PDB Chemical Component XOP
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 XOP
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
C2 |
C1 |
1.393 |
1.382 |
C1 |
C6 |
1.364 |
1.382 |
C1 |
P |
1.727 |
1.815 |
C3 |
C2 |
1.411 |
1.382 |
C2 |
H2 |
1.080 |
1.080 |
C3 |
C4 |
1.360 |
1.382 |
C3 |
H3 |
1.080 |
1.080 |
C4 |
C5 |
1.363 |
1.382 |
C4 |
H4 |
1.080 |
1.080 |
C5 |
C6 |
1.383 |
1.382 |
C5 |
H5 |
1.079 |
1.080 |
C6 |
H6 |
1.080 |
1.080 |
C13 |
C7 |
1.570 |
1.532 |
O2 |
C7 |
1.486 |
1.429 |
C8 |
C7 |
1.543 |
1.532 |
C7 |
H7 |
1.100 |
1.090 |
C9 |
C8 |
1.520 |
1.537 |
C8 |
H8 |
1.100 |
1.090 |
C8 |
H8A |
1.100 |
1.090 |
C10 |
C9 |
1.541 |
1.546 |
N |
C9 |
1.505 |
1.487 |
C9 |
H9 |
1.100 |
1.090 |
C14 |
N |
1.527 |
1.469 |
C12 |
N |
1.492 |
1.488 |
P |
O1 |
1.451 |
1.481 |
O3 |
HO3 |
|
0.967 |
O2 |
P |
1.540 |
1.610 |
O3 |
P |
|
1.610 |
C11 |
C10 |
1.575 |
1.543 |
C10 |
H10 |
1.100 |
1.089 |
C10 |
H10A |
1.100 |
1.090 |
C11 |
C12 |
1.540 |
1.570 |
C11 |
H11 |
1.100 |
1.090 |
C11 |
H11A |
1.100 |
1.090 |
C12 |
C13 |
1.554 |
1.536 |
C12 |
H12 |
1.100 |
1.090 |
C13 |
H13 |
1.100 |
1.090 |
C13 |
H13A |
1.100 |
1.090 |
C14 |
H14 |
1.100 |
1.090 |
C14 |
H14A |
1.100 |
1.090 |
C14 |
H14B |
1.100 |
1.090 |
Bond Angles for XOP
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
C2 |
C1 |
C6 |
113.6 |
120.0 |
C2 |
C1 |
P |
125.8 |
120.0 |
C6 |
C1 |
P |
120.6 |
120.0 |
C1 |
C6 |
C5 |
125.3 |
120.0 |
C1 |
C6 |
H6 |
117.4 |
120.0 |
C1 |
P |
O1 |
114.0 |
109.4 |
C1 |
P |
O2 |
104.9 |
109.5 |
C1 |
P |
O3 |
|
109.5 |
C3 |
C2 |
H2 |
119.1 |
120.0 |
C4 |
C3 |
H3 |
119.1 |
120.0 |
C3 |
C4 |
C5 |
117.0 |
120.0 |
C3 |
C4 |
H4 |
121.5 |
120.0 |
C5 |
C4 |
H4 |
121.5 |
120.0 |
C4 |
C5 |
C6 |
120.5 |
120.0 |
C4 |
C5 |
H5 |
119.8 |
120.0 |
C6 |
C5 |
H5 |
119.8 |
120.0 |
C5 |
C6 |
H6 |
117.4 |
120.0 |
C13 |
C7 |
H7 |
114.9 |
109.4 |
O2 |
C7 |
H7 |
114.5 |
109.4 |
C8 |
C7 |
H7 |
101.7 |
109.4 |
C9 |
C8 |
H8 |
108.0 |
109.6 |
C9 |
C8 |
H8A |
107.0 |
109.6 |
H8 |
C8 |
H8A |
113.0 |
109.6 |
C10 |
C9 |
H9 |
111.2 |
112.2 |
N |
C9 |
H9 |
119.2 |
112.2 |
P |
O3 |
HO3 |
|
114.0 |
O2 |
P |
O3 |
|
109.5 |
C11 |
C10 |
H10 |
110.3 |
110.4 |
C11 |
C10 |
H10A |
110.8 |
110.4 |
H10 |
C10 |
H10A |
107.7 |
110.3 |
C12 |
C11 |
H11 |
111.4 |
110.3 |
C12 |
C11 |
H11A |
112.7 |
110.7 |
C11 |
C12 |
C13 |
107.5 |
107.6 |
C11 |
C12 |
H12 |
113.0 |
112.2 |
