PDB Chemical Component 4DY
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 4DY
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C40 |
C38 |
1.529 |
1.530 |
| C30 |
C33 |
1.530 |
1.530 |
| C30 |
C27 |
1.529 |
1.530 |
| C37 |
C38 |
1.528 |
1.507 |
| C37 |
C36 |
1.530 |
1.310 |
| C33 |
C36 |
1.529 |
1.507 |
| C38 |
C44 |
1.528 |
1.530 |
| C24 |
C27 |
1.530 |
1.531 |
| C24 |
C22 |
1.529 |
1.507 |
| C5 |
C6 |
1.391 |
1.383 |
| C5 |
C4 |
1.392 |
1.385 |
| C6 |
C1 |
1.392 |
1.382 |
| N21 |
C22 |
1.342 |
1.348 |
| N21 |
C17 |
1.468 |
1.465 |
| C22 |
O23 |
1.230 |
1.212 |
| O10 |
C4 |
1.360 |
1.360 |
| C4 |
C3 |
1.391 |
1.392 |
| C1 |
C17 |
1.388 |
1.507 |
| C1 |
C2 |
1.393 |
1.383 |
| C3 |
C2 |
1.388 |
1.385 |
| C3 |
O12 |
1.360 |
1.360 |
| O12 |
C13 |
1.431 |
1.429 |
| C2 |
H2 |
1.080 |
1.080 |
| C5 |
H5 |
1.080 |
1.080 |
| C40 |
H40 |
1.100 |
1.090 |
| C40 |
H6T |
1.100 |
1.090 |
| C40 |
H6S |
1.100 |
1.090 |
| C38 |
H38 |
1.100 |
1.090 |
| C44 |
H6U |
1.100 |
1.089 |
| C44 |
H6V |
1.100 |
1.090 |
| C44 |
H44 |
1.100 |
1.090 |
| C37 |
H37 |
1.080 |
1.080 |
| C36 |
H36 |
1.080 |
1.080 |
| C33 |
H33 |
1.100 |
1.090 |
| C33 |
H6R |
1.099 |
1.090 |
| C30 |
H6Q |
1.100 |
1.090 |
| C30 |
H30 |
1.100 |
1.091 |
| C27 |
H27 |
1.100 |
1.090 |
| C27 |
H6P |
1.100 |
1.090 |
| C24 |
H6O |
1.100 |
1.090 |
| C24 |
H24 |
1.100 |
1.091 |
| N21 |
H21 |
1.000 |
0.970 |
| C17 |
H6N |
1.100 |
1.090 |
| C17 |
H17 |
1.100 |
1.090 |
| C6 |
H6 |
1.080 |
1.080 |
| O10 |
H10 |
0.950 |
0.967 |
| C13 |
H6M |
1.100 |
1.090 |
| C13 |
H6L |
1.100 |
1.090 |
| C13 |
H13 |
1.100 |
1.090 |
Bond Angles for 4DY
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C40 |
C38 |
C44 |
109.5 |
109.5 |
| C38 |
C40 |
H40 |
109.5 |
109.4 |
| C38 |
C40 |
H6T |
109.5 |
109.5 |
| C38 |
C40 |
H6S |
109.5 |
109.5 |
| C40 |
C38 |
H38 |
109.4 |
109.4 |
| C30 |
C33 |
H33 |
109.4 |
109.5 |
| C30 |
C33 |
H6R |
109.4 |
109.4 |
| C27 |
C30 |
H6Q |
109.5 |
109.5 |
| C27 |
C30 |
H30 |
109.5 |
109.5 |
| C30 |
C27 |
H27 |
109.5 |
109.5 |
| C30 |
C27 |
H6P |
109.5 |
109.5 |
| C37 |
C38 |
H38 |
109.4 |
109.5 |
| C36 |
C37 |
