PDB Chemical Component PYL

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 PYL

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
CB2 CG2 1.530 1.530
CB2 HB12 1.100 1.090
CB2 HB22 1.100 1.090
CB2 HB32 1.100 1.090
CG2 CD2 1.527 1.547
CG2 CA2 1.528 1.546
CG2 HG22 1.100 1.090
CD2 CE2 1.531 1.512
CD2 HD32 1.100 1.090
CD2 HD22 1.100 1.090
CE2 N2 1.332 1.273
CE2 HE22 1.080 1.080
N2 CA2 1.471 1.468
CA2 C2 1.531 1.506
CA2 HA2 1.100 1.090
C2 NZ 1.331 1.348
C2 O2 1.230 1.213
NZ CE 1.469 1.465
NZ HZ 1.000 0.970
CE CD 1.530 1.530
CE HE3 1.100 1.090
CE HE2 1.100 1.090
CD CG 1.530 1.529
CD HD3 1.100 1.090
CD HD2 1.099 1.091
CG CB 1.531 1.530
CG HG3 1.100 1.090
CG HG2 1.100 1.090
CB CA 1.531 1.530
CB HB3 1.100 1.090
CB HB2 1.100 1.090
CA C 1.530 1.507
CA HA 1.100 1.090
CA N 1.470 1.469
C OXT 1.250 1.342
C O 1.250 1.208
OXT HXT 0.950 0.967
N H 1.000 1.010
N H2 1.000 1.009

Bond Angles for PYL

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
CG2 CB2 HB12 109.5 109.4
CG2 CB2 HB22 109.5 109.5
CG2 CB2 HB32 109.5 109.5
CB2 CG2 CD2 112.7 111.2
CB2 CG2 CA2 114.3 111.2
CB2 CG2 HG22 109.5 110.9
HB12 CB2 HB22 109.5 109.5
HB12 CB2 HB32 109.5 109.5
HB22 CB2 HB32 109.4 109.5
CD2 CG2 CA2 100.8 100.8
CD2 CG2 HG22 109.6 111.2
CG2 CD2 CE2 101.0 103.8
CG2 CD2 HD32 111.6 110.6
CG2 CD2 HD22 111.5 110.6
CA2 CG2 HG22 109.6 111.2
CG2 CA2 N2 103.3 105.0
CG2 CA2 C2 111.8 110.4
CG2 CA2 HA2 110.0 110.3
CE2 CD2 HD32 111.5 110.6
CE2 CD2 HD22 111.5 110.6
CD2 CE2 N2 109.7 111.2
CD2 CE2 HE22 125.2 124.4
HD32 CD2 HD22 109.5 110.5
N2 CE2 HE22 125.1 124.3
CE2 N2 CA2 110.1 112.6
N2 CA2 C2 110.8 110.3
N2 CA2 HA2 110.8 110.3
C2 CA2 HA2 110.0 110.4
CA2 C2 NZ 114.0 120.0
CA2 C2 O2 121.5 120.0
O2 C2 NZ 124.5 120.0
C2 NZ CE 123.3 120.0
C2 NZ HZ 118.4 120.0
CE NZ HZ 118.4 120.0
NZ CE CD 108.8 109.5
NZ CE HE3 109.6 109.4
NZ CE HE2 109.6 109.4
CD CE HE3 109.7 109.5
CD CE HE2 109.7 109.5
CE CD CG 110.8 109.5
CE CD HD3 109.1 109.5
CE CD HD2 109.1 109.5
HE3 CE HE2 109.5 109.5
CG CD HD3 109.1 109.5
CG CD HD2 109.1 109.5
