PDB Chemical Component UBY
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 UBY
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C6 |
C1 |
1.400 |
1.383 |
| C1 |
C2 |
1.394 |
1.383 |
| C1 |
H1 |
1.080 |
1.080 |
| C3 |
C2 |
1.396 |
1.382 |
| C2 |
H2 |
1.080 |
1.080 |
| C4 |
C3 |
1.388 |
1.383 |
| C3 |
H3 |
1.080 |
1.080 |
| C5 |
C4 |
1.394 |
1.382 |
| C7 |
C4 |
1.504 |
1.506 |
| C5 |
C6 |
1.398 |
1.383 |
| C5 |
H5 |
1.080 |
1.080 |
| C6 |
H6 |
1.080 |
1.080 |
| O8 |
C7 |
1.423 |
1.452 |
| C7 |
H7 |
1.100 |
1.090 |
| C7 |
H7A |
1.100 |
1.090 |
| C9 |
O8 |
1.420 |
1.346 |
| N10 |
C9 |
1.304 |
1.348 |
| O21 |
C9 |
1.234 |
1.215 |
| C11 |
N10 |
1.440 |
1.465 |
| N10 |
HN10 |
1.000 |
0.971 |
| P12 |
C11 |
1.806 |
1.822 |
| C11 |
H11 |
1.100 |
1.090 |
| C11 |
H11A |
1.099 |
1.090 |
| N13 |
P12 |
1.656 |
1.683 |
| P12 |
O22 |
1.481 |
1.481 |
| P12 |
O23 |
1.522 |
1.610 |
| C14 |
N13 |
1.458 |
1.470 |
| N13 |
HN13 |
1.000 |
1.009 |
| C20 |
C14 |
1.534 |
1.529 |
| C14 |
C15 |
1.501 |
1.507 |
| C14 |
H14 |
1.100 |
1.090 |
| C15 |
O24 |
1.241 |
1.213 |
| C15 |
N16 |
1.336 |
1.348 |
| N16 |
C17 |
1.465 |
1.465 |
| N16 |
HN16 |
1.000 |
0.970 |
| C25 |
C17 |
1.533 |
1.529 |
| C17 |
C18 |
1.504 |
1.507 |
| C17 |
H17 |
1.100 |
1.090 |
| C18 |
O32 |
1.253 |
1.209 |
| C18 |
O19 |
1.250 |
1.342 |
| O19 |
HO19 |
0.950 |
0.967 |
| C21 |
C20 |
1.522 |
1.530 |
| C20 |
H20 |
1.100 |
1.090 |
| C20 |
H20A |
1.100 |
1.090 |
| C22 |
C21 |
1.523 |
1.530 |
| C21 |
C23 |
1.527 |
1.530 |
| C21 |
H21 |
1.100 |
1.090 |
| C22 |
H22 |
1.100 |
1.090 |
| C22 |
H22A |
1.100 |
1.090 |
| C22 |
H22B |
1.100 |
1.090 |
| C23 |
H23 |
1.099 |
1.091 |
| C23 |
H23A |
1.100 |
1.090 |
| C23 |
H23B |
1.100 |
1.090 |
| O23 |
HO23 |
0.951 |
0.967 |
| C25 |
H25 |
1.100 |
1.090 |
| C25 |
H25A |
1.100 |
1.090 |
| C25 |
H25B |
1.100 |
1.090 |
Bond Angles for UBY
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C6 |
C1 |
H1 |
120.7 |
120.0 |
| C1 |
C2 |
H2 |
119.6 |
120.0 |
| C3 |
C2 |
H2 |
119.6 |
120.0 |
| C2 |
C3 |
H3 |
119.9 |
120.0 |
| C4 |
C3 |
H3 |
119.9 |
120.0 |
| C4 |
C5 |
H5 |
120.0 |
120.0 |
| C5 |
C6 |
H6 |
119.7 |
120.1 |
| O8 |
C7 |
H7 |
107.6 |
109.4 |
| O8 |
C7 |
H7A |
107.6 |
109.5 |
| H7 |
C7 |
H7A |
111.3 |
109.5 |
| C11 |
N10 |
HN10 |
119.1 |
120.0 |
| P12 |
C11 |
H11 |
108.4 |
109.5 |
| P12 |
C11 |
H11A |
108.4 |
