PDB Chemical Component GBO
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 GBO
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| P1 |
O2 |
1.606 |
1.609 |
| O2 |
HO2 |
0.950 |
0.968 |
| O1 |
P1 |
1.476 |
1.480 |
| O3 |
P1 |
1.593 |
1.610 |
| P1 |
O8 |
1.585 |
1.610 |
| O8 |
HO8 |
0.950 |
0.967 |
| P2 |
O3 |
1.624 |
1.610 |
| O9 |
P2 |
1.502 |
1.480 |
| O5 |
P2 |
1.582 |
1.610 |
| P2 |
O4 |
1.464 |
1.610 |
| O4 |
HO4 |
0.949 |
0.966 |
| C1 |
O5 |
1.398 |
1.429 |
| C1 |
C2 |
1.386 |
1.506 |
| C1 |
H1 |
1.100 |
1.090 |
| C1 |
H1A |
1.100 |
1.090 |
| C3 |
C2 |
1.371 |
1.310 |
| C2 |
H2 |
1.080 |
1.081 |
| C4 |
C3 |
1.553 |
1.507 |
| C3 |
C5 |
1.525 |
1.507 |
| C4 |
H4 |
1.100 |
1.090 |
| C4 |
H4A |
1.100 |
1.089 |
| C4 |
H4B |
1.100 |
1.090 |
| C5 |
C6 |
1.521 |
1.530 |
| C5 |
H5 |
1.100 |
1.090 |
| C5 |
H5A |
1.100 |
1.090 |
| C7 |
C6 |
1.390 |
1.507 |
| C6 |
H6 |
1.100 |
1.090 |
| C6 |
H6A |
1.100 |
1.090 |
| C7 |
C8 |
1.377 |
1.310 |
| C7 |
H7 |
1.080 |
1.080 |
| C10 |
C8 |
1.542 |
1.508 |
| C8 |
C9 |
1.527 |
1.507 |
| C9 |
H9 |
1.100 |
1.090 |
| C9 |
H9A |
1.100 |
1.090 |
| C9 |
H9B |
1.100 |
1.090 |
| N1 |
C10 |
1.447 |
1.465 |
| C10 |
H10 |
1.100 |
1.091 |
| C10 |
H10A |
1.100 |
1.090 |
| C11 |
N1 |
1.321 |
1.347 |
| N1 |
HN1 |
1.000 |
0.970 |
| C12 |
C11 |
1.563 |
1.507 |
| O6 |
C11 |
1.231 |
1.213 |
| C12 |
C13 |
1.567 |
1.531 |
| C12 |
H12 |
1.100 |
1.090 |
| C12 |
H12A |
1.100 |
1.090 |
| C14 |
C13 |
1.535 |
1.530 |
| C13 |
H13 |
1.100 |
1.090 |
| C13 |
H13A |
1.100 |
1.090 |
| C14 |
C15 |
1.532 |
1.530 |
| C14 |
H14 |
1.100 |
1.090 |
| C14 |
H14A |
1.100 |
1.090 |
| C16 |
C15 |
1.561 |
1.530 |
| C15 |
H15 |
1.100 |
1.090 |
| C15 |
H15A |
1.101 |
1.090 |
| S1 |
C16 |
1.861 |
1.839 |
| C19 |
C16 |
1.573 |
1.542 |
| C16 |
H16 |
1.100 |
1.090 |
| C17 |
S1 |
1.833 |
1.838 |
| C18 |
C17 |
1.558 |
1.541 |
| C17 |
H17 |
1.100 |
1.090 |
| C17 |
H17A |
1.100 |
1.090 |
| N3 |
C18 |
1.468 |
1.471 |
| C18 |
C19 |
1.574 |
1.536 |
| C18 |
H18 |
1.100 |
1.090 |
