FAIRMol

NMT-TY0717

Pose ID 2362 Compound 1578 Pose 329

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-TY0717
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 and worth follow-up
Binding strong Geometry medium Native strong SASA done
Strain ΔE
5.3 kcal/mol
Protein clashes
1
Internal clashes
3
Native overlap
contact recall 0.47, Jaccard 0.47, H-bond role recall 0.60
Burial
95%
Hydrophobic fit
68%
Reason: no major geometry red flags detected
1 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Low conformational strain (5.3 kcal/mol) ✓ Excellent LE (-2.168 kcal/mol/HA) ✓ Good fit quality (FQ -14.34) ✓ Good H-bonds (3 bonds) ✓ Deep burial (95% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ Geometry warnings
Score
-26.016
kcal/mol
LE
-2.168
kcal/mol/HA
Fit Quality
-14.34
FQ (Leeson)
HAC
12
heavy atoms
MW
248
Da
LogP
0.69
cLogP
Strain ΔE
5.3 kcal/mol
SASA buried
95%
Lipo contact
68% BSA apolar/total
SASA unbound
356 Ų
Apolar buried
231 Ų

Interaction summary

HB 3 HY 7 PI 1 CLASH 3

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 rank-0.048Score-26.016
Inter norm-2.168Intra norm0.000
Top1000noExcludedno
Contacts9H-bonds3
Artifact reasongeometry warning; 4 clashes; 1 protein clash; 4 cofactor-context clashes
Residues
ARG17 LEU188 LEU226 LEU229 NDP302 PHE113 SER111 TYR194 VAL230

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 overlap9Native recall0.47
Jaccard0.47RMSD-
HB strict3Strict recall0.50
HB same residue+role3HB role recall0.60
HB same residue3HB residue recall0.60

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
266 -0.050247939550237014 -2.1662 -25.9944 3 9 9 0.47 0.60 - no Open
329 -0.04760547293979465 -2.168 -26.016 3 9 9 0.47 0.60 - 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 -26.016kcal/mol
Ligand efficiency (LE) -2.1680kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -14.342
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 12HA

Physicochemical properties
Molecular weight 248.1Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.69
Lipinski: ≤ 5
Rotatable bonds 1

Conformational strain (MMFF94s)
Strain energy (ΔE) 5.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -58.03kcal/mol
Minimised FF energy -63.29kcal/mol

SASA & burial

✓ computed
SASA (unbound) 355.6Ų
Total solvent-accessible surface area of free ligand
BSA total 337.4Ų
Buried surface area upon binding
BSA apolar 230.9Ų
Hydrophobic contacts buried
BSA polar 106.5Ų
Polar contacts buried
Fraction buried 94.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 68.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1398.0Ų
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 1021.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)