FAIRMol

KB_Leish_65

Pose ID 1497 Compound 1142 Pose 142

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 KB_Leish_65

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native strong SASA done
Strain ΔE
21.6 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.70, Jaccard 0.58, H-bond role recall 0.80
Burial
83%
Hydrophobic fit
88%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.713 kcal/mol/HA) ✓ Good fit quality (FQ -7.13) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (88%) ✗ High strain energy (21.6 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (7) ✗ Many internal clashes (11)
Score
-24.230
kcal/mol
LE
-0.713
kcal/mol/HA
Fit Quality
-7.13
FQ (Leeson)
HAC
34
heavy atoms
MW
475
Da
LogP
3.89
cLogP
Strain ΔE
21.6 kcal/mol
SASA buried
83%
Lipo contact
88% BSA apolar/total
SASA unbound
793 Ų
Apolar buried
582 Ų

Interaction summary

HB 7 HY 24 PI 2 CLASH 3
Final rank1.542Score-24.230
Inter norm-0.818Intra norm0.105
Top1000noExcludedno
Contacts18H-bonds7
Artifact reasongeometry warning; 11 clashes; 7 protein contact clashes; moderate strain Δ 21.6
Residues
ALA32 ARG97 GLY157 ILE45 LEU94 LYS57 LYS95 MET53 NDP301 PHE56 PHE91 PRO93 THR61 TYR162 VAL156 VAL30 VAL31 VAL87

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 overlap14Native recall0.70
Jaccard0.58RMSD-
HB strict4Strict recall0.57
HB same residue+role4HB role recall0.80
HB same residue4HB residue recall0.80

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
142 1.542018817237739 -0.817819 -24.2304 7 18 14 0.70 0.80 - no Current
119 2.46774917906516 -0.7188 -19.5282 2 17 0 0.00 0.00 - no Open
134 3.004773157258972 -0.666924 -17.0211 6 19 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 -24.230kcal/mol
Ligand efficiency (LE) -0.7127kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.131
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 475.0Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.89
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 21.62kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -144.73kcal/mol
Minimised FF energy -166.35kcal/mol

SASA & burial

✓ computed
SASA (unbound) 793.0Ų
Total solvent-accessible surface area of free ligand
BSA total 659.7Ų
Buried surface area upon binding
BSA apolar 581.8Ų
Hydrophobic contacts buried
BSA polar 77.9Ų
Polar contacts buried
Fraction buried 83.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 88.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1704.3Ų
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 825.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)