| N2 |
C19 |
1.491 |
1.472 |
| C19 |
H19 |
1.100 |
1.090 |
| C20 |
N2 |
1.328 |
1.340 |
| N2 |
HN2 |
1.000 |
0.970 |
| O7 |
C20 |
1.233 |
1.215 |
| C20 |
N3 |
1.339 |
1.345 |
| N3 |
HN3 |
1.000 |
0.971 |
Bond Angles for GBO
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| P1 |
O2 |
HO2 |
109.5 |
114.0 |
| P1 |
O8 |
HO8 |
109.5 |
114.0 |
| P2 |
O4 |
HO4 |
109.5 |
114.0 |
| C2 |
C1 |
H1 |
109.9 |
109.5 |
| C2 |
C1 |
H1A |
110.2 |
109.5 |
| C1 |
C2 |
H2 |
119.5 |
120.0 |
| H1 |
C1 |
H1A |
108.4 |
109.5 |
| C3 |
C2 |
H2 |
119.5 |
120.0 |
| C4 |
C3 |
C5 |
117.5 |
120.0 |
| C3 |
C5 |
C6 |
116.1 |
109.5 |
| C3 |
C5 |
H5 |
107.3 |
109.5 |
| C3 |
C5 |
H5A |
105.8 |
109.4 |
| H4 |
C4 |
H4A |
109.4 |
109.5 |
| H4 |
C4 |
H4B |
109.5 |
109.4 |
| H4A |
C4 |
H4B |
109.5 |
109.4 |
| C6 |
C5 |
H5 |
107.3 |
109.5 |
| C6 |
C5 |
H5A |
105.8 |
109.5 |
| C5 |
C6 |
H6 |
110.0 |
109.5 |
| C5 |
C6 |
H6A |
110.3 |
109.5 |
| H5 |
C5 |
H5A |
114.8 |
109.5 |
| C7 |
C6 |
H6 |
110.0 |
109.5 |
| C7 |
C6 |
H6A |
110.3 |
109.5 |
| H6 |
C6 |
H6A |
108.3 |
109.4 |
| C8 |
C7 |
H7 |
116.2 |
120.0 |
| C7 |
C8 |
C9 |
118.0 |
120.0 |
| C8 |
C9 |
H9 |
109.5 |
109.5 |
| C8 |
C9 |
H9A |
109.5 |
109.5 |
| C8 |
C9 |
H9B |
109.5 |
109.5 |
| H9 |
C9 |
H9A |
109.4 |
109.5 |
| H9 |
C9 |
H9B |
109.5 |
109.5 |
| H9A |
C9 |
H9B |
109.5 |
109.5 |
| N1 |
C10 |
H10 |
112.8 |
109.5 |
| N1 |
C10 |
H10A |
114.7 |
109.5 |
| H10 |
C10 |
H10A |
102.5 |
109.5 |
| C11 |
N1 |
HN1 |
114.7 |
120.0 |
| C13 |
C12 |
H12 |
107.1 |
109.5 |
| C13 |
C12 |
H12A |
105.3 |
109.5 |
| C12 |
C13 |
H13 |
109.3 |
109.5 |
| C12 |
C13 |
H13A |
109.2 |
109.5 |
| H12 |
C12 |
H12A |
115.5 |
109.5 |
| C14 |
C13 |
H13 |
109.3 |
109.4 |
| C14 |
C13 |
H13A |
109.2 |
109.5 |
| H13 |
C13 |
H13A |
109.9 |
109.6 |
| C15 |
C14 |
H14 |
108.5 |
109.4 |
| C15 |
C14 |
H14A |
107.8 |
109.5 |
| C14 |
C15 |
H15 |
109.3 |
109.5 |
| C14 |
C15 |
H15A |
109.2 |
109.5 |
| H14 |
C14 |
H14A |
111.9 |
109.5 |
| C16 |
C15 |
H15 |
109.3 |
109.5 |
| C16 |
C15 |
H15A |
109.1 |
