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.

✓ Acceptable LE (-0.235 kcal/mol/HA) ✓ Good fit quality (FQ -2.66) ✓ Strong H-bond network (6 bonds) ✗ Very high strain energy (46.3 kcal/mol) ✗ Geometry warnings ℹ SASA not computed

Score

-13.649

kcal/mol

-0.235

kcal/mol/HA

Fit Quality

-2.66

FQ (Leeson)

HAC

heavy atoms

811

LogP

0.36

cLogP

Strain ΔE

46.3 kcal/mol

SASA buried

computing…

Overall: Promising but geometrically suspicious

Binding evidence: strong

Native-like contacts: strong

Ligand efficiency: acceptable

Geometry reliability: low

Reason: geometry warning, clashes, strain 46.3 kcal/mol

Interaction summary

Collapsible panels

H-bonds 6 Hydrophobic 24 π–π 1 Clashes 24 Severe clashes 6

Final rank	70.02141138885924	Score	-13.6495
Inter norm	-0.352638	Intra norm	0.112854
Top1000	no	Excluded	yes
Contacts	20	H-bonds	6
Artifact reason	excluded; geometry warning; 23 clashes; 6 protein clashes
Residues	A:ALA32;A:ARG48;A:ARG92;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:PRO93;A:TYR162;A:VAL156;A:VAL30;A:VAL31;A:VAL87

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

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	H-bonds	9
IFP residues	A:ALA32; A:ARG97; A:ASP52; A:ILE45; A:LEU94; A:LYS57; A:MET53; A:NDP301; A:PHE56; A:PHE91; A:PRO88; A:SER86; A:THR180; A:THR54; A:THR83; A:TYR162; A:VAL156; A:VAL30; A:VAL31; A:VAL87
Current overlap	16	Native recall	0.80
Jaccard	0.67	RMSD	-
H-bond strict	0	Strict recall	0.00
H-bond same residue+role	0	Role recall	0.00
H-bond same residue	0	Residue recall	0.00

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
9	13.325459258586285	-0.334152	-0.965184	3	18	16	0.80	0.20	-	no	Open
22	11.760943129336825	-0.299245	-17.339	2	17	14	0.70	0.20	-	yes	Open
17	12.761484724464736	-0.316773	-1.59097	3	18	14	0.70	0.40	-	yes	Open
23	59.98052726506786	-0.421552	-17.6506	5	19	12	0.60	0.00	-	yes	Open
29	60.31577280944552	-0.299852	7.25978	3	20	17	0.85	0.00	-	yes	Open
26	60.59663818971363	-0.360703	-12.2414	6	17	12	0.60	0.20	-	yes	Open
12	61.38609649517504	-0.371002	-20.1264	7	15	11	0.55	0.20	-	yes	Open
13	61.414446497231125	-0.426789	-10.6427	7	15	11	0.55	0.20	-	yes	Open
11	61.5324330228811	-0.278412	-11.1343	5	14	10	0.50	0.20	-	yes	Open
16	61.78925105950437	-0.317504	-3.7643	6	20	16	0.80	0.20	-	yes	Open
8	61.96984000917183	-0.32562	-14.188	4	17	12	0.60	0.00	-	yes	Open
10	62.14688715416227	-0.392714	-9.15959	3	20	18	0.90	0.20	-	yes	Open
14	62.35515867735744	-0.450017	-11.4909	4	21	18	0.90	0.00	-	yes	Open
6	62.879331909694066	-0.461952	-23.5639	7	19	16	0.80	0.20	-	yes	Open
28	62.88274725756217	-0.46073	-19.3201	5	23	18	0.90	0.20	-	yes	Open
25	63.27097061699387	-0.292962	-24.042	4	20	17	0.85	0.00	-	yes	Open
15	64.47132710717256	-0.447251	-8.82597	5	22	14	0.70	0.20	-	yes	Open
4	64.71227221490146	-0.369835	0.395208	7	16	10	0.50	0.20	-	yes	Open
18	64.79573960870546	-0.42929	-26.9465	9	21	19	0.95	0.20	-	yes	Open
31	65.19941468193234	-0.35032	-3.63977	8	16	11	0.55	0.20	-	yes	Open
30	65.26401004694516	-0.399606	-5.96414	6	18	15	0.75	0.20	-	yes	Open
3	65.50198510870831	-0.404121	2.84679	8	21	17	0.85	0.20	-	yes	Open
24	65.62007994550007	-0.36325	-1.63916	5	18	16	0.80	0.00	-	yes	Open
20	65.80881951412888	-0.313655	-0.785003	3	22	18	0.90	0.00	-	yes	Open
32	65.96630355466264	-0.394604	0.962119	4	19	17	0.85	0.20	-	yes	Open
27	66.40733352043566	-0.403614	-6.59538	5	21	18	0.90	0.00	-	yes	Open
33	66.76375879464149	-0.416966	-9.15118	4	18	16	0.80	0.20	-	yes	Open
5	67.4612805516657	-0.498199	-10.9711	10	21	18	0.90	0.20	-	yes	Open
34	68.79246416550914	-0.509692	-11.9263	7	22	18	0.90	0.20	-	yes	Open
7	69.33706874767066	-0.368499	-1.26329	4	24	19	0.95	0.00	-	yes	Open
21	70.02141138885924	-0.352638	-13.6495	6	20	16	0.80	0.00	-	yes	Current
19	75.49517389022188	-0.349628	0.291842	8	25	17	0.85	0.20	-	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 -13.649kcal/mol

Ligand efficiency (LE) -0.2353kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -2.663

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

Heavy atom count 58HA

Physicochemical properties

Molecular weight 810.8Da

Lipinski: ≤ 500 Da

LogP (cLogP) 0.36

Lipinski: ≤ 5

Rotatable bonds 13

Conformational strain (MMFF94s)

Strain energy (ΔE) 46.32kcal/mol

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

Docked FF energy 133.57kcal/mol

Minimised FF energy 87.25kcal/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.

OHD_Leishmania_45