CD CG CB 112.0 109.5
CD CG HG3 108.8 109.5
CD CG HG2 108.8 109.5
HD3 CD HD2 109.5 109.4
CB CG HG3 108.8 109.4
CB CG HG2 108.8 109.4
CG CB CA 111.5 109.5
CG CB HB3 109.0 109.5
CG CB HB2 109.0 109.5
HG3 CG HG2 109.5 109.5
CA CB HB3 108.9 109.4
CA CB HB2 109.0 109.5
CB CA C 109.6 109.5
CB CA HA 108.9 109.5
CB CA N 110.2 109.4
HB3 CB HB2 109.5 109.5
C CA HA 108.9 109.5
C CA N 109.6 109.5
CA C OXT 116.7 120.0
CA C O 117.0 120.0
N CA HA 109.6 109.5
CA N H 109.5 111.0
CA N H2 109.4 111.0
OXT C O 126.3 120.0
C OXT HXT 109.5 117.0
H N H2 109.5 111.0

Torsion Angles for PYL

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
HB12 CB2 CG2 HB22 240.0 240.0
HB12 CB2 CG2 HB32 120.0 120.0
HB22 CB2 CG2 HB32 240.0 239.9
CD2 CG2 CB2 CA2 114.3 111.5
CD2 CG2 CB2 HG22 237.7 235.7
CB2 CG2 CD2 CE2 202.0 218.6
CB2 CG2 CD2 HD32 320.6 337.1
CB2 CG2 CD2 HD22 83.4 99.9
CA2 CG2 CB2 HG22 123.4 124.2
CB2 CG2 CA2 N2 157.9 141.9
CB2 CG2 CA2 C2 277.1 260.8
CB2 CG2 CA2 HA2 39.5 23.0
CG2 CB2 HB12 HB22 120.0 120.0
CG2 CB2 HB12 HB32 240.0 240.0
HB12 CB2 CG2 CD2 180.0 58.6
HB12 CB2 CG2 CA2 65.7 307.1
HB12 CB2 CG2 HG22 302.3 182.8
HB22 CB2 HB12 HB32 120.0 120.1
CG2 CB2 HB22 HB12 240.0 240.1
CG2 CB2 HB22 HB32 120.0 120.0
HB22 CB2 CG2 CD2 300.0 178.5
HB22 CB2 CG2 CA2 185.8 67.1
HB22 CB2 CG2 HG22 62.3 302.8
HB12 CB2 HB22 HB32 240.0 240.0
CG2 CB2 HB32 HB12 120.0 120.0
CG2 CB2 HB32 HB22 240.0 240.0
HB32 CB2 CG2 CD2 60.0 298.6
HB32 CB2 CG2 CA2 305.7 187.1
HB32 CB2 CG2 HG22 182.3 62.9
HB12 CB2 HB32 HB22 120.0 120.0
CD2 CG2 CB2 HB12 180.0 58.6
CD2 CG2 CB2 HB22 300.0 178.5
CD2 CG2 CB2 HB32 60.0 298.6
CB2 CG2 CD2 CA2 237.7 242.1
CB2 CG2 CD2 HG22 122.3 124.1
CA2 CG2 CD2 HG22 244.5 242.1
CD2 CG2 CA2 N2 36.8 23.9
CD2 CG2 CA2 C2 156.0 142.9
CD2 CG2 CA2 HA2 278.4 265.1
CE2 CD2 CG2 HD32 241.4 241.4
CE2 CD2 CG2 HD22 118.6 118.6
CG2 CD2 CE2 N2 23.6 15.9
CG2 CD2 CE2 HE22 203.6 195.9
HD32 CD2 CG2 HD22 237.3 237.2
CA2 CG2 CB2 HB12 65.7 307.1
CA2 CG2 CB2 HB22 185.8 67.1
CA2 CG2 CB2 HB32 305.7 187.1
CB2 CG2 CA2 CD2 121.1 117.9