109.5 |
| H15 |
C15 |
H15A |
109.9 |
109.4 |
| S1 |
C16 |
H16 |
111.1 |
110.8 |
| C19 |
C16 |
H16 |
114.9 |
110.7 |
| C18 |
C17 |
H17 |
111.5 |
110.7 |
| C18 |
C17 |
H17A |
112.8 |
110.9 |
| H17 |
C17 |
H17A |
104.9 |
110.6 |
| N3 |
C18 |
H18 |
117.4 |
110.5 |
| C19 |
C18 |
H18 |
112.2 |
110.1 |
| C18 |
C19 |
H19 |
113.5 |
110.3 |
| N2 |
C19 |
H19 |
113.1 |
110.5 |
| C20 |
N2 |
HN2 |
124.8 |
125.5 |
| O7 |
C20 |
N3 |
124.1 |
123.0 |
| C20 |
N3 |
HN3 |
123.7 |
125.5 |
Torsion Angles for GBO
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O1 |
P1 |
O2 |
HO2 |
353.7 |
180.0 |
| O1 |
P1 |
O8 |
HO8 |
215.9 |
300.1 |
| O3 |
P1 |
O2 |
HO2 |
117.7 |
300.0 |
| O3 |
P1 |
O8 |
HO8 |
88.7 |
180.1 |
| O8 |
P1 |
O2 |
HO2 |
227.5 |
60.0 |
| O9 |
P2 |
O4 |
HO4 |
57.6 |
179.9 |
| O5 |
P2 |
O4 |
HO4 |
286.4 |
59.9 |
| H1 |
C1 |
C2 |
H1A |
119.4 |
120.0 |
| C3 |
C2 |
C1 |
H2 |
180.0 |
180.0 |
| C2 |
C1 |
H1 |
H1A |
239.5 |
239.9 |
| H1 |
C1 |
C2 |
H2 |
231.3 |
285.0 |
| C2 |
C1 |
H1A |
H1 |
120.4 |
120.1 |
| H1A |
C1 |
C2 |
H2 |
111.9 |
164.9 |
| C3 |
C2 |
C1 |
H1 |
51.4 |
104.9 |
| C3 |
C2 |
C1 |
H1A |
291.9 |
344.9 |
| C1 |
C2 |
C3 |
H2 |
180.0 |
180.0 |
| H2 |
C2 |
C1 |
H1 |
231.3 |
285.0 |
| H2 |
C2 |
C1 |
H1A |
111.9 |
164.9 |
| C4 |
C3 |
C2 |
H2 |
180.8 |
174.4 |
| C4 |
C3 |
C5 |
C6 |
213.0 |
275.0 |
| C4 |
C3 |
C5 |
H5 |
333.0 |
35.0 |
| C4 |
C3 |
C5 |
H5A |
96.0 |
155.0 |
| C5 |
C3 |
C2 |
H2 |
0.2 |
354.4 |
| C6 |
C5 |
C3 |
H5 |
240.0 |
240.0 |
| C6 |
C5 |
C3 |
H5A |
117.0 |
120.0 |
| C3 |
C5 |
C6 |
H6 |
279.3 |
300.0 |
| C3 |
C5 |
C6 |
H6A |
38.8 |
60.0 |
| H5 |
C5 |
C3 |
H5A |
237.0 |
240.0 |
| H4 |
C4 |
C3 |
C5 |
160.2 |
264.8 |
| H4A |
C4 |
H4 |
H4B |
120.0 |
120.0 |
| H4A |
C4 |
C3 |
C5 |
280.1 |
24.8 |
| H4 |
C4 |
H4A |
H4B |
240.0 |
240.0 |
| H4B |
C4 |
C3 |
C5 |
40.2 |
144.8 |
| H4 |
C4 |
H4B |
H4A |
120.0 |
120.0 |
| C3 |
C5 |
C6 |
H5 |
120.0 |
120.0 |
| C3 |
C5 |
C6 |
H5A |
243.0 |
240.0 |
| H5 |
C5 |
C6 |
H5A |
123.0 |
120.0 |
| C7 |
C6 |
C5 |
H6 |
240.0 |
