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
30.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.67, Jaccard 0.42
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.747 kcal/mol/HA)
✓ Good fit quality (FQ -7.59)
✓ Good H-bonds (5 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Very high strain energy (30.8 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Many internal clashes (21)
Score
-26.891
kcal/mol
LE
-0.747
kcal/mol/HA
Fit Quality
-7.59
FQ (Leeson)
HAC
36
heavy atoms
MW
480
Da
LogP
2.23
cLogP
Interaction summary
HB 5
HY 24
PI 0
CLASH 1
Interaction summary
HB 5
HY 24
PI 0
CLASH 1
| Final rank | 2.263 | Score | -26.891 |
|---|---|---|---|
| Inter norm | -0.674 | Intra norm | -0.073 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 5 |
| Artifact reason | geometry warning; 21 clashes; 4 protein contact clashes; high strain Δ 30.8 | ||
| Residues |
ALA209
ALA90
ARG74
ASN91
LEU73
LYS211
LYS89
LYS93
MET70
PRO187
PRO212
PRO213
TRP92
TYR210
VAL88
| ||
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 | 8 | Native recall | 0.67 |
| Jaccard | 0.42 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 448 | 2.1753586768424085 | -0.759862 | -27.2521 | 5 | 18 | 0 | 0.00 | - | - | no | Open |
| 327 | 2.196257409577572 | -1.12511 | -44.4786 | 6 | 25 | 0 | 0.00 | - | - | no | Open |
| 465 | 2.263257935292505 | -0.673764 | -26.8912 | 5 | 15 | 8 | 0.67 | - | - | no | Current |
| 365 | 2.78635018813914 | -0.932024 | -31.3948 | 7 | 21 | 0 | 0.00 | - | - | no | Open |
| 388 | 3.556867624173379 | -0.572201 | -20.9021 | 5 | 12 | 0 | 0.00 | - | - | no | Open |
| 358 | 4.004585156869844 | -0.808049 | -30.127 | 12 | 18 | 0 | 0.00 | - | - | no | Open |
| 391 | 5.477055042660596 | -0.684733 | -29.5647 | 7 | 20 | 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
-26.891kcal/mol
Ligand efficiency (LE)
-0.7470kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.592
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
480.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.23
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
30.76kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-29.08kcal/mol
Minimised FF energy
-59.85kcal/mol
SASA & burial
✓ computed
SASA (unbound)
735.5Ų
Total solvent-accessible surface area of free ligand
BSA total
502.2Ų
Buried surface area upon binding
BSA apolar
390.0Ų
Hydrophobic contacts buried
BSA polar
112.2Ų
Polar contacts buried
Fraction buried
68.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3193.2Ų
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
4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1471.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)