FAIRMol

NMT-TY0665

Pose ID 1714 Compound 1247 Pose 359

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
T03
L. major DHFR L. major
Ligand NMT-TY0665

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 strong SASA done
Strain ΔE
60.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.55, Jaccard 0.50, H-bond role recall 0.40
Burial
91%
Hydrophobic fit
62%
Reason: strain 60.7 kcal/mol
strain ΔE 60.7 kcal/mol 1 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.103 kcal/mol/HA) ✓ Good fit quality (FQ -10.03) ✓ Good H-bonds (5 bonds) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (62%) ✗ Extreme strain energy (60.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-27.576
kcal/mol
LE
-1.103
kcal/mol/HA
Fit Quality
-10.03
FQ (Leeson)
HAC
25
heavy atoms
MW
386
Da
LogP
1.45
cLogP
Strain ΔE
60.7 kcal/mol
SASA buried
91%
Lipo contact
62% BSA apolar/total
SASA unbound
614 Ų
Apolar buried
346 Ų

Interaction summary

HB 5 HY 18 PI 2 CLASH 1

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 rank2.160Score-27.576
Inter norm-1.061Intra norm-0.042
Top1000noExcludedno
Contacts13H-bonds5
Artifact reasongeometry warning; 10 clashes; 1 protein clash; high strain Δ 60.7
Residues
ALA32 ARG97 ASP52 ILE45 LEU94 LYS57 LYS95 MET53 NDP301 PHE56 PHE91 PRO93 VAL31

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name3CL9Contacts20
PoseOpen native poseHB0
IFP residues
ALA32 ARG97 ASP52 ILE45 LEU94 LYS57 MET53 NDP301 PHE56 PHE91 PRO88 SER86 THR180 THR54 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap11Native recall0.55
Jaccard0.50RMSD-
HB strict3Strict recall0.43
HB same residue+role2HB role recall0.40
HB same residue2HB residue recall0.40

Protein summary

225 residues
Protein targetT03Atoms3428
Residues225Chains2
Residue summaryLEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; NDP:74

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
359 2.1601774526580333 -1.06122 -27.5764 5 13 11 0.55 0.40 - no Current
298 3.932577870593009 -1.05653 -27.0195 9 16 1 0.05 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 -27.576kcal/mol
Ligand efficiency (LE) -1.1031kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.028
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 25HA

Physicochemical properties
Molecular weight 386.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.45
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 60.75kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -36.29kcal/mol
Minimised FF energy -97.04kcal/mol

SASA & burial

✓ computed
SASA (unbound) 613.9Ų
Total solvent-accessible surface area of free ligand
BSA total 560.3Ų
Buried surface area upon binding
BSA apolar 346.0Ų
Hydrophobic contacts buried
BSA polar 214.3Ų
Polar contacts buried
Fraction buried 91.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 61.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1399.3Ų
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 1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 800.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)