PDB Chemical Component 8PY
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 8PY
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C32 |
C31 |
1.404 |
1.392 |
| C32 |
C27 |
1.383 |
1.394 |
| C31 |
C30 |
1.379 |
1.392 |
| C28 |
C27 |
1.396 |
1.392 |
| C28 |
C29 |
1.379 |
1.399 |
| C27 |
C23 |
1.460 |
1.475 |
| C30 |
C24 |
1.384 |
1.394 |
| C29 |
C13 |
1.406 |
1.392 |
| C23 |
C24 |
1.446 |
1.474 |
| C23 |
C14 |
1.443 |
1.305 |
| C24 |
C25 |
1.391 |
1.392 |
| C13 |
C14 |
1.378 |
1.474 |
| C13 |
C12 |
1.343 |
1.393 |
| C14 |
C15 |
1.405 |
1.475 |
| C25 |
C26 |
1.398 |
1.399 |
| C12 |
C11 |
1.358 |
1.393 |
| C15 |
C26 |
1.369 |
1.392 |
| C15 |
C16 |
1.366 |
1.392 |
| C11 |
C16 |
1.385 |
1.391 |
| C11 |
N8 |
1.336 |
1.355 |
| C9 |
C7 |
1.503 |
1.507 |
| C7 |
N8 |
1.348 |
1.348 |
| C7 |
O10 |
1.226 |
1.213 |
| N8 |
C8 |
1.336 |
1.387 |
| N7 |
C8 |
1.333 |
1.307 |
| N7 |
C5 |
1.342 |
1.358 |
| O6 |
C6 |
1.260 |
1.219 |
| C8 |
N9 |
1.332 |
1.368 |
| C5 |
C6 |
1.466 |
1.414 |
| C5 |
C4 |
1.477 |
1.398 |
| C6 |
N1 |
1.325 |
1.351 |
| N9 |
C4 |
1.330 |
1.371 |
| N9 |
C1' |
1.489 |
1.465 |
| C4 |
N3 |
1.346 |
1.338 |
| N1 |
C2 |
1.344 |
1.363 |
| C1' |
C2' |
1.520 |
1.545 |
| C1' |
O4' |
1.436 |
1.445 |
| C2' |
C3' |
1.510 |
1.545 |
| N3 |
C2 |
1.333 |
1.314 |
| C2 |
N2 |
1.319 |
1.373 |
| O4' |
C4' |
1.413 |
1.444 |
| C3' |
C4' |
1.511 |
1.545 |
| C3' |
O3' |
1.443 |
1.429 |
| C4' |
C5' |
1.527 |
1.530 |
| O5' |
C5' |
1.415 |
1.429 |
| O5' |
P |
1.609 |
1.610 |
| P |
OP2 |
1.523 |
1.609 |
| P |
OP1 |
1.522 |
1.480 |
| C5' |
H2 |
1.100 |
1.090 |
| C5' |
H3 |
1.100 |
1.089 |
| C4' |
H4 |
1.099 |
1.091 |
| C3' |
H5 |
1.100 |
1.090 |
| O3' |
H6 |
0.950 |
0.967 |
| C2' |
H7 |
1.100 |
1.090 |
| C2' |
H8 |
1.101 |
1.089 |
| C1' |
H9 |
1.100 |
1.090 |
| N2 |
H10 |
1.000 |
0.969 |
| N2 |
H11 |
1.000 |
0.971 |
| N1 |
H12 |
1.000 |
0.970 |
| OP2 |
H13 |
0.950 |
0.967 |
| C9 |
H14 |
1.100 |
1.090 |
| C9 |
H15 |
1.100 |
1.090 |
| C9 |
H16 |
1.099 |
1.090 |
| C12 |
H17 |
1.080 |
1.080 |
| C16 |
H18 |
1.079 |
1.081 |
| C25 |
H19 |
1.080 |
1.080 |
| C26 |
H20 |
1.080 |
1.080 |
| C28 |
H21 |
1.080 |
1.080 |
| C29 |
H22 |
1.080 |
1.081 |
| C30 |
H23 |
1.080 |
1.080 |
| C31 |
H24 |
1.080 |
1.079 |
| C32 |
H25 |
1.080 |
1.080 |
| P |
O1 |
|
1.611 |
| O1 |
H1 |
|
0.966 |
Bond Angles for 8PY
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C32 |
C31 |
H24 |
118.7 |
118.6 |
