PDB Chemical Component PTU
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 PTU
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N1 |
C |
1.478 |
1.374 |
| N1 |
HN11 |
1.020 |
0.970 |
| N1 |
HN12 |
1.020 |
0.969 |
| C |
S |
1.803 |
1.762 |
| C |
N2 |
1.353 |
1.313 |
| S |
C1' |
1.813 |
1.809 |
| N2 |
C1 |
1.360 |
1.369 |
| C1 |
C2 |
1.430 |
1.395 |
| C1 |
C6 |
1.433 |
1.396 |
| C2 |
C3 |
1.421 |
1.379 |
| C2 |
H21 |
1.103 |
1.080 |
| C3 |
C4 |
1.418 |
1.383 |
| C3 |
H31 |
1.103 |
1.081 |
| C4 |
C5 |
1.415 |
1.383 |
| C4 |
H41 |
1.104 |
1.080 |
| C5 |
C6 |
1.417 |
1.380 |
| C5 |
H51 |
1.103 |
1.080 |
| C6 |
H61 |
1.103 |
1.081 |
| C1' |
C2' |
1.517 |
1.530 |
| C1' |
H1'1 |
1.115 |
1.090 |
| C1' |
H1'2 |
1.115 |
1.089 |
| C2' |
H2'1 |
1.115 |
1.090 |
| C2' |
H2'2 |
1.116 |
1.090 |
| C2' |
H2'3 |
1.114 |
1.090 |
Bond Angles for PTU
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C |
N1 |
HN11 |
118.8 |
120.0 |
| C |
N1 |
HN12 |
108.9 |
120.0 |
| N1 |
C |
S |
118.8 |
120.0 |
| N1 |
C |
N2 |
116.7 |
120.0 |
| HN11 |
N1 |
HN12 |
108.8 |
120.0 |
| S |
C |
N2 |
124.5 |
120.0 |
| C |
S |
C1' |
109.9 |
100.0 |
| C |
N2 |
C1 |
138.2 |
120.0 |
| S |
C1' |
C2' |
109.3 |
109.5 |
| S |
C1' |
H1'1 |
112.3 |
109.5 |
| S |
C1' |
H1'2 |
112.2 |
109.5 |
| N2 |
C1 |
C2 |
117.1 |
120.2 |
| N2 |
C1 |
C6 |
124.4 |
120.1 |
| C2 |
C1 |
C6 |
118.5 |
119.7 |
| C1 |
C2 |
C3 |
120.7 |
119.9 |
| C1 |
C2 |
H21 |
120.0 |
120.0 |
| C1 |
C6 |
C5 |
120.6 |
119.9 |
| C1 |
C6 |
H61 |
120.3 |
120.0 |
| C3 |
C2 |
H21 |
119.4 |
120.1 |
| C2 |
C3 |
C4 |
119.9 |
120.2 |
| C2 |
C3 |
H31 |
120.2 |
119.9 |
| C4 |
C3 |
H31 |
119.9 |
119.9 |
| C3 |
C4 |
C5 |
120.0 |
120.2 |
| C3 |
C4 |
H41 |
120.1 |
119.9 |
| C5 |
C4 |
H41 |
119.9 |
119.8 |
| C4 |
C5 |
C6 |
120.3 |
120.2 |
| C4 |
C5 |
H51 |
119.8 |
119.9 |
| C6 |
C5 |
H51 |
120.0 |
119.9 |
| C5 |
C6 |
H61 |
119.2 |
120.1 |
| C2' |
C1' |
H1'1 |
112.3 |
109.5 |
| C2' |
C1' |
H1'2 |
112.3 |
109.5 |
| C1' |
C2' |
H2'1 |
109.3 |
109.5 |
| C1' |
C2' |
H2'2 |
112.2 |
109.5 |
| C1' |
C2' |
H2'3 |
112.3 |
109.5 |
| H1'1 |
C1' |
H1'2 |
98.2 |
109.4 |
| H2'1 |
C2' |
H2'2 |
112.2 |
109.4 |
| H2'1 |
C2' |
H2'3 |
112.3 |
109.5 |
| H2'2 |
C2' |
H2'3 |
98.2 |
109.4 |
Torsion Angles for PTU
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| HN11 |
