Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T09

L. major DHFR-TS L. major

Ligand NMT-TY0960

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 mixed SASA done

Strain ΔE

72.9 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.38, Jaccard 0.32, H-bond role recall 0.17

Burial

86%

Hydrophobic fit

62%

Reason: strain 72.9 kcal/mol

strain ΔE 72.9 kcal/mol 4 protein-contact clashes 4 intramolecular clashes

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Not classified (>100 mg/L)

Daphnia EC₅₀

Not classified (>100 mg/L)

Algae IC₅₀

Not classified (>100 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG Low Ames Clear DILI Low

Molecular report

Full metrics ↗

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

✓ Excellent LE (-1.106 kcal/mol/HA) ✓ Good fit quality (FQ -10.05) ✓ Good H-bonds (3 bonds) ✓ Deep burial (86% SASA buried) ✓ Lipophilic contacts well-matched (62%) ✗ Extreme strain energy (72.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)

Score

-27.642

kcal/mol

-1.106

kcal/mol/HA

Fit Quality

-10.05

FQ (Leeson)

HAC

heavy atoms

386

LogP

1.45

cLogP

Final rank

3.8759

rank score

Inter norm

-1.045

normalised

Contacts

H-bonds 10

Strain ΔE

72.9 kcal/mol

SASA buried

86%

Lipo contact

62% BSA apolar/total

SASA unbound

579 Å²

Apolar buried

310 Å²

Interaction summary

HBD 1 HBA 2 HY 6 PI 2 CLASH 4

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	21
Pose	Open native pose	HB	0
IFP residues	NDP301 ALA32 ARG97 ASP52 GLY157 ILE45 LEU94 LYS57 MET53 PHE55 PHE56 PHE91 PRO88 SER86 THR180 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap	8	Native recall	0.38
Jaccard	0.32	RMSD	-
HB strict	0	Strict recall	0.00
HB same residue+role	1	HB role recall	0.17
HB same residue	1	HB residue recall	0.17

Protein summary

511 residues

Protein target	T09	Atoms	8170
Residues	511	Chains	2
Residue summary	LEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224

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
335	3.875859557844949	-1.04535	-27.6425	10	12	8	0.38	0.17	-	no	Current
287	4.646883205258447	-1.04072	-24.8449	14	14	0	0.00	0.00	-	no	Open
380	5.304743934844145	-0.928245	-23.4355	13	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 -27.642kcal/mol

Ligand efficiency (LE) -1.1057kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -10.052

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

Heavy atom count 25HA

Physicochemical properties

Molecular weight 386.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 1.45

Lipinski: ≤ 5

Rotatable bonds 7

Conformational strain (MMFF94s)

Strain energy (ΔE) 72.86kcal/mol

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

Docked FF energy -53.92kcal/mol

Minimised FF energy -126.78kcal/mol

SASA & burial

✓ computed

SASA (unbound) 578.8Å²

Total solvent-accessible surface area of free ligand

BSA total 496.4Å²

Buried surface area upon binding

BSA apolar 309.8Å²

Hydrophobic contacts buried

BSA polar 186.6Å²

Polar contacts buried

Fraction buried 85.8%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 62.4%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -3112.5Å²

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 4428.5Å²

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

Complex non-polar SASA 1669.1Å²

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