PDB Chemical Component PY6

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 PY6

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
N1 C2 1.383 1.317
N1 C6 1.364 1.319
C2 C2A 1.522 1.507
C2 C3 1.444 1.387
C2A H2A1 1.114 1.089
C2A H2A2 1.115 1.090
C2A H2A3 1.115 1.090
C3 O3 1.352 1.359
C3 C4 1.407 1.392
O3 HO3 0.950 0.967
C4 C4A 1.518 1.507
C4 C5 1.439 1.385
C4A N 1.515 1.468
C4A H4A1 1.115 1.090
C4A H4A2 1.115 1.089
C5 C6 1.383 1.382
C5 C5A 1.528 1.507
C6 H6 1.104 1.080
C5A O4P 1.383 1.429
C5A H5A1 1.115 1.090
C5A H5A2 1.115 1.088
O4P P 1.586 1.609
P O1P 1.426 1.480
P O2P 1.501 1.610
P O3P 1.493 1.609
O2P HOP2 0.951 0.967
O3P HOP3 0.951 0.967
N CA 1.497 1.469
N HN2 1.019 1.009
CA C 1.515 1.508
CA CB 1.528 1.530
CA HA 1.115 1.089
C O 1.349 1.208
C OXT 1.293 1.341
CB CG 1.525 1.529
CB HB1 1.115 1.090
CB HB2 1.116 1.090
CG CD 1.523 1.529
CG HG1 1.115 1.091
CG HG2 1.114 1.089
CD CE 1.520 1.530
CD HD1 1.115 1.090
CD HD2 1.115 1.090
CE HE1 1.116 1.090
CE HE2 1.115 1.088
CE HE3 1.115 1.089
OXT HXT 0.949 0.966

Bond Angles for PY6

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
C2 N1 C6 122.3 121.8
N1 C2 C2A 109.5 119.7
N1 C2 C3 117.9 120.7
N1 C6 C5 118.0 120.9
N1 C6 H6 120.4 119.6
C2A C2 C3 132.5 119.6
C2 C2A H2A1 109.5 109.5
C2 C2A H2A2 112.1 109.5
C2 C2A H2A3 112.1 109.5
C2 C3 O3 110.9 120.5
C2 C3 C4 123.6 119.0
H2A1 C2A H2A2 112.2 109.4
H2A1 C2A H2A3 112.2 109.5
H2A2 C2A H2A3 98.3 109.4
O3 C3 C4 125.5 120.5
C3 O3 HO3 110.8 106.7
C3 C4 C4A 122.3 120.8
C3 C4 C5 112.1 118.4
C4A C4 C5 125.6 120.8
C4 C4A N 103.1 109.4
C4 C4A H4A1 114.6 109.5
C4 C4A H4A2 114.6 109.4
C4 C5 C6 126.1 119.2
C4 C5 C5A 122.4 120.3
N C4A H4A1 114.7 109.5
N C4A H4A2 114.7 109.5
C4A N CA 110.6 106.7
C4A N HN2 111.8 106.7
H4A1 C4A H4A2 95.8 109.5
C6 C5 C5A 111.5 120.4
C5 C6 H6 121.7 119.5
C5 C5A O4P 118.7 109.5
C5 C5A H5A1 108.9 109.4
C5 C5A H5A2 108.9 109.5
O4P C5A H5A1 108.8 109.4
O4P C5A H5A2 108.8 109.5
C5A O4P P 122.7 106.8
H5A1 C5A H5A2 101.2 109.6
O4P P O1P 112.8 109.5
O4P P O2P 104.2 109.5
O4P P O3P 104.5 109.5
O1P P O2P 122.8 109.5
O1P P O3P 101.8 109.4
O2P P O3P 109.5 109.5
P O2P HOP2 104.2 106.8
P O3P HOP3 104.5 106.8
CA N HN2 111.8 106.7
N CA C 108.4 109.4
N CA CB 111.1 109.5
N CA HA 109.8 109.5
C CA CB 111.4 109.5
C CA HA 109.4 109.5
CA C O 110.6 120.0
CA C OXT 124.6 120.1
CB CA HA 106.6 109.5
CA CB CG 115.2 109.5
CA CB HB1 110.2 109.5
CA CB HB2 110.1 109.4
O C OXT 124.8 120.0
C OXT HXT 124.6 120.0
CG CB HB1 110.1 109.5
CG CB HB2 110.1 109.5
CB CG CD 112.0 109.5
CB CG HG1 111.3 109.4
