PDB Chemical Component YNM
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 YNM
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
N |
CA |
1.464 |
1.469 |
N |
CM |
1.479 |
1.469 |
CA |
C |
1.487 |
1.507 |
CA |
CB |
1.538 |
1.530 |
C |
O |
1.249 |
1.208 |
CB |
CG |
1.500 |
1.507 |
CG |
CD1 |
1.409 |
1.383 |
CG |
CD2 |
1.400 |
1.383 |
CD1 |
CE1 |
1.371 |
1.382 |
CD2 |
CE2 |
1.376 |
1.381 |
CE1 |
CZ |
1.381 |
1.387 |
CE2 |
CZ |
1.386 |
1.387 |
OH |
CZ |
1.384 |
1.360 |
C |
OXT |
|
1.342 |
N |
H |
1.000 |
1.009 |
CA |
HA |
1.100 |
1.091 |
CM |
HM1C |
1.100 |
1.090 |
CM |
HM2C |
1.100 |
1.090 |
CM |
HM3C |
1.100 |
1.090 |
CB |
HB1C |
1.100 |
1.090 |
CB |
HB2C |
1.100 |
1.090 |
CD1 |
HD1 |
1.080 |
1.080 |
CD2 |
HD2 |
1.081 |
1.080 |
CE1 |
HE1 |
1.080 |
1.080 |
CE2 |
HE2 |
1.080 |
1.080 |
OH |
HH |
0.950 |
0.967 |
OXT |
HXT |
|
0.967 |
Bond Angles for YNM
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
CA |
N |
CM |
120.3 |
111.0 |
N |
CA |
C |
111.2 |
109.5 |
N |
CA |
CB |
109.1 |
109.5 |
CA |
N |
H |
106.0 |
111.0 |
N |
CA |
HA |
108.4 |
109.5 |
CM |
N |
H |
106.0 |
111.0 |
N |
CM |
HM1C |
109.5 |
109.5 |
N |
CM |
HM2C |
109.5 |
109.4 |
N |
CM |
HM3C |
109.5 |
109.4 |
C |
CA |
CB |
108.9 |
109.5 |
CA |
C |
O |
120.7 |
120.0 |
CA |
C |
OXT |
|
120.0 |
C |
CA |
HA |
108.6 |
109.5 |
CA |
CB |
CG |
116.8 |
109.5 |
CB |
CA |
HA |
110.7 |
109.4 |
CA |
CB |
HB1C |
107.1 |
109.5 |
CA |
CB |
HB2C |
105.4 |
109.4 |
O |
C |
OXT |
|
120.0 |
CB |
CG |
CD1 |
120.1 |
119.9 |
CB |
CG |
CD2 |
122.0 |
120.0 |
CG |
CB |
HB1C |
107.1 |
109.5 |
CG |
CB |
HB2C |
105.4 |
109.5 |
CD1 |
CG |
CD2 |
117.9 |
120.1 |
CG |
CD1 |
CE1 |
120.6 |
120.0 |
CG |
CD1 |
HD1 |
119.7 |
120.0 |
CG |
CD2 |
CE2 |
121.5 |
120.1 |
CG |
CD2 |
HD2 |
119.3 |
119.9 |
CD1 |
CE1 |
CZ |
120.1 |
119.9 |
CE1 |
CD1 |
HD1 |
119.7 |
120.0 |
CD1 |
CE1 |
HE1 |
119.9 |
120.0 |
CD2 |
CE2 |
CZ |
119.1 |
119.9 |
CE2 |
CD2 |
HD2 |
119.3 |
120.0 |
CD2 |
CE2 |
HE2 |
120.5 |
120.0 |
CE1 |
CZ |
CE2 |
