FAIRMol

Z16669877

Pose ID 1987 Compound 1409 Pose 632

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 Z16669877

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 strong SASA done
Strain ΔE
22.5 kcal/mol
Protein clashes
5
Internal clashes
6
Native overlap
contact recall 0.85, Jaccard 0.77, H-bond role recall 0.60
Burial
92%
Hydrophobic fit
74%
Reason: 6 internal clashes
5 protein-contact clashes 6 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.855 kcal/mol/HA) ✓ Good fit quality (FQ -8.48) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (92% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ High strain energy (22.5 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-28.202
kcal/mol
LE
-0.855
kcal/mol/HA
Fit Quality
-8.48
FQ (Leeson)
HAC
33
heavy atoms
MW
485
Da
LogP
3.53
cLogP
Strain ΔE
22.5 kcal/mol
SASA buried
92%
Lipo contact
74% BSA apolar/total
SASA unbound
721 Ų
Apolar buried
491 Ų

Interaction summary

HB 6 HY 24 PI 3 CLASH 6

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 rank3.538Score-28.202
Inter norm-0.890Intra norm0.036
Top1000noExcludedno
Contacts19H-bonds6
Artifact reasongeometry warning; 9 clashes; 2 protein clashes; 1 cofactor-context clash; moderate strain Δ 22.5
Residues
ALA32 ARG97 ASP52 ILE45 LEU94 LYS57 LYS95 MET53 NDP301 PHE56 PHE91 PRO93 THR180 THR83 TYR162 VAL156 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 overlap17Native recall0.85
Jaccard0.77RMSD-
HB strict4Strict recall0.57
HB same residue+role3HB role recall0.60
HB same residue3HB residue recall0.60

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
631 0.22802272933052797 -0.913657 -26.5528 5 16 0 0.00 0.00 - no Open
640 1.0828763374248342 -0.668787 -18.884 4 14 0 0.00 0.00 - no Open
632 3.5383181440115155 -0.890474 -28.2018 6 19 17 0.85 0.60 - no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -28.202kcal/mol
Ligand efficiency (LE) -0.8546kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.479
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 484.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.53
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 22.52kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 32.32kcal/mol
Minimised FF energy 9.80kcal/mol

SASA & burial

✓ computed
SASA (unbound) 720.6Ų
Total solvent-accessible surface area of free ligand
BSA total 666.6Ų
Buried surface area upon binding
BSA apolar 490.7Ų
Hydrophobic contacts buried
BSA polar 175.9Ų
Polar contacts buried
Fraction buried 92.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1553.8Ų
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 800.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)