PDB Chemical Component YCM
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 YCM
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N |
CA |
1.463 |
1.442 |
| N |
H |
1.020 |
1.006 |
| N |
H2 |
1.020 |
1.006 |
| CA |
CB |
1.535 |
1.531 |
| CA |
C |
1.523 |
1.520 |
| CA |
HA |
1.115 |
1.097 |
| CB |
SG |
1.800 |
1.824 |
| CB |
HB2 |
1.114 |
1.095 |
| CB |
HB3 |
1.115 |
1.095 |
| SG |
CD |
1.800 |
1.807 |
| CD |
CE |
1.505 |
1.508 |
| CD |
HD2 |
1.115 |
1.094 |
| CD |
HD3 |
1.114 |
1.093 |
| CE |
OZ1 |
1.226 |
1.229 |
| CE |
NZ2 |
1.325 |
1.376 |
| NZ2 |
HZ21 |
1.020 |
1.015 |
| NZ2 |
HZ22 |
1.020 |
1.015 |
| C |
O |
1.230 |
1.225 |
| C |
OXT |
|
1.355 |
| OXT |
HXT |
|
0.981 |
Bond Angles for YCM
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| CA |
N |
H |
110.2 |
119.0 |
| CA |
N |
H2 |
111.9 |
118.9 |
| N |
CA |
CB |
110.2 |
112.0 |
| N |
CA |
C |
116.0 |
111.9 |
| N |
CA |
HA |
103.8 |
105.3 |
| H |
N |
H2 |
111.9 |
120.6 |
| CB |
CA |
C |
107.7 |
112.4 |
| CB |
CA |
HA |
112.7 |
108.8 |
| CA |
CB |
SG |
114.4 |
113.7 |
| CA |
CB |
HB2 |
110.4 |
109.9 |
| CA |
CB |
HB3 |
110.4 |
110.4 |
| C |
CA |
HA |
106.5 |
106.1 |
| CA |
C |
O |
119.6 |
123.8 |
| CA |
C |
OXT |
|
113.3 |
| SG |
CB |
HB2 |
110.5 |
107.3 |
| SG |
CB |
HB3 |
110.4 |
107.6 |
| CB |
SG |
CD |
104.4 |
98.1 |
| HB2 |
CB |
HB3 |
99.8 |
107.7 |
| SG |
CD |
CE |
117.7 |
109.0 |
| SG |
CD |
HD2 |
109.2 |
109.9 |
| SG |
CD |
HD3 |
109.2 |
109.4 |
| CE |
CD |
HD2 |
109.2 |
108.8 |
| CE |
CD |
HD3 |
109.2 |
111.7 |
| CD |
CE |
OZ1 |
120.8 |
122.6 |
| CD |
CE |
NZ2 |
116.4 |
113.6 |
| HD2 |
CD |
HD3 |
101.0 |
108.2 |
| OZ1 |
CE |
NZ2 |
122.7 |
123.7 |
| CE |
NZ2 |
HZ21 |
122.8 |
118.7 |
| CE |
NZ2 |
HZ22 |
116.4 |
122.7 |
| HZ21 |
NZ2 |
HZ22 |
120.8 |
118.7 |
| O |
C |
OXT |
|
123.0 |
| C |
OXT |
HXT |
|
111.9 |
Torsion Angles for YCM
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| H |
N |
CA |
H2 |
125.2 |
166.6 |
| CB |
CA |
N |
C |
237.3 |
232.8 |
| CB |
CA |
N |
HA |
120.9 |
118.0 |
| N |
CA |
CB |
SG |
304.5 |
67.2 |
| N |
CA |
CB |
HB2 |
69.9 |
307.0 |
| N |
CA |
CB |
HB3 |
179.3 |
188.4 |
| C |
CA |
N |
HA |
243.6 |
245.3 |
| N |
CA |
C |
O |
171.6 |
354.2 |
| N |
CA |
C |
OXT |
|
174.9 |
| CA |
N |
H |
H2 |
234.8 |
193.6 |
| H |
N |
CA |
CB |
180.0 |
245.7 |
| H |
N |
CA |
C |
302.7 |
12.9 |
| H |
N |
CA |
HA |
59.1 |
127.7 |
| CA |
N |
H2 |
H |
124.3 |
166.4 |
| H2 |
N |
CA |
CB |
54.8 |
79.1 |
| H2 |
N |
CA |
C |
177.5 |
206.3 |
| H2 |
N |
CA |
HA |
293.9 |
321.0 |
| CB |
CA |
N |
H |
180.0 |
245.7 |
| CB |
CA |
N |
H2 |
54.8 |
79.1 |
| N |
CA |
CB |
C |
127.5 |
127.0 |
| N |
CA |
CB |
HA |
244.6 |
244.1 |
| C |
CA |
CB |
HA |
117.1 |
117.1 |
| CB |
CA |
C |
O |
295.6 |
121.3 |
| CB |
CA |
C |
OXT |
|
302.0 |
| SG |
CB |
CA |
HB2 |
234.7 |
120.3 |
| SG |
CB |
CA |
HB3 |
125.2 |
238.9 |
| CA |
CB |
SG |
CD |
307.1 |
178.3 |
| HB2 |
CB |
CA |
HB3 |
250.5 |
118.6 |
| C |
CA |
N |
H |
302.7 |
12.9 |
| C |
CA |
N |