| C31 |
C30 |
H23 |
119.4 |
119.7 |
| C29 |
C28 |
H21 |
120.6 |
120.0 |
| C28 |
C29 |
H22 |
120.1 |
119.9 |
| C23 |
C24 |
C25 |
118.9 |
119.5 |
| C24 |
C25 |
C26 |
122.5 |
120.2 |
| C24 |
C25 |
H19 |
118.7 |
119.9 |
| C13 |
C14 |
C15 |
125.5 |
119.2 |
| C13 |
C12 |
H17 |
120.1 |
119.7 |
| C14 |
C15 |
C26 |
121.5 |
119.5 |
| C14 |
C15 |
C16 |
118.6 |
118.3 |
| C15 |
C26 |
C25 |
119.4 |
120.2 |
| C26 |
C25 |
H19 |
118.7 |
120.0 |
| C25 |
C26 |
H20 |
120.3 |
119.9 |
| C12 |
C11 |
C16 |
127.0 |
122.8 |
| C16 |
C15 |
C26 |
119.9 |
122.2 |
| C15 |
C26 |
H20 |
120.3 |
119.9 |
| C11 |
C16 |
C15 |
114.1 |
120.7 |
| C15 |
C16 |
H18 |
123.0 |
119.7 |
| C11 |
C16 |
H18 |
123.0 |
119.7 |
| C9 |
C7 |
O10 |
120.5 |
120.0 |
| N7 |
C5 |
C6 |
132.1 |
134.0 |
| C5 |
C6 |
N1 |
114.8 |
118.3 |
| C5 |
C4 |
N3 |
120.0 |
119.7 |
| C6 |
N1 |
H12 |
118.5 |
119.8 |
| N9 |
C4 |
N3 |
133.4 |
134.1 |
| N9 |
C1' |
H9 |
110.3 |
110.4 |
| C4 |
N3 |
C2 |
116.3 |
121.2 |
| C1' |
C2' |
H7 |
110.4 |
110.5 |
| C1' |
C2' |
H8 |
110.4 |
110.6 |
| O4' |
C1' |
H9 |
111.1 |
110.3 |
| C2' |
C3' |
H5 |
108.7 |
110.6 |
| N3 |
C2 |
N2 |
116.6 |
119.0 |
| C2 |
N2 |
H10 |
120.0 |
120.1 |
| C2 |
N2 |
H11 |
120.0 |
119.9 |
| O4' |
C4' |
H4 |
110.4 |
110.4 |
| C3' |
C4' |
H4 |
109.1 |
110.4 |
| O3' |
C3' |
H5 |
109.6 |
110.5 |
| C3' |
O3' |
H6 |
109.5 |
114.0 |
| C4' |
C5' |
H2 |
109.5 |
109.5 |
| C4' |
C5' |
H3 |
109.5 |
109.5 |
| O5' |
C5' |
H2 |
109.5 |
109.4 |
| O5' |
C5' |
H3 |
109.5 |
109.5 |
| O5' |
P |
OP2 |
112.8 |
109.5 |
| O5' |
P |
O1 |
|
109.5 |
| OP1 |
P |
OP2 |
111.6 |
109.5 |
| P |
OP2 |
H13 |
109.5 |
114.1 |
| OP2 |
P |
O1 |
|
109.4 |
| OP1 |
P |
O1 |
|
109.5 |
| H2 |
C5' |
H3 |
109.5 |
109.5 |
| H7 |
C2' |
H8 |
109.5 |
110.5 |
| H10 |
N2 |
H11 |
120.0 |
120.0 |
| H14 |
C9 |
H15 |
109.5 |
109.4 |
| H14 |
C9 |
H16 |
109.5 |
109.5 |
| H15 |
C9 |
H16 |
109.5 |
109.5 |
| P |
O1 |
H1 |
|
114.0 |
Torsion Angles for 8PY
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C32 |
C31 |
C30 |
H23 |
179.8 |
180.0 |
| C30 |
C24 |
C25 |
H19 |
0.3 |
0.1 |
| C29 |
C13 |
C12 |
H17 |
0.5 |
360.0 |
| C23 |
C24 |
C25 |
C26 |
0.2 |
359.9 |
| C23 |
C24 |
C25 |
H19 |
180.2 |
180.0 |
| C23 |
C14 |
C15 |
C26 |
359.3 |
0.1 |
| C15 |
C26 |
C25 |
C24 |
359.5 |
0.2 |
| C26 |
C25 |
C24 |
H19 |
180.0 |
180.0 |
| C24 |
C25 |
C26 |
H20 |
179.5 |
180.1 |
| C14 |
C13 |
C12 |
H17 |
180.1 |
180.0 |
| C13 |
C14 |
C15 |
C26 |