CB2 CG2 CA2 HG22 236.6 235.9
CD2 CG2 CA2 HG22 115.5 117.9
CA2 CG2 CD2 CE2 324.2 336.5
CA2 CG2 CD2 HD32 82.9 95.1
CA2 CG2 CD2 HD22 205.6 217.9
CE2 N2 CA2 CG2 336.3 343.8
N2 CA2 CG2 C2 240.8 241.1
N2 CA2 CG2 HA2 118.3 118.8
C2 CA2 CG2 HA2 237.5 237.8
CG2 CA2 C2 NZ 225.3 80.0
CG2 CA2 C2 O2 44.3 260.1
HG22 CG2 CB2 HB12 302.3 182.8
HG22 CG2 CB2 HB22 62.3 302.8
HG22 CG2 CB2 HB32 182.3 62.9
CB2 CG2 HG22 CD2 235.9 235.7
CB2 CG2 HG22 CA2 126.2 124.3
CD2 CG2 HG22 CA2 250.3 248.5
HG22 CG2 CD2 CE2 79.7 94.4
HG22 CG2 CD2 HD32 198.3 213.0
HG22 CG2 CD2 HD22 321.1 335.8
HG22 CG2 CA2 N2 281.3 266.0
HG22 CG2 CA2 C2 40.5 24.9
HG22 CG2 CA2 HA2 162.9 147.2
CE2 CD2 CG2 CA2 324.2 336.5
CE2 CD2 CG2 HG22 79.7 94.4
CG2 CD2 CE2 HD32 118.6 118.6
CG2 CD2 CE2 HD22 241.4 241.3
HD32 CD2 CE2 HD22 122.7 122.7
N2 CE2 CD2 HE22 180.0 180.0
CD2 CE2 N2 CA2 359.9 0.1
HD32 CD2 CG2 CA2 82.9 95.1
HD32 CD2 CG2 HG22 198.3 213.0
CG2 CD2 HD32 CE2 247.9 245.6
CG2 CD2 HD32 HD22 123.9 122.9
CE2 CD2 HD32 HD22 236.1 237.2
HD32 CD2 CE2 N2 265.0 257.3
HD32 CD2 CE2 HE22 85.0 77.3
HD22 CD2 CG2 CA2 205.6 217.9
HD22 CD2 CG2 HG22 321.1 335.8
CG2 CD2 HD22 CE2 112.1 114.4
CG2 CD2 HD22 HD32 236.1 237.2
CE2 CD2 HD22 HD32 123.9 122.8
HD22 CD2 CE2 N2 142.2 134.5
HD22 CD2 CE2 HE22 322.2 314.6
CG2 CA2 N2 CE2 336.3 343.8
N2 CE2 CD2 HD32 265.0 257.3
N2 CE2 CD2 HD22 142.2 134.5
CD2 CE2 N2 HE22 180.0 180.0
CE2 N2 CA2 C2 216.4 224.9
CE2 N2 CA2 HA2 94.1 102.7
HE22 CE2 CD2 HD32 85.0 77.3
HE22 CE2 CD2 HD22 322.2 314.6
CD2 CE2 HE22 N2 180.0 180.0
HE22 CE2 N2 CA2 179.9 180.1
N2 CA2 CG2 HG22 281.3 266.0
CG2 CA2 N2 C2 119.9 118.9
CG2 CA2 N2 HA2 242.2 241.2
CA2 N2 CE2 HE22 179.9 180.1
C2 CA2 N2 HA2 122.4 122.2
N2 CA2 C2 NZ 340.0 195.6
N2 CA2 C2 O2 159.0 15.7
C2 CA2 CG2 HG22 40.5 24.9
CG2 CA2 C2 N2 245.3 244.3
CG2 CA2 C2 HA2 122.5 122.2
N2 CA2 C2 HA2 237.1 237.8
O2 C2 CA2 NZ 179.0 180.1
CA2 C2 NZ CE 180.4 180.0
CA2 C2 NZ HZ 0.5 0.1
HA2 CA2 CG2 HG22 162.9 147.2
CG2 CA2 HA2 N2 113.6 115.6
CG2 CA2 HA2 C2 236.5 237.8
N2 CA2 HA2 C2 122.9 122.2
HA2 CA2 C2 NZ 102.9 317.8
