FAIRMol

OHD_Leishmania_376

Pose ID 6113 Compound 1287 Pose 17

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
T10
L. infantum R5P L. infantum
Ligand OHD_Leishmania_376

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
29.6 kcal/mol
Protein clashes
7
Internal clashes
7
Native overlap
contact recall 0.71, Jaccard 0.60, H-bond role recall 0.64
Burial
74%
Hydrophobic fit
86%
Reason: 7 internal clashes
7 protein-contact clashes 7 intramolecular clashes 68% of hydrophobic surface is solvent-exposed (13/19 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.808 kcal/mol/HA) ✓ Good fit quality (FQ -7.45) ✓ Strong H-bond network (12 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (86%) ✗ High strain energy (29.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-21.016
kcal/mol
LE
-0.808
kcal/mol/HA
Fit Quality
-7.45
FQ (Leeson)
HAC
26
heavy atoms
MW
350
Da
LogP
2.08
cLogP
Strain ΔE
29.6 kcal/mol
SASA buried
74%
Lipo contact
86% BSA apolar/total
SASA unbound
625 Ų
Apolar buried
397 Ų

Interaction summary

HB 12 HY 1 PI 2 CLASH 7 ⚠ Exposure 68%
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
68% of hydrophobic surface is solvent-exposed (13/19 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 19 Buried (contacted) 6 Exposed 13 LogP 2.08 H-bonds 12
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
Final rank3.628Score-21.016
Inter norm-0.921Intra norm0.112
Top1000noExcludedno
Contacts15H-bonds12
Artifact reasongeometry warning; 14 clashes; 1 protein clash; moderate strain Δ 29.6
Residues
ALA15 ARG116 ARG140 ARG144 ASN106 ASP13 ASP44 CYS72 GLY73 HIS105 HIS14 HIS141 SER46 THR45 TYR49

Protein summary

155 residues
Protein targetT10Atoms4590
Residues155Chains1
Residue summaryILE:494; ARG:384; ALA:360; VAL:352; LEU:304; GLU:300; THR:280; MET:272; LYS:220; ASP:216; TYR:210; HIS:204; GLY:182; SER:176; GLN:170; ASN:140

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6FXWContacts17
PoseOpen native poseHB0
IFP residues
ALA15 ARG116 ARG140 ARG144 ASN106 ASP13 CYS72 GLY73 GLY75 GLY77 HIS105 HIS14 HIS141 ILE76 LEU101 THR74 TYR49
Current overlap12Native recall0.71
Jaccard0.60RMSD-
HB strict8Strict recall0.62
HB same residue+role7HB role recall0.64
HB same residue7HB residue recall0.64

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
33 1.6930652387964553 -1.3032 -33.8634 6 17 0 0.00 0.00 - no Open
25 2.37677582883771 -1.09051 -30.1724 6 17 0 0.00 0.00 - no Open
12 2.44585948723262 -0.900816 -20.7969 5 15 0 0.00 0.00 - no Open
35 2.5616248823522323 -0.851804 -21.5439 6 20 0 0.00 0.00 - no Open
153 2.897957358189819 -0.8562 -22.5503 4 19 0 0.00 0.00 - no Open
111 3.0202415484740994 -1.0648 -31.0336 6 17 0 0.00 0.00 - no Open
24 3.3091876015919386 -1.08568 -25.0988 6 16 0 0.00 0.00 - no Open
19 3.4171330511542393 -0.834551 -20.0158 4 11 0 0.00 0.00 - no Open
95 3.4786804256067114 -1.14676 -28.8385 7 19 0 0.00 0.00 - no Open
124 3.6213626191011485 -0.903161 -25.3504 6 14 0 0.00 0.00 - no Open
17 3.6275869878240954 -0.920544 -21.0159 12 15 12 0.71 0.64 - no Current
148 3.89202282370617 -0.806911 -21.6887 5 10 0 0.00 0.00 - no Open
25 4.022373065804421 -0.812568 -20.336 5 10 0 0.00 0.00 - no Open
27 4.286510035161286 -1.21476 -29.2815 7 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 -21.016kcal/mol
Ligand efficiency (LE) -0.8083kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.447
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 350.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.08
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 29.59kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -128.52kcal/mol
Minimised FF energy -158.11kcal/mol

SASA & burial

✓ computed
SASA (unbound) 625.2Ų
Total solvent-accessible surface area of free ligand
BSA total 462.9Ų
Buried surface area upon binding
BSA apolar 396.7Ų
Hydrophobic contacts buried
BSA polar 66.2Ų
Polar contacts buried
Fraction buried 74.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 85.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2312.5Ų
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 2417.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 662.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)