FAIRMol

NMT-TY0139

Pose ID 2309 Compound 1819 Pose 276

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 NMT-TY0139
PDB7PXX↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
11.4 kcal/mol
Protein clashes
6
Internal clashes
10
Native overlap
contact recall 0.53, Jaccard 0.53, H-bond role recall 0.80
Burial
95%
Hydrophobic fit
52%
Reason: 10 internal clashes
6 protein-contact clashes 10 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.556 kcal/mol/HA) ✓ Good fit quality (FQ -11.50) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (95% SASA buried) ✗ Moderate strain (11.4 kcal/mol) ✗ Geometry warnings
Score
-23.338
kcal/mol
LE
-1.556
kcal/mol/HA
Fit Quality
-11.50
FQ (Leeson)
HAC
15
heavy atoms
MW
225
Da
LogP
-0.85
cLogP
Strain ΔE
11.4 kcal/mol
SASA buried
95%
Lipo contact
52% BSA apolar/total
SASA unbound
371 Ų
Apolar buried
185 Ų

Interaction summary

HB 6 HY 6 PI 1 CLASH 10

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 rank1.526Score-23.338
Inter norm-1.621Intra norm0.065
Top1000noExcludedno
Contacts10H-bonds6
Artifact reasongeometry warning; 3 clashes; 1 protein clash; 1 severe cofactor-context clash
Residues
ARG17 LEU188 LEU226 LYS198 NDP302 PHE113 SER111 SER112 TYR194 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 overlap10Native recall0.53
Jaccard0.53RMSD-
HB strict4Strict recall0.67
HB same residue+role4HB role recall0.80
HB same residue4HB residue recall0.80

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
283 -1.43235038960848 -2.02036 -29.0308 7 10 0 0.00 0.00 - no Open
251 1.2396203427272454 -1.91109 -30.7021 6 14 12 0.63 0.40 - no Open
276 1.5261822919367496 -1.62124 -23.3378 6 10 10 0.53 0.80 - 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 -23.338kcal/mol
Ligand efficiency (LE) -1.5559kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.496
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 15HA

Physicochemical properties
Molecular weight 225.2Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.85
Lipinski: ≤ 5
Rotatable bonds 2

Conformational strain (MMFF94s)
Strain energy (ΔE) 11.42kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -20.18kcal/mol
Minimised FF energy -31.60kcal/mol

SASA & burial

✓ computed
SASA (unbound) 371.2Ų
Total solvent-accessible surface area of free ligand
BSA total 353.8Ų
Buried surface area upon binding
BSA apolar 185.4Ų
Hydrophobic contacts buried
BSA polar 168.3Ų
Polar contacts buried
Fraction buried 95.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 52.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1344.5Ų
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 1021.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)