FAIRMol

NMT-TY0141

Pose ID 2962 Compound 2011 Pose 252

DB SELECTIONDocking 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 NMT-TY0141
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 high Native strong SASA done
Strain ΔE
7.1 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.59, Jaccard 0.56, H-bond role recall 0.50
Burial
95%
Hydrophobic fit
63%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Low conformational strain (7.1 kcal/mol) ✓ Excellent LE (-1.963 kcal/mol/HA) ✓ Good fit quality (FQ -14.04) ✓ Good H-bonds (5 bonds) ✓ Deep burial (95% SASA buried) ✓ Lipophilic contacts well-matched (63%) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-27.485
kcal/mol
LE
-1.963
kcal/mol/HA
Fit Quality
-14.04
FQ (Leeson)
HAC
14
heavy atoms
MW
214
Da
LogP
-1.13
cLogP
Strain ΔE
7.1 kcal/mol
SASA buried
95%
Lipo contact
63% BSA apolar/total
SASA unbound
379 Ų
Apolar buried
228 Ų

Interaction summary

HB 5 HY 9 PI 1 CLASH 1
Final rank1.152Score-27.485
Inter norm-1.995Intra norm0.032
Top1000noExcludedno
Contacts11H-bonds5
Artifact reasongeometry warning; 6 clashes; 2 protein clashes; 2 severe cofactor-context clashes
Residues
ARG17 GLY225 LEU226 LEU229 MET183 NDP302 PHE113 SER111 TYR194 VAL230 ARG287

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

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 overlap10Native recall0.59
Jaccard0.56RMSD-
HB strict3Strict recall0.43
HB same residue+role3HB role recall0.50
HB same residue3HB residue recall0.60

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
252 1.1524251557210754 -1.99514 -27.4851 5 11 10 0.59 0.50 - 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 -27.485kcal/mol
Ligand efficiency (LE) -1.9632kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -14.037
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 14HA

Physicochemical properties
Molecular weight 214.2Da
Lipinski: ≤ 500 Da
LogP (cLogP) -1.13
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 7.14kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -19.15kcal/mol
Minimised FF energy -26.30kcal/mol

SASA & burial

✓ computed
SASA (unbound) 379.1Ų
Total solvent-accessible surface area of free ligand
BSA total 361.4Ų
Buried surface area upon binding
BSA apolar 228.1Ų
Hydrophobic contacts buried
BSA polar 133.3Ų
Polar contacts buried
Fraction buried 95.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 63.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1397.2Ų
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 1017.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)