CB CG HG2 111.3 109.5
HB1 CB HB2 100.1 109.4
CD CG HG1 111.2 109.5
CD CG HG2 111.3 109.5
CG CD CE 113.5 109.5
CG CD HD1 110.8 109.5
CG CD HD2 110.8 109.5
HG1 CG HG2 99.1 109.4
CE CD HD1 110.7 109.4
CE CD HD2 110.7 109.4
CD CE HE1 113.5 109.5
CD CE HE2 110.8 109.5
CD CE HE3 110.8 109.5
HD1 CD HD2 99.5 109.5
HE1 CE HE2 110.7 109.4
HE1 CE HE3 110.8 109.4
HE2 CE HE3 99.5 109.5

Torsion Angles for PY6

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C2 N1 C6 C5 359.6 359.8
C2 N1 C6 H6 179.6 180.0
C2A C2 N1 C3 179.6 180.0
N1 C2 C2A H2A1 180.0 270.0
N1 C2 C2A H2A2 305.3 30.0
N1 C2 C2A H2A3 54.8 150.0
N1 C2 C3 O3 180.1 180.0
N1 C2 C3 C4 359.5 0.0
C6 N1 C2 C2A 180.1 180.0
C6 N1 C2 C3 0.5 360.0
C4 C5 C6 N1 0.3 0.5
N1 C6 C5 C5A 179.9 180.0
C5 C6 N1 H6 180.0 179.8
C2A C2 N1 C6 180.1 180.0
N1 C2 C2A C3 180.5 180.0
C2A C2 C3 O3 0.6 360.0
C2A C2 C3 C4 180.0 180.0
H2A1 C2A C2 H2A2 234.7 240.0
H2A1 C2A C2 H2A3 125.2 120.1
H2A2 C2A C2 H2A3 250.5 240.0
C3 C2 N1 C6 0.5 360.0
N1 C2 C3 C2A 179.5 180.0
C3 C2 C2A H2A1 359.5 90.1
C3 C2 C2A H2A2 124.8 210.0
C3 C2 C2A H2A3 234.3 330.0
O3 C3 C2 C4 180.5 180.0
C2 C3 O3 HO3 180.0 270.1
C2 C3 C4 C4A 180.2 179.9
C2 C3 C4 C5 0.3 0.3
H2A1 C2A C2 C3 359.5 90.1
C2 C2A H2A1 H2A2 125.2 120.0
C2 C2A H2A1 H2A3 234.8 239.9
H2A2 C2A H2A1 H2A3 109.6 120.0
H2A2 C2A C2 C3 124.8 210.0
C2 C2A H2A2 H2A1 236.2 240.0
C2 C2A H2A2 H2A3 118.0 120.0
H2A1 C2A H2A2 H2A3 241.9 240.0
H2A3 C2A C2 C3 234.3 330.0
C2 C2A H2A3 H2A1 123.8 120.1
C2 C2A H2A3 H2A2 241.9 240.0
H2A1 C2A H2A3 H2A2 118.2 119.9
C2 C3 O3 C4 179.5 180.0
O3 C3 C4 C4A 359.5 360.0
O3 C3 C4 C5 179.7 180.3
C2 C3 C4 O3 180.6 180.0
C4 C3 O3 HO3 0.5 90.0
C4A C4 C3 C5 179.8 179.7
C3 C4 C4A N 331.6 90.0
C3 C4 C4A H4A1 96.9 330.1
C3 C4 C4A H4A2 206.3 210.0
C3 C4 C5 C6 359.7 359.5
C3 C4 C5 C5A 180.2 180.0
HO3 O3 C3 C4 0.5 90.0
C3 C4 C4A C5 180.2 180.3
C4A C4 C5 C6 179.9 179.8
C4A C4 C5 C5A 0.4 0.3
N C4A C4 H4A1 234.7 119.9
N C4A C4 H4A2 125.3 240.0
C4 C4A N CA 157.3 180.0
C4 C4A N HN2 32.0 66.2
H4A1 C4A C4 H4A2 250.6 120.0
N1 C6 C5 C4 0.3 0.5
C3 C4 C5 C4A 179.8 179.7
C5 C4 C4A N 151.4 269.7
C5 C4 C4A H4A1 276.7 149.8
C5 C4 C4A H4A2 26.1 29.7
C6 C5 C4 C5A 179.5 179.5
C4 C5 C6 H6 180.3 180.3
C4 C5 C5A O4P 20.7 179.5
C4 C5 C5A H5A1 145.9 299.4
C4 C5 C5A H5A2 255.4 59.5
N C4A C4 C5 151.4 269.7
C4 C4A N H4A1 125.3 240.1
C4 C4A N H4A2 234.7 120.0
H4A1 C4A N H4A2 109.5 239.9
CA N C4A HN2 125.2 113.8
C4A N CA C 180.1 270.0
C4A N CA CB 57.3 150.0
C4A N CA HA 299.6 30.0
H4A1 C4A C4 C5 276.7 149.8
C4 C4A H4A1 N 241.0 119.9
C4 C4A H4A1 H4A2 120.4 240.0
