FAIRMol

KB_Leish_120

Pose ID 1503 Compound 1105 Pose 148

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_120

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 high Native strong SASA done
Strain ΔE
23.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.85, Jaccard 0.77, H-bond role recall 0.20
Burial
93%
Hydrophobic fit
74%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.897 kcal/mol/HA) ✓ Good fit quality (FQ -8.74) ✓ Deep burial (93% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ High strain energy (23.0 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-27.798
kcal/mol
LE
-0.897
kcal/mol/HA
Fit Quality
-8.74
FQ (Leeson)
HAC
31
heavy atoms
MW
460
Da
LogP
3.38
cLogP
Strain ΔE
23.0 kcal/mol
SASA buried
93%
Lipo contact
74% BSA apolar/total
SASA unbound
741 Ų
Apolar buried
512 Ų

Interaction summary

HB 2 HY 24 PI 3 CLASH 1
Final rank1.240Score-27.798
Inter norm-0.926Intra norm0.029
Top1000noExcludedno
Contacts19H-bonds2
Artifact reasongeometry warning; 6 clashes; 1 protein clash; moderate strain Δ 23.0
Residues
ALA32 ARG97 ASP52 ILE45 LEU94 LYS57 LYS95 MET53 NDP301 PHE56 PHE91 PRO88 PRO93 THR83 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 overlap17Native recall0.85
Jaccard0.77RMSD-
HB strict2Strict recall0.29
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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
148 1.2403718761403133 -0.925706 -27.7982 2 19 17 0.85 0.20 - no Current
648 1.2559919115937181 -0.926046 -27.6044 2 18 16 0.80 0.20 - no Open
92 3.6085021406259115 -0.986882 -27.6733 11 17 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 -27.798kcal/mol
Ligand efficiency (LE) -0.8967kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.736
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 459.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.38
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 23.00kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -0.64kcal/mol
Minimised FF energy -23.64kcal/mol

SASA & burial

✓ computed
SASA (unbound) 740.5Ų
Total solvent-accessible surface area of free ligand
BSA total 687.8Ų
Buried surface area upon binding
BSA apolar 512.2Ų
Hydrophobic contacts buried
BSA polar 175.6Ų
Polar contacts buried
Fraction buried 92.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1572.2Ų
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 796.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)