PDB Chemical Component LYZ
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 LYZ
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N |
CA |
1.447 |
1.469 |
| N |
H |
1.019 |
1.009 |
| N |
H2 |
1.020 |
1.008 |
| CA |
C |
1.523 |
1.506 |
| CA |
CB |
1.541 |
1.529 |
| CA |
HA |
1.115 |
1.090 |
| C |
O |
1.233 |
1.208 |
| C |
OXT |
1.331 |
1.342 |
| CB |
CG |
1.523 |
1.528 |
| CB |
HB2 |
1.115 |
1.090 |
| CB |
HB3 |
1.115 |
1.090 |
| CG |
CD |
1.515 |
1.529 |
| CG |
HG2 |
1.115 |
1.090 |
| CG |
HG3 |
1.116 |
1.090 |
| CD |
CE |
1.523 |
1.529 |
| CD |
OH |
1.448 |
1.430 |
| CD |
HD |
1.115 |
1.089 |
| CE |
NZ |
1.499 |
1.468 |
| CE |
HE2 |
1.115 |
1.091 |
| CE |
HE3 |
1.115 |
1.089 |
| NZ |
HZ1 |
1.019 |
1.008 |
| NZ |
HZ2 |
1.020 |
1.008 |
| OH |
HH |
0.949 |
0.967 |
| OXT |
HXT |
0.951 |
0.967 |
Bond Angles for LYZ
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| CA |
N |
H |
114.0 |
106.7 |
| CA |
N |
H2 |
110.5 |
106.7 |
| N |
CA |
C |
114.0 |
109.4 |
| N |
CA |
CB |
111.9 |
109.5 |
| N |
CA |
HA |
104.8 |
109.4 |
| H |
N |
H2 |
110.6 |
106.7 |
| C |
CA |
CB |
110.6 |
109.6 |
| C |
CA |
HA |
106.3 |
109.4 |
| CA |
C |
O |
120.3 |
120.0 |
| CA |
C |
OXT |
118.9 |
120.0 |
| CB |
CA |
HA |
108.7 |
109.5 |
| CA |
CB |
CG |
113.4 |
109.5 |
| CA |
CB |
HB2 |
110.8 |
109.5 |
| CA |
CB |
HB3 |
110.7 |
109.5 |
| O |
C |
OXT |
120.6 |
119.9 |
| C |
OXT |
HXT |
118.9 |
120.0 |
| CG |
CB |
HB2 |
110.8 |
109.5 |
| CG |
CB |
HB3 |
110.8 |
109.4 |
| CB |
CG |
CD |
112.4 |
109.5 |
| CB |
CG |
HG2 |
111.1 |
109.5 |
| CB |
CG |
HG3 |
111.1 |
109.5 |
| HB2 |
CB |
HB3 |
99.5 |
109.4 |
| CD |
CG |
HG2 |
111.2 |
109.4 |
| CD |
CG |
HG3 |
111.2 |
109.4 |
| CG |
CD |
CE |
110.7 |
109.5 |
| CG |
CD |
OH |
98.6 |
109.5 |
| CG |
CD |
HD |
113.2 |
109.5 |
| HG2 |
CG |
HG3 |
99.2 |
109.5 |
| CE |
CD |
OH |
101.6 |
109.4 |
| CE |
CD |
HD |
110.7 |
109.5 |
| CD |
CE |
NZ |
109.0 |
109.6 |
| CD |
CE |
HE2 |
112.3 |
109.4 |
| CD |
CE |
HE3 |
112.3 |
109.5 |
| OH |
CD |
HD |
120.9 |
109.5 |
| CD |
OH |
HH |
98.7 |
106.8 |
| NZ |
CE |
HE2 |
112.4 |
109.4 |
| NZ |
CE |
HE3 |
112.4 |
109.5 |
| CE |
NZ |
HZ1 |
109.0 |
106.8 |
