PDB Chemical Component TPD
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 TPD
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C3 |
S1 |
1.722 |
1.763 |
| C3 |
C4 |
1.361 |
1.355 |
| C3 |
S2 |
1.717 |
1.785 |
| C9 |
C10 |
1.448 |
1.507 |
| C9 |
N8 |
1.460 |
1.464 |
| C9 |
H91 |
1.100 |
1.090 |
| C9 |
H92 |
1.100 |
1.090 |
| C10 |
C11 |
1.382 |
1.355 |
| C10 |
S14 |
1.735 |
1.785 |
| C11 |
C12 |
1.377 |
1.382 |
| C11 |
H11 |
1.079 |
1.080 |
| C12 |
C13 |
1.385 |
1.356 |
| C12 |
H12 |
1.080 |
1.079 |
| C13 |
S14 |
1.736 |
1.785 |
| C13 |
H13 |
1.080 |
1.080 |
| O1A |
S1 |
1.430 |
1.420 |
| O2A |
S1 |
1.425 |
1.420 |
| N21 |
S1 |
1.489 |
1.656 |
| N21 |
HNL1 |
1.000 |
0.969 |
| N21 |
HNL2 |
1.000 |
0.970 |
| C4 |
C5 |
1.371 |
1.382 |
| C4 |
H4 |
1.080 |
1.080 |
| C5 |
C6 |
1.376 |
1.355 |
| C5 |
H5 |
1.079 |
1.080 |
| C6 |
S2 |
1.699 |
1.785 |
| C6 |
S7 |
1.736 |
1.762 |
| S7 |
O3B |
1.433 |
1.420 |
| S7 |
O4B |
1.436 |
1.421 |
| S7 |
N8 |
1.495 |
1.656 |
| N8 |
HN8 |
1.000 |
0.970 |
Bond Angles for TPD
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| S1 |
C3 |
C4 |
125.4 |
129.0 |
| S1 |
C3 |
S2 |
121.5 |
129.0 |
| C3 |
S1 |
O1A |
107.6 |
105.7 |
| C3 |
S1 |
O2A |
104.9 |
105.7 |
| C3 |
S1 |
N21 |
108.5 |
107.4 |
| C4 |
C3 |
S2 |
113.2 |
102.0 |
| C3 |
C4 |
C5 |
111.5 |
119.0 |
| C3 |
C4 |
H4 |
124.3 |
120.5 |
| C3 |
S2 |
C6 |
90.0 |
98.1 |
| C10 |
C9 |
N8 |
101.2 |
109.5 |
| C10 |
C9 |
H91 |
114.0 |
109.5 |
| C10 |
C9 |
H92 |
112.3 |
109.5 |
| C9 |
C10 |
C11 |
123.5 |
129.0 |
| C9 |
C10 |
S14 |
123.3 |
129.0 |
| N8 |
C9 |
H91 |
114.0 |
109.5 |
| N8 |
C9 |
H92 |
112.3 |
109.5 |
| C9 |
N8 |
S7 |
117.2 |
120.0 |
| C9 |
N8 |
HN8 |
107.0 |
119.9 |
| H91 |
C9 |
H92 |
103.3 |
109.4 |
| C11 |
C10 |
S14 |
113.2 |
101.9 |
| C10 |
C11 |
C12 |
111.4 |
119.0 |
| C10 |
C11 |
H11 |
124.3 |
120.5 |
| C10 |
S14 |
C13 |
89.7 |
98.1 |
| C12 |
C11 |
H11 |
124.3 |
120.5 |
| C11 |
C12 |
C13 |
114.2 |
119.0 |
| C11 |
C12 |
H12 |
122.8 |
120.6 |
| C13 |
C12 |
H12 |
122.9 |
120.5 |
| C12 |
C13 |
S14 |
111.4 |
102.0 |
| C12 |
C13 |
H13 |
124.3 |
129.0 |
| S14 |
C13 |
H13 |
124.3 |
129.0 |
| O1A |
S1 |
O2A |
108.9 |
125.4 |
| O1A |
S1 |
N21 |
112.5 |
105.8 |
| O2A |
S1 |
N21 |
114.0 |
105.8 |
| S1 |
N21 |
HNL1 |
109.5 |
120.0 |
| S1 |
N21 |
HNL2 |
109.5 |
120.0 |
| HNL1 |
N21 |
HNL2 |
109.5 |
120.0 |
| C5 |
C4 |
H4 |
124.3 |
120.5 |
| C4 |
C5 |
