FAIRMol

OHD_Leishmania_310

Pose ID 2733 Compound 243 Pose 23

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
T05
L. major PTR1 L. major
Ligand OHD_Leishmania_310
PDB7PXX↗

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
23.6 kcal/mol
Protein clashes
4
Internal clashes
8
Native overlap
contact recall 0.71, Jaccard 0.57, H-bond role recall 0.50
Burial
93%
Hydrophobic fit
83%
Reason: 8 internal clashes
4 protein-contact clashes 8 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.896 kcal/mol/HA) ✓ Good fit quality (FQ -8.36) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (93% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ High strain energy (23.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (17)
Score
-24.183
kcal/mol
LE
-0.896
kcal/mol/HA
Fit Quality
-8.36
FQ (Leeson)
HAC
27
heavy atoms
MW
360
Da
LogP
2.42
cLogP
Strain ΔE
23.6 kcal/mol
SASA buried
93%
Lipo contact
83% BSA apolar/total
SASA unbound
610 Ų
Apolar buried
469 Ų

Interaction summary

HB 8 HY 24 PI 2 CLASH 8
Final rank3.120Score-24.183
Inter norm-1.075Intra norm0.180
Top1000noExcludedno
Contacts16H-bonds8
Artifact reasongeometry warning; 17 clashes; 1 protein clash; 1 severe cofactor-context clash; moderate strain Δ 23.6
Residues
ARG17 ASP181 GLY225 LEU188 LEU226 LEU229 MET183 NDP302 PHE113 SER111 SER112 SER227 TYR194 VAL228 VAL230 ARG287

Protein summary

274 residues
Protein targetT05Atoms4108
Residues274Chains2
Residue summaryLEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108

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:NDP302

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameligandContacts17
PoseOpen native poseHB0
IFP residues
ARG17 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap12Native recall0.71
Jaccard0.57RMSD-
HB strict3Strict recall0.43
HB same residue+role3HB role recall0.50
HB same residue3HB residue recall0.60

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
24 0.7549739333923433 -1.59413 -34.7747 10 20 0 0.00 0.00 - no Open
329 0.8698098052673956 -1.45049 -32.341 12 17 0 0.00 0.00 - no Open
317 0.8946384457594485 -1.58597 -34.0011 11 20 0 0.00 0.00 - no Open
28 1.0656347282420564 -1.45916 -33.2626 11 19 0 0.00 0.00 - no Open
356 1.3049353307334395 -0.979504 -15.9888 7 14 14 0.82 0.67 - no Open
18 1.588420314889381 -0.911019 -18.1341 8 13 13 0.76 0.83 - no Open
422 1.6628478945064362 -1.05644 -21.9746 9 14 0 0.00 0.00 - no Open
20 3.0361155172718495 -1.0181 -22.5996 8 16 0 0.00 0.00 - no Open
23 3.1202537945072804 -1.07531 -24.183 8 16 12 0.71 0.50 - no Current
27 3.3132689308519394 -0.966783 -22.6379 4 18 0 0.00 0.00 - no Open
356 3.328134667714495 -0.944168 -25.3759 8 17 0 0.00 0.00 - no Open
344 3.624100808087315 -0.981092 -22.542 4 18 0 0.00 0.00 - no Open
388 4.022832904360227 -0.998263 -23.0614 8 15 0 0.00 0.00 - no Open
13 4.626933943246996 -0.776058 -21.6728 5 15 0 0.00 0.00 - no Open
28 4.830200145190352 -0.821899 -16.9858 6 13 0 0.00 0.00 - no Open
345 4.977153414468411 -0.945005 -21.6885 10 15 0 0.00 0.00 - no Open
317 5.527148258279148 -1.01223 -15.9467 14 19 0 0.00 0.00 - no Open
317 5.568677730743583 -1.13532 -21.0205 16 22 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 -24.183kcal/mol
Ligand efficiency (LE) -0.8957kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.356
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 360.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.42
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 23.61kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 117.29kcal/mol
Minimised FF energy 93.69kcal/mol

SASA & burial

✓ computed
SASA (unbound) 609.7Ų
Total solvent-accessible surface area of free ligand
BSA total 568.5Ų
Buried surface area upon binding
BSA apolar 469.4Ų
Hydrophobic contacts buried
BSA polar 99.1Ų
Polar contacts buried
Fraction buried 93.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1663.7Ų
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 2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1020.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)