FAIRMol

Z24565962

Pose ID 7952 Compound 1264 Pose 500

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
T12
T. brucei R5P T. brucei
Ligand Z24565962
PDB6FXS↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
43.6 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.81, Jaccard 0.68, H-bond role recall 0.50
Burial
74%
Hydrophobic fit
76%
Reason: strain 43.6 kcal/mol
strain ΔE 43.6 kcal/mol 4 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.875 kcal/mol/HA) ✓ Good fit quality (FQ -8.68) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ Extreme strain energy (43.6 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (10) ✗ Many internal clashes (11)
Score
-28.868
kcal/mol
LE
-0.875
kcal/mol/HA
Fit Quality
-8.68
FQ (Leeson)
HAC
33
heavy atoms
MW
483
Da
LogP
4.38
cLogP
Strain ΔE
43.6 kcal/mol
SASA buried
74%
Lipo contact
76% BSA apolar/total
SASA unbound
701 Ų
Apolar buried
394 Ų

Interaction summary

HB 10 HY 9 PI 3 CLASH 4
Final rank2.050Score-28.868
Inter norm-0.829Intra norm-0.045
Top1000noExcludedno
Contacts16H-bonds10
Artifact reasongeometry warning; 11 clashes; 10 protein contact clashes; high strain Δ 43.6
Residues
ARG140 ARG144 ASN106 HIS105 HIS141 MET101 TYR97 ARG116 ARG46 ASP13 CYS72 GLY73 HIS14 ILE15 SER74 TYR49

Protein summary

302 residues
Protein targetT12Atoms4598
Residues302Chains2
Residue summaryARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121

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:CSD72

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6FXSContacts16
PoseOpen native poseHB0
IFP residues
ARG140 ARG144 ASN106 HIS105 HIS141 ARG46 ASP13 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 SER74 TYR49
Current overlap13Native recall0.81
Jaccard0.68RMSD-
HB strict6Strict recall0.50
HB same residue+role5HB role recall0.50
HB same residue5HB residue recall0.50

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
500 2.0498656463321923 -0.829319 -28.8676 10 16 13 0.81 0.50 - no Current
527 2.2281217810212235 -0.893909 -32.4636 4 13 0 0.00 0.00 - no Open
540 2.711073966387919 -0.641849 -23.1334 3 14 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 -28.868kcal/mol
Ligand efficiency (LE) -0.8748kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.679
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 482.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.38
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 43.62kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 41.81kcal/mol
Minimised FF energy -1.82kcal/mol

SASA & burial

✓ computed
SASA (unbound) 701.4Ų
Total solvent-accessible surface area of free ligand
BSA total 517.6Ų
Buried surface area upon binding
BSA apolar 394.2Ų
Hydrophobic contacts buried
BSA polar 123.4Ų
Polar contacts buried
Fraction buried 73.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2172.5Ų
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 2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 852.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)