| CE |
NZ |
HZ2 |
112.3 |
106.8 |
| HE2 |
CE |
HE3 |
98.1 |
109.5 |
| HZ1 |
NZ |
HZ2 |
112.5 |
106.8 |
Torsion Angles for LYZ
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| H |
N |
CA |
H2 |
125.3 |
113.8 |
| C |
CA |
N |
CB |
126.5 |
120.1 |
| C |
CA |
N |
HA |
244.1 |
240.1 |
| N |
CA |
C |
O |
187.0 |
329.9 |
| N |
CA |
C |
OXT |
12.5 |
150.0 |
| CB |
CA |
N |
HA |
117.7 |
120.0 |
| N |
CA |
CB |
CG |
301.2 |
300.0 |
| N |
CA |
CB |
HB2 |
66.5 |
179.9 |
| N |
CA |
CB |
HB3 |
175.9 |
60.1 |
| CA |
N |
H |
H2 |
234.7 |
246.2 |
| H |
N |
CA |
C |
180.0 |
173.8 |
| H |
N |
CA |
CB |
53.5 |
53.7 |
| H |
N |
CA |
HA |
295.9 |
293.8 |
| CA |
N |
H2 |
H |
127.3 |
113.8 |
| H2 |
N |
CA |
C |
54.7 |
60.0 |
| H2 |
N |
CA |
CB |
288.2 |
299.9 |
| H2 |
N |
CA |
HA |
170.5 |
180.0 |
| C |
CA |
N |
H |
180.0 |
173.8 |
| C |
CA |
N |
H2 |
54.7 |
60.0 |
| N |
CA |
C |
CB |
232.8 |
240.0 |
| N |
CA |
C |
HA |
115.0 |
119.9 |
| CB |
CA |
C |
HA |
242.1 |
239.9 |
| C |
CA |
CB |
CG |
172.9 |
180.0 |
| C |
CA |
CB |
HB2 |
298.2 |
59.9 |
| C |
CA |
CB |
HB3 |
47.6 |
300.0 |
| O |
C |
CA |
OXT |
174.5 |
179.9 |
| CA |
C |
OXT |
HXT |
179.9 |
179.9 |
| CB |
CA |
N |
H |
53.5 |
53.7 |
| CB |
CA |
N |
H2 |
288.2 |
299.9 |
| N |
CA |
CB |
C |
128.3 |
120.0 |
| N |
CA |
CB |
HA |
244.7 |
240.1 |
| C |
CA |
CB |
HA |
116.4 |
120.0 |
| CB |
CA |
C |
O |
314.2 |
89.9 |
| CB |
CA |
C |
OXT |
139.7 |
270.1 |
| CG |
CB |
CA |
HB2 |
234.7 |
120.1 |
| CG |
CB |
CA |
HB3 |
125.3 |
240.0 |
| CA |
CB |
CG |
CD |
158.2 |
180.0 |
| CA |
CB |
CG |
HG2 |
283.5 |
60.0 |
| CA |
CB |
CG |
HG3 |
32.9 |
300.0 |
| HB2 |
CB |
CA |
HB3 |
250.6 |
119.9 |
| HA |
CA |
N |
H |
295.9 |
293.8 |
| HA |
CA |
N |
H2 |
170.5 |
180.0 |
| N |
CA |
HA |
C |
238.9 |
240.1 |
| N |
CA |
HA |
CB |
119.8 |
120.0 |
| C |
CA |
HA |
CB |
240.9 |
239.9 |
| HA |
CA |
C |
O |
72.0 |
210.0 |
| HA |
CA |
C |
OXT |
257.6 |
30.1 |
| HA |
CA |
CB |
CG |
56.6 |
60.0 |
| HA |
CA |
CB |
HB2 |
181.8 |
299.9 |
| HA |
CA |
CB |
HB3 |
291.3 |
180.0 |
| O |
C |
CA |
CB |
314.2 |
89.9 |
| O |
C |
CA |
HA |
72.0 |
210.0 |
| CA |
C |
O |
OXT |
185.6 |
180.1 |
| O |
C |
OXT |
