FAIRMol

KB_chagas_112

Pose ID 846 Compound 675 Pose 168

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
T02
Human DHFR Human
Ligand KB_chagas_112
PDB5SD8↗

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 strong SASA done
Strain ΔE
30.4 kcal/mol
Protein clashes
0
Internal clashes
11
Native overlap
contact recall 0.76, Jaccard 0.76, H-bond role recall 0.40
Burial
94%
Hydrophobic fit
97%
Reason: 11 internal clashes
11 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.987 kcal/mol/HA) ✓ Good fit quality (FQ -8.85) ✓ Good H-bonds (3 bonds) ✓ Deep burial (94% SASA buried) ✓ Lipophilic contacts well-matched (97%) ✗ Very high strain energy (30.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-23.695
kcal/mol
LE
-0.987
kcal/mol/HA
Fit Quality
-8.85
FQ (Leeson)
HAC
24
heavy atoms
MW
321
Da
LogP
2.17
cLogP
Strain ΔE
30.4 kcal/mol
SASA buried
94%
Lipo contact
97% BSA apolar/total
SASA unbound
563 Ų
Apolar buried
511 Ų

Interaction summary

HB 3 HY 24 PI 1 CLASH 0
Final rank0.404Score-23.695
Inter norm-1.070Intra norm0.083
Top1000noExcludedno
Contacts16H-bonds3
Artifact reasongeometry warning; 11 clashes; 1 protein contact clash; high strain Δ 30.4
Residues
ALA10 ASP22 GLU31 ILE61 ILE8 LEU68 NAP201 PHE32 PHE35 PRO62 SER60 THR137 THR57 TYR122 VAL116 VAL9

Protein summary

200 residues
Protein targetT02Atoms3128
Residues200Chains2
Residue summaryLYS:374; LEU:361; GLU:240; VAL:224; ARG:192; PHE:180; ILE:171; PRO:168; ASN:140; SER:132; TYR:126; GLN:119; ASP:108; MET:102; THR:98; GLY:91

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:NAP201

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name5SD8Contacts21
PoseOpen native poseHB0
IFP residues
ALA10 ASN65 ASP22 GLN36 GLU31 GLY117 GLY21 ILE61 ILE8 LEU23 LEU68 NAP201 PHE32 PHE35 PRO62 SER60 THR137 THR57 TYR122 VAL116 VAL9
Current overlap16Native recall0.76
Jaccard0.76RMSD-
HB strict2Strict recall0.40
HB same residue+role2HB role recall0.40
HB same residue2HB residue recall0.40

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
146 0.19655990329963136 -0.982777 -23.5247 1 16 0 0.00 0.00 - no Open
168 0.4038319057602343 -1.07038 -23.6945 3 16 16 0.76 0.40 - no Current
157 1.3331251010485028 -0.93282 -24.0238 3 12 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 -23.695kcal/mol
Ligand efficiency (LE) -0.9873kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.848
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 321.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.17
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 30.39kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 45.51kcal/mol
Minimised FF energy 15.12kcal/mol

SASA & burial

✓ computed
SASA (unbound) 563.2Ų
Total solvent-accessible surface area of free ligand
BSA total 528.7Ų
Buried surface area upon binding
BSA apolar 510.9Ų
Hydrophobic contacts buried
BSA polar 17.8Ų
Polar contacts buried
Fraction buried 93.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 96.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1606.5Ų
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 1677.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 616.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)