FAIRMol

OHD_Leishmania_93

Pose ID 5422 Compound 3167 Pose 4

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 OHD_Leishmania_93

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry high Native strong SASA done
Strain ΔE
16.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.62, Jaccard 0.54, H-bond role recall 0.33
Burial
93%
Hydrophobic fit
86%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.316 kcal/mol/HA) ✓ Good fit quality (FQ -11.22) ✓ Good H-bonds (4 bonds) ✓ Deep burial (93% SASA buried) ✓ Lipophilic contacts well-matched (86%) ✗ Moderate strain (16.3 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (3) ✗ Internal clashes (7)
Score
-27.632
kcal/mol
LE
-1.316
kcal/mol/HA
Fit Quality
-11.22
FQ (Leeson)
HAC
21
heavy atoms
MW
288
Da
LogP
-0.67
cLogP
Strain ΔE
16.3 kcal/mol
SASA buried
93%
Lipo contact
86% BSA apolar/total
SASA unbound
484 Ų
Apolar buried
388 Ų

Interaction summary

HB 4 HY 24 PI 1 CLASH 1

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 rank0.050Score-27.632
Inter norm-1.293Intra norm-0.023
Top1000noExcludedno
Contacts16H-bonds4
Artifact reasongeometry warning; 7 clashes; 3 protein contact clashes
Residues
NDP301 ALA32 ARG48 ASP52 GLY157 ILE45 MET53 PHE55 PHE56 THR180 TRP47 TYR162 VAL156 VAL30 VAL31 VAL49

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 overlap13Native recall0.62
Jaccard0.54RMSD-
HB strict2Strict recall0.29
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
4 0.04985470824051259 -1.29291 -27.6324 4 16 13 0.62 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 -27.632kcal/mol
Ligand efficiency (LE) -1.3158kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.224
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 21HA

Physicochemical properties
Molecular weight 288.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.67
Lipinski: ≤ 5
Rotatable bonds 2

Conformational strain (MMFF94s)
Strain energy (ΔE) 16.33kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 83.13kcal/mol
Minimised FF energy 66.80kcal/mol

SASA & burial

✓ computed
SASA (unbound) 484.2Ų
Total solvent-accessible surface area of free ligand
BSA total 452.1Ų
Buried surface area upon binding
BSA apolar 387.8Ų
Hydrophobic contacts buried
BSA polar 64.3Ų
Polar contacts buried
Fraction buried 93.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 85.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3161.1Ų
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 1668.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)