FAIRMol

OHD_Leishmania_309

Pose ID 12898 Compound 5307 Pose 19

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_309
PDB9IFH↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
41.9 kcal/mol
Protein clashes
7
Internal clashes
7
Native overlap
contact recall 1.00, Jaccard 0.57, H-bond role recall 0.00
Burial
55%
Hydrophobic fit
84%
Reason: 7 internal clashes
7 protein-contact clashes 7 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.487 kcal/mol/HA) ✓ Good fit quality (FQ -5.26) ✓ Good burial (55% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Extreme strain energy (41.9 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (10) ✗ Many internal clashes (33)
Score
-22.418
kcal/mol
LE
-0.487
kcal/mol/HA
Fit Quality
-5.26
FQ (Leeson)
HAC
46
heavy atoms
MW
616
Da
LogP
2.53
cLogP
Strain ΔE
41.9 kcal/mol
SASA buried
55%
Lipo contact
84% BSA apolar/total
SASA unbound
937 Ų
Apolar buried
432 Ų

Interaction summary

HB 2 HY 13 PI 2 CLASH 7
Final rank4.548Score-22.418
Inter norm-0.472Intra norm-0.017
Top1000noExcludedno
Contacts14H-bonds2
Artifact reasongeometry warning; 33 clashes; 10 protein contact clashes; high strain Δ 41.9
Residues
ASN402 CYS469 GLU466 GLU467 GLY459 HIS461 ILE458 LEU399 LYS407 PHE396 PRO398 SER394 SER470 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 overlap8Native recall1.00
Jaccard0.57RMSD-
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
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
19 4.547810695672186 -0.472135 -22.4181 2 14 8 1.00 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 -22.418kcal/mol
Ligand efficiency (LE) -0.4874kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.260
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 46HA

Physicochemical properties
Molecular weight 615.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.53
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 41.90kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 294.68kcal/mol
Minimised FF energy 252.78kcal/mol

SASA & burial

✓ computed
SASA (unbound) 936.9Ų
Total solvent-accessible surface area of free ligand
BSA total 513.2Ų
Buried surface area upon binding
BSA apolar 432.1Ų
Hydrophobic contacts buried
BSA polar 81.2Ų
Polar contacts buried
Fraction buried 54.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 84.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3367.9Ų
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 1519.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)