FAIRMol

Z56864520

Pose ID 14911 Compound 575 Pose 673

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 Z56864520

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry medium Native mixed SASA done
Strain ΔE
33.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.48, Jaccard 0.40, H-bond role recall 0.45
Burial
79%
Hydrophobic fit
60%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.885 kcal/mol/HA) ✓ Good fit quality (FQ -8.36) ✓ Strong H-bond network (13 bonds) ✓ Deep burial (79% SASA buried) ✓ Lipophilic contacts well-matched (60%) ✗ Very high strain energy (33.6 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-24.782
kcal/mol
LE
-0.885
kcal/mol/HA
Fit Quality
-8.36
FQ (Leeson)
HAC
28
heavy atoms
MW
413
Da
LogP
3.65
cLogP
Strain ΔE
33.6 kcal/mol
SASA buried
79%
Lipo contact
60% BSA apolar/total
SASA unbound
650 Ų
Apolar buried
309 Ų

Interaction summary

HB 13 HY 8 PI 0 CLASH 1

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

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

HY · Hydrophobic contacts

CLASH · Clashes
Final rank2.330Score-24.782
Inter norm-1.121Intra norm0.226
Top1000noExcludedno
Contacts14H-bonds13
Artifact reasongeometry warning; 7 clashes; 1 protein clash; high strain Δ 33.6
Residues
ALA24 ALA48 ASN41 GLN42 GLY23 GLY25 GLY47 ILE46 LEU31 LEU39 LYS127 LYS26 SER27 SER28

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 overlap10Native recall0.48
Jaccard0.40RMSD-
HB strict7Strict recall0.47
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
663 0.2511577254753023 -1.09851 -30.8922 4 15 0 0.00 0.00 - no Open
646 0.8020123366541132 -0.883354 -23.985 2 18 0 0.00 0.00 - no Open
644 2.060226456342705 -0.948105 -29.2566 6 11 0 0.00 0.00 - no Open
673 2.3297314190059755 -1.12086 -24.7821 13 14 10 0.48 0.45 - no Current
671 2.7084623141150126 -0.874177 -26.6575 13 15 0 0.00 0.00 - no Open
643 3.017585003862393 -0.904163 -23.0924 5 16 0 0.00 0.00 - no Open
668 3.3289291970169095 -1.03104 -25.9639 9 19 0 0.00 0.00 - no Open
639 3.377817040032817 -0.950565 -28.199 7 13 0 0.00 0.00 - no Open
662 3.4574628969651684 -0.923998 -27.0934 13 15 0 0.00 0.00 - no Open
655 5.144145577855445 -1.05202 -28.4978 16 20 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 -24.782kcal/mol
Ligand efficiency (LE) -0.8851kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.355
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 412.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.65
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 33.63kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 109.53kcal/mol
Minimised FF energy 75.90kcal/mol

SASA & burial

✓ computed
SASA (unbound) 649.7Ų
Total solvent-accessible surface area of free ligand
BSA total 514.1Ų
Buried surface area upon binding
BSA apolar 309.1Ų
Hydrophobic contacts buried
BSA polar 205.1Ų
Polar contacts buried
Fraction buried 79.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 60.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1264.6Ų
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 544.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)