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.

✓ Good H-bonds (4 bonds) ✗ Very high strain energy (55.5 kcal/mol) ✗ Low LE (-0.108 kcal/mol/HA) ✗ Geometry warnings ✗ Protein contact clashes ℹ SASA not computed

Score

-6.244

kcal/mol

-0.108

kcal/mol/HA

Fit Quality

-1.22

FQ (Leeson)

HAC

heavy atoms

811

LogP

0.36

cLogP

Strain ΔE

55.5 kcal/mol

SASA buried

computing…

Overall: Likely artefact or unreliable pose

Binding evidence: weak

Native-like contacts: strong

Ligand efficiency: weak

Geometry reliability: low

Reason: geometry warning, clashes, protein contact clashes, strain 55.5 kcal/mol

Interaction summary

Collapsible panels

H-bonds 4 Hydrophobic 24 π–π 1 Clashes 13 Severe clashes 0 ⚠ Hydrophobic exposure 36%

⚠️Partial hydrophobic solvent exposure

37% of hydrophobic surface appears solvent-exposed (15/41 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

Non-polar atoms 41 Buried (contacted) 26 Exposed 15 LogP 0.36 H-bonds 4

Exposed fragments: phenyl (3/6 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (7 atoms exposed)

Final rank	59.319339868734374	Score	-6.24402
Inter norm	-0.308009	Intra norm	0.200353
Top1000	no	Excluded	no
Contacts	21	H-bonds	4
Artifact reason	geometry warning; 29 clashes; 13 protein contact clashes
Residues	A:ALA10;A:ARG29;A:ASN65;A:ASP22;A:GLU31;A:ILE61;A:ILE8;A:LEU23;A:LEU28;A:LEU68;A:LYS64;A:NAP201;A:PHE32;A:PHE35;A:PRO27;A:PRO62;A:SER60;A:THR137;A:TRP25;A:TYR34;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	15	Native recall	0.71
Jaccard	0.56	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
31	8.425533844475723	-0.380397	-22.016	3	21	17	0.81	0.60	-	no	Open
23	11.257750680103094	-0.327593	-18.2217	2	18	16	0.76	0.20	-	no	Open
37	11.640071870906773	-0.314286	-5.76513	3	20	17	0.81	0.60	-	no	Open
21	58.36702677466506	-0.347385	-11.1757	5	21	17	0.81	0.60	-	no	Open
18	59.319339868734374	-0.308009	-6.24402	4	21	15	0.71	0.20	-	no	Current
17	60.52840475422638	-0.397137	2.08317	6	21	18	0.86	0.60	-	no	Open
39	58.783221165508124	-0.305712	-0.65496	6	22	17	0.81	0.40	-	yes	Open
36	58.94303154659009	-0.375125	10.2926	7	25	19	0.90	0.60	-	yes	Open
24	59.30261172975436	-0.345465	-6.93005	5	19	16	0.76	1.00	-	yes	Open
8	59.53639892928765	-0.325615	-1.60612	4	22	17	0.81	0.80	-	yes	Open
27	59.68235749441328	-0.349441	4.88142	3	21	15	0.71	0.40	-	yes	Open
38	59.69034817106349	-0.321812	-6.40499	5	20	16	0.76	0.60	-	yes	Open
13	60.26978279199498	-0.420679	-8.48738	6	21	17	0.81	0.20	-	yes	Open
30	60.804582347322224	-0.340259	-7.74974	9	23	18	0.86	1.00	-	yes	Open
11	60.80987913550018	-0.298417	-4.32338	8	21	16	0.76	1.00	-	yes	Open
33	60.89955278719508	-0.299461	-5.40967	3	23	17	0.81	0.40	-	yes	Open
29	61.433157818758566	-0.242312	-9.70003	4	18	14	0.67	0.40	-	yes	Open
26	62.10697060732191	-0.278073	2.18471	6	21	18	0.86	1.00	-	yes	Open
15	62.204729182606556	-0.339563	-9.83817	3	17	14	0.67	0.40	-	yes	Open
10	62.46793478425333	-0.266928	2.99796	9	18	16	0.76	0.80	-	yes	Open
20	62.651341827951036	-0.412405	-9.04773	11	22	16	0.76	0.80	-	yes	Open
35	62.994536147852955	-0.319308	-22.1184	3	24	18	0.86	0.60	-	yes	Open
9	63.240041191810306	-0.376613	3.54285	5	21	16	0.76	0.80	-	yes	Open
19	63.687208589168854	-0.378589	-1.19491	8	20	17	0.81	0.80	-	yes	Open
12	63.78999615320346	-0.313028	-18.1398	8	22	17	0.81	0.40	-	yes	Open
25	63.89545396310958	-0.307773	-21.7118	11	24	18	0.86	1.00	-	yes	Open
28	63.94296760289912	-0.274732	-13.9322	10	23	18	0.86	0.80	-	yes	Open
32	64.11808184675132	-0.330215	9.30956	6	23	17	0.81	0.20	-	yes	Open
34	64.81628222449211	-0.347041	8.46752	6	23	18	0.86	0.80	-	yes	Open
16	65.5840383183634	-0.354847	0.251227	8	20	16	0.76	0.60	-	yes	Open
14	67.8355041402951	-0.32161	-17.0565	14	23	16	0.76	0.80	-	yes	Open
22	71.79890337980143	-0.300888	7.94605	9	24	18	0.86	0.80	-	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 -6.244kcal/mol

Ligand efficiency (LE) -0.1077kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -1.218

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) 55.54kcal/mol

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

Docked FF energy 169.04kcal/mol

Minimised FF energy 113.50kcal/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