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Calculated Physicochemical Properties

The physicochemical properties for lipids in LIPID MAPS Structure Database were calculated using an external open source package named MayaChemTools. The current list of calculated phsicochemical properties is shown below.

NameDescription
Heavy Atoms# of non-hydrogen atoms
Rings# of rings
Aromatic Rings# of aromatic rings
Rotatable Bonds1# of rotatable bonds corresponds to single bonds excluding following types of single bonds: terminal bonds; attached to triple bonds; amide, thioamide and sulfonamide bonds.
van der Waals Molecular
Volume2
(Units: Å3 molecule-1)
van der Waals molecular volume calculated from 2D structure using atomic radii with adjustments for number of bonds, aromatic and non-aromatic rings
Topological Polar Surface
Area3
(Units: Å2 molecule-1)
Topological Polar Surface Area corresponding to nitrogen and oxygen atoms calculated from 2D structure using contributions from pre-defined structure fragments containing these atoms
Hydrogen Bond Donors4,5# of hydrogen bond donors corresponding to sum of nitrogen and oxygen atoms with at least one implicit/explicit hydrogen atom
Hydrogen Bond Acceptors4,5# of hydrogen bond acceptors corresponding to sum of nitrogen atoms without any any implicit/explicit hydrogen atom and all oxygen atoms
logP6logP partition coefficient calculated from 2D structure using contributions from pre-defined structure fragments.
It corresponds to: log(Poctanol/Pwater) = log(SoluteInOctanol/SoluteInWater)
Molar Refractivity6Molar refractivity calculated from 2D structure using contributions from pre-defined structure fragments.

References

[1] Veber, D. F.; Johnson, S. R.; Chend, H. Y.; Smith, B. R.; Ward, K. W.; Kopple, K. D. Molecular properties that influence the oral bioavailability of drug candidates. J. Med. Chem. 45, 2165-2623 (2002).

[2] Zhao, Y. H.; Abraham, M. H.; Zissimos, A. M. Fast calculation of van der Waals volume as a sum of atomic and bond contributions and its application to drug compounds. J. Org. Chem. 68, 7368-7373 (2003).

[3] Ertl, P.; Rohde, B.; Selzer, P. Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport Properties. J. Med. Chem. 43, 3714-3717 (2000).

[4] Schneider, G.; Neidhart, W.; Giller, T.; Schmid, G. Scaffold-hopping by topological pharmacophore search: A contribution to virtual screening. Angew. Chem. Int. Ed. 38, 2894-2896 (1999).

[5] McGregor, M. J.; Muskal, S. M. Pharmacophore fingerprinting. 1. Application to QSAR and focused library design. J. Chem. Inf. Comput. Sci. 39, 569-574 (1999).

[6] Wildman, S. A.; Crippen, G. M.; Prediction of Physicochemical Parameters by Atomic Contributions. J. Chem. Inf. Comput. Sci. 39, 868-873 (1999).

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