Å	Ångström (10−10 m), unit of length
A, B	Protein chain identifiers in PDB structures
ADT	AutoDockTools
ALA	Alanine
ARG	Arginine
ASN	Asparagine
ATCC	American Type Culture Collection
AutoDock-Vina	Molecular docking software
B3LYP	Becke three-parameter Lee–Yang–Parr functional
CFU	Colony Forming Unit
CLSI	Clinical and Laboratory Standards Institute
DFT	Density Functional Theory
EMV	Electron Multiplier Voltage (mode/setting)
GC-MS	Gas Chromatography–Mass Spectrometry
GLU	Glutamic acid
GLY	Glycine
H	Hydrogen atom
HIS	Histidine
ILE	Isoleucine
LEU	Leucine
LPS	Lipopolysaccharide
LYP	Lee-Yang-Parr
m/z	mass-to-charge ratio
MBC	Minimum Bactericidal Concentration
MD	Molecular Dynamics
MDA	Malondialdehyde
MET	Methionine
MHB	Mueller Hinton Broth
MIC	Minimum Inhibitory Concentration
MICs	Minimum Inhibitory Concentrations
NCTC	National Collection of Type Cultures
ND2	Amide nitrogen atom in the side chain of Asparagine
NIST	National Institute of Standards and Technology
O	Oxygen atom
O1	Oxygen atom of Thymoquinone
OG1	Hydroxyl oxygen atom in the side chain of Threonine
PDB	Protein Data Bank
PDB ID	Protein Data Bank Identifier
PHE	Phenylalanine
RMSD	Root Mean Square Deviation
THR	Threonine
TYR	Tyrosine
ΔG	Binding free energy