This dataset contains molecular dynamic simulation data of Loxosceles phospholipase D enzymes, of both clades, in presence of different bilayer compositions. The enzymes simulated are Li_alphaIA1, St_beta1B1, Ll_alphaIII and R44Y/S60Y St_beta1B1. The bilayers are used are a pure POPC, PC:SM:CHOL (70:20:10) and POPC:POPE (50:50) bilayer. The trajectories are in DCD format and the topology file in PSF format.The following simulations are available: 1. Li_alphaIA1 on a pure POPC bilayer; 2. Li_alphaIA1 on a PC:SM:CHOL (70:20:10) bilayer; 3. Li_alphaIA1 on a POPC:POPE (50:50) bilayer; 4. Ll_alphaIII on a pure POPC bilayer; 5. Ll_alphaIII on a PC:SM:CHOL (70:20:10) bilayer; 6. R44Y/S60Y St_beta1B1 on a pure POPC bilayer; 7. St_beta1B1 on a pure POPC bilayer; 8. St_beta1B1 on a PC:SM:CHOL (70:20:10) bilayer; 9. St_beta1B1 on a POPC:POPE (50:50) bilayer;