FAIRMol

Z29484725

Pose ID 5931 Compound 695 Pose 513

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 Z29484725

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
24.8 kcal/mol
Protein clashes
3
Internal clashes
10
Native overlap
contact recall 0.71, Jaccard 0.60, H-bond role recall 0.00
Burial
91%
Hydrophobic fit
68%
Reason: 10 internal clashes
3 protein-contact clashes 10 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.746 kcal/mol/HA) ✓ Good fit quality (FQ -7.46) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ High strain energy (24.8 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (3) ✗ Many internal clashes (10)
Score
-25.348
kcal/mol
LE
-0.746
kcal/mol/HA
Fit Quality
-7.46
FQ (Leeson)
HAC
34
heavy atoms
MW
528
Da
LogP
1.46
cLogP
Strain ΔE
24.8 kcal/mol
SASA buried
91%
Lipo contact
68% BSA apolar/total
SASA unbound
693 Ų
Apolar buried
426 Ų

Interaction summary

HB 2 HY 24 PI 1 CLASH 0
Final rank0.907Score-25.348
Inter norm-0.776Intra norm0.030
Top1000noExcludedno
Contacts19H-bonds2
Artifact reasongeometry warning; 10 clashes; 3 protein contact clashes; moderate strain Δ 24.8
Residues
NDP301 ALA32 ARG48 ASP52 ILE45 LEU94 MET53 PHE56 PRO88 SER44 SER86 THR180 THR83 TRP47 TYR162 VAL156 VAL31 VAL49 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 overlap15Native recall0.71
Jaccard0.60RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
550 0.6761261280243801 -0.770379 -24.7536 1 18 0 0.00 0.00 - no Open
513 0.9072321613567527 -0.775539 -25.3477 2 19 15 0.71 0.00 - no Current
538 3.201542177437042 -0.733884 -23.0948 8 17 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 -25.348kcal/mol
Ligand efficiency (LE) -0.7455kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.460
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 527.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.46
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 24.77kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 31.83kcal/mol
Minimised FF energy 7.06kcal/mol

SASA & burial

✓ computed
SASA (unbound) 693.5Ų
Total solvent-accessible surface area of free ligand
BSA total 628.7Ų
Buried surface area upon binding
BSA apolar 426.5Ų
Hydrophobic contacts buried
BSA polar 202.2Ų
Polar contacts buried
Fraction buried 90.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 67.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3243.8Ų
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 1659.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)