HA2 CA2 C2 O2 281.9 137.9
NZ C2 CA2 HA2 102.9 317.8
CA2 C2 NZ O2 178.9 180.1
CE NZ C2 HZ 180.0 179.9
C2 NZ CE CD 119.2 180.0
C2 NZ CE HE3 239.1 300.0
C2 NZ CE HE2 359.3 60.0
O2 C2 CA2 HA2 281.9 137.9
CA2 C2 O2 NZ 181.1 179.9
O2 C2 NZ CE 1.5 359.9
O2 C2 NZ HZ 181.5 180.0
C2 NZ CE HZ 180.0 180.1
CD CE NZ HE3 240.1 240.0
CD CE NZ HE2 119.9 120.0
NZ CE CD CG 296.6 180.0
NZ CE CD HD3 56.8 300.0
NZ CE CD HD2 176.3 59.9
HE3 CE NZ HE2 239.8 240.0
C2 NZ HZ CE 180.0 179.9
HZ NZ CE CD 299.2 360.0
HZ NZ CE HE3 59.1 120.0
HZ NZ CE HE2 179.3 240.0
CD CE NZ HZ 299.2 360.0
NZ CE CD HE3 119.9 120.0
NZ CE CD HE2 240.1 240.0
HE3 CE CD HE2 120.2 120.1
CG CD CE HD3 239.8 240.0
CG CD CE HD2 120.2 120.1
CE CD CG CB 171.9 180.0
CE CD CG HG3 292.3 300.0
CE CD CG HG2 51.5 60.0
HD3 CD CE HD2 240.4 240.1
HE3 CE NZ HZ 59.1 120.0
NZ CE HE3 CD 240.6 240.0
NZ CE HE3 HE2 120.3 120.0
CD CE HE3 HE2 239.7 240.0
HE3 CE CD CG 176.7 60.0
HE3 CE CD HD3 296.9 180.1
HE3 CE CD HD2 56.5 300.0
HE2 CE NZ HZ 179.3 240.0
NZ CE HE2 CD 119.4 120.0
NZ CE HE2 HE3 239.7 240.0
CD CE HE2 HE3 120.3 120.0
HE2 CE CD CG 56.5 300.0
HE2 CE CD HD3 176.7 60.0
HE2 CE CD HD2 296.2 179.9
CG CD CE HE3 176.7 60.0
CG CD CE HE2 56.5 300.0
CE CD CG HD3 120.2 120.0
CE CD CG HD2 239.8 240.0
HD3 CD CG HD2 119.6 120.0
CB CG CD HG3 239.6 240.0
CB CG CD HG2 120.4 120.0
CD CG CB CA 293.1 180.0
CD CG CB HB3 53.4 300.0
CD CG CB HB2 172.8 60.0
HG3 CG CD HG2 240.8 239.9
HD3 CD CE HE3 296.9 180.1
HD3 CD CE HE2 176.7 60.0
CE CD HD3 CG 238.7 240.0
CE CD HD3 HD2 119.4 120.0
CG CD HD3 HD2 240.6 240.0
HD3 CD CG CB 51.7 60.0
HD3 CD CG HG3 172.1 180.0
HD3 CD CG HG2 291.3 300.0
HD2 CD CE HE3 56.5 300.0
HD2 CD CE HE2 296.2 179.9
CE CD HD2 CG 121.3 120.0
CE CD HD2 HD3 240.6 240.1
CG CD HD2 HD3 119.4 120.0
HD2 CD CG CB 292.1 300.0
HD2 CD CG HG3 52.5 60.0
HD2 CD CG HG2 171.7 180.0
CB CG CD HD3 51.7 60.0
CB CG CD HD2 292.1 300.0
CD CG CB HG3 120.4 120.0
CD CG CB HG2 239.6 240.0
HG3 CG CB HG2 119.2 120.0
CA CB CG HB3 239.7 240.0
CA CB CG HB2 120.3 120.0
CG CB CA C 176.3 175.0
