PDB Chemical Component YFD

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 YFD

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
CAA CAJ 1.528 1.530
CAJ CAL 1.513 1.530
CAL CAM 1.526 1.530
CAM CAN 1.538 1.531
CAN CAS 1.514 1.507
CAS CAV 1.399 1.399
CAS CAI 1.374 1.366
CAV CAQ 1.519 1.471
CAV CAR 1.392 1.403
CAQ OAF 1.254 1.348
CAQ OAE 1.252 1.216
CAR OAG 1.368 1.356
CAR CAU 1.408 1.385
CAI CAT 1.395 1.392
CAT OAO 1.388 1.356
CAT CAU 1.410 1.388
OAO CAB 1.466 1.430
CAU CAK 1.536 1.506
CAK CAH 1.412 1.507
CAH CAP 1.399 1.310
CAP CAD 1.534 1.507
CAP CAC 1.545 1.508
CAA HAA1 1.100 1.090
CAA HAA2 1.100 1.090
CAA HAA3 1.100 1.090
CAJ HAJ1 1.100 1.090
CAJ HAJ2 1.100 1.089
CAL HAL1 1.100 1.090
CAL HAL2 1.100 1.090
CAM HAM1 1.099 1.089
CAM HAM2 1.100 1.090
CAN HAN1 1.100 1.090
CAN HAN2 1.100 1.090
CAI HAI 1.080 1.080
OAF HAF 0.950 0.966
OAG HAG 0.950 0.967
CAB HAB1 1.100 1.090
CAB HAB2 1.100 1.090
CAB HAB3 1.100 1.090
CAK HAK1 1.100 1.090
CAK HAK2 1.100 1.090
CAH HAH 1.080 1.080
CAD HAD1 1.100 1.090
CAD HAD2 1.101 1.090
CAD HAD3 1.100 1.090
CAC HAC1 1.100 1.090
CAC HAC2 1.101 1.090
CAC HAC3 1.100 1.090

Bond Angles for YFD

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
CAA CAJ CAL 105.8 109.4
CAJ CAA HAA1 109.5 109.5
CAJ CAA HAA2 109.4 109.5
CAJ CAA HAA3 109.4 109.4
CAA CAJ HAJ1 110.4 109.5
CAA CAJ HAJ2 110.4 109.5
CAJ CAL CAM 108.6 109.4
CAL CAJ HAJ1 110.4 109.4
CAL CAJ HAJ2 110.4 109.5
CAJ CAL HAL1 109.7 109.5
CAJ CAL HAL2 109.7 109.5
CAL CAM CAN 105.9 109.4
CAM CAL HAL1 109.7 109.5
CAM CAL HAL2 109.7 109.5
CAL CAM HAM1 110.4 109.5
CAL CAM HAM2 110.4 109.5
CAM CAN CAS 109.1 109.4
CAN CAM HAM1 110.4 109.5
CAN CAM HAM2 110.3 109.4
CAM CAN HAN1 109.6 109.5
CAM CAN HAN2 109.6 109.5
CAN CAS CAV 127.1 120.0
CAN CAS CAI 114.6 120.0
CAS CAN HAN1 109.6 109.4
CAS CAN HAN2 109.6 109.5
CAV CAS CAI 118.3 120.1
CAS CAV CAQ 123.0 120.1
CAS CAV CAR 120.8 119.7
CAS CAI CAT 121.7 120.4
CAS CAI HAI 119.1 119.8
CAQ CAV CAR 116.2 120.1
CAV CAQ OAF 116.6 120.0
CAV CAQ OAE 118.7 120.0
CAV CAR OAG 115.6 120.2
CAV CAR CAU 121.6 119.6
OAF CAQ OAE 124.7 120.0
CAQ OAF HAF 109.5 117.0
OAG CAR CAU 122.8 120.1
CAR OAG HAG 109.5 114.0
CAR CAU CAT 116.6 119.9
CAR CAU CAK 120.7 120.1
CAI CAT OAO 116.0 119.9
CAI CAT CAU 121.1 120.3
CAT CAI HAI 119.2 119.8
OAO CAT CAU 122.9 119.9
CAT OAO CAB 110.8 117.0
CAT CAU CAK 122.7 120.0
