FAIRMol

OHD_Leishmania_380

Pose ID 2738 Compound 639 Pose 28

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_380
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
Weak or marginal quality
Binding strong Geometry high Native strong SASA done
Strain ΔE
27.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.76, Jaccard 0.65, H-bond role recall 0.33
Burial
68%
Hydrophobic fit
73%
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 (-0.608 kcal/mol/HA) ✓ Good fit quality (FQ -6.35) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (68% SASA buried) ✓ Lipophilic contacts well-matched (73%) ✗ High strain energy (27.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (20)
Score
-24.337
kcal/mol
LE
-0.608
kcal/mol/HA
Fit Quality
-6.35
FQ (Leeson)
HAC
40
heavy atoms
MW
538
Da
LogP
5.13
cLogP
Strain ΔE
27.6 kcal/mol
SASA buried
68%
Lipo contact
73% BSA apolar/total
SASA unbound
782 Ų
Apolar buried
388 Ų

Interaction summary

HB 8 HY 24 PI 5 CLASH 1
Final rank3.194Score-24.337
Inter norm-0.720Intra norm0.112
Top1000noExcludedno
Contacts16H-bonds8
Artifact reasongeometry warning; 20 clashes; 1 protein clash; 1 severe cofactor-context clash; moderate strain Δ 27.6
Residues
ARG17 GLY225 HIS241 LEU188 LEU226 LEU229 MET183 NDP302 PHE113 PRO115 TYR114 TYR191 TYR194 TYR283 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 overlap13Native recall0.76
Jaccard0.65RMSD-
HB strict2Strict recall0.29
HB same residue+role2HB role recall0.33
HB same residue2HB residue recall0.40

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
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 13 0.76 0.33 - no Current
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 0 0.00 0.00 - no Open
26 4.853888287172083 -0.702973 -26.167 8 19 0 0.00 0.00 - no Open
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 -24.337kcal/mol
Ligand efficiency (LE) -0.6084kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.354
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 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 27.65kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 157.03kcal/mol
Minimised FF energy 129.38kcal/mol

SASA & burial

✓ computed
SASA (unbound) 782.2Ų
Total solvent-accessible surface area of free ligand
BSA total 532.8Ų
Buried surface area upon binding
BSA apolar 388.0Ų
Hydrophobic contacts buried
BSA polar 144.7Ų
Polar contacts buried
Fraction buried 68.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1685.0Ų
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 1057.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)