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