FAIRMol

Z56826892

Pose ID 6558 Compound 960 Pose 462

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 Z56826892

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
23.7 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.94, Jaccard 0.89, H-bond role recall 0.36
Burial
63%
Hydrophobic fit
82%
Reason: 6 internal clashes
6 protein-contact clashes 6 intramolecular clashes 71% of hydrophobic surface is solvent-exposed (15/21 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.688 kcal/mol/HA) ✓ Good fit quality (FQ -6.70) ✓ Good H-bonds (3 bonds) ✓ Good burial (63% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ High strain energy (23.7 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (10) ✗ Many internal clashes (11)
Score
-21.312
kcal/mol
LE
-0.688
kcal/mol/HA
Fit Quality
-6.70
FQ (Leeson)
HAC
31
heavy atoms
MW
478
Da
LogP
4.72
cLogP
Final rank
2.0134
rank score
Inter norm
-0.765
normalised
Contacts
17
H-bonds 5
Strain ΔE
23.7 kcal/mol
SASA buried
63%
Lipo contact
82% BSA apolar/total
SASA unbound
699 Ų
Apolar buried
365 Ų

Interaction summary

HBA 3 HY 2 PI 1 CLASH 6

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

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
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 strict4Strict recall0.31
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
460 1.8777448127256184 -0.865635 -19.3746 4 17 5 0.29 0.09 - no Open
477 1.9436046199643353 -0.914653 -22.7513 6 18 0 0.00 0.00 - no Open
462 2.013375696079133 -0.764934 -21.3119 5 17 16 0.94 0.36 - no Current
452 2.316087839707507 -1.17716 -58.3646 6 17 0 0.00 0.00 - no Open
496 2.3705378259640018 -0.863559 -25.661 1 17 0 0.00 0.00 - no Open
447 2.489012354934417 -1.16168 -31.9315 6 18 0 0.00 0.00 - no Open
516 2.6908538270493585 -0.830365 -21.085 1 19 0 0.00 0.00 - no Open
465 2.715181301617068 -0.904736 -19.1684 10 18 0 0.00 0.00 - no Open
516 2.8199088495293476 -0.821603 -22.806 3 20 0 0.00 0.00 - no Open
478 4.104156564970094 -1.06645 -31.8476 11 23 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 -21.312kcal/mol
Ligand efficiency (LE) -0.6875kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.698
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 478.0Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.72
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 23.72kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -20.40kcal/mol
Minimised FF energy -44.12kcal/mol

SASA & burial

✓ computed
SASA (unbound) 698.6Ų
Total solvent-accessible surface area of free ligand
BSA total 442.8Ų
Buried surface area upon binding
BSA apolar 365.0Ų
Hydrophobic contacts buried
BSA polar 77.8Ų
Polar contacts buried
Fraction buried 63.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2256.9Ų
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 2417.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 734.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)