PDB Chemical Component T5D
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 T5D
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C |
O |
1.394 |
1.429 |
| C1 |
C |
1.539 |
1.530 |
| C2 |
C1 |
1.515 |
1.507 |
| C2 |
N |
1.384 |
1.318 |
| N |
C3 |
1.361 |
1.318 |
| C3 |
C4 |
1.406 |
1.382 |
| C4 |
C5 |
1.391 |
1.387 |
| C5 |
C6 |
1.384 |
1.386 |
| C6 |
C2 |
1.416 |
1.382 |
| C1 |
C7 |
1.534 |
1.543 |
| C7 |
C8 |
1.530 |
1.548 |
| C8 |
C9 |
1.521 |
1.548 |
| C9 |
C10 |
1.528 |
1.542 |
| C10 |
C1 |
1.540 |
1.539 |
| C4 |
H4 |
1.080 |
1.080 |
| C5 |
H5 |
1.080 |
1.080 |
| C6 |
H6 |
1.080 |
1.080 |
| C7 |
H7 |
1.100 |
1.090 |
| C7 |
H8 |
1.100 |
1.090 |
| C8 |
H9 |
1.099 |
1.091 |
| C8 |
H10 |
1.100 |
1.091 |
| C10 |
H14 |
1.100 |
1.090 |
| C10 |
H13 |
1.100 |
1.091 |
| C |
H2 |
1.100 |
1.090 |
| C |
H1 |
1.100 |
1.090 |
| O |
H |
0.950 |
0.967 |
| C3 |
H3 |
1.080 |
1.080 |
| C9 |
H11 |
1.100 |
1.090 |
| C9 |
H12 |
1.100 |
1.090 |
Bond Angles for T5D
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O |
C |
H2 |
109.6 |
109.5 |
| O |
C |
H1 |
109.6 |
109.5 |
| C |
O |
H |
109.5 |
114.0 |
| C10 |
C1 |
C |
109.6 |
110.0 |
| C1 |
C |
H2 |
109.5 |
109.5 |
| C1 |
C |
H1 |
109.6 |
109.5 |
| C6 |
C2 |
C1 |
118.8 |
119.6 |
| C2 |
N |
C3 |
117.0 |
121.8 |
| C6 |
C2 |
N |
122.0 |
120.8 |
| N |
C3 |
H3 |
118.3 |
119.7 |
| C3 |
C4 |
H4 |
120.6 |
120.4 |
| C4 |
C5 |
C6 |
119.6 |
118.5 |
| C5 |
C4 |
H4 |
120.7 |
120.4 |
| C4 |
C5 |
H5 |
120.2 |
120.7 |
| C5 |
C6 |
C2 |
119.3 |
119.2 |
| C6 |
C5 |
H5 |
120.2 |
120.8 |
| C5 |
C6 |
H6 |
120.4 |
120.4 |
| C2 |
C6 |
H6 |
120.3 |
120.4 |
| C1 |
C7 |
H7 |
110.1 |
110.5 |
| C1 |
C7 |
H8 |
110.2 |
110.6 |
| C7 |
C8 |
C9 |
106.9 |
102.8 |
| C8 |
C7 |
H7 |
110.2 |
110.5 |
| C8 |
C7 |
H8 |
110.2 |
110.6 |
| C7 |
C8 |
H9 |
110.1 |
110.8 |
| C7 |
C8 |
H10 |
110.1 |
110.8 |
| C8 |
C9 |
C10 |
105.4 |
104.2 |
| C9 |
C8 |
H9 |
110.1 |
110.8 |
| C9 |
C8 |
H10 |
110.1 |
110.8 |
| C8 |
C9 |
H11 |
110.5 |
110.5 |
