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 (-0.741 kcal/mol/HA) ✓ Good fit quality (FQ -6.43) ✓ Good H-bonds (5 bonds) ✗ Very high strain energy (71.5 kcal/mol) ✗ Geometry warnings ℹ SASA not computed

Score

-16.303

kcal/mol

-0.741

kcal/mol/HA

Fit Quality

-6.43

FQ (Leeson)

HAC

heavy atoms

313

LogP

-1.87

cLogP

Strain ΔE

71.5 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 71.5 kcal/mol

Interaction summary

Collapsible panels

H-bonds 5 Hydrophobic 12 π–π 2 Clashes 11 Severe clashes 2

Final rank	56.918829860887875	Score	-16.3027
Inter norm	-0.701402	Intra norm	-0.0396321
Top1000	no	Excluded	yes
Contacts	12	H-bonds	5
Artifact reason	excluded; geometry warning; 5 clashes; 2 protein clashes
Residues	A:ARG17;A:ASP181;A:HIS241;A:LEU188;A:LEU226;A:LEU229;A:MET233;A:NDP302;A:PHE113;A:SER111;A:TYR194;D:ARG287

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	12	Native recall	0.63
Jaccard	0.63	RMSD	-
H-bond strict	3	Strict recall	0.50
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
507	5.686144961900755	-0.910511	-24.8553	6	13	13	0.68	0.60	-	no	Open
510	6.287494735108774	-0.971726	-22.4279	5	13	13	0.68	0.60	-	no	Open
500	7.073341000747275	-0.871723	-18.4758	5	12	12	0.63	0.60	-	no	Open
513	53.82100798363986	-0.80551	-18.332	5	15	14	0.74	0.40	-	no	Open
503	54.694527863045295	-0.773925	-18.4334	7	12	12	0.63	0.40	-	no	Open
506	53.189690690808916	-0.766778	-19.5941	7	12	12	0.63	0.60	-	yes	Open
498	54.43971156113435	-0.576248	-14.8335	2	13	13	0.68	0.40	-	yes	Open
499	54.73628220238353	-0.921331	-21.6682	7	14	14	0.74	0.60	-	yes	Open
508	54.82562058462894	-0.772498	-18.726	8	13	13	0.68	0.60	-	yes	Open
505	55.72887761220177	-1.00211	-20.3759	9	11	11	0.58	0.40	-	yes	Open
504	56.05524474786222	-0.560875	-14.5935	9	12	12	0.63	0.60	-	yes	Open
509	56.66612662943195	-1.0677	-22.1082	7	12	12	0.63	0.20	-	yes	Open
511	56.918829860887875	-0.701402	-16.3027	5	12	12	0.63	0.40	-	yes	Current
501	57.13425654713693	-0.673914	-16.7727	7	14	14	0.74	0.60	-	yes	Open
512	57.642587123449374	-0.705355	-17.7409	10	13	13	0.68	0.80	-	yes	Open
502	60.944114425953174	-0.689382	-12.6155	6	14	14	0.74	0.60	-	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 -16.303kcal/mol

Ligand efficiency (LE) -0.7410kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -6.434

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

Heavy atom count 22HA

Physicochemical properties

Molecular weight 313.2Da

Lipinski: ≤ 500 Da

LogP (cLogP) -1.87

Lipinski: ≤ 5

Rotatable bonds 4

Conformational strain (MMFF94s)

Strain energy (ΔE) 71.50kcal/mol

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

Docked FF energy 96.51kcal/mol

Minimised FF energy 25.01kcal/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.

MK129