H2 |
177.5 |
206.3 |
| N |
CA |
C |
CB |
236.0 |
233.0 |
| N |
CA |
C |
HA |
114.9 |
114.3 |
| CB |
CA |
C |
HA |
238.9 |
241.3 |
| C |
CA |
CB |
SG |
177.1 |
300.3 |
| C |
CA |
CB |
HB2 |
302.4 |
180.0 |
| C |
CA |
CB |
HB3 |
51.9 |
61.4 |
| O |
C |
CA |
OXT |
|
179.3 |
| CA |
C |
OXT |
HXT |
|
179.3 |
| HA |
CA |
N |
H |
59.1 |
127.7 |
| HA |
CA |
N |
H2 |
293.9 |
321.0 |
| N |
CA |
HA |
CB |
119.3 |
120.2 |
| N |
CA |
HA |
C |
237.1 |
241.3 |
| CB |
CA |
HA |
C |
117.8 |
121.1 |
| HA |
CA |
CB |
SG |
60.0 |
183.1 |
| HA |
CA |
CB |
HB2 |
185.3 |
62.9 |
| HA |
CA |
CB |
HB3 |
294.8 |
304.3 |
| HA |
CA |
C |
O |
56.7 |
240.0 |
| HA |
CA |
C |
OXT |
|
60.7 |
| SG |
CB |
CA |
C |
177.1 |
300.3 |
| SG |
CB |
CA |
HA |
60.0 |
183.1 |
| CA |
CB |
SG |
HB2 |
125.3 |
238.3 |
| CA |
CB |
SG |
HB3 |
234.8 |
122.7 |
| HB2 |
CB |
SG |
HB3 |
109.5 |
244.4 |
| CB |
SG |
CD |
CE |
307.6 |
180.0 |
| CB |
SG |
CD |
HD2 |
72.8 |
299.1 |
| CB |
SG |
CD |
HD3 |
182.4 |
57.7 |
| HB2 |
CB |
CA |
C |
302.4 |
180.0 |
| HB2 |
CB |
CA |
HA |
185.3 |
62.9 |
| CA |
CB |
HB2 |
SG |
232.5 |
124.1 |
| CA |
CB |
HB2 |
HB3 |
116.2 |
239.7 |
| SG |
CB |
HB2 |
HB3 |
243.7 |
115.6 |
| HB2 |
CB |
SG |
CD |
181.8 |
300.0 |
| HB3 |
CB |
CA |
C |
51.9 |
61.4 |
| HB3 |
CB |
CA |
HA |
294.8 |
304.3 |
| CA |
CB |
HB3 |
SG |
127.4 |
235.3 |
| CA |
CB |
HB3 |
HB2 |
243.8 |
119.9 |
| SG |
CB |
HB3 |
HB2 |
116.3 |
244.6 |
| HB3 |
CB |
SG |
CD |
72.3 |
55.6 |
| CD |
SG |
CB |
HB2 |
181.8 |
300.0 |
| CD |
SG |
CB |
HB3 |
72.3 |
55.6 |
| CE |
CD |
SG |
HD2 |
234.8 |
240.9 |
| CE |
CD |
SG |
HD3 |
125.2 |
122.3 |
| SG |
CD |
CE |
OZ1 |
90.6 |
59.3 |
| SG |
CD |
CE |
NZ2 |
271.5 |
239.8 |
| HD2 |
CD |
SG |
HD3 |
250.4 |
241.4 |
| SG |
CD |
CE |
HD2 |
125.2 |
119.8 |
| SG |
CD |
CE |
HD3 |
234.8 |
239.1 |
| HD2 |
CD |
CE |
HD3 |
109.5 |
119.3 |
| OZ1 |
CE |
CD |
NZ2 |
179.2 |
179.5 |
| CD |
CE |
NZ2 |
HZ21 |
359.1 |
179.9 |
| CD |
CE |
NZ2 |
HZ22 |
180.0 |
360.0 |
| SG |
CD |
HD2 |
CE |
230.0 |
240.8 |
| SG |
CD |
HD2 |
HD3 |
115.0 |
119.3 |
| CE |
CD |
HD2 |
HD3 |
245.0 |
238.5 |
| HD2 |
CD |
CE |
OZ1 |
325.4 |
299.5 |
| HD2 |
CD |
CE |
NZ2 |
146.2 |
120.0 |
| SG |
CD |
HD3 |
CE |
130.0 |
120.7 |
| SG |
CD |
HD3 |
HD2 |
245.0 |
240.3 |
| CE |
CD |
HD3 |
HD2 |
114.9 |
119.7 |
| HD3 |
CD |
CE |
OZ1 |
215.9 |
180.2 |
| HD3 |
CD |
CE |
NZ2 |
36.7 |
0.7 |
| OZ1 |
CE |
CD |
HD2 |
325.4 |
299.5 |
| OZ1 |
CE |
CD |
HD3 |
215.9 |
180.2 |
| CD |
CE |
OZ1 |
NZ2 |
180.9 |
180.6 |
| OZ1 |
CE |
NZ2 |
HZ21 |
180.0 |
0.5 |
| OZ1 |
CE |
NZ2 |
HZ22 |
0.9 |
180.5 |
| NZ2 |
CE |
CD |
HD2 |
146.2 |
120.0 |
| NZ2 |
CE |
CD |
HD3 |
36.7 |
0.7 |
| CD |
CE |
NZ2 |
OZ1 |
179.1 |
179.5 |
| HZ21 |
NZ2 |
CE |
HZ22 |
179.1 |
180.0 |
| CE |
NZ2 |
HZ21 |
HZ22 |
180.9 |
180.0 |
| CE |
NZ2 |
HZ22 |
HZ21 |
179.1 |
180.0 |
| O |
C |
CA |
HA |
56.7 |
240.0 |
| CA |
C |
O |
OXT |
|
180.8 |
| O |
C |
OXT |
HXT |
|
360.0 |
| OXT |
C |
CA |
HA |
|
60.7 |
| CA |
C |
OXT |
O |
|
179.3 |