180.1 |
180.0 |
| C13 |
C14 |
C15 |
C16 |
0.5 |
360.0 |
| C13 |
C12 |
C11 |
C16 |
359.5 |
0.1 |
| C14 |
C15 |
C26 |
C25 |
0.8 |
359.8 |
| C16 |
C15 |
C14 |
C26 |
180.4 |
180.0 |
| C14 |
C15 |
C26 |
H20 |
180.8 |
179.9 |
| C11 |
C16 |
C15 |
C14 |
359.3 |
0.0 |
| C14 |
C15 |
C16 |
H18 |
179.3 |
180.3 |
| C24 |
C25 |
C26 |
H19 |
180.0 |
180.0 |
| C16 |
C15 |
C26 |
C25 |
180.4 |
179.9 |
| C15 |
C26 |
C25 |
H20 |
180.0 |
180.1 |
| C12 |
C11 |
C16 |
C15 |
0.8 |
360.0 |
| C12 |
C11 |
C16 |
H18 |
180.8 |
179.7 |
| C24 |
C25 |
C26 |
C15 |
359.5 |
0.2 |
| C14 |
C15 |
C26 |
C16 |
180.4 |
179.9 |
| C15 |
C26 |
C25 |
H19 |
179.5 |
180.1 |
| C25 |
C26 |
C15 |
H20 |
180.0 |
179.9 |
| C11 |
C16 |
C15 |
C26 |
179.6 |
180.0 |
| C26 |
C15 |
C16 |
H18 |
359.6 |
0.2 |
| C14 |
C15 |
C16 |
C26 |
179.6 |
180.1 |
| C16 |
C15 |
C26 |
H20 |
0.4 |
360.0 |
| C11 |
C16 |
C15 |
H18 |
180.0 |
179.7 |
| C14 |
C15 |
C16 |
C11 |
359.3 |
0.0 |
| C15 |
C16 |
C11 |
H18 |
180.0 |
180.3 |
| C8 |
N7 |
C5 |
C6 |
179.9 |
179.7 |
| N7 |
C5 |
C6 |
N1 |
179.1 |
179.9 |
| N7 |
C5 |
C4 |
N3 |
180.4 |
180.1 |
| O6 |
C6 |
N1 |
H12 |
358.5 |
360.0 |
| C8 |
N9 |
C4 |
N3 |
180.9 |
180.2 |
| C8 |
N9 |
C1' |
H9 |
10.2 |
353.1 |
| C6 |
C5 |
C4 |
N3 |
359.6 |
0.1 |
| C5 |
C6 |
N1 |
H12 |
179.7 |
180.1 |
| N9 |
C4 |
C5 |
N3 |
178.5 |
179.9 |
| C5 |
C4 |
N3 |
C2 |
0.9 |
360.0 |
| C5 |
C4 |
N9 |
N3 |
181.8 |
180.1 |
| C4 |
N9 |
C1' |
H9 |
197.9 |
173.5 |
| N9 |
C4 |
N3 |
C2 |
182.9 |
180.1 |
| N9 |
C1' |
C2' |
H7 |
263.5 |
24.2 |
| N9 |
C1' |
C2' |
H8 |
24.6 |
261.5 |
| O4' |
C1' |
N9 |
H9 |
229.4 |
237.8 |
| C4 |
N3 |
C2 |
N2 |
180.8 |
180.0 |
| C5 |
C6 |
N1 |
C2 |
359.7 |
0.1 |
| N1 |
C2 |
N2 |
H10 |
181.8 |
180.0 |
| N1 |
C2 |
N2 |
H11 |
1.8 |
0.1 |
| C1' |
C2' |
C3' |
H5 |
248.8 |
241.3 |
| H7 |
C2' |
C1' |
H8 |
238.9 |
122.7 |
| N9 |
C1' |
O4' |
H9 |
130.3 |
122.3 |
| O4' |
C1' |
C2' |
H7 |
138.9 |
265.3 |
| O4' |
C1' |
C2' |
H8 |
260.0 |
142.6 |
| C1' |
O4' |
C4' |
H4 |
285.2 |
281.5 |
| C2' |
C3' |
C4' |
H4 |
90.4 |
95.0 |
| O3' |
C3' |
C2' |
H5 |
237.9 |
237.3 |
| C2' |
C3' |
O3' |
H6 |
180.0 |
65.4 |
| N3 |
C2 |
N2 |
H10 |
0.0 |
360.0 |
| N3 |
C2 |
N2 |
H11 |
180.0 |
180.0 |
| H10 |
N2 |
C2 |
H11 |
180.0 |
179.9 |
| C3' |
C4' |
O4' |
H4 |
116.8 |
118.9 |
| O4' |
C4' |
C5' |
H2 |
157.8 |
308.0 |
| O4' |
C4' |
C5' |
H3 |
277.8 |
187.9 |
| O4' |
C4' |
C3' |
H4 |
242.3 |
241.1 |
| C3' |
C4' |
C5' |
H2 |
