There are two main types of constraints. For the first type, a specific interacting group in the receptor is selected and an interaction between the ligand (any part of the ligand) and this interacting group must be seen in every docking solution. This is called an interaction constraint. The second type of constraint is a spatial constraint. This takes the form of a spherical volume in the active site, and a specified atom or group of atoms from the ligand must lie within the sphere in the docking solution.

Each constraint can be assigned a priority, making it essential or optional in the docking solution, or a logical expression can be used to define which combinations of constraints are allowed in the docking solution. Once defined in the active site, the set of constraints constitutes the pharmacophore in FlexX-Pharm.

FlexX-Pharm is not a standard module in FlexX. In order to access the FlexX-Pharm functionality, an extra license key is required.