PDB Chemical Component PTR
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 PTR
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N |
CA |
1.479 |
1.468 |
| N |
H |
1.021 |
1.009 |
| N |
H2 |
1.020 |
1.009 |
| CA |
C |
1.521 |
1.508 |
| CA |
CB |
1.532 |
1.529 |
| CA |
HA |
1.115 |
1.090 |
| C |
O |
1.248 |
1.207 |
| C |
OXT |
1.253 |
1.342 |
| OXT |
HXT |
0.949 |
0.967 |
| CB |
CG |
1.518 |
1.507 |
| CB |
HB2 |
1.116 |
1.089 |
| CB |
HB3 |
1.115 |
1.090 |
| CG |
CD1 |
1.399 |
1.382 |
| CG |
CD2 |
1.404 |
1.382 |
| CD1 |
CE1 |
1.408 |
1.381 |
| CD1 |
HD1 |
1.103 |
1.079 |
| CD2 |
CE2 |
1.409 |
1.381 |
| CD2 |
HD2 |
1.104 |
1.080 |
| CE1 |
CZ |
1.406 |
1.387 |
| CE1 |
HE1 |
1.102 |
1.081 |
| CE2 |
CZ |
1.394 |
1.387 |
| CE2 |
HE2 |
1.103 |
1.079 |
| CZ |
OH |
1.438 |
1.359 |
| OH |
P |
1.516 |
1.609 |
| P |
O1P |
1.451 |
1.481 |
| P |
O2P |
1.456 |
1.610 |
| P |
O3P |
1.471 |
1.608 |
| O2P |
HO2P |
0.950 |
0.966 |
| O3P |
HO3P |
0.950 |
0.967 |
Bond Angles for PTR
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| CA |
N |
H |
108.2 |
106.7 |
| CA |
N |
H2 |
112.7 |
106.8 |
| N |
CA |
C |
108.2 |
109.5 |
| N |
CA |
CB |
110.0 |
109.5 |
| N |
CA |
HA |
110.7 |
109.4 |
| H |
N |
H2 |
112.6 |
106.7 |
| C |
CA |
CB |
111.4 |
109.5 |
| C |
CA |
HA |
109.2 |
109.4 |
| CA |
C |
O |
118.5 |
120.0 |
| CA |
C |
OXT |
117.6 |
120.0 |
| CB |
CA |
HA |
107.3 |
109.5 |
| CA |
CB |
CG |
115.7 |
109.5 |
| CA |
CB |
HB2 |
109.9 |
109.5 |
| CA |
CB |
HB3 |
109.9 |
109.4 |
| O |
C |
OXT |
123.9 |
120.0 |
| C |
OXT |
HXT |
117.5 |
120.0 |
| CG |
CB |
HB2 |
110.0 |
109.5 |
| CG |
CB |
HB3 |
110.0 |
109.5 |
| CB |
CG |
CD1 |
120.8 |
119.9 |
| CB |
CG |
CD2 |
120.8 |
119.9 |
| HB2 |
CB |
HB3 |
100.2 |
109.5 |
| CD1 |
CG |
CD2 |
118.3 |
120.1 |
| CG |
CD1 |
CE1 |
121.1 |
120.0 |
| CG |
CD1 |
HD1 |
119.0 |
120.0 |
| CG |
CD2 |
CE2 |
121.6 |
120.0 |
| CG |
CD2 |
HD2 |
119.0 |
120.0 |
| CE1 |
CD1 |
HD1 |
119.8 |
120.0 |
| CD1 |
CE1 |
CZ |
119.4 |
119.9 |
| CD1 |
CE1 |
HE1 |
120.3 |
120.0 |
| CE2 |
CD2 |
HD2 |
119.4 |
119.9 |
| CD2 |
CE2 |
CZ |
119.2 |
119.9 |
| CD2 |
CE2 |
HE2 |
120.9 |
120.1 |
| CZ |
CE1 |