H11 |
C11 |
H11A |
105.1 |
110.4 |
C13 |
C12 |
H12 |
111.4 |
112.7 |
C12 |
C13 |
H13 |
107.6 |
109.6 |
C12 |
C13 |
H13A |
106.3 |
109.6 |
H13 |
C13 |
H13A |
114.1 |
109.7 |
H14 |
C14 |
H14A |
109.5 |
109.5 |
H14 |
C14 |
H14B |
109.5 |
109.5 |
H14A |
C14 |
H14B |
109.5 |
109.4 |
Torsion Angles for XOP
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
C6 |
C1 |
C2 |
P |
180.1 |
180.3 |
C2 |
C1 |
C6 |
C5 |
0.3 |
360.0 |
C2 |
C1 |
C6 |
H6 |
180.3 |
179.7 |
C2 |
C1 |
P |
O1 |
153.5 |
245.3 |
C2 |
C1 |
P |
O2 |
29.5 |
5.3 |
C2 |
C1 |
P |
O3 |
|
125.3 |
C2 |
C1 |
C6 |
P |
179.9 |
179.7 |
C6 |
C1 |
P |
O1 |
333.4 |
65.0 |
C6 |
C1 |
P |
O2 |
209.3 |
185.0 |
C6 |
C1 |
P |
O3 |
|
305.0 |
C4 |
C5 |
C6 |
C1 |
0.9 |
360.0 |
C1 |
C6 |
C5 |
H5 |
180.9 |
180.0 |
C5 |
C6 |
C1 |
H6 |
180.0 |
180.3 |
C2 |
C1 |
P |
C6 |
180.1 |
180.3 |
P |
C1 |
C6 |
C5 |
180.4 |
180.3 |
P |
C1 |
C6 |
H6 |
0.4 |
360.0 |
C1 |
P |
O3 |
HO3 |
|
300.0 |
O2 |
P |
C1 |
O3 |
|
240.0 |
C3 |
C2 |
C1 |
C6 |
0.2 |
0.1 |
C3 |
C2 |
C1 |
P |
180.1 |
179.8 |
H2 |
C2 |
C1 |
C6 |
180.2 |
180.0 |
H2 |
C2 |
C1 |
P |
0.1 |
359.7 |
C4 |
C3 |
C2 |
H2 |
178.0 |
180.0 |
C5 |
C4 |
C3 |
H4 |
180.0 |
180.0 |
C3 |
C4 |
C5 |
C6 |
357.4 |
0.0 |
C3 |
C4 |
C5 |
H5 |
177.4 |
180.0 |
H3 |
C3 |
C2 |
H2 |
358.0 |
360.0 |
H3 |
C3 |
C4 |
C5 |
183.1 |
180.0 |
H3 |
C3 |
C4 |
H4 |
3.1 |
0.0 |
C1 |
C6 |
C5 |
C4 |
0.9 |
360.0 |
C5 |
C4 |
C3 |
H3 |
183.1 |
180.0 |
C3 |
C4 |
C5 |
H4 |
180.0 |
180.0 |
C6 |
C5 |
C4 |
H5 |
180.0 |
180.0 |
C4 |
C5 |
C6 |
H6 |
180.9 |
180.3 |
H4 |
C4 |
C3 |
H3 |
3.1 |
0.0 |
C3 |
C4 |
H4 |
C5 |
180.0 |
180.0 |
H4 |
C4 |
C5 |
C6 |
177.5 |
180.1 |
H4 |
C4 |
C5 |
H5 |
357.4 |
0.0 |
C5 |
C6 |
C1 |
P |
180.4 |
180.3 |
C1 |
C6 |
C5 |
H6 |
180.0 |
179.7 |
C6 |
C5 |
C4 |
H4 |
177.5 |
180.1 |
C4 |
C5 |
C6 |
H5 |
180.0 |
180.0 |
H5 |
C5 |
C4 |
H4 |
357.4 |
0.0 |
C4 |
C5 |
H5 |
C6 |
180.0 |
180.0 |
H5 |
C5 |
C6 |
H6 |
0.9 |
0.3 |
H6 |
C6 |
C1 |
P |
0.4 |
360.0 |
C1 |
C6 |
H6 |
C5 |
180.0 |
180.3 |
H6 |
C6 |
C5 |
H5 |
0.9 |
0.3 |
O2 |
C7 |
C13 |
H7 |
123.0 |
119.9 |
C8 |
C7 |
C13 |
H7 |
243.9 |
240.0 |
C1 |
P |
O2 |
C7 |
201.9 |
185.0 |
C13 |
C7 |
O2 |
H7 |
236.7 |
240.1 |
C8 |
C7 |
O2 |
H7 |
116.1 |
119.9 |
C13 |
C7 |
C8 |
H7 |
123.7 |
120.0 |
O2 |
C7 |
C8 |
H7 |
236.5 |
240.1 |
C9 |
C8 |
C7 |
H7 |
200.3 |
185.9 |
H8 |
C8 |
C9 |
H8A |
122.0 |
120.3 |
H8 |
C8 |
C7 |
H7 |
320.2 |
