FAIRMol

OHD_Leishmania_380

Pose ID 1381 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
T03
L. major DHFR L. major
Ligand OHD_Leishmania_380

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 medium Native strong SASA done
Strain ΔE
19.8 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.90, Jaccard 0.78, H-bond role recall 0.60
Burial
92%
Hydrophobic fit
68%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.739 kcal/mol/HA) ✓ Good fit quality (FQ -7.72) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (92% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ Moderate strain (19.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (19)
Score
-29.574
kcal/mol
LE
-0.739
kcal/mol/HA
Fit Quality
-7.72
FQ (Leeson)
HAC
40
heavy atoms
MW
538
Da
LogP
5.13
cLogP
Strain ΔE
19.8 kcal/mol
SASA buried
92%
Lipo contact
68% BSA apolar/total
SASA unbound
756 Ų
Apolar buried
469 Ų

Interaction summary

HB 8 HY 24 PI 3 CLASH 4

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 rank3.632Score-29.574
Inter norm-0.794Intra norm0.055
Top1000noExcludedno
Contacts21H-bonds8
Artifact reasongeometry warning; 19 clashes; 1 protein clash
Residues
ALA32 ARG48 ASP52 ILE45 LEU94 LYS57 MET53 NDP301 PHE56 PHE91 PRO88 SER86 THR54 THR83 TRP47 TYR162 VAL156 VAL30 VAL31 VAL49 VAL87

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name3CL9Contacts20
PoseOpen native poseHB0
IFP residues
ALA32 ARG97 ASP52 ILE45 LEU94 LYS57 MET53 NDP301 PHE56 PHE91 PRO88 SER86 THR180 THR54 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap18Native recall0.90
Jaccard0.78RMSD-
HB strict3Strict recall0.43
HB same residue+role3HB role recall0.60
HB same residue3HB residue recall0.60

Protein summary

225 residues
Protein targetT03Atoms3428
Residues225Chains2
Residue summaryLEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; NDP:74

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
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 18 0.90 0.60 - no Current
25 3.6473712664434346 -0.864399 -31.0091 12 17 1 0.05 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 1 0.05 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 -29.574kcal/mol
Ligand efficiency (LE) -0.7394kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.722
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) 19.84kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 147.95kcal/mol
Minimised FF energy 128.10kcal/mol

SASA & burial

✓ computed
SASA (unbound) 756.0Ų
Total solvent-accessible surface area of free ligand
BSA total 691.8Ų
Buried surface area upon binding
BSA apolar 469.2Ų
Hydrophobic contacts buried
BSA polar 222.6Ų
Polar contacts buried
Fraction buried 91.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 67.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1562.9Ų
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 1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 780.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)