H37 |
120.0 |
120.0 |
| C37 |
C36 |
H36 |
119.9 |
120.1 |
| C33 |
C36 |
H36 |
119.9 |
120.0 |
| C44 |
C38 |
H38 |
109.4 |
109.5 |
| C38 |
C44 |
H6U |
109.5 |
109.4 |
| C38 |
C44 |
H6V |
109.5 |
109.5 |
| C38 |
C44 |
H44 |
109.5 |
109.5 |
| C24 |
C27 |
H27 |
109.5 |
109.4 |
| C24 |
C27 |
H6P |
109.5 |
109.4 |
| C24 |
C22 |
O23 |
121.1 |
120.0 |
| C22 |
C24 |
H6O |
109.5 |
109.5 |
| C22 |
C24 |
H24 |
109.5 |
109.5 |
| C6 |
C5 |
H5 |
120.3 |
120.0 |
| C5 |
C6 |
H6 |
119.9 |
119.9 |
| C1 |
C17 |
N21 |
109.6 |
109.5 |
| C17 |
N21 |
H21 |
118.9 |
120.0 |
| N21 |
C17 |
H6N |
109.4 |
109.5 |
| N21 |
C17 |
H17 |
109.4 |
109.4 |
| C4 |
C3 |
O12 |
117.0 |
120.1 |
| C2 |
C1 |
C17 |
119.9 |
119.9 |
| C1 |
C17 |
H6N |
109.4 |
109.4 |
| C1 |
C17 |
H17 |
109.4 |
109.5 |
| C1 |
C2 |
H2 |
120.3 |
120.0 |
| C3 |
C2 |
H2 |
120.3 |
120.0 |
| C3 |
O12 |
C13 |
109.7 |
117.0 |
| O12 |
C13 |
H6M |
109.5 |
109.4 |
| O12 |
C13 |
H6L |
109.5 |
109.5 |
| O12 |
C13 |
H13 |
109.5 |
109.5 |
| H40 |
C40 |
H6T |
109.5 |
109.5 |
| H40 |
C40 |
H6S |
109.4 |
109.4 |
| H6T |
C40 |
H6S |
109.5 |
109.5 |
| H6U |
C44 |
H6V |
109.5 |
109.5 |
| H6U |
C44 |
H44 |
109.5 |
109.5 |
| H6V |
C44 |
H44 |
109.5 |
109.5 |
| H33 |
C33 |
H6R |
109.5 |
109.5 |
| H6Q |
C30 |
H30 |
109.4 |
109.4 |
| H27 |
C27 |
H6P |
109.5 |
109.5 |
| H6O |
C24 |
H24 |
109.5 |
109.4 |
| H6N |
C17 |
H17 |
109.5 |
109.5 |
| H6M |
C13 |
H6L |
109.5 |
109.5 |
| H6M |
C13 |
H13 |
109.5 |
109.5 |
| H6L |
C13 |
H13 |
109.4 |
109.5 |
Torsion Angles for 4DY
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C37 |
C38 |
C40 |
H38 |
120.0 |
240.0 |
| C44 |
C38 |
C40 |
H38 |
240.1 |
120.0 |
| C40 |
C38 |
C44 |
H6U |
180.0 |
60.0 |
| C40 |
C38 |
C44 |
H6V |
300.0 |
180.0 |
| C40 |
C38 |
C44 |
H44 |
60.0 |
300.0 |
| H40 |
C40 |
C38 |
H6T |
240.0 |
239.9 |
| H40 |
C40 |
C38 |
H6S |
120.0 |
119.9 |
| H6T |
C40 |
C38 |
H6S |
240.0 |
240.0 |
| C30 |
C33 |
C36 |
H36 |
46.8 |
305.0 |
| H33 |
C33 |
C30 |
H6R |
240.0 |
120.0 |
| C27 |
C30 |
C33 |
H33 |
19.2 |
59.9 |
| C27 |
C30 |
C33 |
H6R |
139.2 |
299.9 |
| C24 |
C27 |
C30 |
H27 |
240.0 |
240.0 |
