PDB Chemical Component 5JY
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 5JY
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O01 |
C02 |
1.405 |
1.359 |
| C02 |
C03 |
1.387 |
1.388 |
| C02 |
C23 |
1.386 |
1.389 |
| C03 |
C04 |
1.389 |
1.378 |
| C23 |
C22 |
1.386 |
1.379 |
| C04 |
C05 |
1.390 |
1.395 |
| C22 |
C05 |
1.391 |
1.394 |
| C05 |
C06 |
1.524 |
1.482 |
| C06 |
C07 |
1.519 |
1.483 |
| C06 |
C14 |
1.363 |
1.339 |
| C13 |
C07 |
1.389 |
1.394 |
| C13 |
C12 |
1.388 |
1.379 |
| C07 |
C08 |
1.389 |
1.394 |
| C12 |
C10 |
1.389 |
1.388 |
| C08 |
C09 |
1.386 |
1.379 |
| C10 |
C09 |
1.387 |
1.388 |
| C10 |
O11 |
1.410 |
1.358 |
| C21 |
C14 |
1.513 |
1.513 |
| C21 |
C20 |
1.510 |
1.537 |
| C14 |
C15 |
1.511 |
1.512 |
| C20 |
C17 |
1.519 |
1.530 |
| C15 |
C16 |
1.517 |
1.532 |
| C17 |
C16 |
1.522 |
1.529 |
| C17 |
C18 |
1.512 |
1.530 |
| C18 |
C19 |
1.512 |
1.530 |
| O01 |
H1 |
0.950 |
0.966 |
| C03 |
H2 |
1.080 |
1.081 |
| C04 |
H3 |
1.080 |
1.080 |
| C08 |
H5 |
1.080 |
1.080 |
| C09 |
H6 |
1.080 |
1.080 |
| O11 |
H7 |
0.950 |
0.966 |
| C12 |
H8 |
1.080 |
1.080 |
| C13 |
H9 |
1.080 |
1.080 |
| C15 |
H11 |
1.100 |
1.090 |
| C15 |
H12 |
1.100 |
1.091 |
| C16 |
H13 |
1.100 |
1.089 |
| C16 |
H14 |
1.100 |
1.089 |
| C17 |
H15 |
1.100 |
1.090 |
| C18 |
H16 |
1.100 |
1.090 |
| C18 |
H17 |
1.100 |
1.091 |
| C19 |
H18 |
1.100 |
1.090 |
| C19 |
H19 |
1.100 |
1.091 |
| C19 |
H20 |
1.100 |
1.089 |
| C20 |
H21 |
1.100 |
1.090 |
| C20 |
H22 |
1.100 |
1.091 |
| C21 |
H23 |
1.100 |
1.090 |
| C21 |
H24 |
1.100 |
1.090 |
| C22 |
H25 |
1.080 |
1.080 |
| C23 |
H26 |
1.080 |
1.080 |
Bond Angles for 5JY
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O01 |
C02 |
C03 |
120.1 |
119.9 |
| O01 |
C02 |
C23 |
119.7 |
119.9 |
| C02 |
O01 |
H1 |
109.5 |
113.9 |
| C03 |
C02 |
C23 |
120.1 |
120.1 |
| C02 |
C03 |
C04 |
119.8 |
120.1 |
| C02 |
C03 |
H2 |
120.1 |
120.0 |
| C02 |
C23 |
C22 |
119.8 |
120.1 |
| C02 |
C23 |
H26 |
120.1 |
119.9 |
| C03 |
C04 |
C05 |
120.5 |
120.0 |
| C04 |
C03 |
H2 |
120.1 |
120.0 |
| C03 |
C04 |
H3 |
119.8 |
120.1 |
| C23 |
C22 |
H25 |
119.7 |
120.0 |
| C04 |
C05 |
C06 |
118.5 |
120.1 |