| C8 |
C9 |
H12 |
110.5 |
110.5 |
| C9 |
C10 |
H14 |
110.8 |
110.1 |
| C9 |
C10 |
H13 |
110.8 |
110.1 |
| C1 |
C10 |
H14 |
110.8 |
110.0 |
| C1 |
C10 |
H13 |
110.8 |
110.0 |
| H7 |
C7 |
H8 |
109.5 |
110.4 |
| H9 |
C8 |
H10 |
109.5 |
110.8 |
| H14 |
C10 |
H13 |
109.5 |
110.0 |
| H2 |
C |
H1 |
109.5 |
109.4 |
| H11 |
C9 |
H12 |
109.5 |
110.5 |
Torsion Angles for T5D
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C10 |
C1 |
C |
O |
77.3 |
180.0 |
| C1 |
C |
O |
H2 |
240.1 |
240.0 |
| C1 |
C |
O |
H1 |
119.9 |
120.0 |
| H2 |
C |
O |
H1 |
239.8 |
240.0 |
| O |
C |
C1 |
H2 |
119.9 |
120.0 |
| O |
C |
C1 |
H1 |
240.1 |
239.9 |
| C1 |
C |
O |
H |
180.0 |
180.0 |
| C6 |
C2 |
C1 |
C |
283.1 |
286.4 |
| C |
C1 |
C7 |
H7 |
28.3 |
145.6 |
| C |
C1 |
C7 |
H8 |
149.2 |
23.1 |
| C |
C1 |
C10 |
H14 |
322.3 |
238.6 |
| C |
C1 |
C10 |
H13 |
200.5 |
359.9 |
| H2 |
C |
C1 |
H1 |
120.1 |
119.9 |
| C2 |
C1 |
C |
H2 |
194.8 |
298.6 |
| C2 |
C1 |
C |
H1 |
74.7 |
178.6 |
| C1 |
C2 |
N |
C3 |
178.4 |
179.8 |
| C6 |
C2 |
C1 |
N |
179.6 |
180.0 |
| C5 |
C6 |
C2 |
C1 |
181.6 |
180.0 |
| C1 |
C2 |
C6 |
H6 |
1.6 |
0.0 |
| C2 |
C1 |
C7 |
H7 |
265.3 |
24.2 |
| C2 |
C1 |
C7 |
H8 |
26.1 |
261.7 |
| C2 |
C1 |
C10 |
H14 |
84.2 |
360.0 |
| C2 |
C1 |
C10 |
H13 |
322.5 |
121.3 |
| C6 |
C2 |
N |
C1 |
180.5 |
180.0 |
| C2 |
N |
C3 |
H3 |
180.2 |
180.1 |
| C5 |
C6 |
C2 |
N |
1.2 |
360.0 |
| N |
C2 |
C6 |
H6 |
181.2 |
180.0 |
| C6 |
C2 |
N |
C3 |
358.9 |
359.8 |
| N |
C3 |
C4 |
H4 |
180.6 |
179.8 |
| C5 |
C4 |
C3 |
H4 |
180.0 |
179.8 |
| C3 |
C4 |
C5 |
H5 |
179.5 |
180.2 |
| C3 |
C4 |
C5 |
H4 |
180.0 |
180.2 |
| C4 |
C5 |
C6 |
C2 |
359.7 |
0.0 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
180.0 |
| C4 |
C5 |
C6 |
H6 |
179.7 |
180.0 |
| C6 |
C5 |
C4 |
H4 |
179.5 |
180.0 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
180.0 |
| C2 |
C6 |
C5 |
H6 |
180.0 |
180.1 |
| C2 |
C6 |
C5 |
H5 |
179.7 |
180.1 |
| C5 |
C6 |
C2 |
H6 |
180.0 |
179.9 |
| C6 |
C2 |
C1 |
C7 |
