PDB Chemical Component PHD
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 PHD
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N |
CA |
1.437 |
1.469 |
| N |
H2 |
1.021 |
1.009 |
| N |
H |
1.020 |
1.008 |
| CA |
C |
1.538 |
1.506 |
| CA |
CB |
1.542 |
1.529 |
| CA |
HA |
1.114 |
1.091 |
| C |
O |
1.240 |
1.208 |
| C |
OXT |
1.323 |
1.342 |
| CB |
CG |
1.601 |
1.506 |
| CB |
HB2 |
1.115 |
1.091 |
| CB |
HB3 |
1.115 |
1.090 |
| CG |
OD1 |
1.326 |
1.342 |
| CG |
OD2 |
1.207 |
1.207 |
| OD1 |
P |
1.650 |
1.609 |
| P |
OP1 |
1.508 |
1.479 |
| P |
OP2 |
1.458 |
1.610 |
| P |
OP3 |
1.512 |
1.609 |
| OP2 |
H2O |
0.949 |
0.967 |
| OP3 |
H3O |
0.949 |
0.967 |
| OXT |
HXT |
0.949 |
0.967 |
Bond Angles for PHD
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| CA |
N |
H2 |
107.9 |
106.7 |
| CA |
N |
H |
112.9 |
106.7 |
| N |
CA |
C |
107.8 |
109.5 |
| N |
CA |
CB |
103.7 |
109.5 |
| N |
CA |
HA |
114.3 |
109.4 |
| H2 |
N |
H |
112.7 |
106.7 |
| C |
CA |
CB |
109.9 |
109.6 |
| C |
CA |
HA |
108.6 |
109.4 |
| CA |
C |
O |
118.0 |
120.0 |
| CA |
C |
OXT |
118.9 |
120.0 |
| CB |
CA |
HA |
112.4 |
109.5 |
| CA |
CB |
CG |
111.4 |
109.5 |
| CA |
CB |
HB2 |
111.5 |
109.5 |
| CA |
CB |
HB3 |
111.5 |
109.5 |
| O |
C |
OXT |
123.1 |
120.0 |
| C |
OXT |
HXT |
118.9 |
120.0 |
| CG |
CB |
HB2 |
111.5 |
109.5 |
| CG |
CB |
HB3 |
111.5 |
109.5 |
| CB |
CG |
OD1 |
116.8 |
120.1 |
| CB |
CG |
OD2 |
116.0 |
120.0 |
| HB2 |
CB |
HB3 |
98.8 |
109.4 |
| OD1 |
CG |
OD2 |
126.3 |
119.9 |
| CG |
OD1 |
P |
132.1 |
120.0 |
| OD1 |
P |
OP1 |
104.3 |
109.5 |
| OD1 |
P |
OP2 |
112.8 |
109.5 |
| OD1 |
P |
OP3 |
104.9 |
109.5 |
| OP1 |
P |
OP2 |
110.3 |
109.4 |
| OP1 |
P |
OP3 |
114.4 |
109.5 |
| OP2 |
P |
OP3 |
110.0 |
109.5 |
| P |
OP2 |
H2O |
112.8 |
106.8 |
| P |
OP3 |
H3O |
104.9 |
106.8 |
Torsion Angles for PHD
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| H2 |
N |
CA |
H |
125.2 |
113.8 |
| C |
CA |
N |
CB |
116.5 |
120.2 |
| C |
CA |
N |
HA |
239.2 |
240.1 |
| N |
CA |
C |
O |
337.9 |
329.9 |
| N |
CA |
C |
OXT |
156.2 |
150.0 |
| CB |
CA |
N |
HA |
122.7 |
119.9 |
| N |
CA |
CB |
CG |
179.9 |
300.1 |
| N |
CA |
CB |
HB2 |
305.2 |
60.1 |
| N |
CA |
CB |
HB3 |
54.6 |
180.0 |
| CA |
N |
H2 |
H |
234.7 |
246.2 |
| H2 |
N |
CA |
C |
180.0 |
173.9 |
| H2 |
N |
CA |
CB |
63.4 |
53.7 |
| H2 |
N |
CA |
HA |
300.8 |
293.8 |
| CA |
N |
H |
H2 |
122.5 |
113.8 |
| H |
N |
CA |
C |
54.7 |
60.1 |
| H |
N |
CA |
CB |
298.2 |
299.9 |
| H |
N |
CA |
HA |
175.6 |
180.0 |
| C |
CA |
N |
H2 |
180.0 |
173.9 |
| C |
CA |
N |
H |
54.7 |
60.1 |
| N |
CA |
C |
CB |
247.6 |
239.9 |
| N |
CA |
C |
HA |
124.4 |
119.9 |
| CB |
CA |
C |
HA |
236.7 |
240.0 |
| C |
CA |
CB |
CG |
64.9 |
180.0 |
| C |
CA |
CB |
HB2 |
190.1 |
300.0 |
| C |
CA |
CB |
HB3 |
299.6 |
59.9 |
| O |
C |
CA |
OXT |
181.7 |
179.8 |
| CA |
C |
OXT |
HXT |
180.1 |
179.9 |
| CB |
CA |
N |
H2 |
63.4 |
53.7 |
| CB |
CA |
N |
