Download eQuilibrator Data
Formats and Data Sources

eQuilibrator data is given in two formats. Tabular data is given as CSV and hierarchical data is given in JSON.

Compound Formation Energies

The standard formation energies of biochemical compounds found in the literature can be downloaded at various pH levels. Note that ionic strength is set to 0.1 M for all the files linked below. The thermodynamic data is drawn mostly from the work of the late Prof. Robert Alberty (references here).

It is also possible to compute the standard transformed formation energy for any pH and ionic strength directly using the chemical formation energy table of the various protonation states (pseudoisomers) of all the compounds (download here). Each row in the CSV file corresponds to one pseudoisomer of one compound. The columns' order is: KEGG compound ID, compound name, chemical formation energy (in kJ/mol), number of hydrogen atoms, net charge, number of magnesium ions, note.

Reaction Energies

The standard Gibbs energies of biochemical reactions in the KEGG database are available for download at various pH levels as well. We use the Component Contribution method to obtain all the given values in the downloadable CSV files. As above, ionic strength is set to 0.1 M for all the files linked below. When a reaction energy cannot be computed, an explanation is given.

It is important not to mix these reaction Gibbs energies with calculations done using the compound formation energies in a single model. These two datasets are not consistent with each other, and mixing could violate the second law of thermodynamics - meaning that a set of reactions that form a cycle might have a total ΔG' different than 0 (a biochemical perpetual motion machine).

Additional Compound Information

The last file is in JSON format and contains many entries, each representing a compound in KEGG (download JSON here). A single compound is represented as follows:

        {
            "CID": "C00631",
            "InChI": "InChI=1S/C3H7O7P/c4-1-2(3(5)6)10-11(7,8)9/h2,4H,1H2,(H,5,6)(H2,7,8,9)/t2-/m1/s1",
            "formula": "C3H7O7P",
            "mass": 185.9929,
            "name": "2-Phospho-D-glycerate",
            "num_electrons": 96,
        }
        

Each listed compound will likely have a KEGG ID ("CID"), a chemical formula ("formula"), an InChI identifier ("InChI"), a mass ("mass"), a common name ("name") and a number of electrons ("num_electrons"). When values are are unknown they are omitted.