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 ↗

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

✓ Excellent LE (-0.498 kcal/mol/HA) ✓ Good fit quality (FQ -4.94) ✗ Very high strain energy (87.5 kcal/mol) ✗ Geometry warnings ℹ SASA not computed

Score

-16.428

kcal/mol

-0.498

kcal/mol/HA

Fit Quality

-4.94

FQ (Leeson)

HAC

heavy atoms

515

LogP

3.54

cLogP

Strain ΔE

87.5 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 87.5 kcal/mol

Interaction summary

Collapsible panels

H-bonds 2 Hydrophobic 19 π–π 6 Clashes 6 Severe clashes 1

Final rank	9.861134013194741	Score	-16.4283
Inter norm	-0.672092	Intra norm	0.174264
Top1000	no	Excluded	yes
Contacts	16	H-bonds	2
Artifact reason	excluded; geometry warning; 12 clashes; 1 protein clash; high strain Δ 92.0
Residues	A:ARG17;A:GLY225;A:HIS241;A:LEU188;A:LEU226;A:LEU229;A:LYS244;A:MET233;A:NDP302;A:PHE113;A:SER111;A:SER227;A:TYR191;A:TYR194;A:VAL230;A:VAL237

Protein summary

308 residues

Protein target	T04	Atoms	4210
Residues	308	Chains	3
Residue summary	LEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108

Native ligand reference

★ reference

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

Name	7PXX	Contacts	19
Pose	Open native pose	H-bonds	8
IFP residues	A:ARG17; A:ASP181; A:GLY225; A:HIS241; A:LEU188; A:LEU226; A:LEU229; A:LYS198; A:MET233; A:NDP302; A:PHE113; A:PRO115; A:SER111; A:SER112; A:SER227; A:TYR191; A:TYR194; A:VAL230; D:ARG287
Current overlap	14	Native recall	0.74
Jaccard	0.67	RMSD	-
H-bond strict	2	Strict recall	0.33
H-bond same residue+role	2	Role recall	0.40
H-bond same residue	2	Residue recall	0.40

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
621	11.843070215384966	-0.501684	-6.82749	7	15	14	0.74	0.40	-	no	Open
755	12.510265020795174	-0.800221	-21.0844	10	21	0	0.00	0.00	-	no	Open
756	12.517436311880019	-0.777335	-21.6609	8	21	0	0.00	0.00	-	no	Open
622	9.861134013194741	-0.672092	-16.4283	2	16	14	0.74	0.40	-	yes	Current
620	13.04205183813502	-0.46004	-7.50613	2	12	12	0.63	0.40	-	yes	Open
619	13.541734180477112	-0.546125	-13.0402	8	14	13	0.68	0.40	-	yes	Open
757	16.859934548743205	-0.640926	-17.5797	6	20	0	0.00	0.00	-	yes	Open
754	21.01681068023511	-0.585086	-13.9002	7	19	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 -16.428kcal/mol

Ligand efficiency (LE) -0.4978kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -4.939

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

Heavy atom count 33HA

Physicochemical properties

Molecular weight 514.9Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.54

Lipinski: ≤ 5

Rotatable bonds 8

Conformational strain (MMFF94s)

Strain energy (ΔE) 87.55kcal/mol

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

Docked FF energy 113.54kcal/mol

Minimised FF energy 25.99kcal/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.

NMT-TY0518