OAO CAB HAB1 109.5 109.4
OAO CAB HAB2 109.5 109.5
OAO CAB HAB3 109.5 109.5
CAU CAK CAH 109.2 109.5
CAU CAK HAK1 109.5 109.5
CAU CAK HAK2 109.5 109.5
CAK CAH CAP 128.2 120.0
CAH CAK HAK1 109.6 109.5
CAH CAK HAK2 109.5 109.5
CAK CAH HAH 115.9 120.0
CAH CAP CAD 119.3 120.0
CAH CAP CAC 120.7 120.0
CAP CAH HAH 115.9 120.0
CAD CAP CAC 120.0 120.0
CAP CAD HAD1 109.5 109.4
CAP CAD HAD2 109.5 109.5
CAP CAD HAD3 109.5 109.5
CAP CAC HAC1 109.5 109.5
CAP CAC HAC2 109.4 109.5
CAP CAC HAC3 109.5 109.5
HAA1 CAA HAA2 109.5 109.5
HAA1 CAA HAA3 109.5 109.4
HAA2 CAA HAA3 109.5 109.5
HAJ1 CAJ HAJ2 109.5 109.5
HAL1 CAL HAL2 109.5 109.5
HAM1 CAM HAM2 109.5 109.5
HAN1 CAN HAN2 109.4 109.5
HAB1 CAB HAB2 109.4 109.5
HAB1 CAB HAB3 109.5 109.4
HAB2 CAB HAB3 109.5 109.5
HAK1 CAK HAK2 109.5 109.4
HAD1 CAD HAD2 109.5 109.5
HAD1 CAD HAD3 109.4 109.5
HAD2 CAD HAD3 109.4 109.5
HAC1 CAC HAC2 109.5 109.5
HAC1 CAC HAC3 109.5 109.5
HAC2 CAC HAC3 109.5 109.5

Torsion Angles for YFD

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
CAA CAJ CAL CAM 181.3 180.0
CAL CAJ CAA HAJ1 240.6 240.1
CAL CAJ CAA HAJ2 119.4 120.0
CAA CAJ CAL HAL1 301.1 299.9
CAA CAJ CAL HAL2 61.4 60.0
HAA1 CAA CAJ HAA2 240.0 239.9
HAA1 CAA CAJ HAA3 120.0 119.9
HAA2 CAA CAJ HAA3 240.0 240.0
HAJ1 CAJ CAA HAJ2 238.8 239.9
CAL CAJ CAA HAA1 180.0 300.0
CAL CAJ CAA HAA2 300.0 60.1
CAL CAJ CAA HAA3 60.0 180.0
CAA CAJ CAL HAJ1 119.4 119.9
CAA CAJ CAL HAJ2 240.6 240.0
CAJ CAL CAM CAN 104.9 180.0
CAM CAL CAJ HAL1 240.1 240.0
CAM CAL CAJ HAL2 119.8 120.0
CAJ CAL CAM HAM1 224.3 300.0
CAJ CAL CAM HAM2 345.4 60.0
HAJ1 CAJ CAL HAJ2 121.2 120.0
HAL1 CAL CAJ HAL2 239.7 239.9
CAM CAL CAJ HAJ1 61.9 60.0
CAM CAL CAJ HAJ2 300.7 300.0
CAJ CAL CAM HAL1 119.9 120.0
CAJ CAL CAM HAL2 240.1 240.0
CAL CAM CAN CAS 146.4 180.0
CAN CAM CAL HAM1 240.6 240.0
CAN CAM CAL HAM2 119.4 119.9
CAL CAM CAN HAN1 266.4 300.0
CAL CAM CAN HAN2 26.5 60.0
HAL1 CAL CAM HAL2 120.3 120.1
HAM1 CAM CAL HAM2 238.9 239.9
CAN CAM CAL HAL1 345.0 60.0
CAN CAM CAL HAL2 224.7 299.9
CAL CAM CAN HAM1 119.4 120.0
CAL CAM CAN HAM2 240.6 240.1
CAM CAN CAS CAV 79.0 85.0
CAM CAN CAS CAI 258.8 264.8
CAS CAN CAM HAN1 240.0 240.0
CAS CAN CAM HAN2 120.0 120.0
HAM1 CAM CAN HAM2 121.1 120.0
HAN1 CAN CAM HAN2 239.9 239.9
CAS CAN CAM HAM1 27.0 60.0
CAS CAN CAM HAM2 265.9 299.9
CAM CAN CAS HAN1 120.0 120.0
CAM CAN CAS HAN2 240.0 240.0
CAV CAS CAN CAI 180.2 180.3