N1 |
C |
HN12 |
125.2 |
180.0 |
| S |
C |
N1 |
N2 |
180.0 |
180.0 |
| N1 |
C |
S |
C1' |
138.5 |
180.0 |
| N1 |
C |
N2 |
C1 |
159.3 |
353.8 |
| C |
N1 |
HN11 |
HN12 |
234.8 |
180.0 |
| HN11 |
N1 |
C |
S |
180.0 |
352.0 |
| HN11 |
N1 |
C |
N2 |
359.9 |
171.9 |
| C |
N1 |
HN12 |
HN11 |
130.8 |
180.0 |
| HN12 |
N1 |
C |
S |
54.8 |
172.0 |
| HN12 |
N1 |
C |
N2 |
234.7 |
351.9 |
| S |
C |
N1 |
HN11 |
180.0 |
352.0 |
| S |
C |
N1 |
HN12 |
54.8 |
172.0 |
| N1 |
C |
S |
N2 |
180.0 |
180.0 |
| S |
C |
N2 |
C1 |
339.3 |
173.8 |
| C |
S |
C1' |
C2' |
136.4 |
180.0 |
| C |
S |
C1' |
H1'1 |
261.7 |
59.9 |
| C |
S |
C1' |
H1'2 |
11.2 |
300.0 |
| N2 |
C |
N1 |
HN11 |
359.9 |
171.9 |
| N2 |
C |
N1 |
HN12 |
234.7 |
351.9 |
| N1 |
C |
N2 |
S |
180.0 |
180.0 |
| N2 |
C |
S |
C1' |
318.6 |
0.0 |
| C |
N2 |
C1 |
C2 |
151.7 |
123.5 |
| C |
N2 |
C1 |
C6 |
331.8 |
303.1 |
| C1' |
S |
C |
N2 |
318.6 |
0.0 |
| C2' |
C1' |
S |
H1'1 |
234.7 |
120.0 |
| C2' |
C1' |
S |
H1'2 |
125.2 |
240.0 |
| S |
C1' |
C2' |
H2'1 |
180.0 |
180.0 |
| S |
C1' |
C2' |
H2'2 |
305.2 |
300.0 |
| S |
C1' |
C2' |
H2'3 |
54.7 |
60.0 |
| H1'1 |
C1' |
S |
H1'2 |
250.5 |
120.0 |
| C2 |
C1 |
N2 |
C6 |
179.9 |
180.4 |
| N2 |
C1 |
C2 |
C3 |
179.7 |
179.9 |
| N2 |
C1 |
C2 |
H21 |
359.7 |
359.9 |
| N2 |
C1 |
C6 |
C5 |
180.3 |
179.8 |
| N2 |
C1 |
C6 |
H61 |
0.3 |
0.4 |
| N2 |
C1 |
C2 |
C6 |
180.1 |
179.6 |
| C2 |
C1 |
C6 |
C5 |
0.4 |
359.5 |
| C2 |
C1 |
C6 |
H61 |
180.4 |
180.0 |
| C3 |
C2 |
C1 |
H21 |
180.0 |
180.0 |
| C1 |
C2 |
C3 |
C4 |
0.3 |
0.0 |
| C1 |
C2 |
C3 |
H31 |
180.3 |
180.0 |
| N2 |
C1 |
C6 |
C2 |
179.9 |
180.4 |
| C6 |
C1 |
C2 |
C3 |
359.6 |
0.3 |
| C6 |
C1 |
C2 |
H21 |
179.6 |
180.3 |
| C4 |
C5 |
C6 |
C1 |
359.8 |
0.5 |
| C1 |
C6 |
C5 |
H51 |
179.8 |
180.3 |
| C5 |
C6 |
C1 |
H61 |
180.0 |
179.5 |
| C3 |
C2 |
C1 |
C6 |
359.6 |
0.3 |
| C1 |
C2 |
C3 |
H21 |
180.0 |
180.0 |
| C4 |
C3 |
C2 |
H31 |
180.0 |
180.0 |
| C2 |
C3 |
C4 |
C5 |
359.9 |
359.9 |
| C2 |
C3 |
C4 |
H41 |
180.0 |
180.0 |
| H21 |
C2 |
C1 |
C6 |
179.6 |
180.3 |
| C1 |
C2 |
H21 |
C3 |
180.0 |
180.0 |
| H21 |
C2 |
C3 |
C4 |
180.2 |
180.0 |
| H21 |
C2 |
C3 |
H31 |
0.3 |
360.0 |
| C4 |
C3 |
C2 |
H21 |
180.2 |
180.0 |
| C2 |
C3 |
C4 |
H31 |
180.0 |
180.0 |
| C5 |
C4 |
C3 |
H41 |
180.0 |
179.9 |
| C3 |
C4 |
C5 |
C6 |
0.0 |
359.8 |
