Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T03

L. major DHFR L. major

Ligand KB_HAT_78

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 mixed SASA done

Strain ΔE

21.7 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.45, Jaccard 0.39, H-bond role recall 0.20

Burial

84%

Hydrophobic fit

78%

Reason: no major geometry red flags detected

2 protein-contact clashes 50% of hydrophobic surface appears solvent-exposed (10/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.959 kcal/mol/HA) ✓ Good fit quality (FQ -8.95) ✓ Good H-bonds (3 bonds) ✓ Deep burial (84% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ High strain energy (21.7 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)

Score

-25.898

kcal/mol

-0.959

kcal/mol/HA

Fit Quality

-8.95

FQ (Leeson)

HAC

heavy atoms

443

LogP

3.91

cLogP

Final rank

3.8220

rank score

Inter norm

-0.982

normalised

Contacts

H-bonds 4

Strain ΔE

21.7 kcal/mol

SASA buried

84%

Lipo contact

78% BSA apolar/total

SASA unbound

620 Å²

Apolar buried

407 Å²

Interaction summary

HBD 1 HBA 2 HY 6 PI 2 CLASH 2

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

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: 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	9	Native recall	0.45
Jaccard	0.39	RMSD	-
HB strict	2	Strict recall	0.29
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
114	3.822031334624506	-0.982374	-25.8976	4	12	9	0.45	0.20	-	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 -25.898kcal/mol

Ligand efficiency (LE) -0.9592kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -8.949

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

Heavy atom count 27HA

Physicochemical properties

Molecular weight 443.3Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.91

Lipinski: ≤ 5

Rotatable bonds 6

Conformational strain (MMFF94s)

Strain energy (ΔE) 21.73kcal/mol

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

Docked FF energy 59.46kcal/mol

Minimised FF energy 37.73kcal/mol

SASA & burial

✓ computed

SASA (unbound) 620.4Å²

Total solvent-accessible surface area of free ligand

BSA total 522.2Å²

Buried surface area upon binding

BSA apolar 407.4Å²

Hydrophobic contacts buried

BSA polar 114.8Å²

Polar contacts buried

Fraction buried 84.2%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 78.0%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1475.8Å²

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 844.0Å²

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