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
27.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.58, Jaccard 0.32
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.902 kcal/mol/HA)
✓ Good fit quality (FQ -8.70)
✓ Good H-bonds (5 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ High strain energy (27.9 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (5)
✗ Internal clashes (9)
Score
-27.062
kcal/mol
LE
-0.902
kcal/mol/HA
Fit Quality
-8.70
FQ (Leeson)
HAC
30
heavy atoms
MW
458
Da
LogP
4.80
cLogP
Interaction summary
HB 5
HY 24
PI 1
CLASH 1
Interaction summary
HB 5
HY 24
PI 1
CLASH 1
| Final rank | 1.124 | Score | -27.062 |
|---|---|---|---|
| Inter norm | -0.831 | Intra norm | -0.071 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 5 |
| Artifact reason | geometry warning; 9 clashes; 5 protein contact clashes; moderate strain Δ 27.9 | ||
| Residues |
ALA209
ALA67
ALA90
ASN91
GLY66
LEU73
LYS211
LYS89
LYS93
MET70
PRO187
PRO212
PRO213
TRP92
TYR210
TYR69
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 | 7 | Native recall | 0.58 |
| Jaccard | 0.32 | 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
Native π–π recall is disabled because no explicit native π–π reference was stored.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 638 | 0.34325018158882725 | -0.807998 | -21.4581 | 1 | 12 | 0 | 0.00 | - | - | no | Open |
| 623 | 0.39759002964385937 | -0.907597 | -28.7047 | 4 | 18 | 0 | 0.00 | - | - | no | Open |
| 626 | 1.1227923024226714 | -1.1074 | -32.2501 | 5 | 18 | 0 | 0.00 | - | - | no | Open |
| 626 | 1.1240171034297752 | -0.831029 | -27.0616 | 5 | 17 | 7 | 0.58 | - | - | no | Current |
| 630 | 1.7563715265578972 | -0.846368 | -25.076 | 4 | 14 | 0 | 0.00 | - | - | no | Open |
| 646 | 2.8590489487856874 | -0.784314 | -23.0842 | 6 | 16 | 0 | 0.00 | - | - | no | Open |
| 639 | 3.474974056717497 | -0.915663 | -28.6397 | 5 | 9 | 0 | 0.00 | - | - | no | Open |
| 649 | 3.8018158212879913 | -0.815353 | -24.1731 | 5 | 14 | 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
-27.062kcal/mol
Ligand efficiency (LE)
-0.9021kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.701
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
457.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.80
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
35.89kcal/mol
Minimised FF energy
7.94kcal/mol
SASA & burial
✓ computed
SASA (unbound)
711.9Ų
Total solvent-accessible surface area of free ligand
BSA total
569.0Ų
Buried surface area upon binding
BSA apolar
397.6Ų
Hydrophobic contacts buried
BSA polar
171.5Ų
Polar contacts buried
Fraction buried
79.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3138.2Ų
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
1441.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)