FAIRMol

Z95963339

Pose ID 14647 Compound 5536 Pose 409

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 Z95963339

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
23.3 kcal/mol
Protein clashes
12
Internal clashes
12
Native overlap
contact recall 0.48, Jaccard 0.36, H-bond role recall 0.27
Burial
75%
Hydrophobic fit
83%
Reason: 12 protein-contact clashes, 12 internal clashes
12 protein-contact clashes 12 intramolecular clashes 73% of hydrophobic surface is solvent-exposed (16/22 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 ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.887 kcal/mol/HA) ✓ Good fit quality (FQ -8.38) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (75% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ High strain energy (23.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-24.843
kcal/mol
LE
-0.887
kcal/mol/HA
Fit Quality
-8.38
FQ (Leeson)
HAC
28
heavy atoms
MW
394
Da
LogP
4.32
cLogP
Final rank
4.0238
rank score
Inter norm
-1.072
normalised
Contacts
17
H-bonds 9
Strain ΔE
23.3 kcal/mol
SASA buried
75%
Lipo contact
83% BSA apolar/total
SASA unbound
656 Ų
Apolar buried
405 Ų

Interaction summary

HBD 1 HBA 5 HY 1 PI 0 CLASH 12

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.

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 overlap10Native recall0.48
Jaccard0.36RMSD-
HB strict5Strict recall0.33
HB same residue+role3HB role recall0.27
HB same residue3HB residue recall0.27

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
409 4.023783690115894 -1.07189 -24.8427 9 17 10 0.48 0.27 - 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 -24.843kcal/mol
Ligand efficiency (LE) -0.8872kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.376
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 394.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.32
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 23.35kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -6.67kcal/mol
Minimised FF energy -30.02kcal/mol

SASA & burial

✓ computed
SASA (unbound) 656.5Ų
Total solvent-accessible surface area of free ligand
BSA total 489.6Ų
Buried surface area upon binding
BSA apolar 405.0Ų
Hydrophobic contacts buried
BSA polar 84.6Ų
Polar contacts buried
Fraction buried 74.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1393.2Ų
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 1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 524.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)