HE1 |
120.2 |
120.1 |
| CE1 |
CZ |
CE2 |
120.4 |
119.9 |
| CE1 |
CZ |
OH |
118.5 |
120.0 |
| CZ |
CE2 |
HE2 |
119.9 |
120.0 |
| CE2 |
CZ |
OH |
121.1 |
120.0 |
| CZ |
OH |
P |
125.9 |
106.8 |
| OH |
P |
O1P |
113.4 |
109.4 |
| OH |
P |
O2P |
98.3 |
109.5 |
| OH |
P |
O3P |
109.6 |
109.5 |
| O1P |
P |
O2P |
111.2 |
109.4 |
| O1P |
P |
O3P |
113.3 |
109.4 |
| O2P |
P |
O3P |
110.0 |
109.5 |
| P |
O2P |
HO2P |
98.2 |
106.9 |
| P |
O3P |
HO3P |
109.6 |
106.8 |
Torsion Angles for PTR
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| H |
N |
CA |
H2 |
125.2 |
246.2 |
| C |
CA |
N |
CB |
121.9 |
120.1 |
| C |
CA |
N |
HA |
240.4 |
240.1 |
| N |
CA |
C |
O |
169.1 |
329.9 |
| N |
CA |
C |
OXT |
350.2 |
150.0 |
| CB |
CA |
N |
HA |
118.4 |
120.0 |
| N |
CA |
CB |
CG |
68.4 |
300.0 |
| N |
CA |
CB |
HB2 |
193.7 |
60.0 |
| N |
CA |
CB |
HB3 |
303.1 |
180.0 |
| CA |
N |
H |
H2 |
234.8 |
113.8 |
| H |
N |
CA |
C |
180.0 |
60.0 |
| H |
N |
CA |
CB |
58.0 |
300.0 |
| H |
N |
CA |
HA |
299.6 |
180.0 |
| CA |
N |
H2 |
H |
122.8 |
246.2 |
| H2 |
N |
CA |
C |
54.8 |
173.8 |
| H2 |
N |
CA |
CB |
292.8 |
53.8 |
| H2 |
N |
CA |
HA |
174.4 |
293.7 |
| C |
CA |
N |
H |
180.0 |
60.0 |
| C |
CA |
N |
H2 |
54.8 |
173.8 |
| N |
CA |
C |
CB |
239.0 |
240.0 |
| N |
CA |
C |
HA |
120.5 |
119.9 |
| CB |
CA |
C |
HA |
241.6 |
240.0 |
| C |
CA |
CB |
CG |
308.4 |
180.0 |
| C |
CA |
CB |
HB2 |
73.7 |
300.0 |
| C |
CA |
CB |
HB3 |
183.0 |
60.0 |
| O |
C |
CA |
OXT |
178.9 |
180.0 |
| CA |
C |
OXT |
HXT |
180.0 |
179.9 |
| CB |
CA |
N |
H |
58.0 |
300.0 |
| CB |
CA |
N |
H2 |
292.8 |
53.8 |
| N |
CA |
CB |
C |
120.0 |
120.0 |
| N |
CA |
CB |
HA |
239.5 |
240.0 |
| C |
CA |
CB |
HA |
119.5 |
120.0 |
| CB |
CA |
C |
O |
290.2 |
90.0 |
| CB |
CA |
C |
OXT |
111.3 |
270.0 |
| CG |
CB |
CA |
HB2 |
234.7 |
240.0 |
| CG |
CB |
CA |
HB3 |
125.3 |
120.0 |
| CA |
CB |
CG |
CD1 |
266.5 |
90.0 |
| CA |
CB |
CG |
CD2 |
90.7 |
269.7 |
| HB2 |
CB |
CA |
HB3 |
250.6 |
240.0 |
| HA |
CA |
N |
H |
299.6 |
180.0 |
| HA |
CA |
N |
H2 |
174.4 |
293.7 |
| N |
CA |
HA |
C |
241.0 |
240.0 |
| N |
CA |
HA |
CB |
120.0 |
120.0 |
| C |
CA |
HA |
CB |
