FAIRMol

Z2752015126

Pose ID 5816 Compound 3331 Pose 398

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
T09
L. major DHFR-TS L. major
Ligand Z2752015126

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
36.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.71, Jaccard 0.65, H-bond role recall 0.33
Burial
91%
Hydrophobic fit
80%
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 (-0.745 kcal/mol/HA) ✓ Good fit quality (FQ -7.11) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Very high strain energy (36.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-21.604
kcal/mol
LE
-0.745
kcal/mol/HA
Fit Quality
-7.11
FQ (Leeson)
HAC
29
heavy atoms
MW
399
Da
LogP
3.60
cLogP
Strain ΔE
36.7 kcal/mol
SASA buried
91%
Lipo contact
80% BSA apolar/total
SASA unbound
608 Ų
Apolar buried
441 Ų

Interaction summary

HB 7 HY 24 PI 1 CLASH 2
Final rank3.224Score-21.604
Inter norm-1.062Intra norm0.317
Top1000noExcludedno
Contacts17H-bonds7
Artifact reasongeometry warning; 13 clashes; 2 protein clashes; 1 severe cofactor-context clash; high strain Δ 36.7
Residues
NDP301 ALA32 GLU43 GLY157 ILE45 LEU94 MET53 PHE56 PRO88 SER44 SER86 THR83 TYR162 VAL156 VAL30 VAL31 VAL87

Protein summary

511 residues
Protein targetT09Atoms8170
Residues511Chains2
Residue summaryLEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224

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.
Name3CL9Contacts21
PoseOpen native poseHB0
IFP residues
NDP301 ALA32 ARG97 ASP52 GLY157 ILE45 LEU94 LYS57 MET53 PHE55 PHE56 PHE91 PRO88 SER86 THR180 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap15Native recall0.71
Jaccard0.65RMSD-
HB strict2Strict recall0.29
HB same residue+role2HB role recall0.33
HB same residue2HB residue recall0.33

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
398 3.223680325206018 -1.06219 -21.604 7 17 15 0.71 0.33 - no Current
374 3.5985658614324247 -0.860019 -17.7772 5 13 0 0.00 0.00 - no Open
392 3.681989993149358 -0.848956 -16.3851 5 12 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 -21.604kcal/mol
Ligand efficiency (LE) -0.7450kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.111
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 399.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.60
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 36.71kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 43.67kcal/mol
Minimised FF energy 6.97kcal/mol

SASA & burial

✓ computed
SASA (unbound) 608.4Ų
Total solvent-accessible surface area of free ligand
BSA total 553.6Ų
Buried surface area upon binding
BSA apolar 441.2Ų
Hydrophobic contacts buried
BSA polar 112.4Ų
Polar contacts buried
Fraction buried 91.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3233.5Ų
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 4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1690.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)