Curated in vivo subset of ZINC15: Correction of formal charge and molecular structure in mol2 format

The database of molecules, referred to as in vivo, was downloaded on
10/12/2021 from ZINC15 (https://zinc15.docking.org/). The database
contained a total of 60,411 molecules, which were available in mol2
format. Errors related to structure (number of atoms) and formal charge
were found when comparing information from the mol2 formats of individual
molecules and their InChI codes present on the ZINC15 website. The
reference number of atoms was obtained from the InChI code, as the sum of
the number of atoms from the formula (main layer of InChI code), which was
modified by adding/subtracting the (de)protonation information from the
protonation sublayer (/p). The reference number of atoms was compared with
the number of atoms from the mol2 format. The reference formal charge was
obtained as the sum of the charges given in the charge sublayer (/q) and
the protonation sublayer (/p) of the InChI code. The reference formal
charge was compared with the formal charge obtained by summing the partial
charges from the mol2 format, with 0.1 e chosen as the acceptable
deviation. Together 1,115 corrected molecules (curated by Open Babel
3.1.1) are provided in mol2 format. In addition, a bash script is
available for downloading the in vivo database, along with detailed
instructions for reproducing the described workflow.