| C24 |
C27 |
C30 |
H6P |
120.0 |
119.9 |
| H6Q |
C30 |
C27 |
H30 |
120.0 |
120.0 |
| H27 |
C27 |
C30 |
H6P |
240.0 |
239.9 |
| C37 |
C38 |
C40 |
H40 |
180.0 |
60.0 |
| C37 |
C38 |
C40 |
H6T |
300.0 |
180.0 |
| C37 |
C38 |
C40 |
H6S |
60.0 |
300.1 |
| C40 |
C38 |
C37 |
H38 |
240.0 |
120.0 |
| C44 |
C38 |
C37 |
H38 |
119.9 |
240.0 |
| C37 |
C38 |
C44 |
H6U |
300.2 |
300.0 |
| C37 |
C38 |
C44 |
H6V |
60.2 |
60.0 |
| C37 |
C38 |
C44 |
H44 |
180.2 |
180.0 |
| C36 |
C37 |
C38 |
H38 |
314.1 |
0.1 |
| C33 |
C36 |
C37 |
H36 |
180.0 |
180.0 |
| C33 |
C36 |
C37 |
H37 |
358.8 |
0.0 |
| C37 |
C36 |
C33 |
H36 |
180.0 |
180.0 |
| C44 |
C38 |
C40 |
H40 |
300.1 |
300.0 |
| C44 |
C38 |
C40 |
H6T |
60.1 |
60.0 |
| C44 |
C38 |
C40 |
H6S |
180.1 |
180.0 |
| C40 |
C38 |
C44 |
H38 |
119.9 |
240.0 |
| C37 |
C38 |
C44 |
H38 |
240.1 |
120.0 |
| H6U |
C44 |
C38 |
H6V |
240.0 |
240.0 |
| H6U |
C44 |
C38 |
H44 |
120.0 |
120.0 |
| H6V |
C44 |
C38 |
H44 |
240.0 |
240.0 |
| C24 |
C27 |
C30 |
H6Q |
76.5 |
59.9 |
| C24 |
C27 |
C30 |
H30 |
316.5 |
300.0 |
| C30 |
C27 |
C24 |
H27 |
120.0 |
120.0 |
| C30 |
C27 |
C24 |
H6P |
240.0 |
240.1 |
| H27 |
C27 |
C24 |
H6P |
120.0 |
120.0 |
| C22 |
C24 |
C27 |
H27 |
76.4 |
60.0 |
| C22 |
C24 |
C27 |
H6P |
316.4 |
300.0 |
| H6O |
C24 |
C22 |
H24 |
120.0 |
120.0 |
| C5 |
C4 |
C3 |
O12 |
180.4 |
180.1 |
| C6 |
C1 |
C17 |
H6N |
178.0 |
30.2 |
| C6 |
C1 |
C17 |
H17 |
58.0 |
150.3 |
| C6 |
C1 |
C2 |
H2 |
179.9 |
179.7 |
| N21 |
C22 |
C24 |
H6O |
82.9 |
60.0 |
| N21 |
C22 |
C24 |
H24 |
322.9 |
300.0 |
| C1 |
C17 |
N21 |
C22 |
214.4 |
180.0 |
| C2 |
C1 |
C17 |
N21 |
117.8 |
90.0 |
| C1 |
C17 |
N21 |
H6N |
240.0 |
120.0 |
| C1 |
C17 |
N21 |
H17 |
120.0 |
240.0 |
| H6N |
C17 |
N21 |
H17 |
240.0 |
120.0 |
| O23 |
C22 |
C24 |
H6O |
262.9 |
240.0 |
| O23 |
C22 |
C24 |
H24 |
142.9 |
120.0 |
| O10 |
C4 |
C3 |
O12 |
0.5 |
0.1 |
| C4 |
C3 |
C2 |
H2 |
180.0 |
180.0 |
| C4 |
C3 |
O12 |
C13 |
264.7 |
180.0 |
| C1 |
C17 |
N21 |
H21 |
34.4 |
360.0 |
| N21 |
C17 |
C1 |
H6N |
120.0 |
240.0 |
| N21 |
C17 |
C1 |
H17 |
240.0 |
120.0 |
| C17 |
C1 |
C2 |
H2 |
0.2 |
0.0 |
| H6N |
C17 |
C1 |
