Structural data and parameters relative to the evaluation of the interaction of an anti aggregating azobioisostere compound with the full-length Aβ42 peptide by replica-exchange molecular dynamics (REMD) simulations. Two different force fields (Amber and CHARMM) were used to simulate the azobioisostere-Abeta42 (AZ-Ab42) complex in a monomeric and dimeric assembly. A brief description of the shared output data is reported below: 1. Amber and CHARMM-adapted parameters for the simulated azobioisostere (AZ) compound. 2. Modified version of the CHARMM36m FF - (CHARMM36mW) 3. Starting (equilibrated) structures (first 5 T-replicas) for REMD on each of the following three systems (PDB): Amber: AZ-Ab42 (monomeric ensemble): Repl.0 (315.0 K), Repl.1 (316.7 K), Repl.2 (318.4 K), Repl.3 (320.1 K), Repl.4 (321.8 K) Amber: AZ-Ab42 (dimeric ensemble): Repl.0 (315.0 K), Repl.1 (316.0 K), Repl.2 (317.0 K), Repl.3 (318.0 K), Repl.4 (319.1 K) CHARMM: AZ-Ab42 (dimeric ensemble): Repl.0 (315.0 K), Repl.1 (316.0 K), Repl.2 (317.0 K), Repl.3 (318.0 K), Repl.4 (319.1 K) 4. Most populated clusters for the three simulated systems (PDB): Amber AZ-Ab42 (monomeric ensemble): 7 clusters (Cl.0: 12.4%, Cl.1: 10.1%, Cl.2: 9.8%, Cl.3: 5.4%, Cl.4: 3.7%, Cl.5: 3.6%, Cl.6: 2.0%) Amber AZ-Ab42 (dimeric ensemble): 5 clusters (Cl.0: 7.1%, Cl.1: 4.3%, Cl.2: 3.5%, Cl.3: 3.2%, Cl.4: 2.4%) CHARMM: AZ-Ab42 (dimeric ensemble): 3 clusters (Cl.0: 4.7%, Cl.1: 4.6%, Cl.2: 2.5%)