FAIRMol

Z56789391

Pose ID 14610 Compound 5555 Pose 372

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
T22
L. donovani rab5a L. donovani
Ligand Z56789391

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 mixed SASA done
Strain ΔE
35.5 kcal/mol
Protein clashes
7
Internal clashes
7
Native overlap
contact recall 0.52, Jaccard 0.38, H-bond role recall 0.45
Burial
93%
Hydrophobic fit
70%
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 ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.376 kcal/mol/HA) ✓ Good fit quality (FQ -12.14) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (93% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ Very high strain energy (35.5 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-31.648
kcal/mol
LE
-1.376
kcal/mol/HA
Fit Quality
-12.14
FQ (Leeson)
HAC
23
heavy atoms
MW
328
Da
LogP
2.88
cLogP
Final rank
4.6412
rank score
Inter norm
-1.468
normalised
Contacts
19
H-bonds 16
Strain ΔE
35.5 kcal/mol
SASA buried
93%
Lipo contact
70% BSA apolar/total
SASA unbound
525 Ų
Apolar buried
343 Ų

Interaction summary

HBD 1 HBA 7 HY 2 PI 0 CLASH 7

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 6.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameRAB5AContacts21
PoseOpen native poseHB0
IFP residues
ALA158 ALA24 ALA40 ASN126 ASN41 ASP129 GLN42 GLU21 GLU73 GLY23 GLY25 LEU130 LEU39 LYS127 LYS159 LYS26 PHE38 SER157 SER22 SER27 SER28
Current overlap11Native recall0.52
Jaccard0.38RMSD-
HB strict6Strict recall0.40
HB same residue+role5HB role recall0.45
HB same residue5HB residue recall0.45

Protein summary

165 residues
Protein targetT22Atoms2561
Residues165Chains1
Residue summaryLEU:363; LYS:242; ALA:231; ARG:214; ILE:190; GLU:180; VAL:144; SER:143; PHE:140; ASN:112; THR:112; TYR:105; GLN:102; ASP:96; GLY:77; TRP:48

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
372 4.641163885384707 -1.46819 -31.6482 16 19 11 0.52 0.45 - 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 -31.648kcal/mol
Ligand efficiency (LE) -1.3760kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -12.144
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 328.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.88
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 35.51kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 107.34kcal/mol
Minimised FF energy 71.84kcal/mol

SASA & burial

✓ computed
SASA (unbound) 525.4Ų
Total solvent-accessible surface area of free ligand
BSA total 488.7Ų
Buried surface area upon binding
BSA apolar 342.5Ų
Hydrophobic contacts buried
BSA polar 146.2Ų
Polar contacts buried
Fraction buried 93.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1227.5Ų
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 1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 495.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)