FAIRMol

Z73416904

Pose ID 14595 Compound 1229 Pose 357

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 Z73416904

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 strong SASA done
Strain ΔE
23.3 kcal/mol
Protein clashes
9
Internal clashes
9
Native overlap
contact recall 0.71, Jaccard 0.52, H-bond role recall 0.36
Burial
89%
Hydrophobic fit
74%
Reason: 9 protein-contact clashes, 9 internal clashes
9 protein-contact clashes 9 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.014 kcal/mol/HA) ✓ Good fit quality (FQ -9.88) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (89% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ High strain energy (23.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-31.424
kcal/mol
LE
-1.014
kcal/mol/HA
Fit Quality
-9.88
FQ (Leeson)
HAC
31
heavy atoms
MW
442
Da
LogP
0.80
cLogP
Final rank
4.4927
rank score
Inter norm
-1.037
normalised
Contacts
23
H-bonds 13
Strain ΔE
23.3 kcal/mol
SASA buried
89%
Lipo contact
74% BSA apolar/total
SASA unbound
705 Ų
Apolar buried
461 Ų

Interaction summary

HBD 1 HBA 8 HY 3 PI 0 CLASH 9

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 7.

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: permissive.
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
Jaccard0.52RMSD-
HB strict5Strict recall0.33
HB same residue+role4HB role recall0.36
HB same residue4HB residue recall0.36

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
355 1.6026500140535416 -0.743905 -21.8571 2 17 0 0.00 0.00 - no Open
354 1.7306580484949365 -0.923116 -29.7352 11 16 0 0.00 0.00 - no Open
407 2.0338986117039672 -0.876746 -27.1056 4 15 0 0.00 0.00 - no Open
358 2.1591494369409356 -0.901399 -28.0656 4 15 0 0.00 0.00 - no Open
383 3.080838426070046 -0.679833 -20.0918 4 11 0 0.00 0.00 - no Open
357 4.492732902768604 -1.03651 -31.4245 13 23 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 -31.424kcal/mol
Ligand efficiency (LE) -1.0137kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.876
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 442.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.80
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 23.33kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 19.63kcal/mol
Minimised FF energy -3.70kcal/mol

SASA & burial

✓ computed
SASA (unbound) 704.6Ų
Total solvent-accessible surface area of free ligand
BSA total 624.0Ų
Buried surface area upon binding
BSA apolar 461.1Ų
Hydrophobic contacts buried
BSA polar 162.9Ų
Polar contacts buried
Fraction buried 88.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1381.5Ų
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 499.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)