The data set contains all the computational files related to mapping the plausible Fe-S species under simulated pre-biotic conditions that connects the initial (up to four iron ions) formation of Fe-S mackinawite-like nanoparticles versus 2Fe-2S rhombs and 4Fe-4S cubanes. The related publication explores the thermodynamic feasibility of proton acting as oxidizing agent that allow for formation of oxidized Fe species with concomitant hydrogen gas evolution. The emergence of the ferric iron in molecular clusters can be stabilized by bisulfide ligands as 'pre-biotic thiolates', which under neutral pH conditions can give rise to the formation of [4Fe-4S] clusters. The estimated enthalpy and free energy values were utilized to establish a reaction network model with PHREEQC package with MinteqA2 database. The depository was organized according to the published figures. Figure 1: provides the XYZ coordinates of the most dominant species in various oxidation states. Figures 2-4: contains the compilation of all the calculations that were used to validate close to 100 density functionals. Figure 5: contains the calculations by some 'old density functionals' such as B3LYP and B(5%HF)P86 and the top five performing functionals for the reference reactions such as water autoionization, hydrogen sulfide acid dissociation, ferrous and ferric iron hydrolysis, and FeS formation. Figure 6: compares and contrasts the energetics of non-solvated and solvated rhombs and cubanes to illustrate the critical functional dependence for describing molecular cluster formation in competition to mackinawite-like nanoparticle formation. The 'lst' files contain the content of each compressed/zip file.