| C3 |
C4 |
C5 |
H51 |
180.1 |
180.0 |
| H31 |
C3 |
C2 |
H21 |
0.3 |
360.0 |
| C2 |
C3 |
H31 |
C4 |
180.0 |
180.0 |
| H31 |
C3 |
C4 |
C5 |
179.9 |
180.0 |
| H31 |
C3 |
C4 |
H41 |
359.9 |
0.0 |
| C1 |
C6 |
C5 |
C4 |
359.8 |
0.5 |
| C5 |
C4 |
C3 |
H31 |
179.9 |
180.0 |
| C3 |
C4 |
C5 |
H41 |
180.0 |
180.1 |
| C6 |
C5 |
C4 |
H51 |
180.0 |
179.8 |
| C4 |
C5 |
C6 |
H61 |
179.8 |
180.0 |
| H41 |
C4 |
C3 |
H31 |
359.9 |
0.0 |
| C3 |
C4 |
H41 |
C5 |
180.0 |
179.9 |
| H41 |
C4 |
C5 |
C6 |
180.0 |
179.8 |
| H41 |
C4 |
C5 |
H51 |
0.0 |
359.9 |
| C1 |
C6 |
C5 |
H61 |
180.0 |
180.5 |
| C6 |
C5 |
C4 |
H41 |
180.0 |
179.8 |
| C4 |
C5 |
C6 |
H51 |
180.0 |
180.2 |
| H51 |
C5 |
C4 |
H41 |
0.0 |
359.9 |
| C4 |
C5 |
H51 |
C6 |
180.0 |
179.8 |
| H51 |
C5 |
C6 |
H61 |
359.8 |
359.8 |
| C1 |
C6 |
H61 |
C5 |
180.0 |
179.5 |
| H61 |
C6 |
C5 |
H51 |
359.8 |
359.8 |
| S |
C1' |
C2' |
H1'1 |
125.3 |
239.9 |
| S |
C1' |
C2' |
H1'2 |
234.8 |
120.0 |
| H1'1 |
C1' |
C2' |
H1'2 |
109.5 |
240.1 |
| H2'1 |
C2' |
C1' |
H2'2 |
234.8 |
240.0 |
| H2'1 |
C2' |
C1' |
H2'3 |
125.3 |
120.0 |
| H2'2 |
C2' |
C1' |
H2'3 |
250.5 |
240.0 |
| S |
C1' |
H1'1 |
C2' |
236.3 |
120.1 |
| S |
C1' |
H1'1 |
H1'2 |
118.2 |
240.0 |
| C2' |
C1' |
H1'1 |
H1'2 |
241.8 |
120.0 |
| H1'1 |
C1' |
C2' |
H2'1 |
54.8 |
300.1 |
| H1'1 |
C1' |
C2' |
H2'2 |
180.0 |
60.1 |
| H1'1 |
C1' |
C2' |
H2'3 |
289.5 |
180.0 |
| S |
C1' |
H1'2 |
C2' |
123.6 |
240.0 |
| S |
C1' |
H1'2 |
H1'1 |
241.8 |
120.0 |
| C2' |
C1' |
H1'2 |
H1'1 |
118.2 |
240.0 |
| H1'2 |
C1' |
C2' |
H2'1 |
305.3 |
60.0 |
| H1'2 |
C1' |
C2' |
H2'2 |
70.4 |
180.0 |
| H1'2 |
C1' |
C2' |
H2'3 |
180.0 |
300.0 |
| H2'1 |
C2' |
C1' |
H1'1 |
54.8 |
300.1 |
| H2'1 |
C2' |
C1' |
H1'2 |
305.3 |
60.0 |
| C1' |
C2' |
H2'1 |
H2'2 |
125.2 |
120.0 |
| C1' |
C2' |
H2'1 |
H2'3 |
234.7 |
240.0 |
| H2'2 |
C2' |
H2'1 |
H2'3 |
109.5 |
119.9 |
| H2'2 |
C2' |
C1' |
H1'1 |
180.0 |
60.1 |
| H2'2 |
C2' |
C1' |
H1'2 |
70.4 |
180.0 |
| C1' |
C2' |
H2'2 |
H2'1 |
236.4 |
240.0 |
| C1' |
C2' |
H2'2 |
H2'3 |
118.2 |
120.0 |
| H2'1 |
C2' |
H2'2 |
H2'3 |
241.8 |
240.0 |
| H2'3 |
C2' |
C1' |
H1'1 |
289.5 |
180.0 |
| H2'3 |
C2' |
C1' |
H1'2 |
180.0 |
300.0 |
| C1' |
C2' |
H2'3 |
H2'1 |
123.7 |
120.0 |
| C1' |
C2' |
H2'3 |
H2'2 |
241.8 |
240.0 |
| H2'1 |
C2' |
H2'3 |
H2'2 |
118.1 |
119.9 |