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 high
Native strong
SASA done
Strain ΔE
29.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.83, Jaccard 0.53, H-bond role recall 1.00
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.486 kcal/mol/HA)
✓ Good fit quality (FQ -4.94)
✓ Good H-bonds (4 bonds)
✓ Deep burial (79% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ High strain energy (29.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (17)
Score
-17.509
kcal/mol
LE
-0.486
kcal/mol/HA
Fit Quality
-4.94
FQ (Leeson)
HAC
36
heavy atoms
MW
484
Da
LogP
2.11
cLogP
Interaction summary
HB 4
HY 24
PI 2
CLASH 2
Interaction summary
HB 4
HY 24
PI 2
CLASH 2
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 | 4.055 | Score | -17.509 |
|---|---|---|---|
| Inter norm | -0.618 | Intra norm | 0.132 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 4 |
| Artifact reason | geometry warning; 17 clashes; 2 protein clashes; moderate strain Δ 29.2 | ||
| Residues |
ARG228
ARG287
ARG331
CYS375
FAD501
GLY197
GLY229
GLY286
GLY376
LEU332
LEU334
MET333
PHE198
PHE230
SER364
THR374
VAL362
| ||
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 | 10 | Native recall | 0.83 |
| Jaccard | 0.53 | RMSD | - |
| HB strict | 1 | Strict recall | 1.00 |
| HB same residue+role | 1 | HB role recall | 1.00 |
| HB same residue | 1 | HB residue recall | 1.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 1.3140367446725727 | -0.804232 | -26.1341 | 3 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 27 | 1.5349452071704826 | -0.772957 | -24.971 | 3 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 31 | 2.9321144294495363 | -0.942471 | -29.4576 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 13 | 3.8886696484394063 | -0.762846 | -21.8866 | 13 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 17 | 4.054842883664916 | -0.618121 | -17.5086 | 4 | 17 | 10 | 0.83 | 1.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-17.509kcal/mol
Ligand efficiency (LE)
-0.4864kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.943
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
484.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.11
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.17kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
176.26kcal/mol
Minimised FF energy
147.09kcal/mol
SASA & burial
✓ computed
SASA (unbound)
758.1Ų
Total solvent-accessible surface area of free ligand
BSA total
596.8Ų
Buried surface area upon binding
BSA apolar
460.3Ų
Hydrophobic contacts buried
BSA polar
136.5Ų
Polar contacts buried
Fraction buried
78.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6545.0Ų
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
2080.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)