FAIRMol

Z56783496

Pose ID 6510 Compound 3527 Pose 414

DB fairmolDocking 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 Z56783496

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
40.3 kcal/mol
Protein clashes
8
Internal clashes
8
Native overlap
contact recall 0.71, Jaccard 0.67, H-bond role recall 0.36
Burial
56%
Hydrophobic fit
78%
Reason: 8 internal clashes
8 protein-contact clashes 8 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 ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.724 kcal/mol/HA) ✓ Good fit quality (FQ -6.98) ✓ Strong H-bond network (16 bonds) ✓ Good burial (56% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ Extreme strain energy (40.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (5)
Score
-21.717
kcal/mol
LE
-0.724
kcal/mol/HA
Fit Quality
-6.98
FQ (Leeson)
HAC
30
heavy atoms
MW
486
Da
LogP
4.57
cLogP
Strain ΔE
40.3 kcal/mol
SASA buried
56%
Lipo contact
78% BSA apolar/total
SASA unbound
657 Ų
Apolar buried
286 Ų

Interaction summary

HB 16 HY 3 PI 2 CLASH 8 ⚠ Exposure 56%

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
⚠️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 4.57 H-bonds 16
Exposed fragments: phenyl (3/5 atoms exposed)aliphatic chain/group (6 atoms exposed)
Final rank4.243Score-21.717
Inter norm-0.868Intra norm0.144
Top1000noExcludedno
Contacts13H-bonds16
Artifact reasongeometry warning; 5 clashes; 2 protein clashes; high strain Δ 40.3
Residues
ALA15 ARG116 ARG140 ARG144 ASN106 ASP13 CYS72 GLY73 HIS105 HIS14 HIS141 SER46 TYR49

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 overlap12Native recall0.71
Jaccard0.67RMSD-
HB strict6Strict recall0.46
HB same residue+role4HB role recall0.36
HB same residue4HB residue recall0.36

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
414 4.243481574384162 -0.868166 -21.7172 16 13 12 0.71 0.36 - 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 -21.717kcal/mol
Ligand efficiency (LE) -0.7239kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.983
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 486.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.57
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 40.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 92.19kcal/mol
Minimised FF energy 51.92kcal/mol

SASA & burial

✓ computed
SASA (unbound) 656.8Ų
Total solvent-accessible surface area of free ligand
BSA total 369.6Ų
Buried surface area upon binding
BSA apolar 286.4Ų
Hydrophobic contacts buried
BSA polar 83.2Ų
Polar contacts buried
Fraction buried 56.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 77.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2224.2Ų
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 721.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)