Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
21.3 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.58, Jaccard 0.33, H-bond role recall 0.00
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.769 kcal/mol/HA)
✓ Good fit quality (FQ -7.42)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (79% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ High strain energy (21.3 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-23.084
kcal/mol
LE
-0.769
kcal/mol/HA
Fit Quality
-7.42
FQ (Leeson)
HAC
30
heavy atoms
MW
458
Da
LogP
4.39
cLogP
Interaction summary
HB 6
HY 18
PI 2
CLASH 3
Interaction summary
HB 6
HY 18
PI 2
CLASH 3
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
| Final rank | 2.859 | Score | -23.084 |
|---|---|---|---|
| Inter norm | -0.784 | Intra norm | 0.015 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 6 |
| Artifact reason | geometry warning; 6 clashes; 2 protein clashes | ||
| Residues |
ARG228
GLY196
GLY197
GLY229
GLY376
ILE378
LEU227
LEU332
LEU334
LEU377
PHE198
PHE230
SER364
TYR221
VAL362
VAL381
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 5S9T | Contacts | 12 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA365
ARG228
ARG331
GLY229
LEU332
LEU334
MET333
PHE198
PHE230
SER364
THR374
VAL366
| ||
| Current overlap | 7 | Native recall | 0.58 |
| Jaccard | 0.33 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
Protein summary
1033 residues
| Protein target | T17 | Atoms | 15160 |
|---|---|---|---|
| Residues | 1033 | Chains | 2 |
| Residue summary | VAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408 | ||
Receptor context
2 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 2
Excluded HETATM 0
Kept cofactors / ions
A:FAD501
B:FAD501
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 638 | 0.34325018158882725 | -0.807998 | -21.4581 | 1 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 623 | 0.39759002964385937 | -0.907597 | -28.7047 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 626 | 1.1227923024226714 | -1.1074 | -32.2501 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 626 | 1.1240171034297752 | -0.831029 | -27.0616 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 630 | 1.7563715265578972 | -0.846368 | -25.076 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 646 | 2.8590489487856874 | -0.784314 | -23.0842 | 6 | 16 | 7 | 0.58 | 0.00 | - | no | Current |
| 639 | 3.474974056717497 | -0.915663 | -28.6397 | 5 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 649 | 3.8018158212879913 | -0.815353 | -24.1731 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.084kcal/mol
Ligand efficiency (LE)
-0.7695kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.423
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
457.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.39
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.33kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-20.51kcal/mol
Minimised FF energy
-41.84kcal/mol
SASA & burial
✓ computed
SASA (unbound)
715.2Ų
Total solvent-accessible surface area of free ligand
BSA total
564.2Ų
Buried surface area upon binding
BSA apolar
395.3Ų
Hydrophobic contacts buried
BSA polar
169.0Ų
Polar contacts buried
Fraction buried
78.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6501.2Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA
8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
2075.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)