C9 |
C10 |
C7 |
H10 |
180.0 |
180.0 |
| C9 |
C8 |
C17 |
H8 |
180.0 |
180.3 |
| C17 |
C8 |
C9 |
H9 |
180.0 |
179.9 |
| C7 |
C10 |
C9 |
C8 |
0.1 |
360.0 |
| C17 |
C8 |
C9 |
H8 |
180.0 |
179.7 |
| C10 |
C9 |
C8 |
H9 |
180.0 |
179.8 |
| C8 |
C9 |
C10 |
H10 |
180.1 |
180.0 |
| H8 |
C8 |
C9 |
C10 |
180.1 |
180.0 |
| H8 |
C8 |
C9 |
H9 |
0.1 |
0.2 |
| C7 |
C10 |
C9 |
H10 |
180.0 |
180.0 |
| C10 |
C9 |
C8 |
H8 |
180.1 |
180.0 |
| C8 |
C9 |
C10 |
H9 |
180.0 |
180.2 |
| H9 |
C9 |
C8 |
H8 |
0.1 |
0.2 |
| C8 |
C9 |
H9 |
C10 |
180.0 |
179.8 |
| H9 |
C9 |
C10 |
H10 |
0.1 |
359.8 |
| C7 |
C10 |
H10 |
C9 |
180.0 |
180.0 |
| H10 |
C10 |
C9 |
H9 |
0.1 |
359.8 |
| O13 |
C11 |
N4 |
HN4 |
180.6 |
180.0 |
| O13 |
C11 |
C12 |
C14 |
138.1 |
180.0 |
| C12 |
C11 |
N4 |
HN4 |
2.0 |
360.0 |
| C11 |
C12 |
C14 |
C15 |
179.7 |
179.9 |
| C11 |
C12 |
C14 |
H14 |
359.7 |
359.9 |
| N6 |
C26 |
C25 |
C12 |
179.8 |
180.0 |
| C25 |
C12 |
C14 |
H14 |
179.4 |
180.0 |
| N5 |
C15 |
C14 |
C12 |
0.4 |
360.0 |
| C15 |
C14 |
C12 |
H14 |
180.0 |
180.1 |
| C12 |
C14 |
C15 |
H15 |
180.4 |
180.0 |
| N5 |
C15 |
C14 |
H15 |
180.0 |
180.0 |
| C12 |
C14 |
C15 |
H14 |
180.0 |
179.9 |
| C12 |
C14 |
H14 |
C15 |
180.0 |
180.1 |
| H14 |
C14 |
C15 |
H15 |
0.4 |
0.1 |
| N5 |
C15 |
H15 |
C14 |
180.0 |
180.0 |
| H15 |
C15 |
C14 |
H14 |
0.4 |
0.1 |
| C19 |
C16 |
N4 |
HN4 |
90.6 |
91.6 |
| C17 |
C16 |
C19 |
H16 |
235.5 |
240.8 |
| C17 |
C16 |
N4 |
HN4 |
324.7 |
335.0 |
| C16 |
C17 |
C8 |
H8 |
0.0 |
359.7 |
| C19 |
C16 |
C17 |
H16 |
119.1 |
119.1 |
| H16 |
C16 |
N4 |
HN4 |
204.0 |
213.3 |
| H16 |
C16 |
C17 |
C18 |
241.3 |
240.6 |
| C18 |
C17 |
C8 |
H8 |
180.0 |
180.0 |
| C18 |
C17 |
C16 |
H16 |
241.3 |
240.6 |
| C24 |
C19 |
C16 |
H16 |
304.4 |
299.3 |
| C20 |
C19 |
C16 |
H16 |
123.8 |
119.4 |
| C23 |
C22 |
C21 |
H21 |
179.8 |
180.0 |
| H22 |
C22 |
C21 |
H21 |
359.8 |
360.0 |
| C24 |
C23 |
C22 |
H22 |
180.2 |
180.0 |
| H23 |
C23 |
C22 |
H22 |
0.2 |
359.9 |
| H23 |
C23 |
C24 |
H24 |
359.8 |
0.1 |
| H24 |
C24 |
C23 |
H23 |
359.8 |
0.1 |
| C25 |
C26 |
N6 |
HN6 |
179.4 |
179.9 |
| C28 |
C27 |
N6 |
HN6 |
180.1 |
180.1 |
| H27 |
C27 |
N6 |
HN6 |
0.1 |
0.0 |
| H28 |
C28 |
C27 |
H27 |
0.3 |
0.1 |
| HN6 |
N6 |
C26 |
C25 |
179.4 |
179.9 |