Calculated Physicochemical Properties

The physicochemical properties for metabolites in Metabolomics 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
(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
(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
Fraction sp3 Carbons7,8,9Fraction of sp3 carbons corresponds to number of sp3 carbons divided by total number of carbon atoms
sp3 Carbons7,8,9# of sp3 carbon atoms


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