FAIRMol

NMT-TY0976

Pose ID 1737 Compound 924 Pose 382

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-TY0976

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native mixed SASA done
Strain ΔE
26.7 kcal/mol
Protein clashes
0
Internal clashes
9
Native overlap
contact recall 0.40, Jaccard 0.36, H-bond role recall 0.20
Burial
80%
Hydrophobic fit
73%
Reason: 9 internal clashes
9 intramolecular clashes 41% of hydrophobic surface appears solvent-exposed (7/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.092 kcal/mol/HA) ✓ Good fit quality (FQ -10.06) ✓ Good H-bonds (4 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (73%) ✗ High strain energy (26.7 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-28.391
kcal/mol
LE
-1.092
kcal/mol/HA
Fit Quality
-10.06
FQ (Leeson)
HAC
26
heavy atoms
MW
388
Da
LogP
2.69
cLogP
Strain ΔE
26.7 kcal/mol
SASA buried
80%
Lipo contact
73% BSA apolar/total
SASA unbound
634 Ų
Apolar buried
373 Ų

Interaction summary

HB 4 HY 14 PI 2 CLASH 0 ⚠ Exposure 41%
⚠️Partial hydrophobic solvent exposure
41% of hydrophobic surface appears solvent-exposed (7/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17 Buried (contacted) 10 Exposed 7 LogP 2.69 H-bonds 4
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank1.846Score-28.391
Inter norm-1.075Intra norm-0.017
Top1000noExcludedno
Contacts10H-bonds4
Artifact reasongeometry warning; 9 clashes; 1 protein clash; moderate strain Δ 26.7
Residues
ARG97 ASP52 ILE45 LEU94 LYS57 LYS95 MET53 PHE56 PHE91 THR61

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

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 overlap8Native recall0.40
Jaccard0.36RMSD-
HB strict2Strict recall0.29
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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
No clash · clashes detected for this pose.

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
352 0.6043615813653308 -0.988227 -26.017 1 13 0 0.00 0.00 - no Open
341 1.0424018304021976 -0.916853 -17.8895 2 16 1 0.05 0.00 - no Open
334 1.5455213211202086 -0.958722 -24.8957 3 17 0 0.00 0.00 - no Open
339 1.7701678738098026 -1.08844 -29.6256 9 14 1 0.05 0.00 - no Open
382 1.845972868808333 -1.07526 -28.3909 4 10 8 0.40 0.20 - no Current
316 1.851249825910153 -1.28271 -34.3935 9 13 0 0.00 0.00 - no Open
350 2.2605111440336363 -0.792669 -20.1687 4 13 0 0.00 0.00 - no Open
399 2.3523012290914926 -1.09868 -26.3499 5 14 0 0.00 0.00 - no Open
294 2.93020983059206 -1.24579 -31.2053 8 20 0 0.00 0.00 - no Open
454 3.1617246535209707 -0.93915 -24.9209 6 16 0 0.00 0.00 - no Open
337 3.545405551412397 -0.83845 -21.4295 9 11 0 0.00 0.00 - no Open
417 3.73364200758271 -0.890396 -21.8774 8 14 0 0.00 0.00 - no Open
382 4.085203326655005 -0.971988 -26.5371 7 17 0 0.00 0.00 - no Open
305 4.467618834823319 -1.27421 -28.5567 10 15 0 0.00 0.00 - no Open
332 5.279291077811236 -1.29833 -31.9328 9 22 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 -28.391kcal/mol
Ligand efficiency (LE) -1.0920kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.061
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 388.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.69
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 26.69kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -74.76kcal/mol
Minimised FF energy -101.45kcal/mol

SASA & burial

✓ computed
SASA (unbound) 634.4Ų
Total solvent-accessible surface area of free ligand
BSA total 507.5Ų
Buried surface area upon binding
BSA apolar 372.6Ų
Hydrophobic contacts buried
BSA polar 134.9Ų
Polar contacts buried
Fraction buried 80.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1478.2Ų
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 816.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)