H17 |
120.0 |
239.9 |
| C2 |
C1 |
C17 |
H6N |
357.8 |
210.0 |
| C2 |
C1 |
C17 |
H17 |
237.8 |
330.0 |
| C3 |
C2 |
C1 |
H2 |
180.0 |
179.9 |
| C3 |
C2 |
C1 |
C17 |
180.2 |
180.0 |
| C1 |
C2 |
C3 |
H2 |
180.0 |
180.1 |
| O12 |
C3 |
C2 |
H2 |
359.7 |
359.9 |
| C3 |
O12 |
C13 |
H6M |
180.0 |
299.9 |
| C3 |
O12 |
C13 |
H6L |
300.0 |
60.0 |
| C3 |
O12 |
C13 |
H13 |
60.0 |
180.0 |
| H6M |
C13 |
O12 |
H6L |
240.0 |
240.0 |
| H6M |
C13 |
O12 |
H13 |
120.0 |
120.0 |
| H6L |
C13 |
O12 |
H13 |
240.0 |
240.0 |
| H2 |
C2 |
C1 |
C17 |
0.2 |
0.0 |
| H5 |
C5 |
C6 |
H6 |
360.0 |
0.5 |
| H40 |
C40 |
C38 |
C44 |
300.1 |
300.0 |
| C38 |
C40 |
H40 |
H6T |
120.0 |
120.0 |
| C38 |
C40 |
H40 |
H6S |
240.0 |
240.1 |
| H40 |
C40 |
C38 |
H38 |
60.0 |
179.9 |
| H6T |
C40 |
H40 |
H6S |
120.0 |
120.0 |
| H6T |
C40 |
C38 |
C44 |
60.1 |
60.0 |
| C38 |
C40 |
H6T |
H40 |
240.0 |
240.0 |
| C38 |
C40 |
H6T |
H6S |
120.0 |
120.0 |
| H6T |
C40 |
C38 |
H38 |
180.0 |
300.0 |
| H40 |
C40 |
H6T |
H6S |
240.0 |
240.0 |
| H6S |
C40 |
C38 |
C44 |
180.1 |
180.0 |
| C38 |
C40 |
H6S |
H40 |
120.0 |
119.9 |
| C38 |
C40 |
H6S |
H6T |
240.0 |
240.0 |
| H6S |
C40 |
C38 |
H38 |
300.0 |
60.0 |
| H40 |
C40 |
H6S |
H6T |
120.0 |
120.1 |
| C40 |
C38 |
H38 |
C44 |
240.0 |
120.0 |
| H38 |
C38 |
C40 |
H40 |
60.0 |
179.9 |
| H38 |
C38 |
C40 |
H6T |
180.0 |
300.0 |
| H38 |
C38 |
C40 |
H6S |
300.0 |
60.0 |
| H38 |
C38 |
C44 |
H6U |
60.1 |
180.0 |
| H38 |
C38 |
C44 |
H6V |
180.1 |
300.0 |
| H38 |
C38 |
C44 |
H44 |
300.1 |
60.0 |
| H6U |
C44 |
C38 |
H38 |
60.1 |
180.0 |
| C38 |
C44 |
H6U |
H6V |
120.0 |
120.0 |
| C38 |
C44 |
H6U |
H44 |
240.0 |
240.0 |
| H6V |
C44 |
H6U |
H44 |
120.0 |
120.0 |
| H6V |
C44 |
C38 |
H38 |
180.1 |
300.0 |
| C38 |
C44 |
H6V |
H6U |
240.0 |
240.0 |
| C38 |
C44 |
H6V |
H44 |
120.0 |
120.0 |
| H6U |
C44 |
H6V |
H44 |
240.0 |
239.9 |
| H44 |
C44 |
C38 |
H38 |
300.1 |
60.0 |
| C38 |
C44 |
H44 |
H6U |
120.0 |
120.0 |
| C38 |
C44 |
H44 |
H6V |
240.0 |
240.0 |
| H6U |
C44 |
H44 |
H6V |
120.0 |
120.0 |
| H37 |
C37 |
C38 |
H38 |
134.1 |
180.0 |
| H37 |
C37 |
C36 |
H36 |
178.8 |
180.0 |
| H36 |
C36 |
C37 |
