FAIRMol

NMT-TY0624

Pose ID 2356 Compound 616 Pose 323

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-TY0624
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 medium Native strong SASA done
Strain ΔE
34.1 kcal/mol
Protein clashes
2
Internal clashes
5
Native overlap
contact recall 0.74, Jaccard 0.70, H-bond role recall 0.40
Burial
80%
Hydrophobic fit
74%
Reason: no major geometry red flags detected
2 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.815 kcal/mol/HA) ✓ Good fit quality (FQ -7.51) ✓ Good H-bonds (3 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ Very high strain energy (34.1 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (2) ✗ Many internal clashes (11)
Score
-21.190
kcal/mol
LE
-0.815
kcal/mol/HA
Fit Quality
-7.51
FQ (Leeson)
HAC
26
heavy atoms
MW
396
Da
LogP
2.16
cLogP
Final rank
0.6040
rank score
Inter norm
-0.943
normalised
Contacts
15
H-bonds 4
Strain ΔE
34.1 kcal/mol
SASA buried
80%
Lipo contact
74% BSA apolar/total
SASA unbound
646 Ų
Apolar buried
380 Ų

Interaction summary

HBD 3 HY 6 PI 4 CLASH 5

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.
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 overlap14Native recall0.74
Jaccard0.70RMSD-
HB strict3Strict recall0.50
HB same residue+role2HB role recall0.40
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
323 0.604003958058523 -0.942657 -21.1902 4 15 14 0.74 0.40 - no Current
291 0.6323186320960439 -1.22038 -30.9952 10 13 0 0.00 0.00 - no Open
329 1.875810958250805 -0.873591 -23.2439 4 10 0 0.00 0.00 - no Open
290 2.002828557753335 -1.14993 -29.8501 9 14 0 0.00 0.00 - no Open
310 2.224044674964138 -0.998085 -25.5439 8 18 0 0.00 0.00 - no Open
274 2.2594370727836455 -1.19735 -30.4625 8 17 0 0.00 0.00 - no Open
363 2.3368706908166565 -1.24065 -32.9492 6 14 0 0.00 0.00 - no Open
296 2.3850699368176747 -1.30385 -33.7876 14 22 0 0.00 0.00 - no Open
256 2.4947555472898184 -0.974719 -18.8557 12 13 0 0.00 0.00 - no Open
354 2.712760058770864 -1.25519 -32.5296 10 15 0 0.00 0.00 - no Open
425 3.1536405973770054 -1.02037 -26.076 10 16 0 0.00 0.00 - no Open
270 3.5240590701875685 -1.13687 -30.0974 8 15 0 0.00 0.00 - no Open
349 3.8084335922387926 -0.992658 -26.3696 8 20 0 0.00 0.00 - no Open
380 3.892965236960112 -1.26373 -32.5926 8 16 0 0.00 0.00 - no Open
394 4.604769733373062 -0.872118 -21.6077 9 12 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 -21.190kcal/mol
Ligand efficiency (LE) -0.8150kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.509
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 395.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.16
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 34.14kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -43.29kcal/mol
Minimised FF energy -77.44kcal/mol

SASA & burial

✓ computed
SASA (unbound) 645.9Ų
Total solvent-accessible surface area of free ligand
BSA total 516.1Ų
Buried surface area upon binding
BSA apolar 380.2Ų
Hydrophobic contacts buried
BSA polar 135.9Ų
Polar contacts buried
Fraction buried 79.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1658.0Ų
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 1001.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)