120.8 |
120.0 |
CE1 |
CZ |
OH |
118.7 |
120.0 |
CZ |
CE1 |
HE1 |
120.0 |
120.0 |
CE2 |
CZ |
OH |
120.4 |
120.0 |
CZ |
CE2 |
HE2 |
120.5 |
120.1 |
CZ |
OH |
HH |
109.5 |
114.0 |
C |
OXT |
HXT |
|
117.0 |
HM1C |
CM |
HM2C |
109.5 |
109.5 |
HM1C |
CM |
HM3C |
109.4 |
109.5 |
HM2C |
CM |
HM3C |
109.5 |
109.5 |
HB1C |
CB |
HB2C |
115.4 |
109.5 |
Torsion Angles for YNM
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
CM |
N |
CA |
H |
240.0 |
236.0 |
CA |
N |
CM |
HM1C |
249.7 |
300.0 |
CA |
N |
CM |
HM2C |
9.7 |
60.0 |
CA |
N |
CM |
HM3C |
129.7 |
180.0 |
C |
CA |
N |
CB |
120.1 |
120.0 |
N |
CA |
C |
O |
289.4 |
0.0 |
N |
CA |
C |
OXT |
|
180.0 |
C |
CA |
N |
HA |
240.7 |
240.0 |
N |
CA |
CB |
CG |
180.3 |
295.0 |
CB |
CA |
N |
HA |
120.6 |
120.0 |
N |
CA |
CB |
HB1C |
300.3 |
55.0 |
N |
CA |
CB |
HB2C |
63.7 |
175.0 |
CM |
N |
CA |
C |
66.4 |
275.0 |
CM |
N |
CA |
CB |
306.2 |
155.0 |
CA |
N |
CM |
H |
120.0 |
124.0 |
CM |
N |
CA |
HA |
185.6 |
35.0 |
HM1C |
CM |
N |
HM2C |
240.0 |
240.0 |
HM1C |
CM |
N |
HM3C |
120.0 |
120.0 |
HM2C |
CM |
N |
HM3C |
240.0 |
240.1 |
C |
CA |
N |
CM |
66.4 |
275.0 |
N |
CA |
C |
CB |
239.7 |
240.0 |
C |
CA |
N |
H |
186.3 |
39.0 |
N |
CA |
C |
HA |
119.1 |
120.0 |
C |
CA |
CB |
CG |
58.8 |
175.0 |
CB |
CA |
C |
HA |
239.4 |
240.0 |
C |
CA |
CB |
HB1C |
178.8 |
295.0 |
C |
CA |
CB |
HB2C |
302.2 |
55.0 |
O |
C |
CA |
OXT |
|
180.1 |
CA |
C |
OXT |
HXT |
|
180.0 |
CB |
CA |
N |
CM |
306.2 |
155.0 |
N |
CA |
CB |
C |
121.5 |
120.0 |
CB |
CA |
N |
H |
66.2 |
278.9 |
N |
CA |
CB |
HA |
240.8 |
240.0 |
CB |
CA |
C |
O |
49.7 |
120.0 |
CB |
CA |
C |
OXT |
|
300.0 |
C |
CA |
CB |
HA |
119.3 |
120.0 |
CA |
CB |
CG |
CD1 |
221.2 |
90.0 |
CA |
CB |
CG |
CD2 |
40.0 |
269.7 |
CG |
CB |
CA |
HB1C |
240.0 |
240.0 |
CG |
CB |
CA |
HB2C |
116.6 |
120.0 |
HB1C |
CB |
CA |
HB2C |
236.6 |
240.0 |
O |
C |
CA |
CB |
49.7 |
120.0 |
CA |
C |
O |
OXT |
|
179.9 |
O |
C |
CA |
HA |
170.3 |
240.0 |
O |
C |
OXT |
HXT |
|
359.9 |
