FAIRMol

Z56815073

Pose ID 2692 Compound 318 Pose 659

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 Z56815073
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 strong SASA done
Strain ΔE
36.0 kcal/mol
Protein clashes
0
Internal clashes
14
Native overlap
contact recall 0.68, Jaccard 0.59, H-bond role recall 0.00
Burial
71%
Hydrophobic fit
70%
Reason: 14 internal clashes
14 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.662 kcal/mol/HA) ✓ Good fit quality (FQ -6.51) ✓ Deep burial (71% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ Very high strain energy (36.0 kcal/mol) ✗ No H-bonds detected ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-21.171
kcal/mol
LE
-0.662
kcal/mol/HA
Fit Quality
-6.51
FQ (Leeson)
HAC
32
heavy atoms
MW
569
Da
LogP
5.67
cLogP
Strain ΔE
36.0 kcal/mol
SASA buried
71%
Lipo contact
70% BSA apolar/total
SASA unbound
750 Ų
Apolar buried
376 Ų

Interaction summary

HB 0 HY 24 PI 3 CLASH 0

HB · H-bonds
No hb · h-bonds detected for this pose.

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 rank0.771Score-21.171
Inter norm-0.754Intra norm0.092
Top1000noExcludedno
Contacts16H-bonds0
Artifact reasongeometry warning; 14 clashes; 1 cofactor-context clash; high strain Δ 36.0
Residues
ARG17 ASP232 GLY225 HIS241 LEU188 LEU226 LEU229 MET233 NDP302 PHE113 PRO234 SER227 TYR191 TYR194 VAL237 ARG287

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 overlap13Native recall0.68
Jaccard0.59RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
662 0.6661725537921506 -1.04002 -28.6522 3 19 0 0.00 0.00 - no Open
659 0.7707737947628458 -0.753505 -21.1708 0 16 13 0.68 0.00 - no Current
652 0.8225922751736459 -1.01993 -29.9798 1 17 0 0.00 0.00 - no Open
642 1.139808952940768 -0.847734 -26.7285 5 14 0 0.00 0.00 - no Open
656 1.7653889637304623 -0.867492 -24.6089 3 18 0 0.00 0.00 - no Open
655 1.8473635475241321 -1.0072 -32.0974 3 18 0 0.00 0.00 - no Open
638 1.9648568381193203 -0.927569 -29.9449 4 16 0 0.00 0.00 - no Open
645 2.1923496622071084 -0.758001 -17.56 2 18 0 0.00 0.00 - no Open
661 2.2567473265764555 -0.765666 -25.1725 7 20 0 0.00 0.00 - no Open
641 2.292373942513122 -0.725642 -22.2969 4 13 0 0.00 0.00 - no Open
641 2.2974884616866427 -0.933418 -28.8424 4 19 0 0.00 0.00 - no Open
654 3.071439811116401 -0.870778 -29.2301 13 16 0 0.00 0.00 - no Open
659 3.8692944863611776 -0.656079 -21.7278 6 10 0 0.00 0.00 - no Open
660 3.931763085408765 -0.81696 -27.3427 3 19 0 0.00 0.00 - no Open
666 5.297500006745246 -0.919049 -23.1364 13 21 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 -21.171kcal/mol
Ligand efficiency (LE) -0.6616kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.506
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 32HA

Physicochemical properties
Molecular weight 568.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.67
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 36.02kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 35.74kcal/mol
Minimised FF energy -0.28kcal/mol

SASA & burial

✓ computed
SASA (unbound) 749.8Ų
Total solvent-accessible surface area of free ligand
BSA total 534.0Ų
Buried surface area upon binding
BSA apolar 376.2Ų
Hydrophobic contacts buried
BSA polar 157.8Ų
Polar contacts buried
Fraction buried 71.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1646.4Ų
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 1115.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)