FAIRMol

OHD_Leishmania_124

Pose ID 2036 Compound 1448 Pose 3

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_124
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
Weak or marginal quality
Binding strong Geometry high Native strong SASA done
Strain ΔE
30.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.68, Jaccard 0.65, H-bond role recall 1.00
Burial
72%
Hydrophobic fit
82%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.935 kcal/mol/HA) ✓ Good fit quality (FQ -9.43) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (72% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ High strain energy (30.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (20)
Score
-32.722
kcal/mol
LE
-0.935
kcal/mol/HA
Fit Quality
-9.43
FQ (Leeson)
HAC
35
heavy atoms
MW
475
Da
LogP
1.25
cLogP
Strain ΔE
30.0 kcal/mol
SASA buried
72%
Lipo contact
82% BSA apolar/total
SASA unbound
772 Ų
Apolar buried
455 Ų

Interaction summary

HB 8 HY 24 PI 4 CLASH 1
Final rank3.458Score-32.722
Inter norm-1.026Intra norm0.091
Top1000noExcludedno
Contacts14H-bonds8
Artifact reasongeometry warning; 20 clashes; 2 protein clashes; 2 cofactor-context clashes; moderate strain Δ 30.0
Residues
ARG17 HIS241 LEU188 LEU189 LEU226 LEU229 LYS198 NDP302 PHE113 PRO115 SER111 TYR191 TYR194 ARG287

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

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 overlap13Native recall0.68
Jaccard0.65RMSD-
HB strict6Strict recall1.00
HB same residue+role5HB role recall1.00
HB same residue5HB residue recall1.00

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
9 1.8278753700939747 -1.06159 -32.4057 8 19 0 0.00 0.00 - no Open
3 3.458347873613621 -1.02586 -32.7223 8 14 13 0.68 1.00 - no Current
7 4.4128156040438125 -0.863725 -24.7338 11 22 0 0.00 0.00 - no Open

Molecular metrics

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

Scoring & efficiency
Docking score -32.722kcal/mol
Ligand efficiency (LE) -0.9349kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.430
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 35HA

Physicochemical properties
Molecular weight 474.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.25
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 29.96kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 6.68kcal/mol
Minimised FF energy -23.29kcal/mol

SASA & burial

✓ computed
SASA (unbound) 772.1Ų
Total solvent-accessible surface area of free ligand
BSA total 557.5Ų
Buried surface area upon binding
BSA apolar 455.2Ų
Hydrophobic contacts buried
BSA polar 102.3Ų
Polar contacts buried
Fraction buried 72.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1772.0Ų
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 1013.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)