Tc-43 Molecular VR Gallery

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Select a dataset tab and click a structure to view it

Dataset—

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Index—

Repr—

2D Ligand

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SMILES

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Therapeutic Area

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Disease Context

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Mechanism of Action

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Drug Discovery Significance

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Notable Compounds

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Key PDB Structures

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⚗️ Torsional Strain

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CSD potentials (CCDC A2 poster): amide 12, ester 8,
aryl-ether 10/8(anti)/4(⊥), aryl-NH 8/6(anti)/3(⊥),
aryl-S 7/7(anti)/4(⊥), aryl-SO2 5/4(⊥),
biaryl 3(45°)/4(75°,bis-ortho), bipyridyl 5(anti),
aryl-2-pyridyl 3(22°), aryl-NR2 3, aryl-CO 5,
benzyl-CH2 2(⊥), benzyl-CHR 2(0°), alkyl 1.5 kcal/mol
+ 1,4 steric + 1,5 ortho-sub steric (mono-ortho bonds only).

⊖ Electrostatic Repulsion

pH FF —

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Coulomb scan: ligand × binding-site atoms. ε=4 (protein interior), cutoff 5 Å. Protein charges via pdb2pqr+PROPKA when server running (start: python3 elec_server.py); falls back to rule-based estimates offline.
Ligand charges: rule-based (backbone/Asp/Glu O ≈ −0.57–0.80, amine/amide N ≈ −0.34–0.42, O/N/F/Cl/S by bonding context).
Positive-charge residues (Lys, Arg) show as attractive — not flagged.
Note: AutoDock Vina has no Coulomb term — this panel fills that gap.

🔄 3D Conformer ✕

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RDKit ETKDGv3 + MMFF94s conformer via local server.
Start first: python3 conformer_server.py
Falls back to bound PDB conformation if server is off.

⚙ Energy Minimize ✕

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OpenMM AMBER14 + GAFF-2.11 energy minimisation via local server.
Start first: python3 minimize_server.py
Tolerance: 10 kJ/mol/nm, max 500 iterations.

💊 Binding Affinity

Empirical Score

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ChEMBL Experimental Data

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PubChem Similar Compound

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Empirical score from geometry (H-bonds, π–π, hydrophobic, salt bridges).
For ML predictions run locally: Boltz-1 (MIT, open-source) or DiffDock-Score.

⚡ Interactions

H-Bond (N/O) always on

H-Bond (weak/S)

π–π Stacking

Hydrophobic

Salt Bridge

🧬 Tc-43 Molecular VR Gallery