| C05 |
C04 |
H3 |
119.8 |
120.0 |
| C05 |
C06 |
C07 |
115.4 |
120.0 |
| C05 |
C06 |
C14 |
123.4 |
120.0 |
| C07 |
C06 |
C14 |
120.9 |
120.0 |
| C06 |
C07 |
C08 |
119.3 |
120.0 |
| C06 |
C14 |
C15 |
122.0 |
120.9 |
| C13 |
C12 |
H8 |
120.0 |
120.0 |
| C07 |
C08 |
C09 |
120.5 |
119.9 |
| C07 |
C08 |
H5 |
119.8 |
120.0 |
| C09 |
C08 |
H5 |
119.8 |
120.1 |
| C08 |
C09 |
H6 |
120.1 |
120.0 |
| C10 |
C09 |
H6 |
120.1 |
120.0 |
| C10 |
O11 |
H7 |
109.5 |
114.0 |
| C21 |
C20 |
H21 |
108.9 |
109.6 |
| C21 |
C20 |
H22 |
108.9 |
109.5 |
| C14 |
C15 |
C16 |
111.2 |
108.6 |
| C14 |
C15 |
H11 |
109.1 |
109.6 |
| C14 |
C15 |
H12 |
109.0 |
109.6 |
| C20 |
C17 |
H15 |
108.9 |
109.4 |
| C16 |
C15 |
H11 |
109.0 |
109.6 |
| C16 |
C15 |
H12 |
109.1 |
109.7 |
| C15 |
C16 |
H13 |
108.9 |
109.4 |
| C15 |
C16 |
H14 |
108.9 |
109.5 |
| C17 |
C16 |
H13 |
108.9 |
109.5 |
| C17 |
C16 |
H14 |
108.9 |
109.5 |
| C17 |
C18 |
C19 |
112.2 |
109.5 |
| C18 |
C17 |
H15 |
108.9 |
109.4 |
| C17 |
C18 |
H16 |
108.8 |
109.5 |
| C17 |
C18 |
H17 |
108.8 |
109.5 |
| C19 |
C18 |
H16 |
108.8 |
109.5 |
| C19 |
C18 |
H17 |
108.8 |
109.4 |
| C18 |
C19 |
H18 |
109.5 |
109.5 |
| C18 |
C19 |
H19 |
109.5 |
109.4 |
| C18 |
C19 |
H20 |
109.5 |
109.5 |
| H11 |
C15 |
H12 |
109.4 |
109.7 |
| H13 |
C16 |
H14 |
109.5 |
109.5 |
| H16 |
C18 |
H17 |
109.5 |
109.5 |
| H18 |
C19 |
H19 |
109.5 |
109.5 |
| H18 |
C19 |
H20 |
109.4 |
109.5 |
| H19 |
C19 |
H20 |
109.5 |
109.5 |
| H21 |
C20 |
H22 |
109.5 |
109.5 |
| H23 |
C21 |
H24 |
109.5 |
109.8 |
Torsion Angles for 5JY
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C03 |
C02 |
O01 |
C23 |
179.8 |
180.3 |
| O01 |
C02 |
C03 |
C04 |
180.1 |
180.0 |
| O01 |
C02 |
C03 |
H2 |
0.1 |
360.0 |
| O01 |
C02 |
C23 |
C22 |
180.3 |
179.8 |
| O01 |
C02 |
C23 |
H26 |
0.3 |
0.0 |
| O01 |
C02 |
C03 |
C23 |
180.2 |
179.7 |
| C03 |
C02 |
O01 |
H1 |
180.0 |
90.0 |
| C03 |
C02 |
C23 |
C22 |
0.5 |
359.5 |
| C03 |
C02 |
C23 |
H26 |
180.5 |
179.7 |
| C02 |
C03 |
C04 |
C05 |
0.4 |
360.0 |
| C04 |
C03 |
C02 |
H2 |
180.0 |
180.0 |
| C02 |
C03 |
C04 |
H3 |
180.4 |
179.9 |
| O01 |
C02 |
C23 |
C03 |
179.8 |
180.3 |
| C23 |
C02 |
O01 |
H1 |
0.2 |
