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
18.3 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.77, Jaccard 0.62
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 (-0.625 kcal/mol/HA)
✓ Good fit quality (FQ -6.31)
✓ Good H-bonds (4 bonds)
✓ Deep burial (66% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Moderate strain (18.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (17)
Score
-21.886
kcal/mol
LE
-0.625
kcal/mol/HA
Fit Quality
-6.31
FQ (Leeson)
HAC
35
heavy atoms
MW
476
Da
LogP
0.67
cLogP
Interaction summary
HB 4
HY 24
PI 3
CLASH 3
Interaction summary
HB 4
HY 24
PI 3
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 | 4.099 | Score | -21.886 |
|---|---|---|---|
| Inter norm | -0.589 | Intra norm | -0.037 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 4 |
| Artifact reason | geometry warning; 17 clashes; 2 protein clashes | ||
| Residues |
CYS52
GLU18
ILE106
ILE339
LEU17
MET113
SER109
SER14
THR335
TRP21
TYR110
VAL53
VAL58
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6RB5 | Contacts | 13 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ASP116
GLU18
GLY112
ILE106
LEU17
MET113
SER109
THR117
THR335
TRP21
TYR110
VAL53
VAL58
| ||
| Current overlap | 10 | Native recall | 0.77 |
| Jaccard | 0.62 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
Protein summary
493 residues
| Protein target | T18 | Atoms | 7550 |
|---|---|---|---|
| Residues | 493 | Chains | 1 |
| Residue summary | VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:276; MET:221 | ||
Receptor context
1 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 1
Excluded HETATM 0
Kept cofactors / ions
A: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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 6 | 1.8442758454334953 | -1.1484 | -34.8941 | 9 | 20 | 0 | 0.00 | - | - | no | Open |
| 6 | 3.2140927104793953 | -0.844147 | -29.4225 | 7 | 17 | 0 | 0.00 | - | - | no | Open |
| 4 | 4.098665573912961 | -0.588615 | -21.8858 | 4 | 13 | 10 | 0.77 | - | - | no | Current |
| 9 | 4.256826637465723 | -0.886547 | -26.2953 | 6 | 17 | 0 | 0.00 | - | - | no | Open |
| 4 | 5.177059448137301 | -0.83407 | -25.8189 | 8 | 22 | 0 | 0.00 | - | - | no | Open |
| 7 | 5.451739153191316 | -0.558397 | -15.3983 | 6 | 15 | 0 | 0.00 | - | - | no | Open |
| 5 | 5.606622137177629 | -0.887957 | -28.3698 | 11 | 19 | 0 | 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
-21.886kcal/mol
Ligand efficiency (LE)
-0.6253kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.307
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
475.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.67
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
8.65kcal/mol
Minimised FF energy
-9.62kcal/mol
SASA & burial
✓ computed
SASA (unbound)
768.9Ų
Total solvent-accessible surface area of free ligand
BSA total
503.6Ų
Buried surface area upon binding
BSA apolar
400.4Ų
Hydrophobic contacts buried
BSA polar
103.2Ų
Polar contacts buried
Fraction buried
65.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3233.1Ų
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
4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1463.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)