FAIRMol

Z30932242

Pose ID 14636 Compound 5517 Pose 398

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 Z30932242

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
14.3 kcal/mol
Protein clashes
0
Internal clashes
9
Native overlap
contact recall 0.71, Jaccard 0.62, H-bond role recall 0.36
Burial
80%
Hydrophobic fit
77%
Reason: 9 internal clashes
9 intramolecular clashes 67% of hydrophobic surface is solvent-exposed (12/18 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 ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.240 kcal/mol/HA) ✓ Good fit quality (FQ -11.11) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ Moderate strain (14.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-29.759
kcal/mol
LE
-1.240
kcal/mol/HA
Fit Quality
-11.11
FQ (Leeson)
HAC
24
heavy atoms
MW
346
Da
LogP
2.56
cLogP
Final rank
3.4317
rank score
Inter norm
-1.281
normalised
Contacts
18
H-bonds 12
Strain ΔE
14.3 kcal/mol
SASA buried
80%
Lipo contact
77% BSA apolar/total
SASA unbound
617 Ų
Apolar buried
377 Ų

Interaction summary

HBD 2 HBA 6 HY 3 PI 1 CLASH 0

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

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
No clash · clashes detected for this pose.

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 overlap15Native recall0.71
Jaccard0.62RMSD-
HB strict6Strict recall0.40
HB same residue+role4HB role recall0.36
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
398 3.4316777561080065 -1.28076 -29.7594 12 18 15 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 -29.759kcal/mol
Ligand efficiency (LE) -1.2400kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.113
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 346.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.56
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 14.35kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -78.41kcal/mol
Minimised FF energy -92.75kcal/mol

SASA & burial

✓ computed
SASA (unbound) 616.6Ų
Total solvent-accessible surface area of free ligand
BSA total 491.5Ų
Buried surface area upon binding
BSA apolar 376.6Ų
Hydrophobic contacts buried
BSA polar 114.9Ų
Polar contacts buried
Fraction buried 79.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1352.3Ų
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 1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 508.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)