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In the current report, 3D structures of the enzyme Lathyrus aphaca Ribulose bisphosphate carboxylase (LArbcL) was modeled using homology modeling. The structures of the synthesized β‐amino carbonyl derivatives were made by means of “Chem Draw ultra‐12.0”, ADMET prediction were conducted to compute physicochemical properties. Pharmacokinetics studies and the molecular docking study of the synthesized compounds were performed against Lathyrus aphaca Ribulose bisphosphate carboxylase. Docking experiments verified a significant Docking Score values between 6.2 to 7.3 kcal mol−1. The highest‐ranking complexes obtained from docking results were subjected to 100 ns Molecular Dynamics simulations using Gromacs program to investigate the constancy of the docked “protein–ligand complexes” as well as the oscillation and conformational variations that occur during protein–ligand interaction. The synthesized derivatives were screened for pre‐emergence and post‐emergence herbicidal activity adjacent to weed species named Lathyrus aphaca with concentrations of “0.005 M, 0.01 M and 0.02 M”, and the activity was compared with Butachlor and penoxulum which are standard herbicide. Every single synthesized compounds show good to moderate activity.