HXT |
5.5 |
0.0 |
| OXT |
C |
CA |
CB |
139.7 |
270.1 |
| OXT |
C |
CA |
HA |
257.6 |
30.1 |
| CA |
C |
OXT |
O |
174.5 |
179.9 |
| CG |
CB |
CA |
HA |
56.6 |
60.0 |
| CA |
CB |
CG |
HB2 |
125.3 |
239.9 |
| CA |
CB |
CG |
HB3 |
234.7 |
120.0 |
| HB2 |
CB |
CG |
HB3 |
109.5 |
240.1 |
| CD |
CG |
CB |
HG2 |
234.7 |
120.0 |
| CD |
CG |
CB |
HG3 |
125.3 |
240.0 |
| CB |
CG |
CD |
CE |
177.8 |
179.9 |
| CB |
CG |
CD |
OH |
71.8 |
60.0 |
| CB |
CG |
CD |
HD |
302.7 |
300.0 |
| HG2 |
CG |
CB |
HG3 |
250.6 |
120.0 |
| HB2 |
CB |
CA |
HA |
181.8 |
299.9 |
| CA |
CB |
HB2 |
CG |
233.2 |
120.1 |
| CA |
CB |
HB2 |
HB3 |
116.6 |
240.0 |
| CG |
CB |
HB2 |
HB3 |
243.3 |
119.9 |
| HB2 |
CB |
CG |
CD |
32.9 |
300.1 |
| HB2 |
CB |
CG |
HG2 |
158.2 |
180.0 |
| HB2 |
CB |
CG |
HG3 |
267.6 |
60.1 |
| HB3 |
CB |
CA |
HA |
291.3 |
180.0 |
| CA |
CB |
HB3 |
CG |
126.7 |
239.9 |
| CA |
CB |
HB3 |
HB2 |
243.4 |
120.0 |
| CG |
CB |
HB3 |
HB2 |
116.7 |
240.0 |
| HB3 |
CB |
CG |
CD |
283.4 |
59.9 |
| HB3 |
CB |
CG |
HG2 |
48.7 |
299.9 |
| HB3 |
CB |
CG |
HG3 |
158.1 |
179.9 |
| CD |
CG |
CB |
HB2 |
32.9 |
300.1 |
| CD |
CG |
CB |
HB3 |
283.4 |
59.9 |
| CB |
CG |
CD |
HG2 |
125.3 |
240.0 |
| CB |
CG |
CD |
HG3 |
234.7 |
120.0 |
| HG2 |
CG |
CD |
HG3 |
109.5 |
240.0 |
| CE |
CD |
CG |
OH |
106.0 |
119.9 |
| CE |
CD |
CG |
HD |
235.1 |
239.9 |
| CG |
CD |
CE |
NZ |
186.7 |
180.0 |
| CG |
CD |
CE |
HE2 |
311.9 |
60.1 |
| CG |
CD |
CE |
HE3 |
61.4 |
300.1 |
| OH |
CD |
CG |
HD |
129.1 |
120.0 |
| CG |
CD |
OH |
HH |
180.1 |
59.9 |
| HG2 |
CG |
CB |
HB2 |
158.2 |
180.0 |
| HG2 |
CG |
CB |
HB3 |
48.7 |
299.9 |
| CB |
CG |
HG2 |
CD |
234.0 |
120.1 |
| CB |
CG |
HG2 |
HG3 |
116.9 |
240.0 |
| CD |
CG |
HG2 |
HG3 |
243.0 |
120.0 |
| HG2 |
CG |
CD |
CE |
52.5 |
300.0 |
| HG2 |
CG |
CD |
OH |
306.5 |
180.0 |
| HG2 |
CG |
CD |
HD |
177.4 |
60.1 |
| HG3 |
CG |
CB |
HB2 |
267.6 |
60.1 |
| HG3 |
CG |
CB |
HB3 |
158.1 |
179.9 |
| CB |
CG |
HG3 |
CD |
126.0 |
240.0 |
| CB |
CG |
HG3 |
HG2 |
243.0 |
120.0 |
| CD |
CG |
HG3 |
HG2 |
117.0 |
240.0 |
| HG3 |
CG |
CD |
CE |
303.0 |
59.9 |
| HG3 |
CG |
CD |
OH |
197.0 |
300.0 |
| HG3 |
CG |
CD |
HD |