109.5 |
| H11 |
C11 |
H11A |
110.5 |
109.5 |
| O22 |
P12 |
O23 |
113.1 |
109.4 |
| P12 |
O23 |
HO23 |
109.5 |
114.0 |
| C14 |
N13 |
HN13 |
105.6 |
110.9 |
| C20 |
C14 |
H14 |
113.2 |
109.5 |
| C15 |
C14 |
H14 |
107.1 |
109.5 |
| C14 |
C15 |
O24 |
120.8 |
120.0 |
| C14 |
C15 |
N16 |
116.6 |
120.0 |
| O24 |
C15 |
N16 |
122.6 |
120.0 |
| C15 |
N16 |
C17 |
124.0 |
120.0 |
| C15 |
N16 |
HN16 |
118.0 |
120.0 |
| C17 |
N16 |
HN16 |
118.0 |
120.0 |
| N16 |
C17 |
C18 |
112.4 |
109.4 |
| N16 |
C17 |
H17 |
108.3 |
109.5 |
| C25 |
C17 |
H17 |
111.4 |
109.5 |
| C18 |
C17 |
H17 |
107.2 |
109.5 |
| C17 |
C18 |
O32 |
116.8 |
120.0 |
| C17 |
C18 |
O19 |
119.2 |
120.0 |
| O32 |
C18 |
O19 |
124.0 |
120.0 |
| C18 |
O19 |
HO19 |
109.5 |
117.0 |
| C21 |
C20 |
H20 |
107.9 |
109.4 |
| C21 |
C20 |
H20A |
107.9 |
109.5 |
| H20 |
C20 |
H20A |
111.0 |
109.5 |
| C22 |
C21 |
C23 |
111.8 |
109.4 |
| C22 |
C21 |
H21 |
107.3 |
109.5 |
| C23 |
C21 |
H21 |
106.9 |
109.4 |
| C21 |
C23 |
H23 |
109.5 |
109.5 |
| C21 |
C23 |
H23A |
109.5 |
109.5 |
| C21 |
C23 |
H23B |
109.5 |
109.5 |
| H22 |
C22 |
H22A |
109.5 |
109.5 |
| H22 |
C22 |
H22B |
109.5 |
109.5 |
| H22A |
C22 |
H22B |
109.5 |
109.4 |
| H23 |
C23 |
H23A |
109.5 |
109.4 |
| H23 |
C23 |
H23B |
109.4 |
109.4 |
| H23A |
C23 |
H23B |
109.5 |
109.5 |
| H25 |
C25 |
H25A |
109.4 |
109.5 |
| H25 |
C25 |
H25B |
109.5 |
109.4 |
| H25A |
C25 |
H25B |
109.5 |
109.5 |
Torsion Angles for UBY
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C6 |
C1 |
C2 |
H2 |
179.0 |
180.0 |
| C3 |
C2 |
C1 |
H2 |
180.0 |
180.0 |
| C1 |
C2 |
C3 |
H3 |
179.6 |
180.0 |
| H1 |
C1 |
C2 |
H2 |
359.0 |
360.0 |
| C1 |
C2 |
C3 |
H2 |
180.0 |
180.0 |
| C4 |
C3 |
C2 |
H3 |
180.0 |
180.3 |
| H2 |
C2 |
C3 |
H3 |
359.7 |
0.0 |
| C4 |
C3 |
C2 |
H2 |
179.6 |
180.3 |
| C2 |
C3 |
C4 |
H3 |
180.0 |
179.7 |
| H3 |
C3 |
C2 |
H2 |
359.7 |
0.0 |
| C5 |
C4 |
C3 |
H3 |
181.2 |
179.7 |
| C4 |
C5 |
C6 |
H6 |
179.4 |
179.7 |
| C7 |
C4 |
C3 |
H3 |
359.0 |
0.3 |
| C7 |
C4 |
C5 |
H5 |
1.4 |
359.4 |
| C5 |
C6 |
C1 |
H1 |
181.5 |
180.0 |
| H5 |
C5 |
C6 |
H6 |
359.4 |
0.3 |
| H6 |
C6 |
C1 |
H1 |
1.5 |
360.0 |
| H7 |
C7 |
O8 |
H7A |
120.0 |
120.0 |
| O8 |
C7 |
H7 |
H7A |
242.3 |
240.0 |
| O8 |
C7 |
H7A |
H7 |
117.7 |
120.0 |
| C9 |
O8 |
C7 |
H7 |
341.9 |
60.1 |
| C9 |
O8 |
C7 |
H7A |
221.8 |
300.1 |
| P12 |
C11 |
N10 |
HN10 |
