FAIRMol

NMT-TY0970

Pose ID 5754 Compound 505 Pose 336

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
T09
L. major DHFR-TS L. major
Ligand NMT-TY0970

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
70.8 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.43, Jaccard 0.35, H-bond role recall 0.17
Burial
86%
Hydrophobic fit
57%
Reason: strain 70.8 kcal/mol
strain ΔE 70.8 kcal/mol 2 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.057 kcal/mol/HA) ✓ Good fit quality (FQ -9.74) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (86% SASA buried) ✗ Extreme strain energy (70.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-27.490
kcal/mol
LE
-1.057
kcal/mol/HA
Fit Quality
-9.74
FQ (Leeson)
HAC
26
heavy atoms
MW
402
Da
LogP
0.13
cLogP
Strain ΔE
70.8 kcal/mol
SASA buried
86%
Lipo contact
57% BSA apolar/total
SASA unbound
578 Ų
Apolar buried
280 Ų

Interaction summary

HB 11 HY 19 PI 0 CLASH 3

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 rank5.033Score-27.490
Inter norm-1.023Intra norm-0.034
Top1000noExcludedno
Contacts14H-bonds11
Artifact reasongeometry warning; 11 clashes; 3 protein clashes; 1 cofactor-context clash; high strain Δ 70.7
Residues
NDP301 ALA32 ARG48 ASP52 ILE45 MET53 PRO46 PRO88 SER44 SER86 THR83 TRP47 VAL49 VAL87

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 overlap9Native recall0.43
Jaccard0.35RMSD-
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
409 2.8379320715057856 -0.987578 -25.03 10 13 0 0.00 0.00 - no Open
342 3.53598991674801 -0.936507 -26.4134 16 15 0 0.00 0.00 - no Open
336 5.033199815846234 -1.02327 -27.4899 11 14 9 0.43 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 -27.490kcal/mol
Ligand efficiency (LE) -1.0573kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.741
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 402.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.13
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 70.80kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 2.92kcal/mol
Minimised FF energy -67.87kcal/mol

SASA & burial

✓ computed
SASA (unbound) 578.0Ų
Total solvent-accessible surface area of free ligand
BSA total 494.2Ų
Buried surface area upon binding
BSA apolar 280.2Ų
Hydrophobic contacts buried
BSA polar 214.0Ų
Polar contacts buried
Fraction buried 85.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 56.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3054.6Ų
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 1706.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)