46.4 |
47.8 |
| C1 |
C7 |
C8 |
C9 |
354.3 |
322.1 |
| C8 |
C7 |
C1 |
H7 |
240.4 |
118.7 |
| C8 |
C7 |
C1 |
H8 |
119.6 |
241.2 |
| C1 |
C7 |
C8 |
H9 |
113.9 |
80.4 |
| C1 |
C7 |
C8 |
H10 |
234.7 |
203.7 |
| H7 |
C7 |
C1 |
H8 |
239.1 |
122.5 |
| C1 |
C7 |
C8 |
H7 |
119.6 |
241.3 |
| C1 |
C7 |
C8 |
H8 |
240.4 |
118.8 |
| C7 |
C8 |
C9 |
C10 |
342.8 |
38.0 |
| C9 |
C8 |
C7 |
H9 |
240.4 |
241.7 |
| C9 |
C8 |
C7 |
H10 |
119.6 |
118.3 |
| C7 |
C8 |
C9 |
H11 |
102.2 |
156.6 |
| C7 |
C8 |
C9 |
H12 |
223.4 |
279.3 |
| H7 |
C7 |
C8 |
H8 |
120.9 |
237.5 |
| H9 |
C8 |
C7 |
H10 |
239.2 |
236.7 |
| C9 |
C8 |
C7 |
H7 |
234.7 |
80.7 |
| C9 |
C8 |
C7 |
H8 |
113.9 |
203.2 |
| C7 |
C8 |
C9 |
H9 |
119.6 |
118.3 |
| C7 |
C8 |
C9 |
H10 |
240.4 |
241.7 |
| C8 |
C9 |
C10 |
H14 |
152.6 |
217.1 |
| C8 |
C9 |
C10 |
H13 |
274.3 |
95.7 |
| H9 |
C8 |
C9 |
H10 |
120.8 |
123.3 |
| H11 |
C9 |
C8 |
H12 |
238.7 |
237.3 |
| C10 |
C9 |
C8 |
H9 |
223.2 |
279.6 |
| C10 |
C9 |
C8 |
H10 |
102.4 |
156.3 |
| C8 |
C9 |
C10 |
H11 |
119.4 |
118.7 |
| C8 |
C9 |
C10 |
H12 |
240.7 |
241.3 |
| C1 |
C10 |
C9 |
H14 |
240.8 |
119.3 |
| C1 |
C10 |
C9 |
H13 |
119.1 |
240.7 |
| H14 |
C10 |
C9 |
H13 |
238.3 |
121.4 |
| C10 |
C1 |
C |
H2 |
317.4 |
60.0 |
| C10 |
C1 |
C |
H1 |
197.3 |
300.0 |
| C6 |
C2 |
C1 |
C10 |
161.4 |
165.0 |
| C10 |
C1 |
C7 |
H7 |
145.6 |
264.9 |
| C10 |
C1 |
C7 |
H8 |
266.5 |
142.4 |
| C8 |
C9 |
C10 |
C1 |
33.4 |
336.4 |
| C9 |
C10 |
C1 |
H14 |
119.1 |
240.7 |
| C9 |
C10 |
C1 |
H13 |
240.9 |
119.3 |
| H14 |
C10 |
C1 |
H13 |
121.7 |
238.7 |
| H4 |
C4 |
C5 |
C6 |
179.5 |
180.0 |
| H4 |
C4 |
C5 |
H5 |
359.5 |
359.9 |
| C4 |
C5 |
H5 |
C6 |
180.0 |
180.0 |
| H5 |
C5 |
C4 |
H4 |
359.5 |
359.9 |
| H5 |
C5 |
C6 |
C2 |
179.7 |
180.1 |
| H5 |
C5 |
C6 |
H6 |
359.7 |
360.0 |
| H6 |
C6 |
C2 |
C1 |
1.6 |
0.0 |
| H6 |
C6 |
C2 |
N |
181.2 |
180.0 |
| C5 |
C6 |
H6 |
C2 |
180.0 |
180.1 |
| H6 |
C6 |
C5 |
H5 |
359.7 |
360.0 |
| C1 |
C7 |
H7 |
H8 |
121.3 |
237.4 |
| H7 |
C7 |
C8 |
C9 |
234.7 |
