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 mixed
SASA done
Strain ΔE
18.9 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.50, Jaccard 0.29
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.709 kcal/mol/HA)
✓ Good fit quality (FQ -7.03)
✓ Good H-bonds (4 bonds)
✓ Deep burial (71% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Moderate strain (18.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-23.394
kcal/mol
LE
-0.709
kcal/mol/HA
Fit Quality
-7.03
FQ (Leeson)
HAC
33
heavy atoms
MW
489
Da
LogP
1.48
cLogP
Interaction summary
HB 4
HY 24
PI 0
CLASH 4
Interaction summary
HB 4
HY 24
PI 0
CLASH 4
| Final rank | 3.255 | Score | -23.394 |
|---|---|---|---|
| Inter norm | -0.735 | Intra norm | 0.026 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 4 |
| Artifact reason | geometry warning; 13 clashes; 1 protein clash | ||
| Residues |
ALA90
ARG74
ASN245
ASN91
GLY214
GLY215
GLY246
LYS211
LYS89
MET70
PRO187
PRO212
PRO213
TRP92
TYR210
| ||
Protein summary
493 residues
| Protein target | T16 | Atoms | 7551 |
|---|---|---|---|
| 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
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6RB5 | Contacts | 12 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA90
ARG74
GLY85
LEU73
LYS89
MET70
PHE83
PRO212
PRO213
SER86
SER87
VAL88
| ||
| Current overlap | 6 | Native recall | 0.50 |
| Jaccard | 0.29 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 104 | 1.1306304036728814 | -0.963491 | -33.1349 | 4 | 15 | 0 | 0.00 | - | - | no | Open |
| 108 | 1.9379363583230258 | -0.690505 | -17.3678 | 1 | 17 | 0 | 0.00 | - | - | no | Open |
| 96 | 2.046857713842369 | -0.866852 | -26.8935 | 3 | 14 | 0 | 0.00 | - | - | no | Open |
| 127 | 2.499006018861275 | -1.07855 | -33.0007 | 4 | 17 | 0 | 0.00 | - | - | no | Open |
| 109 | 2.626930637263631 | -0.627817 | -21.5516 | 5 | 12 | 0 | 0.00 | - | - | no | Open |
| 104 | 2.957960795902455 | -0.791234 | -23.8674 | 4 | 14 | 0 | 0.00 | - | - | no | Open |
| 88 | 3.2552004813490383 | -0.735107 | -23.3941 | 4 | 15 | 6 | 0.50 | - | - | no | Current |
| 80 | 3.2810230026078018 | -0.911782 | -29.5641 | 8 | 22 | 0 | 0.00 | - | - | no | Open |
| 138 | 4.10887258102073 | -0.973846 | -29.3347 | 6 | 16 | 0 | 0.00 | - | - | no | Open |
| 135 | 4.411349043465034 | -0.667356 | -15.746 | 7 | 13 | 0 | 0.00 | - | - | no | Open |
| 74 | 4.525919839894115 | -0.848339 | -24.1956 | 11 | 18 | 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
-23.394kcal/mol
Ligand efficiency (LE)
-0.7089kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.034
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
489.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.48
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.91kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
140.39kcal/mol
Minimised FF energy
121.48kcal/mol
SASA & burial
✓ computed
SASA (unbound)
763.9Ų
Total solvent-accessible surface area of free ligand
BSA total
544.6Ų
Buried surface area upon binding
BSA apolar
432.1Ų
Hydrophobic contacts buried
BSA polar
112.5Ų
Polar contacts buried
Fraction buried
71.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3209.1Ų
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
1491.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)