Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T03

L. major DHFR L. major

Ligand KB_Leish_46

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Reject SASA cached

Promising but geometrically suspicious

Binding strong Geometry low Native strong SASA done

Strain ΔE

45.4 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.60, Jaccard 0.55, H-bond role recall 0.20

Burial

83%

Hydrophobic fit

90%

Reason: strain 45.4 kcal/mol

strain ΔE 45.4 kcal/mol 1 protein-contact clashes

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Cat. 3 — Harmful (10–100 mg/L)

Daphnia EC₅₀

Cat. 3 — Harmful (10–100 mg/L)

Algae IC₅₀

Cat. 2 — Toxic (1–10 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG High Ames Clear DILI Low

Molecular report

Full metrics ↗

Reject Multiple quality flags — this pose should be deprioritised or discarded.

✓ Excellent LE (-0.801 kcal/mol/HA) ✓ Good fit quality (FQ -7.88) ✓ Good H-bonds (3 bonds) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (90%) ✗ Extreme strain energy (45.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)

Score

-25.649

kcal/mol

-0.801

kcal/mol/HA

Fit Quality

-7.88

FQ (Leeson)

HAC

heavy atoms

478

LogP

3.61

cLogP

Final rank

2.8012

rank score

Inter norm

-0.925

normalised

Contacts

H-bonds 3

Strain ΔE

45.4 kcal/mol

SASA buried

83%

Lipo contact

90% BSA apolar/total

SASA unbound

704 Å²

Apolar buried

527 Å²

Interaction summary

HBD 1 HBA 2 HY 7 PI 1 CLASH 1

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.

PI · π–π interactions

Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference

Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.

Name	3CL9	Contacts	20
Pose	Open native pose	HB	0
IFP residues	ALA32 ARG97 ASP52 ILE45 LEU94 LYS57 MET53 NDP301 PHE56 PHE91 PRO88 SER86 THR180 THR54 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap	12	Native recall	0.60
Jaccard	0.55	RMSD	-
HB strict	1	Strict recall	0.14
HB same residue+role	1	HB role recall	0.20
HB same residue	1	HB residue recall	0.20

Protein summary

225 residues

Protein target	T03	Atoms	3428
Residues	225	Chains	2
Residue summary	LEU: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

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
140	2.801213136677595	-0.925317	-25.6492	3	14	12	0.60	0.20	-	no	Current
154	3.198430692215305	-0.587023	-19.525	2	13	0	0.00	0.00	-	no	Open
92	3.8403208941305516	-1.02026	-28.2546	6	20	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 -25.649kcal/mol

Ligand efficiency (LE) -0.8015kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -7.882

LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe

Heavy atom count 32HA

Physicochemical properties

Molecular weight 478.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.61

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 45.39kcal/mol

< 5 good · 5–10 marginal · > 10 problematic

Docked FF energy 107.52kcal/mol

Minimised FF energy 62.14kcal/mol

SASA & burial

✓ computed

SASA (unbound) 704.1Å²

Total solvent-accessible surface area of free ligand

BSA total 585.5Å²

Buried surface area upon binding

BSA apolar 527.2Å²

Hydrophobic contacts buried

BSA polar 58.3Å²

Polar contacts buried

Fraction buried 83.2%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 90.0%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1614.2Å²

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 1820.7Å²

Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)

Complex non-polar SASA 816.3Å²

Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)