269.7 |
| C23 |
C02 |
C03 |
C04 |
359.9 |
0.3 |
| C23 |
C02 |
C03 |
H2 |
179.9 |
180.3 |
| C02 |
C23 |
C22 |
H25 |
178.9 |
180.3 |
| C04 |
C03 |
C02 |
C23 |
359.9 |
0.3 |
| C02 |
C03 |
C04 |
H2 |
180.0 |
180.0 |
| C03 |
C04 |
C05 |
C06 |
180.7 |
180.0 |
| C05 |
C04 |
C03 |
H3 |
180.0 |
180.0 |
| C02 |
C23 |
C22 |
H26 |
180.0 |
180.2 |
| C05 |
C04 |
C03 |
H2 |
180.4 |
180.0 |
| C03 |
C04 |
C05 |
H3 |
180.0 |
180.0 |
| C04 |
C05 |
C06 |
C07 |
37.9 |
295.0 |
| C04 |
C05 |
C06 |
C14 |
223.9 |
115.0 |
| C02 |
C23 |
C22 |
C05 |
358.9 |
0.5 |
| C22 |
C05 |
C04 |
H3 |
178.9 |
180.0 |
| C06 |
C05 |
C04 |
H3 |
0.7 |
0.0 |
| C07 |
C06 |
C05 |
C14 |
174.0 |
180.0 |
| C05 |
C06 |
C07 |
C08 |
67.8 |
295.0 |
| C05 |
C06 |
C14 |
C15 |
193.9 |
180.0 |
| C05 |
C06 |
C07 |
C14 |
185.8 |
180.0 |
| C07 |
C06 |
C14 |
C15 |
20.2 |
360.0 |
| C06 |
C07 |
C08 |
C09 |
180.7 |
180.0 |
| C06 |
C07 |
C08 |
H5 |
0.7 |
359.9 |
| C05 |
C06 |
C14 |
C07 |
173.7 |
180.0 |
| C14 |
C06 |
C07 |
C08 |
242.0 |
115.1 |
| C06 |
C14 |
C15 |
C16 |
234.8 |
231.4 |
| C06 |
C14 |
C15 |
H11 |
355.1 |
351.1 |
| C06 |
C14 |
C15 |
H12 |
114.6 |
111.6 |
| C13 |
C07 |
C06 |
C14 |
63.5 |
294.7 |
| C13 |
C07 |
C08 |
H5 |
179.2 |
180.2 |
| C08 |
C07 |
C06 |
C14 |
242.0 |
115.1 |
| C09 |
C08 |
C07 |
H5 |
180.0 |
180.1 |
| C07 |
C08 |
C09 |
H6 |
180.3 |
180.0 |
| C12 |
C10 |
C09 |
H6 |
180.1 |
180.0 |
| C12 |
C10 |
O11 |
H7 |
180.0 |
270.1 |
| C07 |
C08 |
C09 |
H5 |
180.0 |
179.9 |
| C10 |
C09 |
C08 |
H6 |
180.0 |
179.9 |
| C10 |
C09 |
C08 |
H5 |
180.3 |
180.1 |
| C08 |
C09 |
C10 |
H6 |
180.0 |
180.1 |
| O11 |
C10 |
C09 |
H6 |
0.0 |
360.0 |
| C21 |
C14 |
C15 |
H11 |
171.6 |
171.3 |
| C21 |
C14 |
C15 |
H12 |
291.1 |
291.8 |
| C21 |
C20 |
C17 |
H15 |
65.8 |
56.3 |
| H21 |
C20 |
C21 |
H22 |
240.7 |
120.1 |
| C16 |
C15 |
C14 |
H11 |
239.7 |
240.3 |
| C16 |
C15 |
C14 |
H12 |
120.3 |
119.8 |
| C14 |
C15 |
C16 |
H13 |
67.1 |
65.3 |
| C14 |
C15 |
C16 |
H14 |
186.4 |
185.4 |
| H11 |
C15 |
C14 |
H12 |
240.6 |
239.5 |
| C20 |
C17 |
C16 |
H13 |
295.1 |
303.7 |
| C20 |
C17 |
C16 |
H14 |
175.8 |
183.6 |
| C18 |
C17 |
C20 |
H15 |
118.7 |
119.8 |
| C20 |
C17 |
C18 |
H16 |