H37 |
178.8 |
180.0 |
| C30 |
C33 |
H33 |
H6R |
119.9 |
240.0 |
| H33 |
C33 |
C36 |
H36 |
286.7 |
65.1 |
| C30 |
C33 |
H6R |
H33 |
240.1 |
120.0 |
| H6R |
C33 |
C36 |
H36 |
166.8 |
185.0 |
| H6Q |
C30 |
C33 |
H33 |
139.2 |
180.0 |
| H6Q |
C30 |
C33 |
H6R |
259.2 |
60.0 |
| C27 |
C30 |
H6Q |
H30 |
240.0 |
240.0 |
| H6Q |
C30 |
C27 |
H27 |
196.5 |
179.9 |
| H6Q |
C30 |
C27 |
H6P |
316.5 |
300.0 |
| H30 |
C30 |
C33 |
H33 |
259.2 |
300.0 |
| H30 |
C30 |
C33 |
H6R |
19.2 |
180.0 |
| C27 |
C30 |
H30 |
H6Q |
120.0 |
120.0 |
| H30 |
C30 |
C27 |
H27 |
76.5 |
59.9 |
| H30 |
C30 |
C27 |
H6P |
196.6 |
180.0 |
| H27 |
C27 |
C30 |
H6Q |
196.5 |
179.9 |
| H27 |
C27 |
C30 |
H30 |
76.5 |
59.9 |
| C30 |
C27 |
H27 |
H6P |
120.0 |
120.0 |
| C24 |
C27 |
H27 |
H6P |
240.0 |
240.0 |
| H6P |
C27 |
C30 |
H6Q |
316.5 |
300.0 |
| H6P |
C27 |
C30 |
H30 |
196.6 |
180.0 |
| C30 |
C27 |
H6P |
H27 |
240.0 |
239.9 |
| C24 |
C27 |
H6P |
H27 |
120.0 |
120.0 |
| H6O |
C24 |
C27 |
H27 |
196.4 |
180.0 |
| H6O |
C24 |
C27 |
H6P |
76.4 |
60.0 |
| H6O |
C24 |
C22 |
O23 |
262.9 |
240.0 |
| C22 |
C24 |
H6O |
H24 |
240.0 |
240.0 |
| H24 |
C24 |
C27 |
H27 |
316.4 |
300.0 |
| H24 |
C24 |
C27 |
H6P |
196.4 |
180.0 |
| H24 |
C24 |
C22 |
O23 |
142.9 |
120.0 |
| C22 |
C24 |
H24 |
H6O |
120.0 |
120.0 |
| H21 |
N21 |
C17 |
H6N |
154.4 |
240.0 |
| H21 |
N21 |
C17 |
H17 |
274.4 |
120.0 |
| C1 |
C17 |
H6N |
N21 |
120.1 |
240.0 |
| H6N |
C17 |
N21 |
H21 |
154.4 |
240.0 |
| N21 |
C17 |
H6N |
H17 |
119.9 |
240.0 |
| C1 |
C17 |
H6N |
H17 |
240.1 |
120.0 |
| C1 |
C17 |
H17 |
N21 |
239.9 |
120.0 |
| H17 |
C17 |
N21 |
H21 |
274.4 |
120.0 |
| N21 |
C17 |
H17 |
H6N |
240.1 |
120.0 |
| C1 |
C17 |
H17 |
H6N |
119.9 |
240.0 |
| H6 |
C6 |
C5 |
H5 |
360.0 |
0.5 |
| O12 |
C13 |
H6M |
H6L |
120.0 |
120.0 |
| O12 |
C13 |
H6M |
H13 |
240.0 |
240.0 |
| H6L |
C13 |
H6M |
H13 |
119.9 |
120.0 |
| O12 |
C13 |
H6L |
H6M |
239.9 |
240.0 |
| O12 |
C13 |
H6L |
H13 |
120.0 |
120.0 |
| H6M |
C13 |
H6L |
H13 |
240.1 |
240.0 |
| O12 |
C13 |
H13 |
H6M |
120.0 |
120.0 |
| O12 |
C13 |
H13 |
H6L |
240.0 |
240.0 |
| H6M |
C13 |
H13 |
H6L |
120.0 |
120.0 |