FAIRMol

Z19836822

Pose ID 5919 Compound 3271 Pose 501

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
T09
L. major DHFR-TS L. major
Ligand Z19836822

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
58.0 kcal/mol
Protein clashes
4
Internal clashes
5
Native overlap
contact recall 0.71, Jaccard 0.62, H-bond role recall 0.33
Burial
85%
Hydrophobic fit
80%
Reason: strain 58.0 kcal/mol
strain ΔE 58.0 kcal/mol 4 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.454 kcal/mol/HA) ✓ Good fit quality (FQ -4.78) ✓ Good H-bonds (4 bonds) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Extreme strain energy (58.0 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (7) ✗ Many internal clashes (15)
Score
-18.631
kcal/mol
LE
-0.454
kcal/mol/HA
Fit Quality
-4.78
FQ (Leeson)
HAC
41
heavy atoms
MW
601
Da
LogP
2.00
cLogP
Strain ΔE
58.0 kcal/mol
SASA buried
85%
Lipo contact
80% BSA apolar/total
SASA unbound
913 Ų
Apolar buried
625 Ų

Interaction summary

HB 4 HY 24 PI 2 CLASH 5

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 rank2.263Score-18.631
Inter norm-0.616Intra norm0.161
Top1000noExcludedno
Contacts18H-bonds4
Artifact reasongeometry warning; 15 clashes; 7 protein contact clashes; 1 cofactor-context clash; high strain Δ 58.0
Residues
NDP301 ALA32 ARG97 ASP52 ILE45 LEU94 LYS57 LYS95 MET53 PHE56 PHE91 PRO88 PRO93 SER44 SER86 THR83 VAL156 VAL87

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
Jaccard0.62RMSD-
HB strict3Strict recall0.43
HB same residue+role2HB role recall0.33
HB same residue2HB residue recall0.33

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
501 2.2633637895626286 -0.6159 -18.6312 4 18 15 0.71 0.33 - 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 -18.631kcal/mol
Ligand efficiency (LE) -0.4544kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.775
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 41HA

Physicochemical properties
Molecular weight 600.8Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.00
Lipinski: ≤ 5
Rotatable bonds 10

Conformational strain (MMFF94s)
Strain energy (ΔE) 58.04kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 21.01kcal/mol
Minimised FF energy -37.02kcal/mol

SASA & burial

✓ computed
SASA (unbound) 913.4Ų
Total solvent-accessible surface area of free ligand
BSA total 778.8Ų
Buried surface area upon binding
BSA apolar 624.6Ų
Hydrophobic contacts buried
BSA polar 154.2Ų
Polar contacts buried
Fraction buried 85.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3524.4Ų
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 1643.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)