239.1 |
240.0 |
| HA |
CA |
C |
O |
48.6 |
210.0 |
| HA |
CA |
C |
OXT |
229.7 |
30.0 |
| HA |
CA |
CB |
CG |
188.8 |
60.0 |
| HA |
CA |
CB |
HB2 |
314.1 |
180.0 |
| HA |
CA |
CB |
HB3 |
63.5 |
300.0 |
| O |
C |
CA |
CB |
290.2 |
90.0 |
| O |
C |
CA |
HA |
48.6 |
210.0 |
| CA |
C |
O |
OXT |
181.2 |
180.0 |
| O |
C |
OXT |
HXT |
1.2 |
360.0 |
| OXT |
C |
CA |
CB |
111.3 |
270.0 |
| OXT |
C |
CA |
HA |
229.7 |
30.0 |
| CA |
C |
OXT |
O |
178.8 |
180.0 |
| CG |
CB |
CA |
HA |
188.8 |
60.0 |
| CA |
CB |
CG |
HB2 |
125.3 |
120.0 |
| CA |
CB |
CG |
HB3 |
234.7 |
240.0 |
| HB2 |
CB |
CG |
HB3 |
109.4 |
120.0 |
| CD1 |
CG |
CB |
CD2 |
175.8 |
180.4 |
| CB |
CG |
CD1 |
CE1 |
184.7 |
179.9 |
| CB |
CG |
CD1 |
HD1 |
4.7 |
360.0 |
| CB |
CG |
CD2 |
CE2 |
175.2 |
179.7 |
| CB |
CG |
CD2 |
HD2 |
355.2 |
0.4 |
| HB2 |
CB |
CA |
HA |
314.1 |
180.0 |
| CA |
CB |
HB2 |
CG |
231.5 |
240.0 |
| CA |
CB |
HB2 |
HB3 |
115.7 |
120.0 |
| CG |
CB |
HB2 |
HB3 |
244.2 |
240.0 |
| HB2 |
CB |
CG |
CD1 |
141.2 |
330.0 |
| HB2 |
CB |
CG |
CD2 |
325.4 |
149.6 |
| HB3 |
CB |
CA |
HA |
63.5 |
300.0 |
| CA |
CB |
HB3 |
CG |
128.6 |
120.0 |
| CA |
CB |
HB3 |
HB2 |
244.3 |
240.0 |
| CG |
CB |
HB3 |
HB2 |
115.8 |
120.0 |
| HB3 |
CB |
CG |
CD1 |
31.8 |
210.0 |
| HB3 |
CB |
CG |
CD2 |
216.0 |
29.6 |
| CD1 |
CG |
CB |
HB2 |
141.2 |
330.0 |
| CD1 |
CG |
CB |
HB3 |
31.8 |
210.0 |
| CB |
CG |
CD1 |
CD2 |
184.1 |
179.6 |
| CD1 |
CG |
CD2 |
CE2 |
359.3 |
359.3 |
| CD1 |
CG |
CD2 |
HD2 |
179.3 |
180.0 |
| CE1 |
CD1 |
CG |
HD1 |
180.0 |
179.9 |
| CG |
CD1 |
CE1 |
CZ |
359.9 |
0.0 |
| CG |
CD1 |
CE1 |
HE1 |
179.9 |
179.9 |
| CD2 |
CG |
CB |
HB2 |
325.4 |
149.6 |
| CD2 |
CG |
CB |
HB3 |
216.0 |
29.6 |
| CB |
CG |
CD2 |
CD1 |
175.9 |
180.4 |
| CD2 |
CG |
CD1 |
CE1 |
0.6 |
0.3 |
| CD2 |
CG |
CD1 |
HD1 |
180.6 |
180.4 |
| CE2 |
CD2 |
CG |
HD2 |
180.0 |
179.4 |
| CG |
CD2 |
CE2 |
CZ |
0.2 |
0.7 |
| CG |
CD2 |
CE2 |
HE2 |
180.2 |
180.3 |
| CE1 |
CD1 |
CG |
CD2 |
0.6 |
0.3 |
| CG |
CD1 |
CE1 |
HD1 |
180.0 |
180.0 |
| CZ |
CE1 |
CD1 |
HE1 |
180.0 |
180.1 |
| CD1 |
CE1 |
CZ |
CE2 |
359.6 |
360.0 |
| CD1 |
CE1 |
CZ |
OH |
177.9 |
180.0 |
| HD1 |
CD1 |
