FAIRMol

OHD_Leishmania_93

Pose ID 12885 Compound 5234 Pose 6

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
T20
T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)
Ligand OHD_Leishmania_93
PDB9IFH↗

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
33.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.62, Jaccard 0.56, H-bond role recall 0.00
Burial
48%
Hydrophobic fit
80%
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 (-1.017 kcal/mol/HA) ✓ Good fit quality (FQ -8.67) ✓ Good H-bonds (4 bonds) ✓ Good burial (48% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Very high strain energy (33.0 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-21.349
kcal/mol
LE
-1.017
kcal/mol/HA
Fit Quality
-8.67
FQ (Leeson)
HAC
21
heavy atoms
MW
288
Da
LogP
-0.67
cLogP
Strain ΔE
33.0 kcal/mol
SASA buried
48%
Lipo contact
80% BSA apolar/total
SASA unbound
484 Ų
Apolar buried
186 Ų

Interaction summary

HB 4 HY 9 PI 0 CLASH 2
Final rank2.770Score-21.349
Inter norm-1.033Intra norm0.016
Top1000noExcludedno
Contacts6H-bonds4
Artifact reasongeometry warning; 7 clashes; 2 protein clashes; high strain Δ 33.0
Residues
ASN402 LEU399 LYS407 PHE396 PRO398 THR397

Protein summary

492 residues
Protein targetT20Atoms7539
Residues492Chains1
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:264; 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.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap5Native recall0.62
Jaccard0.56RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
6 2.7702489050082897 -1.0328 -21.3493 4 6 5 0.62 0.00 - 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 -21.349kcal/mol
Ligand efficiency (LE) -1.0166kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.672
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 21HA

Physicochemical properties
Molecular weight 288.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.67
Lipinski: ≤ 5
Rotatable bonds 2

Conformational strain (MMFF94s)
Strain energy (ΔE) 33.00kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 92.28kcal/mol
Minimised FF energy 59.29kcal/mol

SASA & burial

✓ computed
SASA (unbound) 484.1Ų
Total solvent-accessible surface area of free ligand
BSA total 233.1Ų
Buried surface area upon binding
BSA apolar 185.8Ų
Hydrophobic contacts buried
BSA polar 47.3Ų
Polar contacts buried
Fraction buried 48.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2974.5Ų
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 4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1483.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)