Data for Unravelling the Role Played by Non-Covalent Interactions in the Action Mechanism of PCDDs within Cells

1_initial_structure

 ligands 
 - XYZ files: Initial structures of the ligands
 - m1.com: Example of geometry optimization
 - esp_m1.com: Example of ESP charges calculation
 - m1.pdbqt: Example of pdbqt file

 receptor
 - 7zub.pdb: PDB from Protein Data Bank of PDB ID:7ZUB
 - pasb.pdb: PDB of chain D of 7ZUB protein
 - pasb.pdbqt: pdbqt of chain D of 7ZUB protein

 membrane
 - DOPC_128.pdb: PDB file of the relaxed membrane structure 

2_docking(protein)
 - conf.txt: Input for docking

3_MD

 protein
 - 1_min.in: Minimization
 - 2_equil.in: Heating
 - 3_prod.in: Production
 - system_m*.crd and system_m*.parm7: coordinates and parameter for each system
 
 membrane
 - min.in: Minimization
 - heat.in: Heating
 - prod_*.in: Production
 - pull.in: Pulling
 - DOPC_m*.pdb and DOPC_m*.prmtop: coordinates and parameters for each system 

4_MMGBSA(protein)
 - contact.in: cpptraj input to search the contacts between the ligand and the receptor
 - mmgbsa.in: MMGBSA input to calculate the binding free energy, its decomposition and the contribution per residue for the residues with higher contact

5_umbrella_sampling(membrane)
 - prod_window.in: Window production example
 - COM_dist.RST: Window parameter file
 - full_fe_m*.dat: Free energy curve for each system

6_EDA
 - main.inp and tpl.inp: inputs for MoBioTools
 - complex_geom0.com, mon1_geom0.com and mon2_geom0.com: Created inputs from MoBioTools to run single points on Gaussian16
 - input: input for EDA-NCI
 - EDA_m*_memb.dat: Data file with the EDA results on the selected sample for the membrane system
 - EDA_m*_prot.dat: Data file with the EDA results on the selected sample for the protein system