240.0 |
| C7 |
C6 |
C5 |
H6A |
120.6 |
120.0 |
| H6 |
C6 |
C5 |
H6A |
240.6 |
240.0 |
| C3 |
C5 |
H5 |
C6 |
234.6 |
240.0 |
| C3 |
C5 |
H5 |
H5A |
117.3 |
119.9 |
| C6 |
C5 |
H5 |
H5A |
242.7 |
240.0 |
| H5 |
C5 |
C6 |
H6 |
159.4 |
180.0 |
| H5 |
C5 |
C6 |
H6A |
278.8 |
300.0 |
| C3 |
C5 |
H5A |
C6 |
123.7 |
120.0 |
| C3 |
C5 |
H5A |
H5 |
241.9 |
240.1 |
| C6 |
C5 |
H5A |
H5 |
118.2 |
120.1 |
| H5A |
C5 |
C6 |
H6 |
36.3 |
60.0 |
| H5A |
C5 |
C6 |
H6A |
155.8 |
180.0 |
| C7 |
C6 |
C5 |
H5 |
39.4 |
60.0 |
| C7 |
C6 |
C5 |
H5A |
276.4 |
300.0 |
| C5 |
C6 |
C7 |
H6 |
120.0 |
120.0 |
| C5 |
C6 |
C7 |
H6A |
239.4 |
240.0 |
| H6 |
C6 |
C7 |
H6A |
119.4 |
120.0 |
| H6 |
C6 |
C5 |
H5 |
159.4 |
180.0 |
| H6 |
C6 |
C5 |
H5A |
36.3 |
60.0 |
| C5 |
C6 |
H6 |
H6A |
120.6 |
120.0 |
| C7 |
C6 |
H6 |
H6A |
239.4 |
240.0 |
| H6A |
C6 |
C5 |
H5 |
278.8 |
300.0 |
| H6A |
C6 |
C5 |
H5A |
155.8 |
180.0 |
| C5 |
C6 |
H6A |
H6 |
239.6 |
240.0 |
| C7 |
C6 |
H6A |
H6 |
120.4 |
120.0 |
| C8 |
C7 |
C6 |
H6 |
64.5 |
0.8 |
| C8 |
C7 |
C6 |
H6A |
305.1 |
240.8 |
| C7 |
C8 |
C9 |
H9 |
224.5 |
86.5 |
| C7 |
C8 |
C9 |
H9A |
344.5 |
206.5 |
| C7 |
C8 |
C9 |
H9B |
104.5 |
326.5 |
| H7 |
C7 |
C6 |
H6 |
244.5 |
180.8 |
| H7 |
C7 |
C6 |
H6A |
125.1 |
60.8 |
| H7 |
C7 |
C8 |
C9 |
181.7 |
174.2 |
| C10 |
C8 |
C7 |
H7 |
358.2 |
354.2 |
| C10 |
C8 |
C9 |
H9 |
47.9 |
266.4 |
| C10 |
C8 |
C9 |
H9A |
167.9 |
26.4 |
| C10 |
C8 |
C9 |
H9B |
287.9 |
146.4 |
| C9 |
C8 |
C7 |
H7 |
181.7 |
174.2 |
| H9 |
C9 |
C8 |
H9A |
240.0 |
240.0 |
| H9 |
C9 |
C8 |
H9B |
120.0 |
120.0 |
| H9A |
C9 |
C8 |
H9B |
240.0 |
240.0 |
| C8 |
C9 |
H9 |
H9A |
120.0 |
120.0 |
| C8 |
C9 |
H9 |
H9B |
240.0 |
240.0 |
| H9A |
C9 |
H9 |
H9B |
120.0 |
120.0 |
| C8 |
C9 |
H9A |
H9 |
240.0 |
240.0 |
| C8 |
C9 |
H9A |
H9B |
120.0 |
120.0 |
| H9 |
C9 |
H9A |
H9B |
240.0 |
240.0 |
| C8 |
C9 |
H9B |
H9 |
120.0 |
120.0 |
| C8 |
C9 |
H9B |
H9A |
240.0 |
240.0 |
| H9 |
C9 |
H9B |
H9A |
120.0 |
120.1 |
| H10 |
C10 |
N1 |
H10A |
116.8 |
120.0 |
| N1 |
C10 |
H10 |
