FAIRMol

Z199054106

Pose ID 12845 Compound 4084 Pose 644

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
T19
T. brucei TR (NADPH binding site) T. brucei NADPH binding site
Ligand Z199054106
PDB2WOV↗

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
10.3 kcal/mol
Protein clashes
3
Internal clashes
4
Native overlap
contact recall 0.26, Jaccard 0.17, H-bond role recall 0.20
Burial
94%
Hydrophobic fit
92%
Reason: no major geometry red flags detected
3 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.003 kcal/mol/HA) ✓ Good fit quality (FQ -9.68) ✓ Good H-bonds (4 bonds) ✓ Deep burial (94% SASA buried) ✓ Lipophilic contacts well-matched (92%) ✗ Moderate strain (10.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-30.089
kcal/mol
LE
-1.003
kcal/mol/HA
Fit Quality
-9.68
FQ (Leeson)
HAC
30
heavy atoms
MW
393
Da
LogP
6.58
cLogP
Strain ΔE
10.3 kcal/mol
SASA buried
94%
Lipo contact
92% BSA apolar/total
SASA unbound
676 Ų
Apolar buried
584 Ų

Interaction summary

HB 4 HY 23 PI 0 CLASH 4
Final rank2.319Score-30.089
Inter norm-1.068Intra norm0.039
Top1000noExcludedno
Contacts20H-bonds4
Artifact reasongeometry warning; 11 clashes; 1 protein clash; 1 cofactor-context clash
Residues
ALA338 ARG287 ASP327 CYS52 CYS57 GLU202 GLY56 ILE199 LEU334 LYS60 NDP800 PHE182 PHE203 PHE367 PRO336 SER14 SER178 THR335 THR51 VAL55

Protein summary

493 residues
Protein targetT19Atoms7541
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:330; TYR:294; ASP:264; 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
C:NDP800

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name2WOVContacts27
PoseOpen native poseHB0
IFP residues
ALA284 ALA365 ARG222 ARG228 ARG287 ASN223 ASN254 GLN165 GLU202 GLY195 GLY196 GLY197 GLY286 ILE199 ILE285 LEU227 LEU334 LYS60 MET333 NDP800 PHE198 PHE367 PRO167 SER200 TYR221 VAL194 VAL366
Current overlap7Native recall0.26
Jaccard0.17RMSD-
HB strict1Strict recall0.08
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.25

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
631 0.7641378312650706 -0.728918 -20.0211 3 12 0 0.00 0.00 - no Open
647 1.5343132795776104 -0.776554 -18.2427 4 17 0 0.00 0.00 - no Open
644 2.319025147822157 -1.06752 -30.0889 4 20 7 0.26 0.20 - no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -30.089kcal/mol
Ligand efficiency (LE) -1.0030kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.675
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 392.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 6.58
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 10.31kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 86.92kcal/mol
Minimised FF energy 76.62kcal/mol

SASA & burial

✓ computed
SASA (unbound) 676.4Ų
Total solvent-accessible surface area of free ligand
BSA total 637.2Ų
Buried surface area upon binding
BSA apolar 584.2Ų
Hydrophobic contacts buried
BSA polar 53.1Ų
Polar contacts buried
Fraction buried 94.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 91.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3212.2Ų
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 4064.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1475.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)