Research data supporting the publication: Noncovalent Interaction Origins of Substrate Discrimination in LinB: A Combined QM/MM and SAPT Analysis

This repository contains research data (input files and raw data) supporting the publication: Noncovalent Interaction Origins of Substrate Discrimination in LinB: A Combined QM/MM and SAPT Analysis Agata Sowińska(a), Michał Rostkowski(a), Agnieszka Dybala-Defratyka(a), Agnieszka Krzemińska(b) a – Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 114, 90-543 Lodz, Poland b – Institute of Physics, Lodz University of Technology, Wolczanska 217/221, 93-005 Lodz, Poland 1. PDB files of representative structures obtained from cluster analysis. Only clusters representing at least 5% of the total population were considered. File naming convention: Ligand_ConfigurationAndAttackPosition_StationaryPointDesignation.ClusterNumber where: Ligand DBP = 1,2-dibromopropane DCP = 1,2-dichloropropane Configuration R or S stereoisomer AttackPosition Position of the nucleophilic attack (C1 or C2) StationaryPointDesignation RC = reactant complex TS1 = transition state corresponding to the dehalogenation step ClusterNumber Cluster number corresponding to the numbering used in the Supplementary Information of the associated publication. 2. Input files used for Adaptive String Method (ASM) QM/MM simulations. The dataset includes: • Restart files (.rst) corresponding to the reactant complexes (RC) and product states used to initialize ASM calculations. • Topology files (.prmtop) corresponding to individual stereoisomers. File naming convention for .rst files: Ligand_ConfigurationAndAttackPosition_State where: Ligand DBP = 1,2-dibromopropane DCP = 1,2-dichloropropane Configuration R or S stereoisomer AttackPosition Position of the nucleophilic attack (C1 or C2) State RC = reactant complex P = product state The initial string was constructed by assigning the reactant complex structure to nodes 1–25 and the product structure to nodes 26–50 prior to string optimization. Topology files (.prmtop) The topology files correspond to the specified stereoisomers used in the simulations. Each topology file should be used together with the appropriate restart (.rst) file representing the corresponding reactant or product state. 3. PMF data file (.txt) The text file contains the raw potential of mean force (PMF) data obtained from the ASM simulations for all investigated reaction pathways. The columns are defined as follows: s Dimensionless path collective variable describing the progress along the optimized minimum free-energy path. PMF Potential of mean force value (kcal/mol). PMF_CI (95%) Half-width of the 95% confidence interval associated with the PMF value (kcal/mol). Each dataset in the file corresponds to a specific reaction pathway defined by the ligand, stereochemical configuration, and nucleophilic attack position.