FAIRMol

OHD_Leishmania_162

Pose ID 2049 Compound 1546 Pose 16

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
T04
L. major PTR1 L. major
Ligand OHD_Leishmania_162
PDB7PXX↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
22.4 kcal/mol
Protein clashes
2
Internal clashes
9
Native overlap
contact recall 0.63, Jaccard 0.63, H-bond role recall 0.40
Burial
89%
Hydrophobic fit
83%
Reason: 9 internal clashes
2 protein-contact clashes 9 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.521 kcal/mol/HA) ✓ Good fit quality (FQ -11.89) ✓ Good H-bonds (4 bonds) ✓ Deep burial (89% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ High strain energy (22.4 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (2) ✗ Internal clashes (9)
Score
-25.851
kcal/mol
LE
-1.521
kcal/mol/HA
Fit Quality
-11.89
FQ (Leeson)
HAC
17
heavy atoms
MW
227
Da
LogP
1.04
cLogP
Final rank
-0.2402
rank score
Inter norm
-1.688
normalised
Contacts
12
H-bonds 5
Strain ΔE
22.4 kcal/mol
SASA buried
89%
Lipo contact
83% BSA apolar/total
SASA unbound
468 Ų
Apolar buried
345 Ų

Interaction summary

HBD 2 HBA 2 HY 4 PI 2 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

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

HY · Hydrophobic contacts

CLASH · Clashes
No clash · clashes detected for this pose.

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name7PXXContacts19
PoseOpen native poseHB0
IFP residues
ARG17 ASP181 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER112 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap12Native recall0.63
Jaccard0.63RMSD-
HB strict2Strict recall0.33
HB same residue+role2HB role recall0.40
HB same residue2HB residue recall0.40

Protein summary

308 residues
Protein targetT04Atoms4210
Residues308Chains3
Residue summaryLEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108

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:NDP302

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
16 -0.24024462434549526 -1.68838 -25.8508 5 12 12 0.63 0.40 - 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 -25.851kcal/mol
Ligand efficiency (LE) -1.5206kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.891
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 17HA

Physicochemical properties
Molecular weight 227.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.04
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 22.40kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -48.08kcal/mol
Minimised FF energy -70.48kcal/mol

SASA & burial

✓ computed
SASA (unbound) 468.2Ų
Total solvent-accessible surface area of free ligand
BSA total 416.1Ų
Buried surface area upon binding
BSA apolar 345.4Ų
Hydrophobic contacts buried
BSA polar 70.7Ų
Polar contacts buried
Fraction buried 88.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1553.0Ų
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 2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1021.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)