FAIRMol

NMT-TY0623

Pose ID 2987 Compound 343 Pose 277

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
T05
L. major PTR1 L. major
Ligand NMT-TY0623
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 strong SASA done
Strain ΔE
27.7 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.82, Jaccard 0.70, H-bond role recall 0.33
Burial
82%
Hydrophobic fit
73%
Reason: no major geometry red flags detected
1 protein-contact clashes 37% of hydrophobic surface appears solvent-exposed (7/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.986 kcal/mol/HA) ✓ Good fit quality (FQ -9.42) ✓ Good H-bonds (3 bonds) ✓ Deep burial (82% SASA buried) ✓ Lipophilic contacts well-matched (73%) ✗ High strain energy (27.7 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (3) ✗ Many internal clashes (10)
Score
-28.607
kcal/mol
LE
-0.986
kcal/mol/HA
Fit Quality
-9.42
FQ (Leeson)
HAC
29
heavy atoms
MW
430
Da
LogP
2.95
cLogP
Final rank
0.7836
rank score
Inter norm
-0.966
normalised
Contacts
17
H-bonds 8
Strain ΔE
27.7 kcal/mol
SASA buried
82%
Lipo contact
73% BSA apolar/total
SASA unbound
684 Ų
Apolar buried
408 Ų

Interaction summary

HBD 2 HBA 1 HY 5 PI 3 CLASH 2

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

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 overlap14Native recall0.82
Jaccard0.70RMSD-
HB strict2Strict recall0.29
HB same residue+role2HB role recall0.33
HB same residue2HB residue recall0.40

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
290 -0.07584312586851832 -1.13056 -32.0626 7 15 0 0.00 0.00 - no Open
322 0.30845358684249946 -0.891961 -22.9586 1 16 13 0.76 0.17 - no Open
277 0.7836269283764385 -0.966102 -28.607 8 17 14 0.82 0.33 - no Current
393 1.7697479735872257 -0.888141 -25.7806 6 15 0 0.00 0.00 - no Open
379 2.0583001140760584 -1.04849 -30.952 5 15 0 0.00 0.00 - no Open
424 2.557044498817305 -0.988533 -28.1895 8 17 0 0.00 0.00 - no Open
342 2.7977411127516505 -0.78462 -22.2614 10 10 0 0.00 0.00 - no Open
328 2.9974190872298045 -0.816997 -22.4353 4 15 0 0.00 0.00 - no Open
309 3.050671063739145 -0.980479 -28.998 6 18 0 0.00 0.00 - no Open
331 3.103020756997463 -0.788626 -21.3481 8 19 0 0.00 0.00 - no Open
353 3.2612201780631067 -1.05701 -30.407 7 17 0 0.00 0.00 - no Open
362 3.7208953487922924 -0.983933 -23.2803 7 17 0 0.00 0.00 - no Open
348 3.795992434048253 -0.864899 -26.6158 8 20 0 0.00 0.00 - no Open
289 3.87862843107247 -0.963867 -29.2468 8 19 0 0.00 0.00 - no Open
328 4.137080334224266 -0.976406 -27.277 12 18 0 0.00 0.00 - no Open
309 4.286815840501966 -0.801912 -23.8944 5 20 0 0.00 0.00 - no Open
269 4.88188196770325 -1.1395 -32.34 11 17 0 0.00 0.00 - no Open
255 5.815034729044303 -0.891682 -22.7371 13 16 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 -28.607kcal/mol
Ligand efficiency (LE) -0.9864kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.416
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 429.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.95
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 27.69kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -46.63kcal/mol
Minimised FF energy -74.32kcal/mol

SASA & burial

✓ computed
SASA (unbound) 683.5Ų
Total solvent-accessible surface area of free ligand
BSA total 562.1Ų
Buried surface area upon binding
BSA apolar 408.2Ų
Hydrophobic contacts buried
BSA polar 153.9Ų
Polar contacts buried
Fraction buried 82.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1640.8Ų
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 1046.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)