. Author manuscript; available in PMC: 2019 Sep 1.

Published in final edited form as: J Mol Graph Model. 2018 Jun 18;84:96–108. doi: 10.1016/j.jmgm.2018.06.005

Table 1:

The 35 atom types used in gnina. Carbon atoms are distinguished by aromaticity and adjacency to polar atoms (“NonHydrophobe”). Polar atoms are distinguished by hydrogen bonding propensity.

Receptor Atom Types	Ligand Atom Types
AliphaticCarbonXSHydrophobe	AliphaticCarbonXSHydrophobe
AliphaticCarbonXSNonHydrophobe	AliphaticCarbonXSNonHydrophobe
AromaticCarbonXSHydrophobe	AromaticCarbonXSHydrophobe
AromaticCarbonXSNonHydrophobe	AromaticCarbonXSNonHydrophobe
Calcium	Bromine
Iron	Chlorine
Magnesium	Fluorine
Nitrogen	Nitrogen
NitrogenXSAcceptor	NitrogenXSAcceptor
NitrogenXSDonor	NitrogenXSDonor
NitrogenXSDonorAcceptor	NitrogenXSDonorAcceptor
OxygenXSAcceptor	Oxygen
OxygenXSDonorAcceptor	OxygenXSAcceptor
Phosphorus	OxygenXSDonorAcceptor
Sulfur	Phosphorus
Zinc	Sulfur
	SulfurAcceptor
	Iodine
	Boron