FAIRMol

Z49582855

Pose ID 1814 Compound 1194 Pose 459

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 Z49582855

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
63.5 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.40, Jaccard 0.38, H-bond role recall 0.20
Burial
76%
Hydrophobic fit
77%
Reason: strain 63.5 kcal/mol
strain ΔE 63.5 kcal/mol 3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.549 kcal/mol/HA) ✓ Good fit quality (FQ -5.44) ✓ Good H-bonds (4 bonds) ✓ Deep burial (76% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ Extreme strain energy (63.5 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (6) ✗ Many internal clashes (14)
Score
-18.104
kcal/mol
LE
-0.549
kcal/mol/HA
Fit Quality
-5.44
FQ (Leeson)
HAC
33
heavy atoms
MW
466
Da
LogP
4.22
cLogP
Strain ΔE
63.5 kcal/mol
SASA buried
76%
Lipo contact
77% BSA apolar/total
SASA unbound
713 Ų
Apolar buried
417 Ų

Interaction summary

HB 4 HY 19 PI 3 CLASH 3
Final rank1.830Score-18.104
Inter norm-0.833Intra norm0.285
Top1000noExcludedno
Contacts9H-bonds4
Artifact reasongeometry warning; 14 clashes; 6 protein contact clashes; high strain Δ 63.5
Residues
ARG97 ASP52 LEU94 LYS57 LYS95 MET53 PHE56 PHE91 THR54

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 overlap8Native recall0.40
Jaccard0.38RMSD-
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
459 1.829936886186891 -0.833233 -18.1042 4 9 8 0.40 0.20 - no Current
400 2.919528348790917 -0.992687 -29.4876 8 20 0 0.00 0.00 - no Open
443 5.2170465664104695 -0.651954 -13.936 6 9 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 -18.104kcal/mol
Ligand efficiency (LE) -0.5486kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.443
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 466.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.22
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 63.50kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 79.83kcal/mol
Minimised FF energy 16.34kcal/mol

SASA & burial

✓ computed
SASA (unbound) 713.0Ų
Total solvent-accessible surface area of free ligand
BSA total 544.9Ų
Buried surface area upon binding
BSA apolar 417.4Ų
Hydrophobic contacts buried
BSA polar 127.5Ų
Polar contacts buried
Fraction buried 76.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1551.0Ų
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 820.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)