CG |
CD2 |
180.6 |
180.4 |
| CG |
CD1 |
HD1 |
CE1 |
180.0 |
180.0 |
| HD1 |
CD1 |
CE1 |
CZ |
179.9 |
180.0 |
| HD1 |
CD1 |
CE1 |
HE1 |
359.9 |
359.9 |
| CG |
CD2 |
CE2 |
HD2 |
180.0 |
180.6 |
| CE1 |
CZ |
CE2 |
CD2 |
0.3 |
359.7 |
| CZ |
CE2 |
CD2 |
HE2 |
180.0 |
180.3 |
| CD2 |
CE2 |
CZ |
OH |
182.1 |
179.7 |
| CG |
CD2 |
HD2 |
CE2 |
180.0 |
179.4 |
| HD2 |
CD2 |
CE2 |
CZ |
180.2 |
180.0 |
| HD2 |
CD2 |
CE2 |
HE2 |
0.2 |
359.7 |
| CZ |
CE1 |
CD1 |
HD1 |
179.9 |
180.0 |
| CD1 |
CE1 |
CZ |
HE1 |
180.0 |
179.9 |
| CD2 |
CE2 |
CZ |
CE1 |
0.3 |
359.7 |
| CE1 |
CZ |
CE2 |
HE2 |
180.3 |
180.0 |
| CE2 |
CZ |
CE1 |
OH |
181.7 |
180.0 |
| CE1 |
CZ |
OH |
P |
245.5 |
89.9 |
| HE1 |
CE1 |
CD1 |
HD1 |
359.9 |
359.9 |
| CD1 |
CE1 |
HE1 |
CZ |
180.0 |
180.1 |
| HE1 |
CE1 |
CZ |
CE2 |
179.6 |
180.1 |
| HE1 |
CE1 |
CZ |
OH |
357.9 |
0.1 |
| CZ |
CE2 |
CD2 |
HD2 |
180.2 |
180.0 |
| CD2 |
CE2 |
CZ |
HE2 |
180.0 |
179.7 |
| CE2 |
CZ |
CE1 |
HE1 |
179.6 |
180.1 |
| CE1 |
CZ |
CE2 |
OH |
178.2 |
180.0 |
| CE2 |
CZ |
OH |
P |
63.8 |
269.9 |
| HE2 |
CE2 |
CD2 |
HD2 |
0.2 |
359.7 |
| CD2 |
CE2 |
HE2 |
CZ |
180.0 |
180.3 |
| HE2 |
CE2 |
CZ |
OH |
2.1 |
0.0 |
| OH |
CZ |
CE1 |
HE1 |
357.9 |
0.1 |
| CE1 |
CZ |
OH |
CE2 |
181.8 |
180.0 |
| OH |
CZ |
CE2 |
HE2 |
2.1 |
0.0 |
| CZ |
OH |
P |
O1P |
309.6 |
60.0 |
| CZ |
OH |
P |
O2P |
192.1 |
179.9 |
| CZ |
OH |
P |
O3P |
77.3 |
300.1 |
| O1P |
P |
OH |
O2P |
117.5 |
240.1 |
| O1P |
P |
OH |
O3P |
232.3 |
119.9 |
| O2P |
P |
OH |
O3P |
114.7 |
239.9 |
| OH |
P |
O2P |
HO2P |
180.0 |
180.0 |
| OH |
P |
O3P |
HO3P |
180.0 |
299.9 |
| OH |
P |
O1P |
O2P |
250.3 |
120.0 |
| OH |
P |
O1P |
O3P |
125.8 |
240.0 |
| O2P |
P |
O1P |
O3P |
235.4 |
120.0 |
| O1P |
P |
O2P |
HO2P |
60.9 |
299.9 |
| O1P |
P |
O3P |
HO3P |
307.8 |
180.0 |
| OH |
P |
O2P |
O1P |
119.2 |
240.1 |
| OH |
P |
O2P |
O3P |
245.6 |
120.1 |
| O1P |
P |
O2P |
O3P |
126.4 |
240.0 |
| O2P |
P |
O3P |
HO3P |
73.0 |
60.1 |
| OH |
P |
O3P |
O1P |
232.2 |
119.9 |
| OH |
P |
O3P |
O2P |
107.0 |
239.9 |
| O1P |
P |
O3P |
O2P |
234.8 |
120.0 |
| O3P |
P |
O2P |
HO2P |
294.4 |
59.9 |
| HO2P |
O2P |
P |
O3P |
294.4 |
59.9 |