H10A |
236.2 |
239.9 |
| N1 |
C10 |
H10A |
H10 |
122.5 |
120.0 |
| C11 |
N1 |
C10 |
H10 |
72.0 |
60.0 |
| C11 |
N1 |
C10 |
H10A |
315.2 |
300.0 |
| HN1 |
N1 |
C10 |
H10 |
252.0 |
240.1 |
| HN1 |
N1 |
C10 |
H10A |
135.2 |
120.0 |
| C12 |
C11 |
N1 |
HN1 |
0.4 |
359.9 |
| O6 |
C11 |
N1 |
HN1 |
178.3 |
180.0 |
| H12 |
C12 |
C13 |
H12A |
123.5 |
120.0 |
| C14 |
C13 |
C12 |
H13 |
240.0 |
240.1 |
| C14 |
C13 |
C12 |
H13A |
119.8 |
120.0 |
| H13 |
C13 |
C12 |
H13A |
239.8 |
239.9 |
| C13 |
C12 |
H12 |
H12A |
243.1 |
240.0 |
| H12 |
C12 |
C13 |
H13 |
168.5 |
179.9 |
| H12 |
C12 |
C13 |
H13A |
288.8 |
300.0 |
| C13 |
C12 |
H12A |
H12 |
117.9 |
120.0 |
| H12A |
C12 |
C13 |
H13 |
45.0 |
59.9 |
| H12A |
C12 |
C13 |
H13A |
165.3 |
180.1 |
| C14 |
C13 |
C12 |
H12 |
48.5 |
60.0 |
| C14 |
C13 |
C12 |
H12A |
285.0 |
300.0 |
| C12 |
C13 |
C14 |
H13 |
120.0 |
119.9 |
| C12 |
C13 |
C14 |
H13A |
240.2 |
240.0 |
| H13 |
C13 |
C14 |
H13A |
120.2 |
120.1 |
| H13 |
C13 |
C12 |
H12 |
168.5 |
179.9 |
| H13 |
C13 |
C12 |
H12A |
45.0 |
59.9 |
| C12 |
C13 |
H13 |
H13A |
119.8 |
120.1 |
| C14 |
C13 |
H13 |
H13A |
240.2 |
240.0 |
| H13A |
C13 |
C12 |
H12 |
288.8 |
300.0 |
| H13A |
C13 |
C12 |
H12A |
165.3 |
180.1 |
| C12 |
C13 |
H13A |
H13 |
240.1 |
240.0 |
| C14 |
C13 |
H13A |
H13 |
119.9 |
120.0 |
| C15 |
C14 |
C13 |
H13 |
104.7 |
60.1 |
| C15 |
C14 |
C13 |
H13A |
344.5 |
300.0 |
| H14 |
C14 |
C15 |
H14A |
121.3 |
120.0 |
| C16 |
C15 |
C14 |
H15 |
240.0 |
240.0 |
| C16 |
C15 |
C14 |
H15A |
119.8 |
120.0 |
| H15 |
C15 |
C14 |
H15A |
239.8 |
240.0 |
| H14 |
C14 |
C13 |
H13 |
224.7 |
180.0 |
| H14 |
C14 |
C13 |
H13A |
104.5 |
60.0 |
| C15 |
C14 |
H14 |
H14A |
241.2 |
240.0 |
| H14 |
C14 |
C15 |
H15 |
184.0 |
180.0 |
| H14 |
C14 |
C15 |
H15A |
304.3 |
300.0 |
| H14A |
C14 |
C13 |
H13 |
346.0 |
300.1 |
| H14A |
C14 |
C13 |
H13A |
225.8 |
180.0 |
| C15 |
C14 |
H14A |
H14 |
119.1 |
120.0 |
| H14A |
C14 |
C15 |
H15 |
62.7 |
60.0 |
| H14A |
C14 |
C15 |
H15A |
183.0 |
180.0 |
| C16 |
C15 |
C14 |
H14 |
64.0 |
