Docking pose detail

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 ↗

Weak Marginal quality. Consider only alongside better-scoring alternatives.

✓ Excellent LE (-1.255 kcal/mol/HA) ✓ Good fit quality (FQ -10.89) ✓ Strong H-bond network (7 bonds) ✗ High strain energy (19.6 kcal/mol) ✗ Geometry warnings ✗ Protein contact clashes ℹ SASA not computed

Score

-27.606

kcal/mol

-1.255

kcal/mol/HA

Fit Quality

-10.89

FQ (Leeson)

HAC

heavy atoms

341

LogP

1.26

cLogP

Strain ΔE

19.6 kcal/mol

SASA buried

computing…

Interaction summary

Collapsible panels

H-bonds 7 Hydrophobic 24 π–π 2 Clashes 12 Severe clashes 0

Final rank	4.688193311484323	Score	-27.6063
Inter norm	-1.23878	Intra norm	-0.0160541
Top1000	no	Excluded	no
Contacts	15	H-bonds	7
Artifact reason	geometry warning; 6 clashes; 12 protein contact clashes; high strain Δ 25.1
Residues	A:ALA10;A:ARG29;A:GLU31;A:GLY117;A:ILE8;A:LEU23;A:LEU28;A:NAP201;A:PHE32;A:PHE35;A:PRO27;A:TRP25;A:TYR122;A:VAL116;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	11	Native recall	0.52
Jaccard	0.44	RMSD	-
H-bond strict	3	Strict recall	0.60
H-bond same residue+role	4	Role recall	0.80
H-bond same residue	4	Residue recall	0.80

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
2861	3.6164297562044743	-1.32008	-28.8892	9	16	0	0.00	0.00	-	no	Open
2863	3.969540372062586	-1.09904	-24.9808	7	16	0	0.00	0.00	-	no	Open
2134	4.688193311484323	-1.23878	-27.6063	7	15	11	0.52	0.80	-	no	Current
2227	4.802075810609685	-1.30938	-28.0234	11	14	0	0.00	0.00	-	no	Open
2864	5.37486062420216	-1.10854	-25.2361	8	16	0	0.00	0.00	-	yes	Open
2225	6.265002448680948	-1.27167	-28.6738	10	14	0	0.00	0.00	-	yes	Open
2862	6.514321868725696	-1.06736	-23.0307	7	16	0	0.00	0.00	-	yes	Open
2865	6.732307314856408	-1.07055	-23.9724	9	16	0	0.00	0.00	-	yes	Open
2226	12.12563218092324	-1.09615	-24.0266	9	9	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 -27.606kcal/mol

Ligand efficiency (LE) -1.2548kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -10.894

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

Heavy atom count 22HA

Physicochemical properties

Molecular weight 341.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 1.26

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 19.61kcal/mol

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

Docked FF energy -26.70kcal/mol

Minimised FF energy -46.31kcal/mol

SASA & burial (FreeSASA)

not yet run

SASA has not been computed yet for this pose. It will be calculated automatically the next time this pose is loaded if a receptor PDB path is stored.

NMT-TY0608