FAIRMol

Z27873696

Pose ID 1846 Compound 1398 Pose 491

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 Z27873696

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native mixed SASA done
Strain ΔE
59.6 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.50, Jaccard 0.43, H-bond role recall 0.20
Burial
84%
Hydrophobic fit
76%
Reason: strain 59.6 kcal/mol
strain ΔE 59.6 kcal/mol 5 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.979 kcal/mol/HA) ✓ Good fit quality (FQ -9.54) ✓ Good H-bonds (4 bonds) ✓ Deep burial (84% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ Extreme strain energy (59.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-30.345
kcal/mol
LE
-0.979
kcal/mol/HA
Fit Quality
-9.54
FQ (Leeson)
HAC
31
heavy atoms
MW
472
Da
LogP
1.58
cLogP
Strain ΔE
59.6 kcal/mol
SASA buried
84%
Lipo contact
76% BSA apolar/total
SASA unbound
707 Ų
Apolar buried
447 Ų

Interaction summary

HB 4 HY 23 PI 2 CLASH 5

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
Final rank3.365Score-30.345
Inter norm-0.902Intra norm-0.077
Top1000noExcludedno
Contacts13H-bonds4
Artifact reasongeometry warning; 13 clashes; 1 protein clash; high strain Δ 59.6
Residues
ARG97 ASP52 ILE45 LEU94 LYS57 LYS90 LYS95 MET53 PHE56 PHE91 PRO93 THR54 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 overlap10Native recall0.50
Jaccard0.43RMSD-
HB strict1Strict recall0.14
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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
449 0.9543235955270444 -0.805705 -26.6154 4 20 1 0.05 0.00 - no Open
477 1.999555085717567 -0.6289 -18.9999 6 11 0 0.00 0.00 - no Open
491 3.364629749418482 -0.902193 -30.345 4 13 10 0.50 0.20 - no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -30.345kcal/mol
Ligand efficiency (LE) -0.9789kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.536
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 471.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.58
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 59.58kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 106.30kcal/mol
Minimised FF energy 46.72kcal/mol

SASA & burial

✓ computed
SASA (unbound) 707.3Ų
Total solvent-accessible surface area of free ligand
BSA total 590.4Ų
Buried surface area upon binding
BSA apolar 447.5Ų
Hydrophobic contacts buried
BSA polar 143.0Ų
Polar contacts buried
Fraction buried 83.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 75.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1552.5Ų
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 1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 807.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)