34.8 |
55.4 |
| C20 |
C17 |
C18 |
H17 |
154.0 |
175.4 |
| C14 |
C15 |
C16 |
H11 |
120.3 |
119.7 |
| C14 |
C15 |
C16 |
H12 |
239.7 |
240.3 |
| C17 |
C16 |
C15 |
H13 |
239.7 |
240.1 |
| C17 |
C16 |
C15 |
H14 |
120.3 |
120.0 |
| H11 |
C15 |
C16 |
H12 |
119.5 |
120.5 |
| H13 |
C16 |
C15 |
H14 |
240.7 |
239.9 |
| C17 |
C16 |
C15 |
H11 |
186.4 |
185.6 |
| C17 |
C16 |
C15 |
H12 |
67.0 |
65.1 |
| C15 |
C16 |
C17 |
H13 |
120.3 |
119.9 |
| C15 |
C16 |
C17 |
H14 |
239.7 |
240.0 |
| H13 |
C16 |
C17 |
H14 |
119.3 |
120.1 |
| C20 |
C17 |
C18 |
H15 |
241.3 |
240.2 |
| C18 |
C17 |
C16 |
H13 |
56.0 |
63.8 |
| C18 |
C17 |
C16 |
H14 |
296.7 |
303.6 |
| C19 |
C18 |
C17 |
H16 |
239.6 |
240.0 |
| C19 |
C18 |
C17 |
H17 |
120.4 |
119.9 |
| C17 |
C18 |
C19 |
H18 |
180.0 |
300.1 |
| C17 |
C18 |
C19 |
H19 |
300.0 |
60.0 |
| C17 |
C18 |
C19 |
H20 |
60.0 |
180.0 |
| H16 |
C18 |
C17 |
H17 |
240.8 |
240.0 |
| C19 |
C18 |
C17 |
H15 |
33.0 |
55.1 |
| C17 |
C18 |
C19 |
H16 |
120.4 |
120.1 |
| C17 |
C18 |
C19 |
H17 |
239.6 |
240.0 |
| H16 |
C18 |
C19 |
H17 |
119.2 |
119.9 |
| H18 |
C19 |
C18 |
H19 |
240.0 |
240.1 |
| H18 |
C19 |
C18 |
H20 |
120.0 |
120.1 |
| H19 |
C19 |
C18 |
H20 |
240.0 |
240.0 |
| H1 |
O01 |
C02 |
C03 |
180.0 |
90.0 |
| H1 |
O01 |
C02 |
C23 |
0.2 |
269.7 |
| H2 |
C03 |
C02 |
C23 |
179.9 |
180.3 |
| C02 |
C03 |
H2 |
C04 |
180.0 |
180.0 |
| H2 |
C03 |
C04 |
C05 |
180.4 |
180.0 |
| H2 |
C03 |
C04 |
H3 |
0.4 |
360.0 |
| C03 |
C04 |
H3 |
C05 |
180.0 |
180.0 |
| H3 |
C04 |
C03 |
H2 |
0.4 |
360.0 |
| H3 |
C04 |
C05 |
C06 |
0.7 |
0.0 |
| C07 |
C08 |
H5 |
C09 |
180.0 |
180.1 |
| H5 |
C08 |
C09 |
H6 |
0.3 |
0.1 |
| H6 |
C09 |
C08 |
H5 |
0.3 |
0.1 |
| H9 |
C13 |
C12 |
H8 |
359.4 |
360.0 |
| C14 |
C15 |
H11 |
C16 |
238.4 |
240.9 |
| C14 |
C15 |
H11 |
H12 |
119.2 |
120.4 |
| C16 |
C15 |
H11 |
H12 |
240.8 |
239.5 |
| H11 |
C15 |
C16 |
H13 |
306.8 |
305.6 |
| H11 |
C15 |
C16 |
H14 |
66.1 |
65.7 |
| C14 |
C15 |
H12 |
C16 |
121.6 |
119.1 |
| C14 |
C15 |
H12 |
H11 |
240.8 |
239.5 |
| C16 |
C15 |
H12 |
H11 |
119.2 |
120.4 |
| H12 |
C15 |
C16 |
H13 |
187.3 |
185.0 |
| H12 |
C15 |
C16 |
H14 |
306.6 |
305.1 |
| H13 |
C16 |
C15 |
H11 |
