Docking pose detail

Molecular metrics status: done

Cached molecular metrics are available for this pose.

Metrics cached · SASA missing

py3Dmol interaction viewer

Left: interactive complex viewer. Right: clickable PLIP-like interaction summary. Clicking an interaction thickens and highlights it in the 3D view.

Strict H-bonds Permissive H-bonds

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.678 kcal/mol/HA) ✓ Good fit quality (FQ -6.73) ✓ Strong H-bond network (7 bonds) ✗ Very high strain energy (21.6 kcal/mol) ✗ Geometry warnings ℹ SASA not computed

Score

-22.381

kcal/mol

-0.678

kcal/mol/HA

Fit Quality

-6.73

FQ (Leeson)

HAC

heavy atoms

454

LogP

3.86

cLogP

Strain ΔE

21.6 kcal/mol

SASA buried

computing…

Overall: Promising but geometrically suspicious

Binding evidence: strong

Native-like contacts: strong

Ligand efficiency: excellent

Geometry reliability: low

Reason: geometry warning, clashes, strain 21.6 kcal/mol

Interaction summary

Collapsible panels

H-bonds 7 Hydrophobic 20 π–π 1 Clashes 11 Severe clashes 1

Final rank	7.822824542312068	Score	-22.3807
Inter norm	-0.854858	Intra norm	0.176655
Top1000	no	Excluded	yes
Contacts	19	H-bonds	7
Artifact reason	excluded; geometry warning; 13 clashes; 1 protein clash; high strain Δ 33.5
Residues	A:ALA10;A:ASP22;A:GLU31;A:GLY21;A:ILE61;A:ILE8;A:LEU23;A:NAP201;A:PHE32;A:PHE35;A:PRO26;A:PRO27;A:PRO62;A:SER60;A:THR57;A:TRP25;A:TYR122;A:VAL116;A:VAL9

Protein summary

200 residues

Protein target	T02	Atoms	3128
Residues	200	Chains	2
Residue summary	LYS:374; LEU:361; GLU:240; VAL:224; ARG:192; PHE:180; ILE:171; PRO:168; ASN:140; SER:132; TYR:126; GLN:119; ASP:108; MET:102; THR:98; GLY:91

Native ligand reference

★ reference

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

Name	5SD8	Contacts	21
Pose	Open native pose	H-bonds	5
IFP residues	A:ALA10; A:ASN65; A:ASP22; A:GLN36; A:GLU31; A:GLY117; A:GLY21; A:ILE61; A:ILE8; A:LEU23; A:LEU68; A:NAP201; A:PHE32; A:PHE35; A:PRO62; A:SER60; A:THR137; A:THR57; A:TYR122; A:VAL116; A:VAL9
Current overlap	16	Native recall	0.76
Jaccard	0.67	RMSD	-
H-bond strict	1	Strict recall	0.20
H-bond same residue+role	1	Role recall	0.20
H-bond same residue	1	Residue recall	0.20

Hydrogen bonds

Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

π–π interactions

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

Hydrophobic contacts

Clashes

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	Contacts	Native overlap	Native recall	HB role recall	RMSD	Excluded
2071	4.146993863723905	-0.726869	-17.6699	3	18	14	0.67	0.20	-	no	Open
1154	5.831207691736963	-0.657314	-10.7425	9	17	0	0.00	0.00	-	no	Open
658	7.030741241965613	-0.791369	-16.6012	4	20	0	0.00	0.00	-	no	Open
1153	7.491677553996237	-0.695516	-20.8755	4	14	0	0.00	0.00	-	no	Open
2070	7.822824542312068	-0.854858	-22.3807	7	19	16	0.76	0.20	-	yes	Current
657	10.36186575723464	-0.622288	-16.9641	1	18	0	0.00	0.00	-	yes	Open

Molecular metrics

FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.

✓ Metrics available

Scoring & efficiency

Docking score -22.381kcal/mol

Ligand efficiency (LE) -0.6782kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -6.729

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

Heavy atom count 33HA

Physicochemical properties

Molecular weight 453.5Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.86

Lipinski: ≤ 5

Rotatable bonds 7

Conformational strain (MMFF94s)

Strain energy (ΔE) 21.63kcal/mol

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

Docked FF energy 76.85kcal/mol

Minimised FF energy 55.22kcal/mol

SASA & burial (FreeSASA)

not yet run

SASA has not been computed yet for this pose. Queue a background recompute to populate FreeSASA burial metrics without blocking the page.

MK152