CG CB CA HA 57.3 55.0
CG CB CA N 297.0 295.0
HB3 CB CG HB2 240.6 240.0
HG3 CG CD HD3 172.1 180.0
HG3 CG CD HD2 52.5 60.0
CD CG HG3 CB 237.7 240.0
CD CG HG3 HG2 118.8 120.1
CB CG HG3 HG2 241.2 240.0
HG3 CG CB CA 172.7 60.0
HG3 CG CB HB3 293.0 180.0
HG3 CG CB HB2 52.4 300.0
HG2 CG CD HD3 291.3 300.0
HG2 CG CD HD2 171.7 180.0
CD CG HG2 CB 122.4 120.0
CD CG HG2 HG3 241.2 240.0
CB CG HG2 HG3 118.8 120.0
HG2 CG CB CA 53.5 300.0
HG2 CG CB HB3 173.8 60.0
HG2 CG CB HB2 293.2 180.0
CA CB CG HG3 172.7 60.0
CA CB CG HG2 53.5 300.0
CG CB CA HB3 120.3 120.0
CG CB CA HB2 239.7 239.9
HB3 CB CA HB2 119.4 119.9
C CA CB HA 119.0 120.0
C CA CB N 239.3 240.0
CB CA C OXT 272.2 280.0
CB CA C O 92.5 100.0
N CA CB HA 239.7 240.0
CB CA N H 180.0 176.0
CB CA N H2 300.0 300.0
HB3 CB CG HG3 293.0 180.0
HB3 CB CG HG2 173.8 60.0
CG CB HB3 CA 238.2 240.0
CG CB HB3 HB2 119.1 120.1
CA CB HB3 HB2 240.9 240.1
HB3 CB CA C 56.0 55.0
HB3 CB CA HA 297.0 295.0
HB3 CB CA N 176.7 175.0
HB2 CB CG HG3 52.4 300.0
HB2 CB CG HG2 293.2 180.0
CG CB HB2 CA 121.9 120.1
CG CB HB2 HB3 240.9 240.0
CA CB HB2 HB3 119.1 119.9
HB2 CB CA C 296.6 295.0
HB2 CB CA HA 177.6 175.0
HB2 CB CA N 57.3 55.0
C CA CB HB3 56.0 55.0
C CA CB HB2 296.6 295.0
CB CA C HA 241.0 240.0
CB CA C N 121.1 120.0
N CA C HA 119.9 120.0
C CA N H 300.7 296.0
C CA N H2 60.8 60.0
OXT C CA O 179.7 179.9
CA C OXT HXT 180.3 180.0
HA CA CB HB3 297.0 295.0
HA CA CB HB2 177.6 175.0
CB CA HA C 119.5 120.0
CB CA HA N 239.3 240.0
C CA HA N 119.9 120.0
HA CA C OXT 31.2 40.0
HA CA C O 211.4 220.0
HA CA N H 60.1 56.0
HA CA N H2 180.2 180.0
N CA CB HB3 176.7 175.0
N CA CB HB2 57.3 55.0
CB CA N C 239.3 240.0
CB CA N HA 119.8 120.0
C CA N HA 240.6 240.0
N CA C OXT 151.1 160.0
N CA C O 331.4 340.0
H N CA H2 240.0 236.0
OXT C CA HA 31.2 40.0
OXT C CA N 151.1 160.0
CA C OXT O 180.3 180.1
O C CA HA 211.4 220.0
O C CA N 331.4 340.0
CA C O OXT 179.7 179.9
O C OXT HXT 0.0 359.9
HXT OXT C O 0.0 359.9
H N CA HA 60.1 56.0
CA N H H2 120.0 124.0
H2 N CA HA 180.2 180.0
CA N H2 H 240.0 236.0