60.0 |
| C16 |
C15 |
C14 |
H14A |
302.7 |
300.0 |
| C14 |
C15 |
C16 |
H15 |
120.0 |
120.0 |
| C14 |
C15 |
C16 |
H15A |
240.2 |
240.0 |
| H15 |
C15 |
C16 |
H15A |
120.2 |
120.0 |
| H15 |
C15 |
C14 |
H14 |
184.0 |
180.0 |
| H15 |
C15 |
C14 |
H14A |
62.7 |
60.0 |
| C14 |
C15 |
H15 |
H15A |
119.8 |
120.0 |
| C16 |
C15 |
H15 |
H15A |
240.3 |
240.0 |
| H15A |
C15 |
C14 |
H14 |
304.3 |
300.0 |
| H15A |
C15 |
C14 |
H14A |
183.0 |
180.0 |
| C14 |
C15 |
H15A |
H15 |
240.1 |
240.0 |
| C16 |
C15 |
H15A |
H15 |
119.8 |
120.0 |
| S1 |
C16 |
C15 |
H15 |
233.4 |
171.0 |
| S1 |
C16 |
C15 |
H15A |
113.2 |
51.0 |
| C19 |
C16 |
S1 |
H16 |
237.1 |
241.7 |
| C19 |
C16 |
C15 |
H15 |
115.2 |
57.5 |
| C19 |
C16 |
C15 |
H15A |
354.9 |
297.6 |
| S1 |
C16 |
C19 |
H16 |
120.3 |
118.4 |
| H16 |
C16 |
C15 |
H15 |
352.9 |
294.3 |
| H16 |
C16 |
C15 |
H15A |
232.6 |
174.3 |
| C17 |
S1 |
C16 |
H16 |
80.8 |
83.8 |
| H17 |
C17 |
C18 |
H17A |
117.8 |
123.2 |
| C18 |
C17 |
H17 |
H17A |
237.6 |
236.6 |
| C18 |
C17 |
H17A |
H17 |
121.6 |
123.3 |
| N3 |
C18 |
C17 |
H17 |
324.3 |
331.9 |
| N3 |
C18 |
C17 |
H17A |
206.5 |
208.7 |
| C19 |
C18 |
N3 |
H18 |
237.4 |
241.8 |
| N3 |
C18 |
C19 |
H19 |
122.7 |
118.4 |
| C18 |
C19 |
C16 |
H16 |
272.0 |
266.0 |
| C19 |
C18 |
C17 |
H17 |
214.8 |
216.9 |
| C19 |
C18 |
C17 |
H17A |
97.0 |
93.6 |
| N3 |
C18 |
C19 |
H18 |
126.1 |
118.5 |
| N2 |
C19 |
C18 |
H19 |
237.1 |
241.5 |
| H18 |
C18 |
C17 |
H17 |
90.9 |
93.6 |
| H18 |
C18 |
C17 |
H17A |
333.1 |
330.3 |
| H18 |
C18 |
C19 |
H19 |
356.5 |
359.9 |
| N2 |
C19 |
C16 |
H16 |
159.1 |
151.3 |
| N2 |
C19 |
C18 |
H18 |
233.6 |
241.4 |
| C18 |
C19 |
N2 |
H19 |
123.2 |
118.3 |
| H19 |
C19 |
C16 |
H16 |
35.7 |
29.6 |
| H19 |
C19 |
C18 |
H18 |
356.5 |
359.9 |
| C20 |
N2 |
C19 |
H19 |
235.9 |
241.7 |
| HN2 |
N2 |
C19 |
H19 |
55.9 |
61.6 |
| O7 |
C20 |
N2 |
HN2 |
1.2 |
0.0 |
| O7 |
C20 |
N3 |
HN3 |
358.5 |
0.1 |
| C20 |
N3 |
C18 |
H18 |
123.9 |
118.4 |
| N3 |
C20 |
N2 |
HN2 |
181.8 |
180.1 |
| HN3 |
N3 |
C18 |
H18 |
304.0 |
298.2 |