Many reports describe the influence of additives or impurities on the physicochemical properties of crystals. On having obtained trans-[RuCl₂(C₅H₅N)₄] as brown, needle-shaped crystals contrary to red ororange-red blocks reported previously, we herein revisit its study. This complex was obtained from the filtrate of an ensuing reaction mixture of RuCl₃.3H₂O, bis(2-hydroxy-l-naphthaldehyde)adipoyldihydrazone (npahH₄) and pyridine in methanol. Findings from X-ray crystallographic data and spectra of IR, UV-Visible,¹H and ¹³C NMR along with other analytical studies of the complex are presented here. A comparative study with previously reported crystal forms was performed to understand the accompanying molecular structuraldifferences in the physical (shape, size and color) morphological alteration. Further probing into molecular dynamics, the molecular interactions were analyzed and quantified using computational methods. The symmetry of intermolecular interaction in C—H_Cl is different from earlier reported crystal forms. The intercontact H_H showed a major contribution (62.9%) for Hirshfeld surfaces. Also, we report antibacterial activity of the complex against methicillin-resistant Staphylococcus aureus followed by the in silico docking study that revealed its interaction with the residue Glu58 of ATPase subunit of S. aureus GyrB. Additional studies on its toxicity using rat models revealed this complex as non-toxic to animals