FAIRMol

Z25831748

Pose ID 2457 Compound 1909 Pose 424

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
T04
L. major PTR1 L. major
Ligand Z25831748
PDB7PXX↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native mixed SASA done
Strain ΔE
41.2 kcal/mol
Protein clashes
0
Internal clashes
10
Native overlap
contact recall 0.53, Jaccard 0.53, H-bond role recall 0.40
Burial
70%
Hydrophobic fit
75%
Reason: 10 internal clashes
10 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.274 kcal/mol/HA) ✓ Good fit quality (FQ -12.29) ✓ Good H-bonds (3 bonds) ✓ Deep burial (70% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ Extreme strain energy (41.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-38.207
kcal/mol
LE
-1.274
kcal/mol/HA
Fit Quality
-12.29
FQ (Leeson)
HAC
30
heavy atoms
MW
447
Da
LogP
3.90
cLogP
Strain ΔE
41.2 kcal/mol
SASA buried
70%
Lipo contact
75% BSA apolar/total
SASA unbound
732 Ų
Apolar buried
380 Ų

Interaction summary

HB 3 HY 21 PI 5 CLASH 0

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
No clash · clashes detected for this pose.
Final rank2.570Score-38.207
Inter norm-1.049Intra norm-0.224
Top1000noExcludedno
Contacts10H-bonds3
Artifact reasongeometry warning; 10 clashes; 2 protein clashes; 1 cofactor-context clash; high strain Δ 41.2
Residues
HIS241 LEU188 LEU226 LEU229 NDP302 PHE113 PRO115 SER111 TYR191 TYR194

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name7PXXContacts19
PoseOpen native poseHB0
IFP residues
ARG17 ASP181 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER112 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap10Native recall0.53
Jaccard0.53RMSD-
HB strict2Strict recall0.33
HB same residue+role2HB role recall0.40
HB same residue2HB residue recall0.40

Protein summary

308 residues
Protein targetT04Atoms4210
Residues308Chains3
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
411 1.2238300291495845 -0.8053 -32.4178 3 17 0 0.00 0.00 - no Open
453 2.5515372806796917 -0.693794 -25.6657 6 13 0 0.00 0.00 - no Open
424 2.5699954615836487 -1.04947 -38.2072 3 10 10 0.53 0.40 - 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 -38.207kcal/mol
Ligand efficiency (LE) -1.2736kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -12.285
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 446.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.90
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 41.16kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 46.64kcal/mol
Minimised FF energy 5.48kcal/mol

SASA & burial

✓ computed
SASA (unbound) 732.4Ų
Total solvent-accessible surface area of free ligand
BSA total 509.0Ų
Buried surface area upon binding
BSA apolar 380.3Ų
Hydrophobic contacts buried
BSA polar 128.7Ų
Polar contacts buried
Fraction buried 69.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1680.5Ų
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 2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1055.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)