27.3 |
274.9 |
| H11 |
C11 |
P12 |
H11A |
120.0 |
120.1 |
| H11 |
C11 |
N10 |
HN10 |
147.3 |
34.9 |
| P12 |
C11 |
H11 |
H11A |
241.3 |
240.0 |
| H11A |
C11 |
N10 |
HN10 |
267.3 |
154.9 |
| P12 |
C11 |
H11A |
H11 |
118.7 |
120.1 |
| N13 |
P12 |
C11 |
H11 |
64.8 |
60.0 |
| N13 |
P12 |
C11 |
H11A |
304.8 |
300.0 |
| N13 |
P12 |
O23 |
HO23 |
234.3 |
60.0 |
| O22 |
P12 |
C11 |
H11 |
305.0 |
300.0 |
| O22 |
P12 |
C11 |
H11A |
185.0 |
180.0 |
| O22 |
P12 |
O23 |
HO23 |
0.0 |
180.0 |
| O23 |
P12 |
C11 |
H11 |
180.2 |
180.0 |
| O23 |
P12 |
C11 |
H11A |
60.2 |
60.0 |
| C20 |
C14 |
N13 |
HN13 |
41.2 |
331.1 |
| C15 |
C14 |
C20 |
H14 |
118.5 |
120.1 |
| C20 |
C14 |
C15 |
N16 |
80.9 |
286.0 |
| C15 |
C14 |
N13 |
HN13 |
160.3 |
91.1 |
| C20 |
C14 |
C15 |
H14 |
237.7 |
239.9 |
| O24 |
C15 |
C14 |
N16 |
182.7 |
180.1 |
| C14 |
C15 |
N16 |
C17 |
184.4 |
184.9 |
| C14 |
C15 |
N16 |
HN16 |
4.4 |
5.0 |
| H14 |
C14 |
N13 |
HN13 |
278.8 |
211.1 |
| H14 |
C14 |
C15 |
O24 |
25.9 |
226.2 |
| H14 |
C14 |
C15 |
N16 |
203.2 |
46.1 |
| O24 |
C15 |
C14 |
H14 |
25.9 |
226.2 |
| C14 |
C15 |
O24 |
N16 |
177.1 |
179.9 |
| O24 |
C15 |
N16 |
C17 |
1.7 |
4.9 |
| O24 |
C15 |
N16 |
HN16 |
181.7 |
184.9 |
| N16 |
C15 |
C14 |
H14 |
203.2 |
46.1 |
| C14 |
C15 |
N16 |
O24 |
182.7 |
180.1 |
| C17 |
N16 |
C15 |
HN16 |
180.0 |
180.0 |
| C15 |
N16 |
C17 |
C18 |
236.4 |
205.0 |
| C15 |
N16 |
C17 |
H17 |
354.6 |
325.0 |
| C15 |
N16 |
C17 |
HN16 |
180.0 |
180.0 |
| C25 |
C17 |
N16 |
H17 |
120.9 |
120.0 |
| C18 |
C17 |
N16 |
H17 |
241.8 |
240.0 |
| N16 |
C17 |
C18 |
O32 |
160.2 |
360.0 |
| N16 |
C17 |
C18 |
O19 |
338.7 |
180.0 |
| C15 |
N16 |
HN16 |
C17 |
180.0 |
180.0 |
| HN16 |
N16 |
C17 |
C18 |
56.4 |
25.0 |
| HN16 |
N16 |
C17 |
H17 |
174.6 |
145.0 |
| C25 |
C17 |
N16 |
HN16 |
295.6 |
265.0 |
| N16 |
C17 |
C25 |
H17 |
241.0 |
240.0 |
| C18 |
C17 |
C25 |
H17 |
118.3 |
120.0 |
| C25 |
C17 |
C18 |
O19 |
99.0 |
300.0 |
| C18 |
C17 |
N16 |
HN16 |
56.4 |
25.0 |
| N16 |
C17 |
C18 |
H17 |
118.9 |
120.0 |
| C25 |
C17 |
C18 |
H17 |
239.1 |
240.0 |
| O32 |
C18 |
C17 |
O19 |
181.5 |
180.0 |
| C17 |
C18 |
O19 |
HO19 |
181.6 |
180.0 |
| H17 |
C17 |
N16 |
HN16 |
174.6 |
145.0 |
| N16 |
C17 |
H17 |
C18 |
238.5 |
240.0 |
| H17 |
C17 |
C18 |
O32 |
41.3 |
240.0 |
| H17 |
C17 |
C18 |
O19 |
219.9 |
60.0 |
| O32 |
C18 |
C17 |
H17 |
41.3 |
240.0 |
| C17 |
