FAIRMol

Z20253414

Pose ID 3199 Compound 2 Pose 489

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
T05
L. major PTR1 L. major
Ligand Z20253414
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
32.2 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.71, Jaccard 0.63, H-bond role recall 0.33
Burial
80%
Hydrophobic fit
68%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.048 kcal/mol/HA) ✓ Good fit quality (FQ -9.66) ✓ Good H-bonds (5 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ Very high strain energy (32.2 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-27.260
kcal/mol
LE
-1.048
kcal/mol/HA
Fit Quality
-9.66
FQ (Leeson)
HAC
26
heavy atoms
MW
371
Da
LogP
2.19
cLogP
Strain ΔE
32.2 kcal/mol
SASA buried
80%
Lipo contact
68% BSA apolar/total
SASA unbound
627 Ų
Apolar buried
338 Ų

Interaction summary

HB 5 HY 15 PI 3 CLASH 5

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 rank2.929Score-27.260
Inter norm-1.069Intra norm0.020
Top1000noExcludedno
Contacts14H-bonds5
Artifact reasongeometry warning; 6 clashes; 2 protein clashes; 1 cofactor-context clash; high strain Δ 32.2
Residues
ARG17 ASP181 GLY225 LEU188 LEU226 LEU229 MET183 MET233 NDP302 PHE113 TYR191 TYR194 VAL230 ARG287

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 overlap12Native recall0.71
Jaccard0.63RMSD-
HB strict2Strict recall0.29
HB same residue+role2HB role recall0.33
HB same residue2HB residue recall0.40

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
545 -0.19688936144560998 -1.00883 -27.6012 5 18 0 0.00 0.00 - no Open
489 2.929054263771643 -1.0687 -27.2601 5 14 12 0.71 0.33 - no Current
514 3.9749964876293937 -0.911876 -25.92 6 13 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 -27.260kcal/mol
Ligand efficiency (LE) -1.0485kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.660
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 371.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.19
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 32.17kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -60.83kcal/mol
Minimised FF energy -93.00kcal/mol

SASA & burial

✓ computed
SASA (unbound) 627.1Ų
Total solvent-accessible surface area of free ligand
BSA total 500.5Ų
Buried surface area upon binding
BSA apolar 337.8Ų
Hydrophobic contacts buried
BSA polar 162.7Ų
Polar contacts buried
Fraction buried 79.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 67.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1597.3Ų
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 1038.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)