Drug–Receptor Binding Pocket Simulator

Ligand Properties

Size scale ×1.00

Net charge q 0.00

Binding mode

Target Protein — key residue

Docking Results

Binding affinity ΔG0.00 kcal/mol

Steric fit0%

Off-target risk0%

How it works

The ligand's atoms and the pocket's residues are real 3D coordinates. For every ligand–residue atom pair at distance d the sim sums a Lennard-Jones steric term and a Coulomb electrostatic term:

E_LJ  = 4ε[(σ/d)^12 − (σ/d)^6]   (σ = sum of atomic radii)
E_elec = k · q_lig · q_res / d
ΔG ≈ scale·(Σ E_LJ + w·Σ E_elec) + offset

Size changes each ligand atom's radius, so it changes σ and therefore how much steric clash (positive E_LJ) is generated against the pocket walls.
Charge sets the ligand's electrostatic character; it only lowers ΔG (stronger binding) when it is complementary to the key residue's charge — same-sign charges repel and raise ΔG.
Flexible mode halves the repulsive part of E_LJ, modelling induced-fit deformation that relieves steric clash the rigid pose can't avoid.
Key residue mutation changes the target's own charge (Acidic/Neutral/Basic) — the same lock the ligand's "key" charge has to fit, exactly like a real point mutation changing drug efficacy.
Off-target risk compares this pocket's affinity against an identical-shape decoy pocket with no charge pattern (steric-only). A ligand that binds mainly by charge complementarity scores low risk; one that binds mainly by generic shape/size also sticks to unrelated surfaces — high risk, a real-world proxy for side effects from promiscuous binding.

Acidic residue (−) Basic residue (+) Neutral residue

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