FAIRMol

Z24181579

Pose ID 1949 Compound 1273 Pose 594

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 Z24181579

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
32.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.70, Jaccard 0.67, H-bond role recall 0.20
Burial
82%
Hydrophobic fit
76%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.909 kcal/mol/HA) ✓ Good fit quality (FQ -9.02) ✓ Good H-bonds (4 bonds) ✓ Deep burial (82% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ Very high strain energy (32.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-29.996
kcal/mol
LE
-0.909
kcal/mol/HA
Fit Quality
-9.02
FQ (Leeson)
HAC
33
heavy atoms
MW
467
Da
LogP
3.11
cLogP
Strain ΔE
32.7 kcal/mol
SASA buried
82%
Lipo contact
76% BSA apolar/total
SASA unbound
753 Ų
Apolar buried
466 Ų

Interaction summary

HB 4 HY 24 PI 3 CLASH 1

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 rank2.280Score-29.996
Inter norm-0.963Intra norm0.054
Top1000noExcludedno
Contacts15H-bonds4
Artifact reasongeometry warning; 10 clashes; 1 protein clash; moderate strain Δ 29.9
Residues
ALA32 ARG97 ASP52 ILE45 LEU94 LYS57 LYS95 MET53 NDP301 PHE56 PHE91 TYR162 VAL156 VAL30 VAL31

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
Jaccard0.67RMSD-
HB strict2Strict recall0.29
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
606 2.0387116795349516 -0.783773 -26.6302 4 17 0 0.00 0.00 - no Open
594 2.280406481965539 -0.963317 -29.9961 4 15 14 0.70 0.20 - no Current
593 4.016783419434528 -0.82401 -26.1742 12 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 -29.996kcal/mol
Ligand efficiency (LE) -0.9090kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.019
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 466.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.11
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 32.70kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 61.36kcal/mol
Minimised FF energy 28.66kcal/mol

SASA & burial

✓ computed
SASA (unbound) 753.4Ų
Total solvent-accessible surface area of free ligand
BSA total 613.8Ų
Buried surface area upon binding
BSA apolar 466.3Ų
Hydrophobic contacts buried
BSA polar 147.6Ų
Polar contacts buried
Fraction buried 81.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1591.5Ų
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 811.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)