C6 |
113.3 |
119.0 |
| C4 |
C5 |
H5 |
123.3 |
120.5 |
| C6 |
C5 |
H5 |
123.3 |
120.5 |
| C5 |
C6 |
S2 |
112.1 |
102.0 |
| C5 |
C6 |
S7 |
128.0 |
129.0 |
| S2 |
C6 |
S7 |
119.9 |
129.0 |
| C6 |
S7 |
O3B |
107.1 |
105.7 |
| C6 |
S7 |
O4B |
108.2 |
105.8 |
| C6 |
S7 |
N8 |
109.0 |
107.4 |
| O3B |
S7 |
O4B |
110.0 |
125.3 |
| O3B |
S7 |
N8 |
113.7 |
105.8 |
| O4B |
S7 |
N8 |
108.7 |
105.8 |
| S7 |
N8 |
HN8 |
107.0 |
120.0 |
Torsion Angles for TPD
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C4 |
C3 |
S1 |
S2 |
178.5 |
179.7 |
| S1 |
C3 |
C4 |
C5 |
181.6 |
179.8 |
| S1 |
C3 |
C4 |
H4 |
1.6 |
0.3 |
| S1 |
C3 |
S2 |
C6 |
178.5 |
180.0 |
| O1A |
S1 |
C3 |
O2A |
244.1 |
134.8 |
| O1A |
S1 |
C3 |
N21 |
122.0 |
247.4 |
| O2A |
S1 |
C3 |
N21 |
237.8 |
112.6 |
| C3 |
S1 |
N21 |
HNL1 |
88.2 |
180.0 |
| C3 |
S1 |
N21 |
HNL2 |
328.2 |
359.8 |
| S1 |
C3 |
C4 |
S2 |
181.4 |
180.2 |
| C4 |
C3 |
S1 |
O1A |
86.6 |
337.1 |
| C4 |
C3 |
S1 |
O2A |
202.5 |
202.3 |
| C4 |
C3 |
S1 |
N21 |
324.6 |
89.7 |
| C4 |
C3 |
S2 |
C6 |
359.8 |
0.2 |
| C5 |
C4 |
C3 |
H4 |
180.0 |
179.6 |
| C3 |
C4 |
C5 |
C6 |
359.9 |
0.5 |
| C3 |
C4 |
C5 |
H5 |
179.9 |
180.3 |
| S1 |
C3 |
S2 |
C4 |
178.7 |
179.8 |
| S2 |
C3 |
S1 |
O1A |
268.1 |
157.4 |
| S2 |
C3 |
S1 |
O2A |
23.9 |
22.6 |
| S2 |
C3 |
S1 |
N21 |
146.1 |
270.0 |
| S2 |
C3 |
C4 |
C5 |
0.2 |
359.6 |
| S2 |
C3 |
C4 |
H4 |
180.2 |
180.1 |
| C5 |
C6 |
S2 |
C3 |
0.1 |
0.0 |
| C3 |
S2 |
C6 |
S7 |
179.8 |
180.0 |
| N8 |
C9 |
C10 |
H91 |
122.9 |
120.1 |
| N8 |
C9 |
C10 |
H92 |
240.0 |
240.0 |
| C10 |
C9 |
N8 |
S7 |
143.2 |
180.0 |
| C10 |
C9 |
N8 |
HN8 |
263.2 |
0.0 |
| H91 |
C9 |
C10 |
H92 |
117.1 |
119.9 |
| C11 |
C10 |
C9 |
S14 |
182.8 |
179.7 |
| C9 |
C10 |
C11 |
C12 |
176.9 |
179.8 |
| C9 |
C10 |
C11 |
H11 |
356.9 |
0.3 |
| C9 |
C10 |
S14 |
C13 |
183.0 |
180.0 |
| C10 |
C9 |
N8 |
H91 |
237.1 |
240.0 |
| C10 |
C9 |
N8 |
H92 |
120.0 |
120.0 |
| N8 |
C9 |
C10 |
C11 |
268.6 |
89.7 |
| N8 |
C9 |
C10 |
S14 |
85.8 |
270.1 |
| H91 |
C9 |
N8 |
H92 |
242.9 |
240.0 |
| C6 |
S7 |
N8 |
C9 |
72.5 |
60.0 |
| O3B |
S7 |
N8 |
C9 |
313.1 |
307.4 |
| O4B |
S7 |
N8 |
C9 |
190.2 |
172.6 |
| S7 |
N8 |
C9 |
HN8 |
240.0 |
180.0 |
| C10 |
C9 |
H91 |
N8 |
115.6 |
120.1 |
| C10 |
C9 |
H91 |
H92 |
237.8 |
240.0 |
| H91 |
C9 |
C10 |
C11 |
145.8 |
329.7 |
| H91 |
C9 |
C10 |
S14 |
322.9 |
150.0 |
| N8 |
C9 |
H91 |
H92 |
122.2 |
120.0 |
| H91 |
C9 |
