FAIRMol

NMT-TY0973

Pose ID 5755 Compound 485 Pose 337

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
T09
L. major DHFR-TS L. major
Ligand NMT-TY0973

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native mixed SASA done
Strain ΔE
77.7 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.52, Jaccard 0.42, H-bond role recall 0.17
Burial
88%
Hydrophobic fit
64%
Reason: strain 77.7 kcal/mol
strain ΔE 77.7 kcal/mol 5 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.164 kcal/mol/HA) ✓ Good fit quality (FQ -10.72) ✓ Strong H-bond network (12 bonds) ✓ Deep burial (88% SASA buried) ✓ Lipophilic contacts well-matched (64%) ✗ Extreme strain energy (77.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-30.262
kcal/mol
LE
-1.164
kcal/mol/HA
Fit Quality
-10.72
FQ (Leeson)
HAC
26
heavy atoms
MW
400
Da
LogP
2.09
cLogP
Strain ΔE
77.7 kcal/mol
SASA buried
88%
Lipo contact
64% BSA apolar/total
SASA unbound
576 Ų
Apolar buried
325 Ų

Interaction summary

HB 12 HY 24 PI 2 CLASH 5

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 rank4.674Score-30.262
Inter norm-1.064Intra norm-0.100
Top1000noExcludedno
Contacts16H-bonds12
Artifact reasongeometry warning; 14 clashes; 2 protein clashes; high strain Δ 77.7
Residues
NDP301 ALA32 ARG48 ASP52 ILE182 ILE45 MET53 PHE56 PRO50 THR180 TRP47 TYR162 VAL156 VAL30 VAL31 VAL49

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name3CL9Contacts21
PoseOpen native poseHB0
IFP residues
NDP301 ALA32 ARG97 ASP52 GLY157 ILE45 LEU94 LYS57 MET53 PHE55 PHE56 PHE91 PRO88 SER86 THR180 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap11Native recall0.52
Jaccard0.42RMSD-
HB strict0Strict recall0.00
HB same residue+role1HB role recall0.17
HB same residue1HB residue recall0.17

Protein summary

511 residues
Protein targetT09Atoms8170
Residues511Chains2
Residue summaryLEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224

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:NDP301

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
412 2.7698275766177316 -0.991513 -27.6873 5 15 0 0.00 0.00 - no Open
397 3.390660755693382 -1.01571 -28.7401 5 15 0 0.00 0.00 - no Open
337 4.6744520542981975 -1.06368 -30.2621 12 16 11 0.52 0.17 - 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 -30.262kcal/mol
Ligand efficiency (LE) -1.1639kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.724
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 400.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.09
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 77.69kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -42.68kcal/mol
Minimised FF energy -120.38kcal/mol

SASA & burial

✓ computed
SASA (unbound) 576.2Ų
Total solvent-accessible surface area of free ligand
BSA total 506.5Ų
Buried surface area upon binding
BSA apolar 324.5Ų
Hydrophobic contacts buried
BSA polar 182.0Ų
Polar contacts buried
Fraction buried 87.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 64.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3124.7Ų
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 4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1680.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)