CG |
CB |
CA |
HA |
299.5 |
55.0 |
CA |
CB |
CG |
HB1C |
120.0 |
120.0 |
CA |
CB |
CG |
HB2C |
243.4 |
240.0 |
CD1 |
CG |
CB |
CD2 |
181.3 |
180.3 |
CB |
CG |
CD1 |
CE1 |
179.9 |
180.0 |
CB |
CG |
CD1 |
HD1 |
359.9 |
359.9 |
CB |
CG |
CD2 |
CE2 |
179.9 |
180.0 |
CB |
CG |
CD2 |
HD2 |
359.9 |
0.0 |
HB1C |
CB |
CG |
HB2C |
123.4 |
120.0 |
CB |
CG |
CD1 |
CD2 |
178.8 |
179.7 |
CD1 |
CG |
CB |
HB1C |
101.2 |
330.0 |
CD1 |
CG |
CB |
HB2C |
337.8 |
210.0 |
CD1 |
CG |
CD2 |
CE2 |
358.6 |
359.7 |
CD1 |
CG |
CD2 |
HD2 |
178.6 |
179.7 |
CG |
CD1 |
CE1 |
CZ |
360.0 |
359.9 |
CE1 |
CD1 |
CG |
HD1 |
180.0 |
180.1 |
CG |
CD1 |
CE1 |
HE1 |
180.0 |
180.0 |
CB |
CG |
CD2 |
CD1 |
181.2 |
180.3 |
CD2 |
CG |
CB |
HB1C |
280.0 |
149.7 |
CD2 |
CG |
CB |
HB2C |
156.6 |
29.7 |
CD2 |
CG |
CD1 |
CE1 |
1.1 |
0.3 |
CD2 |
CG |
CD1 |
HD1 |
181.1 |
180.2 |
CG |
CD2 |
CE2 |
CZ |
0.5 |
0.0 |
CE2 |
CD2 |
CG |
HD2 |
180.0 |
180.0 |
CG |
CD2 |
CE2 |
HE2 |
180.5 |
179.9 |
CE1 |
CD1 |
CG |
CD2 |
1.1 |
0.3 |
CG |
CD1 |
CE1 |
HD1 |
180.0 |
179.9 |
CD1 |
CE1 |
CZ |
CE2 |
359.1 |
359.8 |
CD1 |
CE1 |
CZ |
OH |
179.8 |
180.0 |
CZ |
CE1 |
CD1 |
HE1 |
180.0 |
180.0 |
CG |
CD2 |
CE2 |
HD2 |
180.0 |
180.0 |
CE1 |
CZ |
CE2 |
CD2 |
0.7 |
0.2 |
CD2 |
CE2 |
CZ |
OH |
180.0 |
180.0 |
CZ |
CE2 |
CD2 |
HE2 |
180.0 |
180.1 |
CZ |
CE1 |
CD1 |
HD1 |
180.0 |
180.0 |
CD1 |
CE1 |
CZ |
HE1 |
180.0 |
180.0 |
CD2 |
CE2 |
CZ |
CE1 |
0.7 |
0.2 |
CE2 |
CZ |
CE1 |
OH |
179.3 |
179.8 |
CE1 |
CZ |
CE2 |
HE2 |
180.7 |
180.3 |
CE1 |
CZ |
OH |
HH |
64.6 |
90.0 |
CZ |
CE2 |
CD2 |
HD2 |
180.5 |
180.0 |
CD2 |
CE2 |
CZ |
HE2 |
180.0 |
179.9 |
CE1 |
CZ |
CE2 |
OH |
180.7 |
180.2 |
CE2 |
CZ |
CE1 |
HE1 |
179.1 |
179.8 |
CE2 |
CZ |
OH |
HH |
245.2 |
270.2 |
CE1 |
CZ |
OH |
CE2 |
179.3 |
179.8 |
OH |
CZ |
CE1 |
HE1 |
359.8 |
360.0 |
OH |
CZ |
CE2 |
HE2 |
0.0 |
0.1 |
OXT |
C |
CA |
CB |
|
300.0 |
CA |
C |
OXT |
O |
|
180.1 |
OXT |
C |
CA |
HA |
|
59.9 |
CA |
N |
H |
CM |
231.1 |
236.0 |
H |
N |
CA |
C |
186.3 |
39.0 |
H |