CAN CAS CAV CAQ 0.5 0.0
CAN CAS CAV CAR 180.7 179.9
CAN CAS CAI CAT 179.2 180.1
CAN CAS CAI HAI 359.2 0.0
HAN1 CAN CAS HAN2 120.1 120.0
CAN CAS CAV CAI 179.8 179.7
CAV CAS CAN HAN1 319.0 325.0
CAV CAS CAN HAN2 199.0 205.0
CAV CAS CAI CAT 359.1 359.8
CAV CAS CAI HAI 179.1 179.8
CAQ CAV CAS CAR 179.9 180.1
CAS CAV CAQ OAF 176.0 269.9
CAS CAV CAQ OAE 354.5 90.0
CAS CAV CAR OAG 180.6 180.0
CAS CAV CAR CAU 359.1 0.1
CAN CAS CAI CAV 180.2 180.3
CAI CAS CAN HAN1 138.9 144.7
CAI CAS CAN HAN2 18.8 24.7
CAI CAS CAV CAQ 180.7 180.3
CAI CAS CAV CAR 0.9 0.2
CAS CAI CAT OAO 180.4 180.0
CAS CAI CAT CAU 1.1 359.9
CAT CAI CAS HAI 180.0 180.1
CAQ CAV CAS CAI 180.7 180.3
CAS CAV CAQ CAR 180.1 179.9
CAQ CAV CAR OAG 0.7 360.0
CAQ CAV CAR CAU 179.2 180.0
OAF CAQ CAV OAE 181.5 179.9
CAV CAQ OAF HAF 178.5 180.0
CAR CAV CAS CAI 0.9 0.2
CAS CAV CAR CAQ 179.9 180.1
CAR CAV CAQ OAF 355.8 90.0
CAR CAV CAQ OAE 174.4 270.1
OAG CAR CAV CAU 181.5 180.0
CAV CAR OAG HAG 180.0 90.1
CAV CAR CAU CAT 1.0 359.6
CAV CAR CAU CAK 180.7 180.0
OAF CAQ CAV CAR 355.8 90.0
CAV CAQ OAF OAE 178.4 180.1
OAE CAQ CAV CAR 174.4 270.1
CAV CAQ OAE OAF 181.6 179.9
OAE CAQ OAF HAF 0.0 360.0
CAV CAR OAG CAU 178.4 180.0
OAG CAR CAU CAT 179.4 179.7
OAG CAR CAU CAK 359.1 0.0
CAV CAR CAU OAG 181.6 180.0
CAU CAR OAG HAG 1.6 270.0
CAI CAT CAU CAR 358.9 0.4
OAO CAT CAU CAR 179.6 180.3
CAT CAU CAR CAK 180.3 179.6
CAR CAU CAK CAH 74.8 89.9
CAR CAU CAK HAK1 194.7 210.0
CAR CAU CAK HAK2 314.8 329.9
CAS CAI CAT HAI 180.0 179.9
CAR CAU CAT CAI 358.9 0.4
OAO CAT CAI CAU 179.3 180.1
CAI CAT OAO CAB 11.8 359.9
CAI CAT CAU CAK 179.2 180.1
CAR CAU CAT OAO 179.6 180.3
CAI CAT OAO CAU 180.7 179.9
OAO CAT CAI HAI 0.4 0.1
OAO CAT CAU CAK 359.9 359.9
CAT OAO CAB HAB1 180.0 180.0
CAT OAO CAB HAB2 300.0 300.0
CAT OAO CAB HAB3 60.0 60.1
CAR CAU CAT CAK 179.7 180.4
CAI CAT CAU OAO 179.3 180.1
CAU CAT CAI HAI 181.1 180.0
CAU CAT OAO CAB 191.1 180.1
CAT CAU CAK CAH 254.5 270.3
CAT CAU CAK HAK1 14.4 30.3
CAT CAU CAK HAK2 134.6 150.3
CAB OAO CAT CAU 191.1 180.1
HAB1 CAB OAO HAB2 240.0 240.0
HAB1 CAB OAO HAB3 120.0 119.9
HAB2 CAB OAO HAB3 240.0 240.0
CAR CAU CAK CAT 180.3 179.6
CAU CAK CAH CAP 165.4 125.9
CAH CAK CAU HAK1 240.1 240.0
CAH CAK CAU HAK2 119.9 120.0
CAU CAK CAH HAH 345.3 306.0
HAK1 CAK CAU HAK2 239.9 240.1
CAU CAK CAH HAK1 119.9 120.1
CAU CAK CAH HAK2 240.1 240.0
CAK CAH CAP CAD 358.7 353.8
