FAIRMol

Z56765335

Pose ID 1832 Compound 1212 Pose 477

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 Z56765335

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 strong SASA done
Strain ΔE
35.3 kcal/mol
Protein clashes
7
Internal clashes
7
Native overlap
contact recall 0.55, Jaccard 0.44, H-bond role recall 0.40
Burial
92%
Hydrophobic fit
87%
Reason: 7 internal clashes
7 protein-contact clashes 7 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.916 kcal/mol/HA) ✓ Good fit quality (FQ -8.64) ✓ Good H-bonds (5 bonds) ✓ Deep burial (92% SASA buried) ✓ Lipophilic contacts well-matched (87%) ✗ Very high strain energy (35.3 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (11) ✗ Internal clashes (9)
Score
-25.637
kcal/mol
LE
-0.916
kcal/mol/HA
Fit Quality
-8.64
FQ (Leeson)
HAC
28
heavy atoms
MW
374
Da
LogP
3.28
cLogP
Strain ΔE
35.3 kcal/mol
SASA buried
92%
Lipo contact
87% BSA apolar/total
SASA unbound
682 Ų
Apolar buried
541 Ų

Interaction summary

HB 5 HY 24 PI 3 CLASH 7

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 rank1.919Score-25.637
Inter norm-0.954Intra norm0.038
Top1000noExcludedno
Contacts16H-bonds5
Artifact reasongeometry warning; 9 clashes; 11 protein contact clashes; high strain Δ 35.3
Residues
ALA32 ARG48 ARG97 ASP52 ILE45 LEU94 LYS57 LYS95 MET53 NDP301 PHE56 PHE91 PRO88 PRO93 TRP47 VAL49

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 overlap11Native recall0.55
Jaccard0.44RMSD-
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
477 1.9185062916126276 -0.954005 -25.6366 5 16 11 0.55 0.40 - no Current
495 2.0281070354192057 -0.815998 -23.2531 3 16 0 0.00 0.00 - no Open
436 3.47512672009095 -1.11523 -30.328 14 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 -25.637kcal/mol
Ligand efficiency (LE) -0.9156kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.643
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 374.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.28
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 35.31kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 107.24kcal/mol
Minimised FF energy 71.93kcal/mol

SASA & burial

✓ computed
SASA (unbound) 682.4Ų
Total solvent-accessible surface area of free ligand
BSA total 625.3Ų
Buried surface area upon binding
BSA apolar 541.4Ų
Hydrophobic contacts buried
BSA polar 83.9Ų
Polar contacts buried
Fraction buried 91.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 86.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1595.6Ų
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 819.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)