N |
CA |
CB |
66.2 |
278.9 |
H |
N |
CA |
HA |
305.6 |
159.0 |
H |
N |
CM |
HM1C |
129.7 |
176.0 |
H |
N |
CM |
HM2C |
249.7 |
296.1 |
H |
N |
CM |
HM3C |
9.7 |
56.0 |
HA |
CA |
N |
CM |
185.6 |
35.0 |
N |
CA |
HA |
C |
239.1 |
240.0 |
N |
CA |
HA |
CB |
119.6 |
120.0 |
HA |
CA |
N |
H |
305.6 |
159.0 |
C |
CA |
HA |
CB |
240.5 |
240.0 |
HA |
CA |
C |
O |
170.3 |
240.0 |
HA |
CA |
C |
OXT |
|
59.9 |
HA |
CA |
CB |
CG |
299.5 |
55.0 |
HA |
CA |
CB |
HB1C |
59.5 |
175.0 |
HA |
CA |
CB |
HB2C |
182.8 |
295.0 |
HM1C |
CM |
N |
H |
129.7 |
176.0 |
N |
CM |
HM1C |
HM2C |
120.0 |
120.0 |
N |
CM |
HM1C |
HM3C |
240.0 |
240.0 |
HM2C |
CM |
HM1C |
HM3C |
120.0 |
120.0 |
HM2C |
CM |
N |
H |
249.7 |
296.1 |
N |
CM |
HM2C |
HM1C |
240.0 |
240.0 |
N |
CM |
HM2C |
HM3C |
120.0 |
119.9 |
HM1C |
CM |
HM2C |
HM3C |
240.0 |
239.9 |
HM3C |
CM |
N |
H |
9.7 |
56.0 |
N |
CM |
HM3C |
HM1C |
120.0 |
120.0 |
N |
CM |
HM3C |
HM2C |
240.0 |
240.1 |
HM1C |
CM |
HM3C |
HM2C |
120.0 |
120.1 |
CA |
CB |
HB1C |
CG |
233.9 |
240.0 |
HB1C |
CB |
CA |
HA |
59.5 |
175.0 |
CA |
CB |
HB1C |
HB2C |
116.9 |
120.0 |
HB1C |
CB |
CG |
CD1 |
101.2 |
330.0 |
HB1C |
CB |
CG |
CD2 |
280.0 |
149.7 |
CG |
CB |
HB1C |
HB2C |
243.0 |
240.0 |
CA |
CB |
HB2C |
CG |
124.2 |
120.0 |
HB2C |
CB |
CA |
HA |
182.8 |
295.0 |
CA |
CB |
HB2C |
HB1C |
242.1 |
240.0 |
HB2C |
CB |
CG |
CD1 |
337.8 |
210.0 |
HB2C |
CB |
CG |
CD2 |
156.6 |
29.7 |
CG |
CB |
HB2C |
HB1C |
118.0 |
120.0 |
HD1 |
CD1 |
CG |
CD2 |
181.1 |
180.2 |
CG |
CD1 |
HD1 |
CE1 |
180.0 |
180.1 |
HD1 |
CD1 |
CE1 |
CZ |
180.0 |
180.0 |
HD1 |
CD1 |
CE1 |
HE1 |
0.0 |
0.1 |
CG |
CD2 |
HD2 |
CE2 |
180.0 |
180.0 |
HD2 |
CD2 |
CE2 |
CZ |
180.5 |
180.0 |
HD2 |
CD2 |
CE2 |
HE2 |
0.5 |
359.9 |
CD1 |
CE1 |
HE1 |
CZ |
180.0 |
180.0 |
HE1 |
CE1 |
CD1 |
HD1 |
0.0 |
0.1 |
HE1 |
CE1 |
CZ |
CE2 |
179.1 |
179.8 |
HE1 |
CE1 |
CZ |
OH |
359.8 |
360.0 |
CD2 |
CE2 |
HE2 |
CZ |
180.0 |
180.1 |
HE2 |
CE2 |
CD2 |
HD2 |
0.5 |
359.9 |
HE2 |
CE2 |
CZ |
OH |
0.0 |
0.1 |