CAK CAH CAP CAC 178.2 173.8
CAP CAH CAK HAH 180.0 179.9
HAK1 CAK CAH HAK2 120.1 119.9
CAP CAH CAK HAK1 45.4 5.9
CAP CAH CAK HAK2 285.3 246.0
CAK CAH CAP HAH 180.0 180.1
CAD CAP CAH CAC 180.5 180.0
CAH CAP CAD HAD1 180.0 84.4
CAH CAP CAD HAD2 300.0 204.4
CAH CAP CAD HAD3 60.0 324.4
CAH CAP CAC HAC1 180.0 90.1
CAH CAP CAC HAC2 300.0 210.0
CAH CAP CAC HAC3 60.0 330.0
CAH CAP CAD CAC 179.5 180.0
CAD CAP CAH HAH 178.8 173.7
CAD CAP CAC HAC1 359.5 270.0
CAD CAP CAC HAC2 119.5 30.0
CAD CAP CAC HAC3 239.5 150.0
HAD1 CAD CAP HAD2 240.0 240.0
HAD1 CAD CAP HAD3 120.0 120.0
HAD2 CAD CAP HAD3 240.0 240.0
CAH CAP CAC CAD 180.5 180.0
CAC CAP CAH HAH 358.3 353.7
CAC CAP CAD HAD1 0.5 264.4
CAC CAP CAD HAD2 120.5 24.4
CAC CAP CAD HAD3 240.5 144.4
HAC1 CAC CAP HAC2 240.0 240.0
HAC1 CAC CAP HAC3 120.0 120.0
HAC2 CAC CAP HAC3 240.0 240.0
HAA1 CAA CAJ CAL 180.0 300.0
CAJ CAA HAA1 HAA2 120.0 120.1
CAJ CAA HAA1 HAA3 240.0 240.1
HAA1 CAA CAJ HAJ1 299.4 59.9
HAA1 CAA CAJ HAJ2 60.6 180.0
HAA2 CAA HAA1 HAA3 120.0 120.0
HAA2 CAA CAJ CAL 300.0 60.1
CAJ CAA HAA2 HAA1 240.0 239.9
CAJ CAA HAA2 HAA3 120.0 119.9
HAA2 CAA CAJ HAJ1 59.4 180.0
HAA2 CAA CAJ HAJ2 180.6 300.1
HAA1 CAA HAA2 HAA3 240.0 240.0
HAA3 CAA CAJ CAL 60.0 180.0
CAJ CAA HAA3 HAA1 120.0 120.0
CAJ CAA HAA3 HAA2 240.1 240.0
HAA3 CAA CAJ HAJ1 179.4 300.0
HAA3 CAA CAJ HAJ2 300.6 60.0
HAA1 CAA HAA3 HAA2 120.0 120.1
CAA CAJ HAJ1 CAL 243.4 240.1
HAJ1 CAJ CAA HAA1 299.4 59.9
HAJ1 CAJ CAA HAA2 59.4 180.0
HAJ1 CAJ CAA HAA3 179.4 300.0
CAA CAJ HAJ1 HAJ2 121.7 120.1
HAJ1 CAJ CAL CAM 61.9 60.0
CAL CAJ HAJ1 HAJ2 238.3 240.0
HAJ1 CAJ CAL HAL1 181.7 180.0
HAJ1 CAJ CAL HAL2 302.0 300.1
CAA CAJ HAJ2 CAL 116.6 120.0
HAJ2 CAJ CAA HAA1 60.6 180.0
HAJ2 CAJ CAA HAA2 180.6 300.1
HAJ2 CAJ CAA HAA3 300.6 60.0
CAA CAJ HAJ2 HAJ1 238.3 240.0
HAJ2 CAJ CAL CAM 300.7 300.0
CAL CAJ HAJ2 HAJ1 121.7 120.0
HAJ2 CAJ CAL HAL1 60.5 59.9
HAJ2 CAJ CAL HAL2 180.9 180.0
CAJ CAL HAL1 CAM 240.8 240.1
HAL1 CAL CAJ HAJ1 181.7 180.0
HAL1 CAL CAJ HAJ2 60.5 59.9
CAJ CAL HAL1 HAL2 120.4 120.0
HAL1 CAL CAM CAN 345.0 60.0
CAM CAL HAL1 HAL2 239.6 240.0
HAL1 CAL CAM HAM1 104.4 180.0
HAL1 CAL CAM HAM2 225.6 300.1
CAJ CAL HAL2 CAM 119.2 119.9
HAL2 CAL CAJ HAJ1 302.0 300.1
HAL2 CAL CAJ HAJ2 180.9 180.0
CAJ CAL HAL2 HAL1 239.6 239.9
HAL2 CAL CAM CAN 224.7 299.9
CAM CAL HAL2 HAL1 120.4 120.0
HAL2 CAL CAM HAM1 344.2 59.9
HAL2 CAL CAM HAM2 105.3 180.0
