This study explores the molecular interactions between two drugs, diclofenac, and heparin, through computational docking to understand the impact of complex formation on binding affinity, orientation, and pharmacological properties. Using molecular modeling and docking simulations, we analyzed how diclofenac and heparin bind individually and as complexes to target receptor Factor Xa, critical in coagulation pathways. Results demonstrate that forming diclofenac-heparin complexes significantly enhances binding affinity, with lower binding energies compared to individual drugs, indicating more stable interactions. Notably, the orientation of the complex (diclofenac_heparin versus heparin_diclofenac) affected the binding site and binding energy, suggesting that sequence and orientation in complex formation are crucial factors in drug-target interaction. Additionally, differences in lipophilicity (logP values) between the complexes suggest that binding orientation may influence bioavailability and membrane permeability. These findings underscore the potential for dual-drug complex formation to enhance pharmacological efficacy, paving the way for optimized drug combinations in therapeutic applications