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.
|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|
|logP6||logP partition coefficient calculated from 2D structure using contributions from pre-defined structure fragments. |
It corresponds to: log(Poctanol/Pwater) = log(SoluteInOctanol/SoluteInWater)
|Molar Refractivity6||Molar refractivity calculated from 2D structure using contributions from pre-defined structure fragments.|
 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).
 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).
 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).
 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).
 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).
 Wildman, S. A.; Crippen, G. M.; Prediction of Physicochemical Parameters by Atomic Contributions. J. Chem. Inf. Comput. Sci. 39, 868-873 (1999).