CAL CAM HAM1 CAN 243.3 240.0
HAM1 CAM CAL HAL1 104.4 180.0
HAM1 CAM CAL HAL2 344.2 59.9
CAL CAM HAM1 HAM2 121.7 120.1
HAM1 CAM CAN CAS 27.0 60.0
CAN CAM HAM1 HAM2 238.4 240.0
HAM1 CAM CAN HAN1 147.0 179.9
HAM1 CAM CAN HAN2 267.0 300.0
CAL CAM HAM2 CAN 116.7 119.9
HAM2 CAM CAL HAL1 225.6 300.1
HAM2 CAM CAL HAL2 105.3 180.0
CAL CAM HAM2 HAM1 238.3 239.9
HAM2 CAM CAN CAS 265.9 299.9
CAN CAM HAM2 HAM1 121.7 120.0
HAM2 CAM CAN HAN1 25.8 59.9
HAM2 CAM CAN HAN2 145.9 180.0
CAM CAN HAN1 CAS 240.3 240.0
HAN1 CAN CAM HAM1 147.0 179.9
HAN1 CAN CAM HAM2 25.8 59.9
CAM CAN HAN1 HAN2 120.1 120.0
HAN1 CAN CAS CAV 319.0 325.0
HAN1 CAN CAS CAI 138.9 144.7
CAS CAN HAN1 HAN2 239.8 240.0
CAM CAN HAN2 CAS 119.7 120.0
HAN2 CAN CAM HAM1 267.0 300.0
HAN2 CAN CAM HAM2 145.9 180.0
CAM CAN HAN2 HAN1 239.9 239.9
HAN2 CAN CAS CAV 199.0 205.0
HAN2 CAN CAS CAI 18.8 24.7
CAS CAN HAN2 HAN1 120.2 120.0
CAS CAI HAI CAT 180.0 180.1
HAI CAI CAT OAO 0.4 0.1
HAI CAI CAT CAU 181.1 180.0
HAF OAF CAQ OAE 0.0 360.0
HAG OAG CAR CAU 1.6 270.0
OAO CAB HAB1 HAB2 120.0 120.0
OAO CAB HAB1 HAB3 240.0 240.0
HAB2 CAB HAB1 HAB3 120.0 120.0
OAO CAB HAB2 HAB1 240.0 240.0
OAO CAB HAB2 HAB3 120.0 120.0
HAB1 CAB HAB2 HAB3 240.0 240.0
OAO CAB HAB3 HAB1 120.1 119.9
OAO CAB HAB3 HAB2 240.0 240.0
HAB1 CAB HAB3 HAB2 119.9 120.0
CAU CAK HAK1 CAH 240.3 239.9
CAU CAK HAK1 HAK2 120.2 120.0
HAK1 CAK CAH CAP 45.4 5.9
CAH CAK HAK1 HAK2 239.9 240.0
HAK1 CAK CAH HAH 225.4 186.0
CAU CAK HAK2 CAH 119.7 120.1
CAU CAK HAK2 HAK1 239.8 240.0
HAK2 CAK CAH CAP 285.3 246.0
CAH CAK HAK2 HAK1 120.2 120.0
HAK2 CAK CAH HAH 105.3 66.1
CAK CAH HAH CAP 180.0 179.9
HAH CAH CAK HAK1 225.4 186.0
HAH CAH CAK HAK2 105.3 66.1
HAH CAH CAP CAD 178.8 173.7
HAH CAH CAP CAC 358.3 353.7
HAD1 CAD CAP CAC 0.5 264.4
CAP CAD HAD1 HAD2 120.0 120.0
CAP CAD HAD1 HAD3 240.0 240.0
HAD2 CAD HAD1 HAD3 119.9 120.1
HAD2 CAD CAP CAC 120.5 24.4
CAP CAD HAD2 HAD1 239.9 240.1
CAP CAD HAD2 HAD3 120.0 120.0
HAD1 CAD HAD2 HAD3 240.1 240.0
HAD3 CAD CAP CAC 240.5 144.4
CAP CAD HAD3 HAD1 120.0 119.9
CAP CAD HAD3 HAD2 240.0 240.0
HAD1 CAD HAD3 HAD2 120.0 120.1
CAP CAC HAC1 HAC2 120.0 120.0
CAP CAC HAC1 HAC3 240.0 240.0
HAC2 CAC HAC1 HAC3 120.0 120.0
CAP CAC HAC2 HAC1 240.0 240.0
CAP CAC HAC2 HAC3 120.0 120.0
HAC1 CAC HAC2 HAC3 240.0 240.0
CAP CAC HAC3 HAC1 120.0 120.0
CAP CAC HAC3 HAC2 240.0 240.0
HAC1 CAC HAC3 HAC2 120.0 120.0