For each registered compound in Labguru's Compound Collection, a variety of chemical properties are automatically calculated based on the chemical structure provided. These calculations, powered by OpenBabel, ensure accurate and consistent chemical data across your inventory, streamlining property tracking and analysis.
These calculations, powered by OpenBabel, ensure accurate and consistent chemical data across your inventory, streamlining property tracking and analysis.
For more information click here.
Key Auto-Calculated Chemical Properties
Formula
The chemical formula of the molecule
MW (g/mol)
The mass of one molecule of a substance, calculated as a sum of all the atomic weights.
cLogP
LogP (also known as octanol-water partition coefficient) is a measure used to describe the ability of chemical compounds to dissolve in water or lipids. It represents the ratio of the concentration of a compound in an octanol phase to its concentration in an aqueous phase, both at equilibrium.
TPSA
TPSA is defined as the sum of the absolute values of the signed area of the van der Waals surfaces associated with each heavy atom in a molecule.
Composition
Calculates the percentage by weight (or mass) of each element in a compound, based on its chemical formula.
SMILES
Simplified Molecular Input Line Entry System- a text-based representation method used to describe the structure of organic and some inorganic molecules in chemistry and computer-aided molecular design.
Canonical SMILES
Refer to a unique, standardized SMILES representation for each distinct molecular structure.
InChI
International Chemical Identifier (InChI) is a unique, text-based representation system for defining the structural identity of chemical compounds.
HBD
Refers to the total number of atoms in a molecule that can act as hydrogen bond donors.
HBA
Refers to the total number of atoms in a molecule that can act as hydrogen bond acceptors.
Non-hydrogen atom count
A molecular property that represents the total number of heavy atoms (excluding hydrogen atoms) present in a molecule. This includes all atoms except hydrogen, which are typically carbon (C), nitrogen (N), oxygen (O), sulfur (S), phosphorus (P), halogens (F, Cl, Br, I), and other heavy metal ions.
Rotatable bond count
Represents the total number of rotatable bonds present in a molecule.
Fraction cSP3
Represents the ratio of sp3 hybridized carbon atoms to the total number of carbon atoms present in a molecule.
Aromatic ring count
Refer to the number of aromatic rings present in a molecule.
Aliphatic ring count
Refer to the number of aliphatic (saturated) rings present in a molecule.
Lipinski Rule of Five
A set of guidelines aims to predict the oral bioavailability (the ability of a drug to be effectively absorbed into a living system when administered orally) of small organic molecules based on their molecular structures.
HBD<5
HBA1<10
MW<500
logP<5
For each compound, the system assesses these properties and returns a 'Yes' or 'No' indication for meeting Lipinski’s Rule of Five
Please note:
The auto-calculated chemical properties were upgraded as part of Labguru version 6.26.
Previous chemical properties calculated using Chemaxon services are no longer available, as well as the formula field allowing free text values. Those fields are considered legacy fields.
All previously inserted and calculated values for those fields are saved in Labguru database and are available for users at all times.
In order to present the legacy data, admin users can enable its presentation on the compounds collection customization page.
This will present the legacy data as part of the show page of compounds created previously to version 6.26.
Be aware that the structure modification of those compounds will cause the deletion of the legacy data.