N8 |
S7 |
266.1 |
300.0 |
| H91 |
C9 |
N8 |
HN8 |
26.1 |
120.0 |
| C10 |
C9 |
H92 |
N8 |
246.6 |
240.0 |
| C10 |
C9 |
H92 |
H91 |
123.3 |
120.0 |
| H92 |
C9 |
C10 |
C11 |
28.7 |
209.7 |
| H92 |
C9 |
C10 |
S14 |
205.8 |
30.1 |
| N8 |
C9 |
H92 |
H91 |
236.7 |
240.0 |
| H92 |
C9 |
N8 |
S7 |
23.2 |
60.0 |
| H92 |
C9 |
N8 |
HN8 |
143.2 |
240.0 |
| C11 |
C10 |
C9 |
N8 |
268.6 |
89.7 |
| C11 |
C10 |
C9 |
H91 |
145.8 |
329.7 |
| C11 |
C10 |
C9 |
H92 |
28.7 |
209.7 |
| C9 |
C10 |
C11 |
S14 |
177.4 |
180.3 |
| C11 |
C10 |
S14 |
C13 |
0.5 |
0.2 |
| C12 |
C11 |
C10 |
H11 |
180.0 |
179.5 |
| C10 |
C11 |
C12 |
C13 |
0.4 |
0.5 |
| C10 |
C11 |
C12 |
H12 |
180.4 |
180.3 |
| S14 |
C10 |
C9 |
N8 |
85.8 |
270.1 |
| S14 |
C10 |
C9 |
H91 |
322.9 |
150.0 |
| S14 |
C10 |
C9 |
H92 |
205.8 |
30.1 |
| C9 |
C10 |
S14 |
C11 |
182.6 |
179.7 |
| S14 |
C10 |
C11 |
C12 |
359.4 |
359.6 |
| S14 |
C10 |
C11 |
H11 |
179.4 |
180.1 |
| C12 |
C13 |
S14 |
C10 |
359.7 |
360.0 |
| C10 |
S14 |
C13 |
H13 |
179.8 |
179.9 |
| C12 |
C11 |
C10 |
S14 |
359.4 |
359.6 |
| C10 |
C11 |
C12 |
H11 |
180.0 |
180.5 |
| C13 |
C12 |
C11 |
H12 |
180.0 |
180.2 |
| C11 |
C12 |
C13 |
S14 |
360.0 |
359.7 |
| C11 |
C12 |
C13 |
H13 |
180.0 |
179.8 |
| H11 |
C11 |
C10 |
S14 |
179.4 |
180.1 |
| C10 |
C11 |
H11 |
C12 |
180.0 |
179.5 |
| H11 |
C11 |
C12 |
C13 |
180.4 |
180.0 |
| H11 |
C11 |
C12 |
H12 |
0.4 |
359.8 |
| C10 |
S14 |
C13 |
C12 |
359.7 |
360.0 |
| C13 |
C12 |
C11 |
H11 |
180.4 |
180.0 |
| C11 |
C12 |
C13 |
H12 |
180.0 |
179.8 |
| S14 |
C13 |
C12 |
H13 |
180.0 |
179.9 |
| H12 |
C12 |
C11 |
H11 |
0.4 |
359.8 |
| C11 |
C12 |
H12 |
C13 |
180.0 |
180.2 |
| H12 |
C12 |
C13 |
S14 |
180.0 |
180.0 |
| H12 |
C12 |
C13 |
H13 |
360.0 |
0.0 |
| S14 |
C13 |
C12 |
H12 |
180.0 |
180.0 |
| C12 |
C13 |
S14 |
H13 |
180.0 |
180.1 |
| H13 |
C13 |
C12 |
H12 |
360.0 |
0.0 |
| C12 |
C13 |
H13 |
S14 |
180.0 |
179.9 |
| O1A |
S1 |
C3 |
C4 |
86.6 |
337.1 |
| O1A |
S1 |
C3 |
S2 |
268.1 |
157.4 |
| C3 |
S1 |
O1A |
O2A |
113.2 |
236.9 |
| C3 |
S1 |
O1A |
N21 |
240.5 |
113.7 |
| O2A |
S1 |
O1A |
N21 |
127.3 |
236.8 |
| O1A |
S1 |
N21 |
HNL1 |
329.2 |
292.6 |
| O1A |
S1 |
N21 |
HNL2 |
209.2 |
112.3 |
| O2A |
S1 |
C3 |
C4 |
202.5 |
202.3 |
| O2A |
S1 |
C3 |
S2 |
23.9 |
22.6 |
| C3 |
S1 |
O2A |
O1A |
245.0 |
123.1 |
| C3 |
S1 |
O2A |
N21 |
118.5 |
246.3 |
| O1A |
S1 |
O2A |
N21 |
233.5 |
123.2 |
| O2A |
S1 |
N21 |
HNL1 |
204.7 |