80.7 |
| C8 |
C7 |
H7 |
H8 |
238.7 |
122.6 |
| H7 |
C7 |
C8 |
H9 |
354.3 |
199.1 |
| H7 |
C7 |
C8 |
H10 |
115.1 |
322.4 |
| C1 |
C7 |
H8 |
H7 |
238.7 |
122.6 |
| H8 |
C7 |
C8 |
C9 |
113.9 |
203.2 |
| C8 |
C7 |
H8 |
H7 |
121.3 |
237.4 |
| H8 |
C7 |
C8 |
H9 |
233.5 |
321.6 |
| H8 |
C7 |
C8 |
H10 |
354.3 |
84.9 |
| C7 |
C8 |
H9 |
C9 |
242.3 |
246.6 |
| H9 |
C8 |
C7 |
H7 |
354.3 |
199.1 |
| H9 |
C8 |
C7 |
H8 |
233.5 |
321.6 |
| C7 |
C8 |
H9 |
H10 |
121.2 |
123.3 |
| H9 |
C8 |
C9 |
C10 |
223.2 |
279.6 |
| C9 |
C8 |
H9 |
H10 |
238.8 |
236.7 |
| H9 |
C8 |
C9 |
H11 |
342.6 |
38.3 |
| H9 |
C8 |
C9 |
H12 |
103.8 |
160.9 |
| C7 |
C8 |
H10 |
C9 |
117.6 |
113.4 |
| H10 |
C8 |
C7 |
H7 |
115.1 |
322.4 |
| H10 |
C8 |
C7 |
H8 |
354.3 |
84.9 |
| C7 |
C8 |
H10 |
H9 |
238.8 |
236.7 |
| H10 |
C8 |
C9 |
C10 |
102.4 |
156.3 |
| C9 |
C8 |
H10 |
H9 |
121.2 |
123.3 |
| H10 |
C8 |
C9 |
H11 |
221.7 |
274.9 |
| H10 |
C8 |
C9 |
H12 |
343.0 |
37.6 |
| H14 |
C10 |
C1 |
C |
322.3 |
238.6 |
| C9 |
C10 |
H14 |
H13 |
122.5 |
238.5 |
| C1 |
C10 |
H14 |
H13 |
237.5 |
121.3 |
| H13 |
C10 |
C1 |
C |
200.5 |
359.9 |
| C9 |
C10 |
H13 |
H14 |
237.5 |
121.5 |
| C1 |
C10 |
H13 |
H14 |
122.5 |
238.7 |
| O |
C |
H2 |
H1 |
120.2 |
120.0 |
| H2 |
C |
O |
H |
299.9 |
300.0 |
| C1 |
C |
H2 |
H1 |
239.8 |
240.0 |
| O |
C |
H1 |
H2 |
239.8 |
240.0 |
| H1 |
C |
O |
H |
60.1 |
60.0 |
| C1 |
C |
H1 |
H2 |
120.2 |
120.0 |
| H |
O |
C |
H2 |
299.9 |
300.0 |
| H |
O |
C |
H1 |
60.1 |
60.0 |
| H3 |
C3 |
C4 |
H4 |
0.6 |
0.2 |
| C8 |
C9 |
H11 |
C10 |
243.8 |
245.2 |
| H11 |
C9 |
C8 |
H9 |
342.6 |
38.3 |
| H11 |
C9 |
C8 |
H10 |
221.7 |
274.9 |
| C8 |
C9 |
H11 |
H12 |
121.9 |
122.7 |
| H11 |
C9 |
C10 |
H14 |
33.2 |
98.4 |
| H11 |
C9 |
C10 |
H13 |
155.0 |
337.0 |
| C8 |
C9 |
H12 |
C10 |
116.2 |
114.8 |
| H12 |
C9 |
C8 |
H9 |
103.8 |
160.9 |
| H12 |
C9 |
C8 |
H10 |
343.0 |
37.6 |
| C8 |
C9 |
H12 |
H11 |
238.1 |
237.4 |
| H12 |
C9 |
C10 |
H14 |
271.9 |
335.8 |
| H12 |
C9 |
C10 |
H13 |
33.7 |
214.4 |