FAIRMol

NMT-TY0623

Pose ID 1708 Compound 343 Pose 353

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
T03
L. major DHFR L. major
Ligand NMT-TY0623

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native strong SASA done
Strain ΔE
40.3 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.65, Jaccard 0.54, H-bond role recall 0.80
Burial
91%
Hydrophobic fit
71%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.048 kcal/mol/HA) ✓ Good fit quality (FQ -10.01) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ Extreme strain energy (40.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-30.407
kcal/mol
LE
-1.048
kcal/mol/HA
Fit Quality
-10.01
FQ (Leeson)
HAC
29
heavy atoms
MW
430
Da
LogP
2.54
cLogP
Strain ΔE
40.3 kcal/mol
SASA buried
91%
Lipo contact
71% BSA apolar/total
SASA unbound
647 Ų
Apolar buried
417 Ų

Interaction summary

HB 7 HY 24 PI 2 CLASH 3

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 rank3.261Score-30.407
Inter norm-1.057Intra norm0.008
Top1000noExcludedno
Contacts17H-bonds7
Artifact reasongeometry warning; 12 clashes; 1 protein clash; high strain Δ 40.3
Residues
ALA32 ARG48 ASP52 GLY157 ILE45 MET53 NDP301 PHE56 PRO88 SER86 TRP47 TYR162 VAL156 VAL30 VAL31 VAL49 VAL87

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 overlap13Native recall0.65
Jaccard0.54RMSD-
HB strict4Strict recall0.57
HB same residue+role4HB role recall0.80
HB same residue4HB residue recall0.80

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
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 0 0.00 0.00 - no Open
277 0.7836269283764385 -0.966102 -28.607 8 17 0 0.00 0.00 - no Open
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 13 0.65 0.80 - no Current
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 1 0.05 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 1 0.05 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 -30.407kcal/mol
Ligand efficiency (LE) -1.0485kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.009
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 429.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.54
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 40.28kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -32.69kcal/mol
Minimised FF energy -72.97kcal/mol

SASA & burial

✓ computed
SASA (unbound) 646.6Ų
Total solvent-accessible surface area of free ligand
BSA total 588.9Ų
Buried surface area upon binding
BSA apolar 417.2Ų
Hydrophobic contacts buried
BSA polar 171.7Ų
Polar contacts buried
Fraction buried 91.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1472.1Ų
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 819.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)