306.8 |
305.6 |
| H13 |
C16 |
C15 |
H12 |
187.3 |
185.0 |
| C15 |
C16 |
H13 |
H14 |
118.9 |
120.1 |
| C17 |
C16 |
H13 |
H14 |
241.0 |
239.9 |
| H14 |
C16 |
C15 |
H11 |
66.1 |
65.7 |
| H14 |
C16 |
C15 |
H12 |
306.6 |
305.1 |
| C15 |
C16 |
H14 |
H13 |
241.1 |
240.0 |
| C17 |
C16 |
H14 |
H13 |
119.0 |
120.1 |
| H15 |
C17 |
C16 |
H13 |
175.0 |
183.6 |
| H15 |
C17 |
C16 |
H14 |
55.6 |
63.5 |
| H15 |
C17 |
C18 |
C19 |
33.0 |
55.1 |
| H15 |
C17 |
C18 |
H16 |
153.4 |
175.2 |
| H15 |
C17 |
C18 |
H17 |
272.6 |
295.2 |
| C17 |
C18 |
H16 |
C19 |
237.5 |
239.9 |
| H16 |
C18 |
C17 |
H15 |
153.4 |
175.2 |
| C17 |
C18 |
H16 |
H17 |
118.7 |
120.0 |
| C19 |
C18 |
H16 |
H17 |
241.2 |
240.1 |
| H16 |
C18 |
C19 |
H18 |
59.6 |
180.0 |
| H16 |
C18 |
C19 |
H19 |
179.6 |
299.9 |
| H16 |
C18 |
C19 |
H20 |
299.6 |
59.9 |
| C17 |
C18 |
H17 |
C19 |
122.5 |
120.0 |
| H17 |
C18 |
C17 |
H15 |
272.6 |
295.2 |
| C17 |
C18 |
H17 |
H16 |
241.3 |
239.9 |
| C19 |
C18 |
H17 |
H16 |
118.8 |
120.0 |
| H17 |
C18 |
C19 |
H18 |
300.4 |
60.1 |
| H17 |
C18 |
C19 |
H19 |
60.4 |
180.0 |
| H17 |
C18 |
C19 |
H20 |
180.4 |
300.0 |
| H18 |
C19 |
C18 |
H16 |
59.6 |
180.0 |
| H18 |
C19 |
C18 |
H17 |
300.4 |
60.1 |
| C18 |
C19 |
H18 |
H19 |
120.0 |
119.9 |
| C18 |
C19 |
H18 |
H20 |
240.0 |
239.9 |
| H19 |
C19 |
H18 |
H20 |
120.0 |
120.0 |
| H19 |
C19 |
C18 |
H16 |
179.6 |
299.9 |
| H19 |
C19 |
C18 |
H17 |
60.4 |
180.0 |
| C18 |
C19 |
H19 |
H18 |
240.0 |
240.0 |
| C18 |
C19 |
H19 |
H20 |
120.0 |
120.0 |
| H18 |
C19 |
H19 |
H20 |
240.0 |
240.0 |
| H20 |
C19 |
C18 |
H16 |
299.6 |
59.9 |
| H20 |
C19 |
C18 |
H17 |
180.4 |
300.0 |
| C18 |
C19 |
H20 |
H18 |
120.0 |
120.0 |
| C18 |
C19 |
H20 |
H19 |
240.0 |
240.0 |
| H18 |
C19 |
H20 |
H19 |
120.0 |
120.0 |
| C21 |
C20 |
H21 |
H22 |
119.0 |
239.9 |
| H21 |
C20 |
C17 |
H15 |
305.5 |
176.5 |
| C21 |
C20 |
H22 |
H21 |
241.0 |
120.2 |
| H22 |
C20 |
C17 |
H15 |
186.1 |
296.5 |
| H23 |
C21 |
C20 |
H21 |
51.5 |
175.2 |
| H23 |
C21 |
C20 |
H22 |
170.9 |
55.1 |
| H24 |
C21 |
C20 |
H21 |
292.4 |
54.5 |
| H24 |
C21 |
C20 |
H22 |
51.7 |
294.4 |
| C02 |
C23 |
H26 |
C22 |
180.0 |
179.8 |
| H26 |
C23 |
C22 |
H25 |
358.9 |
0.1 |