FAIRMol

Z56789391

Pose ID 6445 Compound 3479 Pose 349

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
T10
L. infantum R5P L. infantum
Ligand Z56789391

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
13.2 kcal/mol
Protein clashes
7
Internal clashes
7
Native overlap
contact recall 0.94, Jaccard 0.89, H-bond role recall 0.55
Burial
77%
Hydrophobic fit
62%
Reason: 7 internal clashes
7 protein-contact clashes 7 intramolecular clashes 56% of hydrophobic surface appears solvent-exposed (9/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.178 kcal/mol/HA) ✓ Good fit quality (FQ -10.40) ✓ Strong H-bond network (16 bonds) ✓ Deep burial (77% SASA buried) ✓ Lipophilic contacts well-matched (62%) ✗ Moderate strain (13.2 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-27.099
kcal/mol
LE
-1.178
kcal/mol/HA
Fit Quality
-10.40
FQ (Leeson)
HAC
23
heavy atoms
MW
328
Da
LogP
2.78
cLogP
Strain ΔE
13.2 kcal/mol
SASA buried
77%
Lipo contact
62% BSA apolar/total
SASA unbound
566 Ų
Apolar buried
271 Ų

Interaction summary

HB 16 HY 7 PI 1 CLASH 7 ⚠ Exposure 56%
⚠️Partial hydrophobic solvent exposure
56% of hydrophobic surface appears solvent-exposed (9/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 16 Buried (contacted) 7 Exposed 9 LogP 2.78 H-bonds 16
Exposed fragments: phenyl (4/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank3.511Score-27.099
Inter norm-1.538Intra norm0.360
Top1000noExcludedno
Contacts17H-bonds16
Artifact reasongeometry warning; 6 clashes; 2 protein clashes
Residues
ALA15 ARG116 ARG140 ARG144 ASN106 ASP13 CYS72 GLY73 GLY75 GLY77 HIS105 HIS14 HIS141 ILE76 SER46 THR74 TYR49

Protein summary

155 residues
Protein targetT10Atoms4590
Residues155Chains1
Residue summaryILE:494; ARG:384; ALA:360; VAL:352; LEU:304; GLU:300; THR:280; MET:272; LYS:220; ASP:216; TYR:210; HIS:204; GLY:182; SER:176; GLN:170; ASN:140

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6FXWContacts17
PoseOpen native poseHB0
IFP residues
ALA15 ARG116 ARG140 ARG144 ASN106 ASP13 CYS72 GLY73 GLY75 GLY77 HIS105 HIS14 HIS141 ILE76 LEU101 THR74 TYR49
Current overlap16Native recall0.94
Jaccard0.89RMSD-
HB strict7Strict recall0.54
HB same residue+role6HB role recall0.55
HB same residue8HB residue recall0.73

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
369 2.775244022661589 -1.30197 -28.0283 12 15 0 0.00 0.00 - no Open
399 2.8909886841250687 -0.814991 -15.9798 5 9 0 0.00 0.00 - no Open
349 3.510896952791053 -1.5379 -27.0993 16 17 16 0.94 0.55 - 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 -27.099kcal/mol
Ligand efficiency (LE) -1.1782kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.399
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 328.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.78
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 13.25kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 100.62kcal/mol
Minimised FF energy 87.38kcal/mol

SASA & burial

✓ computed
SASA (unbound) 565.8Ų
Total solvent-accessible surface area of free ligand
BSA total 434.1Ų
Buried surface area upon binding
BSA apolar 270.9Ų
Hydrophobic contacts buried
BSA polar 163.2Ų
Polar contacts buried
Fraction buried 76.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 62.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2132.3Ų
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 2417.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 670.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)