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
22.3 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.83, Jaccard 0.50
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.661 kcal/mol/HA)
✓ Good fit quality (FQ -6.62)
✓ Good H-bonds (4 bonds)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ High strain energy (22.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-22.479
kcal/mol
LE
-0.661
kcal/mol/HA
Fit Quality
-6.62
FQ (Leeson)
HAC
34
heavy atoms
MW
475
Da
LogP
3.63
cLogP
Interaction summary
HB 4
HY 24
PI 1
CLASH 2
Interaction summary
HB 4
HY 24
PI 1
CLASH 2
| Final rank | 3.721 | Score | -22.479 |
|---|---|---|---|
| Inter norm | -0.724 | Intra norm | 0.062 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 4 |
| Artifact reason | geometry warning; 14 clashes; 2 protein clashes; moderate strain Δ 22.0 | ||
| Residues |
ALA209
ALA77
ALA90
ARG74
GLU82
GLY214
GLY215
GLY85
LEU73
LYS211
LYS89
MET70
PHE83
PRO212
PRO213
TRP81
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 | 10 | Native recall | 0.83 |
| Jaccard | 0.50 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 95 | 1.1841529654796734 | -0.696503 | -23.591 | 1 | 18 | 0 | 0.00 | - | - | no | Open |
| 170 | 2.576240317442257 | -0.774875 | -25.0845 | 3 | 19 | 0 | 0.00 | - | - | no | Open |
| 131 | 2.6803510726405357 | -0.711682 | -23.8607 | 3 | 17 | 10 | 0.83 | - | - | no | Open |
| 144 | 2.9957812529215895 | -0.72733 | -25.9487 | 4 | 19 | 0 | 0.00 | - | - | no | Open |
| 140 | 3.1434613533924827 | -0.737044 | -24.0613 | 2 | 18 | 0 | 0.00 | - | - | no | Open |
| 109 | 3.414601892745689 | -0.892323 | -31.238 | 4 | 20 | 0 | 0.00 | - | - | no | Open |
| 72 | 3.7212335604547015 | -0.723532 | -22.4786 | 4 | 18 | 10 | 0.83 | - | - | no | Current |
| 79 | 3.810645461348144 | -0.888646 | -27.5234 | 3 | 16 | 0 | 0.00 | - | - | no | Open |
| 165 | 4.940385607351782 | -0.876029 | -29.5071 | 4 | 15 | 1 | 0.08 | - | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-22.479kcal/mol
Ligand efficiency (LE)
-0.6611kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.615
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
474.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.63
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.32kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
42.84kcal/mol
Minimised FF energy
20.52kcal/mol
SASA & burial
✓ computed
SASA (unbound)
790.1Ų
Total solvent-accessible surface area of free ligand
BSA total
582.0Ų
Buried surface area upon binding
BSA apolar
435.3Ų
Hydrophobic contacts buried
BSA polar
146.7Ų
Polar contacts buried
Fraction buried
73.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3222.4Ų
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
1465.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)