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 (-0.671 kcal/mol/HA) ✓ Good fit quality (FQ -6.33) ✓ Strong H-bond network (6 bonds) ✗ Very high strain energy (71.9 kcal/mol) ✗ Geometry warnings ℹ SASA not computed

Score

-18.779

kcal/mol

-0.671

kcal/mol/HA

Fit Quality

-6.33

FQ (Leeson)

HAC

heavy atoms

395

LogP

0.29

cLogP

Strain ΔE

71.9 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 71.9 kcal/mol

Interaction summary

Collapsible panels

H-bonds 6 Hydrophobic 11 π–π 3 Clashes 13 Severe clashes 4 ⚠ Hydrophobic exposure 37%

⚠️Partial hydrophobic solvent exposure

38% of hydrophobic surface appears solvent-exposed (6/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

Non-polar atoms 16 Buried (contacted) 10 Exposed 6 LogP 0.29 H-bonds 6

Exposed fragments: cyclohexyl (6/6 atoms exposed)

Final rank	60.73871815021003	Score	-18.7793
Inter norm	-0.456546	Intra norm	-0.214142
Top1000	no	Excluded	yes
Contacts	14	H-bonds	6
Artifact reason	excluded; geometry warning; 9 clashes; 4 protein clashes
Residues	A:GLY225;A:HIS241;A:LEU188;A:LEU226;A:LEU229;A:LYS198;A:MET233;A:NDP302;A:PHE113;A:SER111;A:SER227;A:TYR191;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	14	Native recall	0.74
Jaccard	0.74	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
527	5.891409740024111	-0.515279	-16.7059	4	9	7	0.37	0.20	-	no	Open
528	6.359922493989476	-0.36283	-14.6109	3	13	8	0.42	0.00	-	no	Open
1235	7.032734784611533	-0.628431	-18.4734	8	14	0	0.00	0.00	-	no	Open
517	8.364022583352615	-0.41136	-8.84547	0	11	11	0.58	0.00	-	no	Open
1225	8.441691451085614	-0.789636	-20.1777	9	16	0	0.00	0.00	-	no	Open
1231	9.082657087162138	-0.666685	-19.8599	11	15	0	0.00	0.00	-	yes	Open
521	53.702263615319715	-0.390491	-16.0943	4	10	9	0.47	0.00	-	yes	Open
529	54.40281540057171	-0.540214	-19.3742	3	13	12	0.63	0.20	-	yes	Open
1224	55.183818795300816	-0.739943	-20.637	15	14	0	0.00	0.00	-	yes	Open
515	55.41281723541009	-0.630571	-19.9357	2	11	11	0.58	0.20	-	yes	Open
1230	55.49832959546925	-0.731818	-23.2743	12	15	0	0.00	0.00	-	yes	Open
1232	55.83797235404214	-0.685282	-19.7783	11	17	0	0.00	0.00	-	yes	Open
525	56.42092736058264	-0.543513	-19.2566	4	15	13	0.68	0.20	-	yes	Open
1234	56.67463624307634	-0.752278	-24.7967	13	18	0	0.00	0.00	-	yes	Open
518	56.92548383250641	-0.756829	-23.5876	4	14	14	0.74	0.20	-	yes	Open
1233	57.23049033369077	-0.724255	-14.9267	16	17	0	0.00	0.00	-	yes	Open
524	57.72942329726388	-0.405152	-12.6321	1	11	11	0.58	0.20	-	yes	Open
519	58.431984108837334	-0.854976	-22.2617	5	13	12	0.63	0.20	-	yes	Open
1228	58.575904788600795	-0.676444	-24.3564	14	14	0	0.00	0.00	-	yes	Open
514	58.71522466402821	-0.567157	-15.3722	7	12	12	0.63	0.40	-	yes	Open
1229	58.73567817729465	-0.684721	-18.1648	13	15	0	0.00	0.00	-	yes	Open
1227	59.42598692321233	-0.78197	-22.6204	16	15	0	0.00	0.00	-	yes	Open
1222	59.744342673684294	-0.678639	-23.7778	16	15	0	0.00	0.00	-	yes	Open
1223	60.12723507982641	-0.732825	-19.5077	16	15	0	0.00	0.00	-	yes	Open
1236	60.481300868577115	-0.797444	-20.7781	13	15	0	0.00	0.00	-	yes	Open
516	60.546706941921016	-0.56026	-12.719	4	13	13	0.68	0.20	-	yes	Open
526	60.73871815021003	-0.456546	-18.7793	6	14	14	0.74	0.40	-	yes	Current
1226	61.77427913488611	-0.635959	-20.9696	14	13	0	0.00	0.00	-	yes	Open
1237	62.22107286502941	-0.738013	-24.4913	15	16	0	0.00	0.00	-	yes	Open
522	62.691023796287	-0.662376	-21.0398	7	14	13	0.68	0.40	-	yes	Open
523	62.85254899909571	-0.579875	-13.9285	6	13	12	0.63	0.40	-	yes	Open
520	69.91948374176653	-0.448124	-16.1368	10	12	11	0.58	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 -18.779kcal/mol

Ligand efficiency (LE) -0.6707kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -6.332

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

Heavy atom count 28HA

Physicochemical properties

Molecular weight 395.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 0.29

Lipinski: ≤ 5

Rotatable bonds 6

Conformational strain (MMFF94s)

Strain energy (ΔE) 71.90kcal/mol

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

Docked FF energy 91.42kcal/mol

Minimised FF energy 19.51kcal/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.

MK131