N C4A H4A1 H4A2 239.5 120.1
H4A1 C4A N CA 32.0 300.0
H4A1 C4A N HN2 266.8 186.1
H4A2 C4A C4 C5 26.1 29.7
C4 C4A H4A2 N 119.0 240.1
C4 C4A H4A2 H4A1 239.5 120.0
N C4A H4A2 H4A1 120.5 240.0
H4A2 C4A N CA 282.5 60.1
H4A2 C4A N HN2 157.3 306.2
N1 C6 C5 H6 180.0 180.2
C4 C5 C6 C5A 180.4 180.5
C6 C5 C5A O4P 201.1 0.0
C6 C5 C5A H5A1 326.4 119.9
C6 C5 C5A H5A2 75.9 239.9
C4 C5 C5A C6 179.6 179.5
C5A C5 C6 H6 359.9 359.8
O4P C5A C5 H5A1 234.8 240.1
O4P C5A C5 H5A2 125.3 120.1
C5 C5A O4P P 151.2 180.0
H5A1 C5A C5 H5A2 250.5 239.9
N1 C6 H6 C5 180.0 179.8
H6 C6 C5 C5A 359.9 359.8
C5 C5A O4P H5A1 125.3 119.9
C5 C5A O4P H5A2 234.7 240.0
H5A1 C5A O4P H5A2 109.4 120.1
C5A O4P P O1P 308.2 59.9
C5A O4P P O2P 172.8 180.0
C5A O4P P O3P 57.9 300.0
C5 C5A H5A1 O4P 229.2 240.1
C5 C5A H5A1 H5A2 114.6 120.0
O4P C5A H5A1 H5A2 245.5 239.9
H5A1 C5A O4P P 25.9 60.1
C5 C5A H5A2 O4P 130.9 120.0
C5 C5A H5A2 H5A1 245.4 240.0
O4P C5A H5A2 H5A1 114.5 120.0
H5A2 C5A O4P P 276.5 300.0
P O4P C5A H5A1 25.9 60.1
P O4P C5A H5A2 276.5 300.0
O1P P O4P O2P 135.3 240.0
O1P P O4P O3P 250.3 120.0
O2P P O4P O3P 114.9 240.0
O4P P O2P HOP2 180.0 180.0
O4P P O3P HOP3 180.0 300.0
O4P P O1P O2P 234.1 120.0
O4P P O1P O3P 111.4 240.0
O2P P O1P O3P 237.3 120.0
O1P P O2P HOP2 50.4 300.0
O1P P O3P HOP3 297.6 180.0
O4P P O2P O1P 129.6 240.0
O4P P O2P O3P 248.7 120.0
O1P P O2P O3P 119.1 240.0
O2P P O3P HOP3 68.9 60.0
O4P P O3P O1P 242.5 120.0
O4P P O3P O2P 111.1 239.9
O1P P O3P O2P 228.6 120.0
O3P P O2P HOP2 291.3 60.0
HOP2 O2P P O3P 291.3 60.0
CA N C4A H4A1 32.0 300.0
CA N C4A H4A2 282.5 60.1
C4A N CA HN2 234.8 246.2
C CA N CB 122.8 120.0
C CA N HA 240.5 240.0
N CA C O 48.8 150.0
N CA C OXT 229.0 330.0
CB CA N HA 117.7 120.0
N CA CB CG 56.7 300.0
N CA CB HB1 182.0 179.9
N CA CB HB2 291.4 60.0
HN2 N C4A H4A1 266.8 186.1
HN2 N C4A H4A2 157.3 306.2
C4A N HN2 CA 124.5 113.8
HN2 N CA C 305.3 23.8
HN2 N CA CB 182.6 263.8
HN2 N CA HA 64.9 143.8
C CA N HN2 305.3 23.8
N CA C CB 237.5 240.0
N CA C HA 119.8 120.0
CB CA C HA 242.3 240.0
C CA CB CG 295.7 180.0
C CA CB HB1 60.9 60.0
C CA CB HB2 170.4 300.1
O C CA OXT 179.7 179.9
CA C OXT HXT 180.0 180.0
CB CA N HN2 182.6 263.8
N CA CB C 121.0 120.0
N CA CB HA 240.4 240.0
C CA CB HA 119.4 120.0
CB CA C O 171.3 270.0
CB CA C OXT 351.6 90.0
CG CB CA HB1 234.7 120.1
CG CB CA HB2 125.3 239.9
CA CB CG CD 191.8 180.0
CA CB CG HG1 317.0 60.0
CA CB CG HG2 66.6 300.0
HB1 CB CA HB2 250.5 119.9
HA CA N HN2 64.9 143.8
N CA HA C 241.1 240.0
N CA HA CB 120.4 120.0
C CA HA CB 239.3 240.0
HA CA C O 289.0 30.0
