FAIRMol

OHD_Leishmania_380

Pose ID 7478 Compound 639 Pose 26

DB fairmolDocking 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
T12
T. brucei R5P T. brucei
Ligand OHD_Leishmania_380
PDB6FXS↗

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
19.8 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.81, Jaccard 0.59, H-bond role recall 0.20
Burial
67%
Hydrophobic fit
70%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.654 kcal/mol/HA) ✓ Good fit quality (FQ -6.83) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (67% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ Moderate strain (19.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (21)
Score
-26.167
kcal/mol
LE
-0.654
kcal/mol/HA
Fit Quality
-6.83
FQ (Leeson)
HAC
40
heavy atoms
MW
538
Da
LogP
5.13
cLogP
Strain ΔE
19.8 kcal/mol
SASA buried
67%
Lipo contact
70% BSA apolar/total
SASA unbound
778 Ų
Apolar buried
363 Ų

Interaction summary

HB 8 HY 12 PI 3 CLASH 2

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 rank4.854Score-26.167
Inter norm-0.703Intra norm0.049
Top1000noExcludedno
Contacts19H-bonds8
Artifact reasongeometry warning; 21 clashes; 2 protein clashes
Residues
ARG140 ASN106 GLN104 GLU138 HIS105 HIS141 MET101 SER136 TYR97 ARG116 ASP13 CYS72 GLY73 GLY77 HIS14 ILE15 ILE76 SER74 TYR49

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6FXSContacts16
PoseOpen native poseHB0
IFP residues
ARG140 ARG144 ASN106 HIS105 HIS141 ARG46 ASP13 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 SER74 TYR49
Current overlap13Native recall0.81
Jaccard0.59RMSD-
HB strict2Strict recall0.17
HB same residue+role2HB role recall0.20
HB same residue4HB residue recall0.40

Protein summary

302 residues
Protein targetT12Atoms4598
Residues302Chains2
Residue summaryARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121

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:CSD72

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
34 2.037464332345491 -0.816862 -31.8466 6 16 0 0.00 0.00 - no Open
25 2.378437056644811 -0.79296 -25.1786 11 20 0 0.00 0.00 - no Open
28 3.1939535201530846 -0.720039 -24.3367 8 16 0 0.00 0.00 - no Open
12 3.2679598625087527 -0.927293 -34.1568 6 15 0 0.00 0.00 - no Open
20 3.495100387591973 -0.687709 -25.9631 8 13 0 0.00 0.00 - no Open
26 3.6318101855931193 -0.794213 -29.5742 8 21 0 0.00 0.00 - no Open
25 3.6473712664434346 -0.864399 -31.0091 12 17 0 0.00 0.00 - no Open
11 3.756350175949824 -0.818637 -30.0821 11 18 0 0.00 0.00 - no Open
36 4.328059027755822 -0.664103 -25.5651 8 12 0 0.00 0.00 - no Open
13 4.367243655754057 -0.718582 -25.2048 10 15 0 0.00 0.00 - no Open
30 4.3947619074725255 -0.797581 -32.0325 7 21 0 0.00 0.00 - no Open
27 4.675590440132758 -0.575435 -21.4762 7 13 0 0.00 0.00 - no Open
18 4.709489958919522 -0.661154 -21.8688 6 14 5 0.31 0.20 - no Open
26 4.853888287172083 -0.702973 -26.167 8 19 13 0.81 0.20 - no Current
25 5.0046255959625645 -0.602508 -21.2208 5 13 0 0.00 0.00 - no Open
20 5.305300875417073 -0.744562 -26.4698 11 17 0 0.00 0.00 - no Open
17 5.662829045447725 -0.771959 -29.8084 10 17 0 0.00 0.00 - no Open
12 6.260876601403174 -0.803018 -30.5918 10 16 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 -26.167kcal/mol
Ligand efficiency (LE) -0.6542kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.832
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 40HA

Physicochemical properties
Molecular weight 538.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.13
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 19.81kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 141.05kcal/mol
Minimised FF energy 121.24kcal/mol

SASA & burial

✓ computed
SASA (unbound) 778.1Ų
Total solvent-accessible surface area of free ligand
BSA total 521.7Ų
Buried surface area upon binding
BSA apolar 362.8Ų
Hydrophobic contacts buried
BSA polar 158.9Ų
Polar contacts buried
Fraction buried 67.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 69.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2171.1Ų
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 2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 818.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)