The data described here are derived from insights into binding selectivity of inhibitors toward BRD4 and CBP by using MD simulations. The analyses were performed on six systems, including the F3J-BRD4/CBP, EX1-BRD4/CBP, and E2T-BRD4/CBP complexes. There are four folder: Eigenvalue, Porcupine, MSA, and Loop. The Eigenvalue folder includes the data of the eigenvalues against eigenvector indexes obtained from the diagonalization of the covariance matrix constructed by utilizing atomic coordinates saved at MD trajectories of six complexes. The Porcupine folder shows the first six eigenvectors (fort.71-fort.76), the initialized structure of six complexes, and k.txt file. Take fort.71 as an example, the first triple of numbers determine coordinates of the Cα atoms of the residues 53-166 in BRD4 and that of the residues 1083–1196 in CBP. They defined the starting point, and the unit is Å. The second triple of numbers show the motion directions of BRD4 and CBP, and they represent the movement vectors. The MSA folder includes the data of Molecular surface area (MSA) of six systems were calculated by the CPPTRAJ module in AMBER18, each *.dat file gives the MSA of 100,000 conformations, and the number in the second column represents MSA of each conformation, and the unit is the square of Å. The Loop folder indicates the data of the distance between the Cα atoms of Leu92/Leu1120 in the ZA-loop of BRD4/CBP and that of Pro142/Lys1170 in the BC-loop of BRD4/CBP, representing the distance of the ZA-loop away from the BC-loop, each *.dat file gives the distance of 100,000 conformations, and the number in the second column represents distance of the ZA-loop away from the BC-loop in each conformation, and the unit is Å. The two frequency.xlsx files give the data of the frequency distributions of MSA and that of distance, respectively . These data are useful for understanding internal dynamics and conformations of BRD4 and CBP due to inhibitor bindings.