FAIRMol

NMT-TY0324

Pose ID 2319 Compound 1600 Pose 286

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-TY0324
PDB7PXX↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry high Native mixed SASA done
Strain ΔE
22.8 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.53, Jaccard 0.53, H-bond role recall 0.20
Burial
94%
Hydrophobic fit
39%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-2.015 kcal/mol/HA) ✓ Good fit quality (FQ -13.33) ✓ Good H-bonds (3 bonds) ✓ Deep burial (94% SASA buried) ✗ High strain energy (22.8 kcal/mol) ✗ Geometry warnings
Score
-24.180
kcal/mol
LE
-2.015
kcal/mol/HA
Fit Quality
-13.33
FQ (Leeson)
HAC
12
heavy atoms
MW
202
Da
LogP
-1.00
cLogP
Strain ΔE
22.8 kcal/mol
SASA buried
94%
Lipo contact
39% BSA apolar/total
SASA unbound
354 Ų
Apolar buried
130 Ų

Interaction summary

HB 3 HY 9 PI 0 CLASH 2

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes
Final rank0.047Score-24.180
Inter norm-2.015Intra norm0.000
Top1000noExcludedno
Contacts10H-bonds3
Artifact reasongeometry warning; 3 clashes; 1 protein clash; moderate strain Δ 22.8
Residues
ARG17 ASP181 HIS241 LEU188 LEU226 LEU229 NDP302 PHE113 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 strict1Strict recall0.17
HB same residue+role1HB role recall0.20
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
286 0.04657961052787923 -2.01498 -24.1797 3 10 10 0.53 0.20 - 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 -24.180kcal/mol
Ligand efficiency (LE) -2.0150kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -13.329
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 12HA

Physicochemical properties
Molecular weight 202.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) -1.00
Lipinski: ≤ 5
Rotatable bonds 0

Conformational strain (MMFF94s)
Strain energy (ΔE) 22.78kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -84.63kcal/mol
Minimised FF energy -107.41kcal/mol

SASA & burial

✓ computed
SASA (unbound) 354.0Ų
Total solvent-accessible surface area of free ligand
BSA total 331.5Ų
Buried surface area upon binding
BSA apolar 129.7Ų
Hydrophobic contacts buried
BSA polar 201.8Ų
Polar contacts buried
Fraction buried 93.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 39.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1297.2Ų
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 1022.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)