HA CA C OXT 109.3 210.0
HA CA CB CG 176.3 60.0
HA CA CB HB1 301.6 299.9
HA CA CB HB2 51.0 180.1
O C CA CB 171.3 270.0
O C CA HA 289.0 30.0
CA C O OXT 180.3 180.1
O C OXT HXT 0.3 0.1
OXT C CA CB 351.6 90.0
OXT C CA HA 109.3 210.0
CA C OXT O 179.7 179.9
CG CB CA HA 176.3 60.0
CA CB CG HB1 125.3 240.0
CA CB CG HB2 234.7 120.0
HB1 CB CG HB2 109.4 240.0
CD CG CB HG1 234.8 120.0
CD CG CB HG2 125.3 239.9
CB CG CD CE 79.9 180.0
CB CG CD HD1 205.2 60.1
CB CG CD HD2 314.7 300.0
HG1 CG CB HG2 250.5 119.9
HB1 CB CA HA 301.6 299.9
CA CB HB1 CG 231.9 120.0
CA CB HB1 HB2 116.0 240.1
CG CB HB1 HB2 244.1 120.0
HB1 CB CG CD 66.5 300.0
HB1 CB CG HG1 191.7 180.0
HB1 CB CG HG2 301.3 60.1
HB2 CB CA HA 51.0 180.1
CA CB HB2 CG 128.1 240.0
CA CB HB2 HB1 244.0 119.9
CG CB HB2 HB1 116.0 240.0
HB2 CB CG CD 317.1 60.0
HB2 CB CG HG1 82.3 300.0
HB2 CB CG HG2 191.8 180.0
CD CG CB HB1 66.5 300.0
CD CG CB HB2 317.1 60.0
CB CG CD HG1 125.2 240.0
CB CG CD HG2 234.7 120.1
HG1 CG CD HG2 109.5 240.0
CE CD CG HD1 234.7 120.0
CE CD CG HD2 125.2 240.0
CG CD CE HE1 180.0 180.0
CG CD CE HE2 305.3 300.0
CG CD CE HE3 54.7 60.0
HD1 CD CG HD2 250.5 120.1
HG1 CG CB HB1 191.7 180.0
HG1 CG CB HB2 82.3 300.0
CB CG HG1 CD 234.3 120.0
CB CG HG1 HG2 117.2 240.0
CD CG HG1 HG2 242.8 120.0
HG1 CG CD CE 314.7 300.0
HG1 CG CD HD1 80.0 180.0
HG1 CG CD HD2 189.5 60.0
HG2 CG CB HB1 301.3 60.1
HG2 CG CB HB2 191.8 180.0
CB CG HG2 CD 125.7 240.0
CB CG HG2 HG1 242.8 120.0
CD CG HG2 HG1 117.1 240.0
HG2 CG CD CE 205.2 60.0
HG2 CG CD HD1 330.5 300.0
HG2 CG CD HD2 79.9 179.9
CE CD CG HG1 314.7 300.0
CE CD CG HG2 205.2 60.0
CG CD CE HD1 125.3 240.0
CG CD CE HD2 234.8 120.0
HD1 CD CE HD2 109.4 240.0
HE1 CE CD HE2 234.8 240.0
HE1 CE CD HE3 125.3 119.9
HE2 CE CD HE3 250.5 239.9
HD1 CD CG HG1 80.0 180.0
HD1 CD CG HG2 330.5 300.0
CG CD HD1 CE 233.2 120.0
CG CD HD1 HD2 116.6 239.9
CE CD HD1 HD2 243.4 120.0
HD1 CD CE HE1 54.7 300.0
HD1 CD CE HE2 179.9 59.9
HD1 CD CE HE3 289.4 180.0
HD2 CD CG HG1 189.5 60.0
HD2 CD CG HG2 79.9 179.9
CG CD HD2 CE 126.8 240.0
CG CD HD2 HD1 243.3 120.1
CE CD HD2 HD1 116.6 240.0
HD2 CD CE HE1 305.3 60.0
HD2 CD CE HE2 70.5 179.9
HD2 CD CE HE3 180.0 300.0
HE1 CE CD HD1 54.7 300.0
HE1 CE CD HD2 305.3 60.0
CD CE HE1 HE2 125.3 120.0
CD CE HE1 HE3 234.7 240.0
HE2 CE HE1 HE3 109.4 120.0
HE2 CE CD HD1 179.9 59.9
HE2 CE CD HD2 70.5 179.9
CD CE HE2 HE1 233.2 240.0
CD CE HE2 HE3 116.6 120.1
HE1 CE HE2 HE3 243.4 240.1
HE3 CE CD HD1 289.4 180.0
HE3 CE CD HD2 180.0 300.0
CD CE HE3 HE1 126.8 120.0
CD CE HE3 HE2 243.4 239.9
HE1 CE HE3 HE2 116.5 119.9