67.4 |
| O2A |
S1 |
N21 |
HNL2 |
84.7 |
247.2 |
| N21 |
S1 |
C3 |
C4 |
324.6 |
89.7 |
| N21 |
S1 |
C3 |
S2 |
146.1 |
270.0 |
| C3 |
S1 |
N21 |
O1A |
119.0 |
247.4 |
| C3 |
S1 |
N21 |
O2A |
243.5 |
112.6 |
| O1A |
S1 |
N21 |
O2A |
124.6 |
225.1 |
| HNL1 |
N21 |
S1 |
HNL2 |
120.0 |
180.2 |
| S1 |
N21 |
HNL1 |
HNL2 |
240.0 |
179.8 |
| S1 |
N21 |
HNL2 |
HNL1 |
120.0 |
180.2 |
| C5 |
C4 |
C3 |
S2 |
0.2 |
359.6 |
| C3 |
C4 |
C5 |
H4 |
180.0 |
180.4 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
180.2 |
| C4 |
C5 |
C6 |
S2 |
360.0 |
359.7 |
| C4 |
C5 |
C6 |
S7 |
180.3 |
179.7 |
| H4 |
C4 |
C3 |
S2 |
180.2 |
180.1 |
| C3 |
C4 |
H4 |
C5 |
180.0 |
179.5 |
| H4 |
C4 |
C5 |
C6 |
179.9 |
180.0 |
| H4 |
C4 |
C5 |
H5 |
359.9 |
359.8 |
| C3 |
S2 |
C6 |
C5 |
0.1 |
0.0 |
| C6 |
C5 |
C4 |
H4 |
179.9 |
180.0 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
179.8 |
| S2 |
C6 |
C5 |
S7 |
179.7 |
180.0 |
| C5 |
C6 |
S7 |
O3B |
62.0 |
202.6 |
| C5 |
C6 |
S7 |
O4B |
180.5 |
337.4 |
| C5 |
C6 |
S7 |
N8 |
298.5 |
90.0 |
| H5 |
C5 |
C4 |
H4 |
359.9 |
359.8 |
| C4 |
C5 |
H5 |
C6 |
180.0 |
180.2 |
| H5 |
C5 |
C6 |
S2 |
180.0 |
180.0 |
| H5 |
C5 |
C6 |
S7 |
0.3 |
360.0 |
| S2 |
C6 |
C5 |
H5 |
180.0 |
180.0 |
| C5 |
C6 |
S2 |
S7 |
180.3 |
180.0 |
| S2 |
C6 |
S7 |
O3B |
242.4 |
22.6 |
| S2 |
C6 |
S7 |
O4B |
0.9 |
157.4 |
| S2 |
C6 |
S7 |
N8 |
118.9 |
270.0 |
| C9 |
N8 |
S7 |
C6 |
72.5 |
60.0 |
| S7 |
C6 |
C5 |
H5 |
0.3 |
360.0 |
| C5 |
C6 |
S7 |
S2 |
179.7 |
180.0 |
| O3B |
S7 |
C6 |
O4B |
241.5 |
225.2 |
| O3B |
S7 |
C6 |
N8 |
123.5 |
112.6 |
| O4B |
S7 |
C6 |
N8 |
242.0 |
247.4 |
| C6 |
S7 |
N8 |
HN8 |
312.5 |
240.0 |
| C9 |
N8 |
S7 |
O3B |
313.1 |
307.4 |
| C6 |
S7 |
O3B |
O4B |
117.4 |
123.1 |
| C6 |
S7 |
O3B |
N8 |
239.5 |
246.3 |
| O4B |
S7 |
O3B |
N8 |
122.1 |
123.2 |
| O3B |
S7 |
N8 |
HN8 |
193.1 |
127.4 |
| C9 |
N8 |
S7 |
O4B |
190.2 |
172.6 |
| C6 |
S7 |
O4B |
O3B |
243.3 |
236.9 |
| C6 |
S7 |
O4B |
N8 |
118.3 |
113.7 |
| O3B |
S7 |
O4B |
N8 |
234.9 |
236.8 |
| O4B |
S7 |
N8 |
HN8 |
70.3 |
352.6 |
| S7 |
N8 |
C9 |
H91 |
266.1 |
300.0 |
| S7 |
N8 |
C9 |
H92 |
23.2 |
60.0 |
| C9 |
N8 |
S7 |
HN8 |
120.0 |
180.0 |
| C6 |
S7 |
N8 |
O3B |
119.4 |
112.6 |
| C6 |
S7 |
N8 |
O4B |
242.3 |
247.4 |
| O3B |
S7 |
N8 |
O4B |
122.8 |
134.8 |
| HN8 |
N8 |
C9 |
H91 |
26.1 |
120.0 |
| HN8 |
N8 |
C9 |
H92 |
143.2 |
240.0 |
| C9 |
N8 |
HN8 |
S7 |
233.6 |
180.0 |