FAIRMol

Z2786555116

Pose ID 1970 Compound 1106 Pose 615

DB fairmolDocking 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 Z2786555116

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
33.0 kcal/mol
Protein clashes
3
Internal clashes
15
Native overlap
contact recall 0.85, Jaccard 0.85, H-bond role recall 0.40
Burial
88%
Hydrophobic fit
87%
Reason: 15 internal clashes
3 protein-contact clashes 15 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.888 kcal/mol/HA) ✓ Good fit quality (FQ -8.57) ✓ Good H-bonds (3 bonds) ✓ Deep burial (88% SASA buried) ✓ Lipophilic contacts well-matched (87%) ✗ Very high strain energy (33.0 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (3) ✗ Many internal clashes (15)
Score
-26.652
kcal/mol
LE
-0.888
kcal/mol/HA
Fit Quality
-8.57
FQ (Leeson)
HAC
30
heavy atoms
MW
421
Da
LogP
3.94
cLogP
Strain ΔE
33.0 kcal/mol
SASA buried
88%
Lipo contact
87% BSA apolar/total
SASA unbound
680 Ų
Apolar buried
521 Ų

Interaction summary

HB 3 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 rank1.246Score-26.652
Inter norm-0.954Intra norm0.066
Top1000noExcludedno
Contacts17H-bonds3
Artifact reasongeometry warning; 15 clashes; 3 protein contact clashes; high strain Δ 33.0
Residues
ALA32 ARG97 ASP52 ILE45 LEU94 LYS57 MET53 NDP301 PHE56 PRO88 SER86 THR83 TYR162 VAL156 VAL30 VAL31 VAL87

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 overlap17Native recall0.85
Jaccard0.85RMSD-
HB strict3Strict recall0.43
HB same residue+role2HB role recall0.40
HB same residue2HB residue recall0.40

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
615 1.2459304674828053 -0.954123 -26.6523 3 17 17 0.85 0.40 - no Current
600 2.3579498767405274 -0.89371 -24.4846 3 19 1 0.05 0.00 - no Open
612 3.200337542338984 -0.919186 -26.9863 9 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 -26.652kcal/mol
Ligand efficiency (LE) -0.8884kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.570
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 420.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.94
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 32.99kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 56.11kcal/mol
Minimised FF energy 23.12kcal/mol

SASA & burial

✓ computed
SASA (unbound) 680.0Ų
Total solvent-accessible surface area of free ligand
BSA total 596.8Ų
Buried surface area upon binding
BSA apolar 520.5Ų
Hydrophobic contacts buried
BSA polar 76.3Ų
Polar contacts buried
Fraction buried 87.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 87.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1602.6Ų
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 815.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)