FAIRMol

Z104500108

Pose ID 1806 Compound 1154 Pose 451

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
T03
L. major DHFR L. major
Ligand Z104500108

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
37.7 kcal/mol
Protein clashes
0
Internal clashes
6
Native overlap
contact recall 0.75, Jaccard 0.71, H-bond role recall 0.80
Burial
89%
Hydrophobic fit
79%
Reason: 6 internal clashes
6 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.906 kcal/mol/HA) ✓ Good fit quality (FQ -8.45) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (89% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ Very high strain energy (37.7 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-24.455
kcal/mol
LE
-0.906
kcal/mol/HA
Fit Quality
-8.45
FQ (Leeson)
HAC
27
heavy atoms
MW
368
Da
LogP
3.37
cLogP
Strain ΔE
37.7 kcal/mol
SASA buried
89%
Lipo contact
79% BSA apolar/total
SASA unbound
663 Ų
Apolar buried
464 Ų

Interaction summary

HB 6 HY 24 PI 2 CLASH 0

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.
Final rank1.625Score-24.455
Inter norm-1.010Intra norm0.104
Top1000noExcludedno
Contacts16H-bonds6
Artifact reasongeometry warning; 6 clashes; 1 protein clash; high strain Δ 35.6
Residues
ALA32 ARG97 ASP52 ILE45 LEU94 LYS57 LYS95 MET53 NDP301 PHE56 PHE91 THR83 TYR162 VAL156 VAL30 VAL31

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name3CL9Contacts20
PoseOpen native poseHB0
IFP residues
ALA32 ARG97 ASP52 ILE45 LEU94 LYS57 MET53 NDP301 PHE56 PHE91 PRO88 SER86 THR180 THR54 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap15Native recall0.75
Jaccard0.71RMSD-
HB strict4Strict recall0.57
HB same residue+role4HB role recall0.80
HB same residue4HB residue recall0.80

Protein summary

225 residues
Protein targetT03Atoms3428
Residues225Chains2
Residue summaryLEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; NDP:74

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
451 1.62513760502491 -1.0097 -24.4552 6 16 15 0.75 0.80 - no Current
441 2.439082481465908 -0.928261 -18.0333 13 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 -24.455kcal/mol
Ligand efficiency (LE) -0.9057kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.450
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 368.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.37
Lipinski: ≤ 5
Rotatable bonds 10

Conformational strain (MMFF94s)
Strain energy (ΔE) 37.67kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 84.67kcal/mol
Minimised FF energy 47.00kcal/mol

SASA & burial

✓ computed
SASA (unbound) 663.3Ų
Total solvent-accessible surface area of free ligand
BSA total 589.4Ų
Buried surface area upon binding
BSA apolar 464.1Ų
Hydrophobic contacts buried
BSA polar 125.3Ų
Polar contacts buried
Fraction buried 88.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 78.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1532.3Ų
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 1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 799.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)