C18 |
O32 |
O19 |
178.4 |
180.0 |
| O32 |
C18 |
O19 |
HO19 |
360.0 |
360.0 |
| O19 |
C18 |
C17 |
H17 |
219.9 |
60.0 |
| C17 |
C18 |
O19 |
O32 |
181.6 |
180.0 |
| C21 |
C20 |
C14 |
H14 |
302.9 |
305.7 |
| H20 |
C20 |
C21 |
H20A |
120.0 |
120.0 |
| H20 |
C20 |
C14 |
H14 |
62.9 |
65.7 |
| C21 |
C20 |
H20 |
H20A |
242.0 |
240.0 |
| H20A |
C20 |
C14 |
H14 |
182.9 |
185.7 |
| C21 |
C20 |
H20A |
H20 |
118.0 |
120.0 |
| C22 |
C21 |
C20 |
H20 |
75.2 |
306.9 |
| C22 |
C21 |
C20 |
H20A |
315.2 |
186.9 |
| C23 |
C21 |
C22 |
H21 |
243.1 |
119.9 |
| C22 |
C21 |
C23 |
H23 |
54.2 |
180.0 |
| C22 |
C21 |
C23 |
H23A |
174.2 |
300.0 |
| C22 |
C21 |
C23 |
H23B |
294.2 |
60.0 |
| C23 |
C21 |
C20 |
H20 |
309.2 |
66.9 |
| C23 |
C21 |
C20 |
H20A |
189.2 |
306.9 |
| C22 |
C21 |
C23 |
H21 |
117.1 |
240.0 |
| H23 |
C23 |
C21 |
H23A |
240.0 |
240.0 |
| H23 |
C23 |
C21 |
H23B |
120.0 |
120.0 |
| H23A |
C23 |
C21 |
H23B |
240.0 |
240.0 |
| H21 |
C21 |
C20 |
H20 |
192.3 |
186.9 |
| H21 |
C21 |
C20 |
H20A |
72.3 |
66.9 |
| C22 |
C21 |
H21 |
C23 |
239.9 |
120.0 |
| H21 |
C21 |
C23 |
H23 |
297.1 |
300.0 |
| H21 |
C21 |
C23 |
H23A |
57.1 |
60.0 |
| H21 |
C21 |
C23 |
H23B |
177.1 |
180.0 |
| H22 |
C22 |
C21 |
C23 |
306.0 |
64.2 |
| H22 |
C22 |
C21 |
H21 |
62.8 |
304.2 |
| H22A |
C22 |
H22 |
H22B |
120.0 |
120.0 |
| H22A |
C22 |
C21 |
C23 |
65.9 |
184.2 |
| H22A |
C22 |
C21 |
H21 |
182.8 |
64.2 |
| H22 |
C22 |
H22A |
H22B |
240.0 |
239.9 |
| H22B |
C22 |
C21 |
C23 |
185.9 |
304.1 |
| H22B |
C22 |
C21 |
H21 |
302.8 |
184.2 |
| H22 |
C22 |
H22B |
H22A |
120.0 |
120.1 |
| H23 |
C23 |
C21 |
H21 |
297.1 |
300.0 |
| C21 |
C23 |
H23 |
H23A |
120.0 |
120.0 |
| C21 |
C23 |
H23 |
H23B |
240.0 |
240.0 |
| H23A |
C23 |
H23 |
H23B |
120.0 |
120.0 |
| H23A |
C23 |
C21 |
H21 |
57.1 |
60.0 |
| C21 |
C23 |
H23A |
H23 |
240.0 |
240.0 |
| C21 |
C23 |
H23A |
H23B |
120.0 |
120.0 |
| H23 |
C23 |
H23A |
H23B |
240.0 |
240.1 |
| H23B |
C23 |
C21 |
H21 |
177.1 |
180.0 |
| C21 |
C23 |
H23B |
H23 |
120.0 |
120.0 |
| C21 |
C23 |
H23B |
H23A |
240.0 |
239.9 |
| H23 |
C23 |
H23B |
H23A |
120.0 |
119.9 |
| H25 |
C25 |
C17 |
H17 |
299.0 |
300.0 |
| H25A |
C25 |
H25 |
H25B |
120.0 |
120.0 |
| H25A |
C25 |
C17 |
H17 |
59.0 |
60.0 |
| H25 |
C25 |
H25A |
H25B |
240.0 |
240.0 |
| H25B |
C25 |
C17 |
H17 |
179.0 |
180.0 |
| H25 |
C25 |
H25B |
H25A |
120.0 |
120.0 |