FAIRMol

Z56773052

Pose ID 5826 Compound 3179 Pose 408

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
T09
L. major DHFR-TS L. major
Ligand Z56773052

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
22.1 kcal/mol
Protein clashes
3
Internal clashes
4
Native overlap
contact recall 0.76, Jaccard 0.64, H-bond role recall 0.17
Burial
95%
Hydrophobic fit
75%
Reason: no major geometry red flags detected
3 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.578 kcal/mol/HA) ✓ Good fit quality (FQ -5.46) ✓ Good H-bonds (4 bonds) ✓ Deep burial (95% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ High strain energy (22.1 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (3) ✗ Many internal clashes (10)
Score
-16.180
kcal/mol
LE
-0.578
kcal/mol/HA
Fit Quality
-5.46
FQ (Leeson)
HAC
28
heavy atoms
MW
406
Da
LogP
5.56
cLogP
Strain ΔE
22.1 kcal/mol
SASA buried
95%
Lipo contact
75% BSA apolar/total
SASA unbound
652 Ų
Apolar buried
467 Ų

Interaction summary

HB 4 HY 24 PI 2 CLASH 4

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 rank0.686Score-16.180
Inter norm-0.912Intra norm0.334
Top1000noExcludedno
Contacts20H-bonds4
Artifact reasongeometry warning; 10 clashes; 3 protein contact clashes; 1 cofactor-context clash; moderate strain Δ 22.1
Residues
NDP301 ALA32 ARG48 ASP52 ILE45 LEU94 MET53 PHE55 PHE56 PRO88 SER44 SER86 THR180 THR83 TRP47 VAL156 VAL30 VAL31 VAL49 VAL87

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
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 overlap16Native recall0.76
Jaccard0.64RMSD-
HB strict1Strict recall0.14
HB same residue+role1HB role recall0.17
HB same residue1HB residue recall0.17

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
408 0.6856936610759928 -0.912214 -16.18 4 20 16 0.76 0.17 - no Current
385 1.7574554438791103 -0.85316 -21.8276 3 16 0 0.00 0.00 - no Open
405 2.3914850059656008 -0.780922 -21.2429 6 11 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 -16.180kcal/mol
Ligand efficiency (LE) -0.5779kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.455
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 405.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.56
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 22.11kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 73.67kcal/mol
Minimised FF energy 51.56kcal/mol

SASA & burial

✓ computed
SASA (unbound) 651.7Ų
Total solvent-accessible surface area of free ligand
BSA total 619.6Ų
Buried surface area upon binding
BSA apolar 466.6Ų
Hydrophobic contacts buried
BSA polar 152.9Ų
Polar contacts buried
Fraction buried 95.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 75.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3250.6Ų
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 1673.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)