Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T03

L. major DHFR L. major

Ligand Z47741866

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

27.1 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.65, Jaccard 0.57, H-bond role recall 0.80

Burial

89%

Hydrophobic fit

75%

Reason: 10 internal clashes

2 protein-contact clashes 10 intramolecular 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. 3 — Harmful (10–100 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG Medium Ames Clear DILI Low

Molecular report

Full metrics ↗

Weak Marginal quality. Consider only alongside better-scoring alternatives.

✓ Excellent LE (-0.991 kcal/mol/HA) ✓ Good fit quality (FQ -9.13) ✓ Good H-bonds (4 bonds) ✓ Deep burial (89% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ High strain energy (27.1 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (2) ✗ Many internal clashes (10)

Score

-25.774

kcal/mol

-0.991

kcal/mol/HA

Fit Quality

-9.13

FQ (Leeson)

HAC

heavy atoms

369

LogP

2.83

cLogP

Final rank

0.4530

rank score

Inter norm

-1.114

normalised

Contacts

H-bonds 8

Strain ΔE

27.1 kcal/mol

SASA buried

89%

Lipo contact

75% BSA apolar/total

SASA unbound

634 Å²

Apolar buried

424 Å²

Interaction summary

HBD 2 HBA 2 HY 10 PI 1 CLASH 0

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.

PI · π–π interactions

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

HY · Hydrophobic contacts

CLASH · Clashes

No clash · clashes detected for this pose.

Native ligand reference

★ reference

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

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	13	Native recall	0.65
Jaccard	0.57	RMSD	-
HB strict	4	Strict recall	0.57
HB same residue+role	4	HB role recall	0.80
HB same residue	4	HB residue recall	0.80

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
495	0.45297170136575826	-1.1141	-25.774	8	16	13	0.65	0.80	-	no	Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.

✓ Metrics available

Scoring & efficiency

Docking score -25.774kcal/mol

Ligand efficiency (LE) -0.9913kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -9.133

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

Heavy atom count 26HA

Physicochemical properties

Molecular weight 369.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.83

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 27.05kcal/mol

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

Docked FF energy -21.14kcal/mol

Minimised FF energy -48.19kcal/mol

SASA & burial

✓ computed

SASA (unbound) 634.2Å²

Total solvent-accessible surface area of free ligand

BSA total 565.3Å²

Buried surface area upon binding

BSA apolar 423.5Å²

Hydrophobic contacts buried

BSA polar 141.8Å²

Polar contacts buried

Fraction buried 89.1%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 74.9%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1491.1Å²

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 816.1Å²

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