68.0 |
180.0 |
| CE |
CD |
CG |
HG2 |
52.5 |
300.0 |
| CE |
CD |
CG |
HG3 |
303.0 |
59.9 |
| CG |
CD |
CE |
OH |
256.0 |
240.0 |
| CG |
CD |
CE |
HD |
126.3 |
120.1 |
| OH |
CD |
CE |
HD |
230.3 |
240.1 |
| CE |
CD |
OH |
HH |
66.7 |
299.9 |
| NZ |
CE |
CD |
HE2 |
234.7 |
119.9 |
| NZ |
CE |
CD |
HE3 |
125.3 |
239.9 |
| CD |
CE |
NZ |
HZ1 |
180.0 |
180.0 |
| CD |
CE |
NZ |
HZ2 |
54.7 |
293.9 |
| HE2 |
CE |
CD |
HE3 |
250.5 |
120.0 |
| OH |
CD |
CG |
HG2 |
306.5 |
180.0 |
| OH |
CD |
CG |
HG3 |
197.0 |
300.0 |
| CG |
CD |
OH |
CE |
113.3 |
120.0 |
| CG |
CD |
OH |
HD |
236.3 |
240.0 |
| CE |
CD |
OH |
HD |
123.0 |
120.0 |
| OH |
CD |
CE |
NZ |
290.6 |
300.0 |
| OH |
CD |
CE |
HE2 |
55.9 |
180.0 |
| OH |
CD |
CE |
HE3 |
165.4 |
60.0 |
| HD |
CD |
CG |
HG2 |
177.4 |
60.1 |
| HD |
CD |
CG |
HG3 |
68.0 |
180.0 |
| CG |
CD |
HD |
CE |
235.1 |
239.9 |
| CG |
CD |
HD |
OH |
116.5 |
120.0 |
| CE |
CD |
HD |
OH |
241.5 |
240.1 |
| HD |
CD |
CE |
NZ |
60.3 |
59.9 |
| HD |
CD |
CE |
HE2 |
185.6 |
300.0 |
| HD |
CD |
CE |
HE3 |
295.1 |
180.0 |
| HD |
CD |
OH |
HH |
303.8 |
180.0 |
| NZ |
CE |
CD |
OH |
290.6 |
300.0 |
| NZ |
CE |
CD |
HD |
60.3 |
59.9 |
| CD |
CE |
NZ |
HE2 |
125.2 |
240.1 |
| CD |
CE |
NZ |
HE3 |
234.8 |
120.1 |
| HE2 |
CE |
NZ |
HE3 |
109.5 |
240.1 |
| HZ1 |
NZ |
CE |
HZ2 |
125.3 |
246.1 |
| HE2 |
CE |
CD |
OH |
55.9 |
180.0 |
| HE2 |
CE |
CD |
HD |
185.6 |
300.0 |
| CD |
CE |
HE2 |
NZ |
236.6 |
120.0 |
| CD |
CE |
HE2 |
HE3 |
118.3 |
240.0 |
| NZ |
CE |
HE2 |
HE3 |
241.7 |
119.9 |
| HE2 |
CE |
NZ |
HZ1 |
54.8 |
299.9 |
| HE2 |
CE |
NZ |
HZ2 |
289.5 |
53.8 |
| HE3 |
CE |
CD |
OH |
165.4 |
60.0 |
| HE3 |
CE |
CD |
HD |
295.1 |
180.0 |
| CD |
CE |
HE3 |
NZ |
123.4 |
239.9 |
| CD |
CE |
HE3 |
HE2 |
241.8 |
120.0 |
| NZ |
CE |
HE3 |
HE2 |
118.4 |
240.1 |
| HE3 |
CE |
NZ |
HZ1 |
305.2 |
59.9 |
| HE3 |
CE |
NZ |
HZ2 |
179.9 |
173.8 |
| HZ1 |
NZ |
CE |
HE2 |
54.8 |
299.9 |
| HZ1 |
NZ |
CE |
HE3 |
305.2 |
59.9 |
| CE |
NZ |
HZ1 |
HZ2 |
234.8 |
113.9 |
| HZ2 |
NZ |
CE |
HE2 |
289.5 |
53.8 |
| HZ2 |
NZ |
CE |
HE3 |
179.9 |
173.8 |
| CE |
NZ |
HZ2 |
HZ1 |
123.4 |
246.0 |
| HH |
OH |
CD |
HD |
303.8 |
180.0 |