FAIRMol

NMT-TY0929

Pose ID 1727 Compound 484 Pose 372

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-TY0929

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
32.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.80, Jaccard 0.73, H-bond role recall 0.20
Burial
91%
Hydrophobic fit
75%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.038 kcal/mol/HA) ✓ Good fit quality (FQ -9.68) ✓ Good H-bonds (4 bonds) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ Very high strain energy (32.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-28.013
kcal/mol
LE
-1.038
kcal/mol/HA
Fit Quality
-9.68
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
2.03
cLogP
Strain ΔE
32.6 kcal/mol
SASA buried
91%
Lipo contact
75% BSA apolar/total
SASA unbound
642 Ų
Apolar buried
437 Ų

Interaction summary

HB 4 HY 24 PI 3 CLASH 2

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 rank3.962Score-28.013
Inter norm-1.104Intra norm0.066
Top1000noExcludedno
Contacts18H-bonds4
Artifact reasongeometry warning; 13 clashes; 3 protein clashes; high strain Δ 32.6
Residues
ALA32 ARG97 ASP52 ILE45 LEU94 LYS57 LYS95 MET53 NDP301 PHE56 PHE91 PRO88 PRO93 THR54 TYR162 VAL30 VAL31 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 overlap16Native recall0.80
Jaccard0.73RMSD-
HB strict2Strict recall0.29
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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
346 0.35538722495997677 -0.978913 -25.6036 2 13 0 0.00 0.00 - no Open
293 1.274900942951345 -1.03583 -28.5719 7 12 0 0.00 0.00 - no Open
323 1.3627403067812827 -0.906394 -18.7308 3 16 1 0.05 0.00 - no Open
375 2.0500114754417558 -1.04631 -29.6312 5 15 0 0.00 0.00 - no Open
318 2.0823117440239103 -1.13317 -28.9361 12 15 1 0.05 0.00 - no Open
322 2.294639162656896 -0.986167 -29.4161 5 20 0 0.00 0.00 - no Open
441 2.5220455662358785 -0.89302 -25.8372 8 15 0 0.00 0.00 - no Open
338 2.659289984590069 -0.997905 -24.9728 12 15 0 0.00 0.00 - no Open
392 2.7685730244744846 -1.12247 -31.1016 6 15 0 0.00 0.00 - no Open
333 3.6903577688505305 -0.859379 -21.1312 9 16 0 0.00 0.00 - no Open
343 3.8983164634663794 -0.849572 -21.6991 9 14 0 0.00 0.00 - no Open
372 3.9624227153920875 -1.10356 -28.0126 4 18 16 0.80 0.20 - no Current
282 4.021294943242523 -1.239 -35.8435 9 17 0 0.00 0.00 - no Open
316 4.705477255827921 -1.17836 -28.5533 9 21 0 0.00 0.00 - no Open
287 4.830955251729373 -1.16188 -25.6924 10 15 0 0.00 0.00 - no Open
353 5.092204702816937 -0.795238 -22.7627 7 12 0 0.00 0.00 - no Open
272 5.40909853377186 -0.937498 -19.6641 16 12 0 0.00 0.00 - no Open
409 5.703467463727863 -0.909529 -26.8524 10 16 0 0.00 0.00 - no Open
296 6.199766084150915 -1.0563 -30.5291 13 17 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 -28.013kcal/mol
Ligand efficiency (LE) -1.0375kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.680
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 403.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.03
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 32.55kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 3.81kcal/mol
Minimised FF energy -28.74kcal/mol

SASA & burial

✓ computed
SASA (unbound) 641.6Ų
Total solvent-accessible surface area of free ligand
BSA total 584.5Ų
Buried surface area upon binding
BSA apolar 436.9Ų
Hydrophobic contacts buried
BSA polar 147.7Ų
Polar contacts buried
Fraction buried 91.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1486.3Ų
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 804.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)