FAIRMol

Z226217786

Pose ID 3038 Compound 2302 Pose 328

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
T05
L. major PTR1 L. major
Ligand Z226217786
PDB7PXX↗

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
30.8 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.53, Jaccard 0.43, H-bond role recall 0.50
Burial
88%
Hydrophobic fit
80%
Reason: no major geometry red flags detected
2 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.289 kcal/mol/HA) ✓ Good fit quality (FQ -12.17) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (88% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Very high strain energy (30.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-36.088
kcal/mol
LE
-1.289
kcal/mol/HA
Fit Quality
-12.17
FQ (Leeson)
HAC
28
heavy atoms
MW
379
Da
LogP
1.01
cLogP
Strain ΔE
30.8 kcal/mol
SASA buried
88%
Lipo contact
80% BSA apolar/total
SASA unbound
654 Ų
Apolar buried
459 Ų

Interaction summary

HB 9 HY 10 PI 2 CLASH 3
Final rank4.406Score-36.088
Inter norm-1.302Intra norm0.013
Top1000noExcludedno
Contacts13H-bonds9
Artifact reasongeometry warning; 12 clashes; 3 protein clashes; 2 cofactor-context clashes; high strain Δ 30.8
Residues
ARG17 ASP181 GLY225 LEU188 LEU226 MET183 NDP302 PHE113 SER112 TYR114 TYR194 VAL230 ARG287

Protein summary

274 residues
Protein targetT05Atoms4108
Residues274Chains2
Residue summaryLEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108

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:NDP302

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameligandContacts17
PoseOpen native poseHB0
IFP residues
ARG17 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap9Native recall0.53
Jaccard0.43RMSD-
HB strict3Strict recall0.43
HB same residue+role3HB role recall0.50
HB same residue3HB residue recall0.60

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
380 0.9814085371023361 -1.15237 -32.9195 5 18 0 0.00 0.00 - no Open
359 1.4395845830790477 -0.886124 -25.2086 2 16 0 0.00 0.00 - no Open
328 4.406034356198507 -1.30168 -36.088 9 13 9 0.53 0.50 - 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 -36.088kcal/mol
Ligand efficiency (LE) -1.2889kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -12.167
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 379.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.01
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 30.76kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 71.83kcal/mol
Minimised FF energy 41.08kcal/mol

SASA & burial

✓ computed
SASA (unbound) 654.2Ų
Total solvent-accessible surface area of free ligand
BSA total 574.0Ų
Buried surface area upon binding
BSA apolar 459.1Ų
Hydrophobic contacts buried
BSA polar 114.9Ų
Polar contacts buried
Fraction buried 87.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1651.0Ų
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 2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1052.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)