FAIRMol

KB_Leish_34

Pose ID 10972 Compound 1355 Pose 129

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
T17
T. brucei TR (Doorstop site) T. brucei Doorstop site
Ligand KB_Leish_34
PDB5S9T↗

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
26.2 kcal/mol
Protein clashes
0
Internal clashes
16
Native overlap
contact recall 0.58, Jaccard 0.33, H-bond role recall 0.00
Burial
79%
Hydrophobic fit
84%
Reason: 16 internal clashes
16 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.720 kcal/mol/HA) ✓ Good fit quality (FQ -7.01) ✓ Good H-bonds (5 bonds) ✓ Deep burial (79% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ High strain energy (26.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)
Score
-22.309
kcal/mol
LE
-0.720
kcal/mol/HA
Fit Quality
-7.01
FQ (Leeson)
HAC
31
heavy atoms
MW
418
Da
LogP
3.00
cLogP
Final rank
3.7459
rank score
Inter norm
-0.795
normalised
Contacts
16
H-bonds 9
Strain ΔE
26.2 kcal/mol
SASA buried
79%
Lipo contact
84% BSA apolar/total
SASA unbound
724 Ų
Apolar buried
479 Ų

Interaction summary

HBD 2 HBA 3 HY 6 PI 2 CLASH 0

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

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.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap7Native recall0.58
Jaccard0.33RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

1033 residues
Protein targetT17Atoms15160
Residues1033Chains2
Residue summaryVAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408

Receptor context

2 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 2 Excluded HETATM 0
Kept cofactors / ions
A:FAD501 B:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
26 1.4101122879884354 -0.906264 -23.329 4 16 0 0.00 0.00 - no Open
110 2.103604095285442 -0.923564 -26.714 6 20 0 0.00 0.00 - no Open
134 2.947754247818082 -0.927731 -23.7117 7 18 0 0.00 0.00 - no Open
21 3.346236366062366 -0.860096 -25.5696 5 16 0 0.00 0.00 - no Open
129 3.7459393641572074 -0.795054 -22.3086 9 16 7 0.58 0.00 - no Current
116 3.774010796698115 -0.852737 -25.5275 6 17 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 -22.309kcal/mol
Ligand efficiency (LE) -0.7196kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.011
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 418.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.00
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 26.20kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -155.93kcal/mol
Minimised FF energy -182.14kcal/mol

SASA & burial

✓ computed
SASA (unbound) 724.4Ų
Total solvent-accessible surface area of free ligand
BSA total 571.2Ų
Buried surface area upon binding
BSA apolar 479.1Ų
Hydrophobic contacts buried
BSA polar 92.1Ų
Polar contacts buried
Fraction buried 78.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6607.9Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2079.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)