FAIRMol

Z56799026

Pose ID 8104 Compound 3885 Pose 652

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
T12
T. brucei R5P T. brucei
Ligand Z56799026
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
66.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.75, Jaccard 0.67, H-bond role recall 0.30
Burial
66%
Hydrophobic fit
63%
Reason: strain 66.5 kcal/mol
strain ΔE 66.5 kcal/mol 1 protein-contact clashes 67% of hydrophobic surface is solvent-exposed (14/21 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 ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.161 kcal/mol/HA) ✓ Good fit quality (FQ -11.31) ✓ Good H-bonds (4 bonds) ✓ Deep burial (66% SASA buried) ✓ Lipophilic contacts well-matched (63%) ✗ Extreme strain energy (66.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-35.985
kcal/mol
LE
-1.161
kcal/mol/HA
Fit Quality
-11.31
FQ (Leeson)
HAC
31
heavy atoms
MW
449
Da
LogP
6.13
cLogP
Final rank
3.1832
rank score
Inter norm
-0.932
normalised
Contacts
14
H-bonds 8
Strain ΔE
66.5 kcal/mol
SASA buried
66%
Lipo contact
63% BSA apolar/total
SASA unbound
710 Ų
Apolar buried
295 Ų

Interaction summary

HBA 4 HY 3 PI 2 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 2.

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

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.
Name6FXSContacts16
PoseOpen native poseHB0
IFP residues
ARG140 ARG144 ASN106 HIS105 HIS141 ARG46 ASP13 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 SER74 TYR49
Current overlap12Native recall0.75
Jaccard0.67RMSD-
HB strict5Strict recall0.42
HB same residue+role3HB role recall0.30
HB same residue4HB residue recall0.40

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
652 3.18316293059357 -0.931922 -35.9853 8 14 12 0.75 0.30 - no Current
665 4.464983918621528 -0.978845 -31.0499 15 22 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 -35.985kcal/mol
Ligand efficiency (LE) -1.1608kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.309
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 449.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 6.13
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 66.55kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 64.47kcal/mol
Minimised FF energy -2.07kcal/mol

SASA & burial

✓ computed
SASA (unbound) 710.4Ų
Total solvent-accessible surface area of free ligand
BSA total 467.8Ų
Buried surface area upon binding
BSA apolar 295.2Ų
Hydrophobic contacts buried
BSA polar 172.6Ų
Polar contacts buried
Fraction buried 65.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 63.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2147.2Ų
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 2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 796.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)