FAIRMol

Z26394837

Pose ID 5887 Compound 1088 Pose 469

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
T09
L. major DHFR-TS L. major
Ligand Z26394837

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native mixed SASA done
Strain ΔE
24.3 kcal/mol
Protein clashes
0
Internal clashes
8
Native overlap
contact recall 0.48, Jaccard 0.40, H-bond role recall 0.00
Burial
82%
Hydrophobic fit
81%
Reason: 8 internal clashes
8 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.941 kcal/mol/HA) ✓ Good fit quality (FQ -8.78) ✓ Deep burial (82% SASA buried) ✓ Lipophilic contacts well-matched (81%) ✗ High strain energy (24.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-25.416
kcal/mol
LE
-0.941
kcal/mol/HA
Fit Quality
-8.78
FQ (Leeson)
HAC
27
heavy atoms
MW
368
Da
LogP
2.08
cLogP
Final rank
2.5281
rank score
Inter norm
-0.998
normalised
Contacts
14
H-bonds 5
Strain ΔE
24.3 kcal/mol
SASA buried
82%
Lipo contact
81% BSA apolar/total
SASA unbound
632 Ų
Apolar buried
416 Ų

Interaction summary

HBA 2 HY 8 PI 0 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 2.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes
No clash · clashes detected for this pose.

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
Name3CL9Contacts21
PoseOpen native poseHB0
IFP residues
NDP301 ALA32 ARG97 ASP52 GLY157 ILE45 LEU94 LYS57 MET53 PHE55 PHE56 PHE91 PRO88 SER86 THR180 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap10Native recall0.48
Jaccard0.40RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

511 residues
Protein targetT09Atoms8170
Residues511Chains2
Residue summaryLEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224

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
489 1.0553398923708686 -0.994766 -22.3642 2 15 1 0.05 0.00 - no Open
469 2.528091285632924 -0.99771 -25.4163 5 14 10 0.48 0.00 - no Current
490 2.7046869720375177 -0.827874 -19.6462 5 14 0 0.00 0.00 - no Open
504 2.958579191911424 -0.882871 -23.9816 4 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 -25.416kcal/mol
Ligand efficiency (LE) -0.9413kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.782
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 368.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.08
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 24.26kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -16.37kcal/mol
Minimised FF energy -40.63kcal/mol

SASA & burial

✓ computed
SASA (unbound) 631.8Ų
Total solvent-accessible surface area of free ligand
BSA total 515.5Ų
Buried surface area upon binding
BSA apolar 415.6Ų
Hydrophobic contacts buried
BSA polar 99.9Ų
Polar contacts buried
Fraction buried 81.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3276.6Ų
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 4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1680.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)