TABLE 5.

Number of atom clashes between atoms of chlorpromazine and amitriptyline and those of substrates norfloxacin and ethidium bromide and those of the inhibitor MBX3132 bound to AcrB_EC (PDB ID 5ENQ)^a

Compoundb	No. of atomic clashes
	Norfloxacin	Ethidium bromide	MBX3132
CPZEC	4	11	14
AMIEC	3	0	3
CPZST	6	3	15c
AMIST	5	4	Nonec

^aThe calculation was performed on the representative structure of the most populated cluster extracted from each MD trajectory (in the case of amitriptyline and chlorpromazine, we selected the trajectories associated with the more negative binding free energies among those displaying a stable position of the ligand in the last 50 ns of the production run). In addition, we used the crystal structure of E. coli AcrB in which the inhibitor MBX3132 has been cocrystallized (PDB ID 5ENQ). To evaluate the number of clashes, these structures were superimposed, and the number of heavy atoms of amitriptyline/chlorpromazine that overlap the other compounds was recorded.

^bCPZ, chlorpromazine; AMI, amitriptyline.

^cUnder the hypothesis that MBX3132 binds to AcrB_ST similarly to the mode found in the X-ray structure 5ENQ of AcrB_EC.