H |
298.2 |
299.9 |
| N |
CA |
CB |
C |
115.1 |
120.1 |
| N |
CA |
CB |
HA |
236.1 |
240.1 |
| C |
CA |
CB |
HA |
121.0 |
120.0 |
| CB |
CA |
C |
O |
90.3 |
89.9 |
| CB |
CA |
C |
OXT |
268.6 |
270.1 |
| CG |
CB |
CA |
HB2 |
234.7 |
240.0 |
| CG |
CB |
CA |
HB3 |
125.3 |
120.1 |
| CA |
CB |
CG |
OD1 |
38.7 |
180.0 |
| CA |
CB |
CG |
OD2 |
208.4 |
359.9 |
| HB2 |
CB |
CA |
HB3 |
250.6 |
240.1 |
| HA |
CA |
N |
H2 |
300.8 |
293.8 |
| HA |
CA |
N |
H |
175.6 |
180.0 |
| N |
CA |
HA |
C |
239.6 |
240.1 |
| N |
CA |
HA |
CB |
117.8 |
119.9 |
| C |
CA |
HA |
CB |
238.2 |
239.9 |
| HA |
CA |
C |
O |
213.5 |
209.9 |
| HA |
CA |
C |
OXT |
31.9 |
30.1 |
| HA |
CA |
CB |
CG |
303.9 |
60.0 |
| HA |
CA |
CB |
HB2 |
69.1 |
180.0 |
| HA |
CA |
CB |
HB3 |
178.6 |
299.9 |
| O |
C |
CA |
CB |
90.3 |
89.9 |
| O |
C |
CA |
HA |
213.5 |
209.9 |
| CA |
C |
O |
OXT |
178.2 |
180.2 |
| O |
C |
OXT |
HXT |
358.3 |
0.1 |
| OXT |
C |
CA |
CB |
268.6 |
270.1 |
| OXT |
C |
CA |
HA |
31.9 |
30.1 |
| CA |
C |
OXT |
O |
181.8 |
179.8 |
| CG |
CB |
CA |
HA |
303.9 |
60.0 |
| CA |
CB |
CG |
HB2 |
125.3 |
120.0 |
| CA |
CB |
CG |
HB3 |
234.7 |
239.9 |
| HB2 |
CB |
CG |
HB3 |
109.4 |
119.9 |
| OD1 |
CG |
CB |
OD2 |
190.3 |
180.0 |
| CB |
CG |
OD1 |
P |
203.5 |
179.9 |
| HB2 |
CB |
CA |
HA |
69.1 |
180.0 |
| CA |
CB |
HB2 |
CG |
234.8 |
239.9 |
| CA |
CB |
HB2 |
HB3 |
117.4 |
120.0 |
| CG |
CB |
HB2 |
HB3 |
242.6 |
240.0 |
| HB2 |
CB |
CG |
OD1 |
273.4 |
60.0 |
| HB2 |
CB |
CG |
OD2 |
83.1 |
239.9 |
| HB3 |
CB |
CA |
HA |
178.6 |
299.9 |
| CA |
CB |
HB3 |
CG |
125.2 |
120.1 |
| CA |
CB |
HB3 |
HB2 |
242.6 |
240.1 |
| CG |
CB |
HB3 |
HB2 |
117.4 |
120.0 |
| HB3 |
CB |
CG |
OD1 |
164.0 |
300.1 |
| HB3 |
CB |
CG |
OD2 |
333.7 |
120.0 |
| OD1 |
CG |
CB |
HB2 |
273.4 |
60.0 |
| OD1 |
CG |
CB |
HB3 |
164.0 |
300.1 |
| CB |
CG |
OD1 |
OD2 |
168.5 |
180.0 |
| CG |
OD1 |
P |
OP1 |
217.3 |
60.1 |
| CG |
OD1 |
P |
OP2 |
337.0 |
180.0 |
| CG |
OD1 |
P |
OP3 |
96.7 |
300.0 |
| OD2 |
CG |
CB |
HB2 |
83.1 |
239.9 |
| OD2 |
CG |
CB |
HB3 |
333.7 |
120.0 |
| CB |
CG |
OD2 |
OD1 |
191.4 |
180.0 |
| OD2 |
CG |
OD1 |
P |
35.0 |
360.0 |
| P |
OD1 |
CG |
OD2 |
35.0 |
360.0 |
| OP1 |
P |
OD1 |
OP2 |
240.3 |
240.1 |
| OP1 |
P |
OD1 |
OP3 |
120.6 |
120.0 |
| OP2 |
P |
OD1 |
OP3 |
240.3 |
240.0 |
| OD1 |
P |
OP2 |
H2O |
180.0 |
180.0 |
| OD1 |
P |
OP3 |
H3O |
180.0 |
300.0 |
| OD1 |
P |
OP1 |
OP2 |
121.4 |
120.0 |
| OD1 |
P |
OP1 |
OP3 |
246.0 |
240.0 |
| OP2 |
P |
OP1 |
OP3 |
124.6 |
120.0 |
| OP1 |
P |
OP2 |
H2O |
296.2 |
300.0 |
| OP1 |
P |
OP3 |
H3O |
66.3 |
180.0 |
| OD1 |
P |
OP2 |
OP1 |
243.8 |
240.0 |
| OD1 |
P |
OP2 |
OP3 |
116.7 |
120.1 |
| OP1 |
P |
OP2 |
OP3 |
232.9 |
240.0 |
| OP2 |
P |
OP3 |
H3O |
301.6 |
60.0 |
| OD1 |
P |
OP3 |
OP1 |
113.7 |
120.0 |
| OD1 |
P |
OP3 |
OP2 |
238.4 |
240.0 |
| OP1 |
P |
OP3 |
OP2 |
124.8 |
120.0 |
| OP3 |
P |
OP2 |
H2O |
63.3 |
60.0 |
| H2O |
OP2 |
P |
OP3 |
63.3 |
60.0 |