274.1 |
63.5 |
| C3' |
C4' |
C5' |
H3 |
34.1 |
303.4 |
| C2' |
C3' |
O3' |
H5 |
121.6 |
122.8 |
| O3' |
C3' |
C4' |
H4 |
327.6 |
336.3 |
| O5' |
C5' |
C4' |
H2 |
240.0 |
120.0 |
| O5' |
C5' |
C4' |
H3 |
120.0 |
240.0 |
| H2 |
C5' |
C4' |
H3 |
239.9 |
120.1 |
| C4' |
C5' |
O5' |
H2 |
120.0 |
240.0 |
| C4' |
C5' |
O5' |
H3 |
240.0 |
120.0 |
| C5' |
O5' |
P |
OP2 |
36.7 |
295.0 |
| C5' |
O5' |
P |
O1 |
|
175.0 |
| H2 |
C5' |
O5' |
H3 |
120.0 |
240.0 |
| OP1 |
P |
O5' |
OP2 |
233.0 |
120.0 |
| O5' |
P |
OP2 |
H13 |
232.8 |
300.0 |
| OP2 |
P |
O5' |
O1 |
|
120.0 |
| OP1 |
P |
O5' |
O1 |
|
240.0 |
| O5' |
P |
O1 |
H1 |
|
180.0 |
| O5' |
P |
OP2 |
O1 |
|
240.0 |
| OP1 |
P |
OP2 |
O1 |
|
120.0 |
| OP2 |
P |
O1 |
H1 |
|
60.0 |
| O5' |
P |
OP1 |
OP2 |
127.6 |
240.0 |
| O5' |
P |
OP1 |
O1 |
|
120.0 |
| OP1 |
P |
OP2 |
H13 |
0.0 |
180.0 |
| OP2 |
P |
OP1 |
O1 |
|
240.0 |
| OP1 |
P |
O1 |
H1 |
|
300.0 |
| C4' |
C5' |
H2 |
H3 |
120.1 |
239.9 |
| O5' |
C5' |
H2 |
H3 |
240.0 |
120.0 |
| C4' |
C5' |
H3 |
H2 |
239.9 |
120.0 |
| O5' |
C5' |
H3 |
H2 |
120.0 |
240.0 |
| H4 |
C4' |
C5' |
H2 |
33.2 |
185.8 |
| H4 |
C4' |
C5' |
H3 |
153.3 |
65.7 |
| H5 |
C3' |
C4' |
H4 |
206.0 |
213.7 |
| H5 |
C3' |
O3' |
H6 |
58.4 |
302.6 |
| H6 |
O3' |
C3' |
H5 |
58.4 |
302.6 |
| C1' |
C2' |
H7 |
H8 |
121.6 |
237.2 |
| H7 |
C2' |
C3' |
H5 |
129.4 |
359.9 |
| C1' |
C2' |
H8 |
H7 |
238.4 |
122.7 |
| H8 |
C2' |
C3' |
H5 |
8.3 |
122.5 |
| H9 |
C1' |
C2' |
H7 |
20.6 |
146.5 |
| H9 |
C1' |
C2' |
H8 |
141.7 |
23.8 |
| C2 |
N2 |
H10 |
H11 |
180.0 |
180.1 |
| C2 |
N2 |
H11 |
H10 |
180.0 |
179.9 |
| H13 |
OP2 |
P |
O1 |
|
60.0 |
| H14 |
C9 |
C7 |
O10 |
0.0 |
264.3 |
| H15 |
C9 |
H14 |
H16 |
120.0 |
120.1 |
| H15 |
C9 |
C7 |
O10 |
120.0 |
24.2 |
| H14 |
C9 |
H15 |
H16 |
240.0 |
239.9 |
| H16 |
C9 |
C7 |
O10 |
240.0 |
144.2 |
| H14 |
C9 |
H16 |
H15 |
120.0 |
120.0 |
| H17 |
C12 |
C11 |
C16 |
179.5 |
180.0 |
| H18 |
C16 |
C15 |
C26 |
359.6 |
0.2 |
| C11 |
C16 |
H18 |
C15 |
180.0 |
180.3 |
| C24 |
C25 |
H19 |
C26 |
180.0 |
180.0 |
| H19 |
C25 |
C26 |
H20 |
359.4 |
0.0 |
| C15 |
C26 |
H20 |
C25 |
180.0 |
179.9 |
| H20 |
C26 |
C25 |
H19 |
359.4 |
0.0 |
| H21 |
C28 |
C29 |
H22 |
359.6 |
360.0 |
| H22 |
C29 |
C28 |
H21 |
359.6 |
360.0 |
| H24 |
C31 |
C30 |
H23 |
359.7 |
0.1 |
| H25 |
C32 |
C31 |
H24 |
0.4 |
360.0 |
| O5' |
P |
O1 |
OP2 |
|
120.0 |
| OP1 |
P |
O1 |
OP2 |
|
240.0 |
| O1 |
P |
OP2 |
H13 |
|
60.0 |