FAIRMol

OHD_Leishmania_479

Pose ID 11549 Compound 175 Pose 28

DB SELECTIONDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T18
T. brucei TR (Mepacrine binding site (MBS, site 1)) T. brucei Mepacrine binding site (MBS, site 1)
Ligand OHD_Leishmania_479
PDB6RB5↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
36.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.77, Jaccard 0.53
Burial
65%
Hydrophobic fit
88%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.446 kcal/mol/HA) ✓ Good fit quality (FQ -4.53) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (65% SASA buried) ✓ Lipophilic contacts well-matched (88%) ✗ Very high strain energy (36.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (15)
Score
-16.052
kcal/mol
LE
-0.446
kcal/mol/HA
Fit Quality
-4.53
FQ (Leeson)
HAC
36
heavy atoms
MW
497
Da
LogP
5.77
cLogP
Strain ΔE
36.2 kcal/mol
SASA buried
65%
Lipo contact
88% BSA apolar/total
SASA unbound
801 Ų
Apolar buried
462 Ų

Interaction summary

HB 6 HY 24 PI 2 CLASH 2
Final rank3.880Score-16.052
Inter norm-0.640Intra norm0.194
Top1000noExcludedno
Contacts16H-bonds6
Artifact reasongeometry warning; 15 clashes; 2 protein clashes; high strain Δ 36.2
Residues
CYS52 CYS57 GLU18 GLY13 ILE106 ILE339 LEU17 MET113 PRO336 SER109 SER14 THR335 TRP21 TYR110 VAL53 VAL58

Protein summary

493 residues
Protein targetT18Atoms7550
Residues493Chains1
Residue summaryVAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:276; MET:221

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:FAD501

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6RB5Contacts13
PoseOpen native poseHB0
IFP residues
ASP116 GLU18 GLY112 ILE106 LEU17 MET113 SER109 THR117 THR335 TRP21 TYR110 VAL53 VAL58
Current overlap10Native recall0.77
Jaccard0.53RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
39 1.389938486693102 -0.754924 -24.0057 3 17 0 0.00 - - no Open
35 3.793209517544306 -0.797642 -20.3455 6 15 0 0.00 - - no Open
28 3.8800022506745635 -0.63976 -16.0523 6 16 10 0.77 - - no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -16.052kcal/mol
Ligand efficiency (LE) -0.4459kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.532
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 36HA

Physicochemical properties
Molecular weight 497.0Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.77
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 36.19kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 53.23kcal/mol
Minimised FF energy 17.05kcal/mol

SASA & burial

✓ computed
SASA (unbound) 801.1Ų
Total solvent-accessible surface area of free ligand
BSA total 522.5Ų
Buried surface area upon binding
BSA apolar 462.1Ų
Hydrophobic contacts buried
BSA polar 60.4Ų
Polar contacts buried
Fraction buried 65.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 88.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3242.8Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1523.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)