FAIRMol

KB_chagas_104

Pose ID 5553 Compound 3309 Pose 135

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
T09
L. major DHFR-TS L. major
Ligand KB_chagas_104

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 mixed SASA done
Strain ΔE
37.6 kcal/mol
Protein clashes
0
Internal clashes
14
Native overlap
contact recall 0.38, Jaccard 0.31, H-bond role recall 0.17
Burial
69%
Hydrophobic fit
72%
Reason: 14 internal clashes
14 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.662 kcal/mol/HA) ✓ Good fit quality (FQ -6.68) ✓ Good H-bonds (5 bonds) ✓ Deep burial (69% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ Very high strain energy (37.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-23.168
kcal/mol
LE
-0.662
kcal/mol/HA
Fit Quality
-6.68
FQ (Leeson)
HAC
35
heavy atoms
MW
490
Da
LogP
2.72
cLogP
Strain ΔE
37.6 kcal/mol
SASA buried
69%
Lipo contact
72% BSA apolar/total
SASA unbound
753 Ų
Apolar buried
379 Ų

Interaction summary

HB 5 HY 22 PI 2 CLASH 0
Final rank2.873Score-23.168
Inter norm-0.749Intra norm0.087
Top1000noExcludedno
Contacts13H-bonds5
Artifact reasongeometry warning; 14 clashes; 1 protein clash; high strain Δ 37.5
Residues
ARG97 LEU94 LYS57 LYS90 LYS95 MET53 PHE56 PHE91 PRO50 PRO88 PRO93 THR54 VAL87

Protein summary

511 residues
Protein targetT09Atoms8170
Residues511Chains2
Residue summaryLEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224

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:NDP301

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name3CL9Contacts21
PoseOpen native poseHB0
IFP residues
NDP301 ALA32 ARG97 ASP52 GLY157 ILE45 LEU94 LYS57 MET53 PHE55 PHE56 PHE91 PRO88 SER86 THR180 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap8Native recall0.38
Jaccard0.31RMSD-
HB strict2Strict recall0.29
HB same residue+role1HB role recall0.17
HB same residue1HB residue recall0.17

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
No clash · clashes detected for this pose.

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
135 2.873105287369656 -0.749158 -23.1682 5 13 8 0.38 0.17 - no Current
93 3.613209796741848 -0.724488 -23.198 12 17 0 0.00 0.00 - no Open
112 5.761302332405041 -1.04951 -35.638 14 16 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 -23.168kcal/mol
Ligand efficiency (LE) -0.6619kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.677
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 35HA

Physicochemical properties
Molecular weight 489.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.72
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 37.60kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 118.80kcal/mol
Minimised FF energy 81.20kcal/mol

SASA & burial

✓ computed
SASA (unbound) 753.4Ų
Total solvent-accessible surface area of free ligand
BSA total 522.8Ų
Buried surface area upon binding
BSA apolar 379.2Ų
Hydrophobic contacts buried
BSA polar 143.6Ų
Polar contacts buried
Fraction buried 69.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3301.4Ų
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 4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1724.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)