FAIRMol

Z56902329

Pose ID 1774 Compound 1435 Pose 419

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 Z56902329

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
50.2 kcal/mol
Protein clashes
8
Internal clashes
8
Native overlap
contact recall 0.70, Jaccard 0.56, H-bond role recall 0.20
Burial
94%
Hydrophobic fit
77%
Reason: 8 internal clashes, strain 50.2 kcal/mol
strain ΔE 50.2 kcal/mol 8 protein-contact clashes 8 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.854 kcal/mol/HA) ✓ Good fit quality (FQ -7.87) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (94% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ Extreme strain energy (50.2 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-22.215
kcal/mol
LE
-0.854
kcal/mol/HA
Fit Quality
-7.87
FQ (Leeson)
HAC
26
heavy atoms
MW
435
Da
LogP
1.98
cLogP
Strain ΔE
50.2 kcal/mol
SASA buried
94%
Lipo contact
77% BSA apolar/total
SASA unbound
625 Ų
Apolar buried
450 Ų

Interaction summary

HB 10 HY 24 PI 3 CLASH 8
Final rank4.090Score-22.215
Inter norm-1.054Intra norm0.199
Top1000noExcludedno
Contacts19H-bonds10
Artifact reasongeometry warning; 8 clashes; 2 protein clashes; high strain Δ 50.2
Residues
ALA32 ARG48 ASP52 ILE182 ILE45 MET53 NDP301 PHE55 PHE56 SER86 THR180 THR83 TRP47 TYR162 VAL156 VAL30 VAL31 VAL49 VAL87

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

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 overlap14Native recall0.70
Jaccard0.56RMSD-
HB strict2Strict recall0.29
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
336 0.10214502245811838 -1.26749 -33.2096 7 13 0 0.00 0.00 - no Open
398 2.060629453322421 -0.798133 -17.2509 8 11 0 0.00 0.00 - no Open
419 4.090345340807407 -1.05369 -22.2147 10 19 14 0.70 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 -22.215kcal/mol
Ligand efficiency (LE) -0.8544kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.872
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 435.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.98
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 50.23kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 104.33kcal/mol
Minimised FF energy 54.10kcal/mol

SASA & burial

✓ computed
SASA (unbound) 624.7Ų
Total solvent-accessible surface area of free ligand
BSA total 584.9Ų
Buried surface area upon binding
BSA apolar 450.0Ų
Hydrophobic contacts buried
BSA polar 134.9Ų
Polar contacts buried
Fraction buried 93.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1489.0Ų
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 821.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)