305.8 |
C9 |
C8 |
H8 |
H8A |
241.8 |
239.6 |
H8A |
C8 |
C7 |
H7 |
82.2 |
66.0 |
C9 |
C8 |
H8A |
H8 |
118.8 |
120.3 |
C10 |
C9 |
C8 |
H8 |
187.2 |
191.9 |
C10 |
C9 |
C8 |
H8A |
65.2 |
71.6 |
N |
C9 |
C10 |
H9 |
126.9 |
122.0 |
N |
C9 |
C8 |
H8 |
296.8 |
304.3 |
N |
C9 |
C8 |
H8A |
174.8 |
184.0 |
C10 |
C9 |
N |
H9 |
238.7 |
238.0 |
H9 |
C9 |
C8 |
H8 |
64.3 |
67.9 |
H9 |
C9 |
C8 |
H8A |
302.3 |
307.6 |
C14 |
N |
C9 |
H9 |
44.9 |
44.8 |
C12 |
N |
C9 |
H9 |
164.6 |
163.9 |
C1 |
P |
O1 |
O2 |
240.4 |
120.0 |
C1 |
P |
O1 |
O3 |
|
240.0 |
O2 |
P |
O3 |
HO3 |
|
60.0 |
C1 |
P |
O2 |
O1 |
124.7 |
240.0 |
C1 |
P |
O2 |
O3 |
|
120.0 |
P |
O2 |
C7 |
H7 |
356.5 |
0.0 |
C1 |
P |
O3 |
O1 |
|
120.0 |
C1 |
P |
O3 |
O2 |
|
240.0 |
C11 |
C10 |
C9 |
H9 |
204.1 |
212.5 |
H10 |
C10 |
C11 |
H10A |
119.1 |
122.3 |
H10 |
C10 |
C9 |
H9 |
324.1 |
331.4 |
C11 |
C10 |
H10 |
H10A |
239.0 |
237.7 |
H10A |
C10 |
C9 |
H9 |
83.2 |
93.6 |
C11 |
C10 |
H10A |
H10 |
120.7 |
122.3 |
C12 |
C11 |
C10 |
H10 |
245.7 |
241.4 |
C12 |
C11 |
C10 |
H10A |
126.6 |
119.1 |
H11 |
C11 |
C12 |
H11A |
117.9 |
122.5 |
C13 |
C12 |
C11 |
H12 |
123.3 |
124.5 |
C11 |
C12 |
C13 |
H13 |
300.2 |
287.8 |
C11 |
C12 |
C13 |
H13A |
177.6 |
167.4 |
H11 |
C11 |
C10 |
H10 |
5.7 |
360.0 |
H11 |
C11 |
C10 |
H10A |
246.6 |
237.7 |
C12 |
C11 |
H11 |
H11A |
237.6 |
237.4 |
H11 |
C11 |
C12 |
C13 |
148.5 |
152.7 |
H11 |
C11 |
C12 |
H12 |
25.2 |
28.1 |
H11A |
C11 |
C10 |
H10 |
123.6 |
122.3 |
H11A |
C11 |
C10 |
H10A |
4.5 |
0.0 |
C12 |
C11 |
H11A |
H11 |
121.6 |
122.4 |
H11A |
C11 |
C12 |
C13 |
30.6 |
30.2 |
H11A |
C11 |
C12 |
H12 |
267.3 |
265.7 |
C12 |
C13 |
C7 |
H7 |
149.2 |
174.1 |
C13 |
C12 |
C11 |
H11 |
148.5 |
152.7 |
C13 |
C12 |
C11 |
H11A |
30.6 |
30.2 |
C11 |
C12 |
C13 |
H12 |
235.7 |
235.8 |
H13 |
C13 |
C12 |
H13A |
122.6 |
120.4 |
H12 |
C12 |
C11 |
H11 |
25.2 |
28.1 |
H12 |
C12 |
C11 |
H11A |
267.3 |
265.7 |
C11 |
C12 |
H12 |
C13 |
121.1 |
121.7 |
H12 |
C12 |
C13 |
H13 |
64.5 |
52.1 |
H12 |
C12 |
C13 |
H13A |
301.8 |
291.7 |
H13 |
C13 |
C7 |
H7 |
269.2 |
293.7 |
H13 |
C13 |
C12 |
H12 |
64.5 |
52.1 |
C12 |
C13 |
H13 |
H13A |
242.4 |
239.7 |
H13A |
C13 |
C7 |
H7 |
31.7 |
54.1 |
H13A |
C13 |
C12 |
H12 |
301.8 |
291.7 |
C12 |
C13 |
H13A |
H13 |
118.4 |
120.4 |
H14A |
C14 |
H14 |
H14B |
120.0 |
120.0 |
H14 |
C14 |
H14A |
H14B |
240.0 |
240.0 |
H14 |
C14 |
H14B |
H14A |
120.0 |
120.0 |