FAIRMol

Z56762066

Pose ID 12025 Compound 923 Pose 504

DB SELECTIONDocking 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
T18
T. brucei TR (Mepacrine binding site (MBS, site 1)) T. brucei Mepacrine binding site (MBS, site 1)
Ligand Z56762066
PDB6RB5↗

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 high Native mixed SASA done
Strain ΔE
18.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.54, Jaccard 0.47
Burial
65%
Hydrophobic fit
83%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.722 kcal/mol/HA) ✓ Good fit quality (FQ -6.82) ✓ Deep burial (65% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ Moderate strain (18.4 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (2) ✗ Many internal clashes (12)
Score
-20.213
kcal/mol
LE
-0.722
kcal/mol/HA
Fit Quality
-6.82
FQ (Leeson)
HAC
28
heavy atoms
MW
386
Da
LogP
4.93
cLogP
Strain ΔE
18.4 kcal/mol
SASA buried
65%
Lipo contact
83% BSA apolar/total
SASA unbound
602 Ų
Apolar buried
328 Ų

Interaction summary

HB 2 HY 24 PI 2 CLASH 2
Final rank0.864Score-20.213
Inter norm-0.746Intra norm0.024
Top1000noExcludedno
Contacts9H-bonds2
Artifact reasongeometry warning; 12 clashes; 2 protein contact clashes
Residues
GLU18 ILE106 ILE339 LEU17 MET113 SER109 SER14 TRP21 TYR110

Protein summary

493 residues
Protein targetT18Atoms7550
Residues493Chains1
Residue summaryVAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:276; MET:221

Receptor context

1 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 1 Excluded HETATM 0
Kept cofactors / ions
A:FAD501

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6RB5Contacts13
PoseOpen native poseHB0
IFP residues
ASP116 GLU18 GLY112 ILE106 LEU17 MET113 SER109 THR117 THR335 TRP21 TYR110 VAL53 VAL58
Current overlap7Native recall0.54
Jaccard0.47RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

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

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

HY · Hydrophobic contacts

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
504 0.8643933819477166 -0.745954 -20.2128 2 9 7 0.54 - - no Current
514 2.3450903609637552 -0.936825 -24.3398 1 18 0 0.00 - - no Open
460 4.055199461620027 -0.872882 -25.292 9 11 0 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 -20.213kcal/mol
Ligand efficiency (LE) -0.7219kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.815
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 386.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.93
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 18.38kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -13.44kcal/mol
Minimised FF energy -31.81kcal/mol

SASA & burial

✓ computed
SASA (unbound) 601.8Ų
Total solvent-accessible surface area of free ligand
BSA total 393.6Ų
Buried surface area upon binding
BSA apolar 327.7Ų
Hydrophobic contacts buried
BSA polar 65.9Ų
Polar contacts buried
Fraction buried 65.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3127.1Ų
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 4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1482.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)