FAIRMol

NMT-TY0615

Pose ID 1704 Compound 624 Pose 349

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-TY0615

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 mixed SASA done
Strain ΔE
23.3 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.40, Jaccard 0.35, H-bond role recall 0.20
Burial
84%
Hydrophobic fit
71%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.067 kcal/mol/HA) ✓ Good fit quality (FQ -10.07) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (84% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ High strain energy (23.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-29.864
kcal/mol
LE
-1.067
kcal/mol/HA
Fit Quality
-10.07
FQ (Leeson)
HAC
28
heavy atoms
MW
418
Da
LogP
2.07
cLogP
Strain ΔE
23.3 kcal/mol
SASA buried
84%
Lipo contact
71% BSA apolar/total
SASA unbound
674 Ų
Apolar buried
400 Ų

Interaction summary

HB 9 HY 21 PI 3 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 rank3.925Score-29.864
Inter norm-1.050Intra norm-0.016
Top1000noExcludedno
Contacts11H-bonds9
Artifact reasongeometry warning; 10 clashes; 2 protein clashes; moderate strain Δ 23.3
Residues
ALA32 ARG97 ASP52 LEU94 LYS57 LYS90 LYS95 MET53 PHE56 PHE91 PRO93

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
Jaccard0.35RMSD-
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
286 0.1465605854321825 -1.19394 -32.9525 8 16 0 0.00 0.00 - no Open
319 0.36642347467445924 -0.879437 -22.3358 1 16 0 0.00 0.00 - no Open
419 0.8391962853228202 -0.877673 -24.4346 5 16 0 0.00 0.00 - no Open
304 1.173755634996843 -0.883006 -24.7401 4 20 1 0.05 0.00 - no Open
302 2.436367550694648 -0.950939 -25.3338 9 16 0 0.00 0.00 - no Open
355 2.444543107656295 -1.08753 -30.4423 6 15 0 0.00 0.00 - no Open
322 2.4446601818421776 -0.791024 -19.9765 6 14 0 0.00 0.00 - no Open
336 2.463593334913157 -0.803657 -21.4576 9 10 0 0.00 0.00 - no Open
330 2.5563520520351584 -0.78044 -19.9576 8 16 0 0.00 0.00 - no Open
263 3.041922657056329 -1.11762 -30.5736 10 16 0 0.00 0.00 - no Open
389 3.368666501110512 -0.85198 -23.3125 6 13 1 0.05 0.00 - no Open
349 3.9250362007127744 -1.05025 -29.8637 9 11 8 0.40 0.20 - no Current
372 4.026339219876199 -1.18223 -30.309 8 16 0 0.00 0.00 - no Open
291 4.327872741509822 -1.07289 -25.4854 16 24 0 0.00 0.00 - no Open
342 4.655876379256122 -0.889836 -26.7374 6 17 0 0.00 0.00 - no Open
251 5.021275157969677 -0.869737 -21.4644 11 14 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 -29.864kcal/mol
Ligand efficiency (LE) -1.0666kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.069
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 417.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.07
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 23.30kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -44.21kcal/mol
Minimised FF energy -67.51kcal/mol

SASA & burial

✓ computed
SASA (unbound) 674.4Ų
Total solvent-accessible surface area of free ligand
BSA total 566.3Ų
Buried surface area upon binding
BSA apolar 399.8Ų
Hydrophobic contacts buried
BSA polar 166.5Ų
Polar contacts buried
Fraction buried 84.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1524.0Ų
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 792.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)