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
Reject
SASA cached
Likely artefact or unreliable pose
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
23.1 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.58, Jaccard 0.33
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.861 kcal/mol/HA)
✓ Good fit quality (FQ -8.13)
✓ Good H-bonds (5 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ High strain energy (23.1 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (6)
✗ Many internal clashes (11)
Score
-24.115
kcal/mol
LE
-0.861
kcal/mol/HA
Fit Quality
-8.13
FQ (Leeson)
HAC
28
heavy atoms
MW
384
Da
LogP
4.16
cLogP
Interaction summary
HB 5
HY 24
PI 0
CLASH 1
Interaction summary
HB 5
HY 24
PI 0
CLASH 1
| Final rank | 1.315 | Score | -24.115 |
|---|---|---|---|
| Inter norm | -0.957 | Intra norm | 0.095 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 5 |
| Artifact reason | geometry warning; 11 clashes; 6 protein contact clashes; moderate strain Δ 23.1 | ||
| Residues |
ALA209
ALA90
ASN91
GLY214
GLY215
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 | 7 | Native recall | 0.58 |
| Jaccard | 0.33 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 483 | 1.0853100332132994 | -1.15783 | -26.9741 | 5 | 17 | 0 | 0.00 | - | - | no | Open |
| 533 | 1.3030885157662433 | -0.984884 | -24.6447 | 3 | 20 | 0 | 0.00 | - | - | no | Open |
| 539 | 1.3153312150478562 | -0.956507 | -24.115 | 5 | 16 | 7 | 0.58 | - | - | no | Current |
| 468 | 1.4983376621522455 | -1.21454 | -29.8472 | 7 | 21 | 0 | 0.00 | - | - | no | Open |
| 487 | 1.829623080713065 | -0.906153 | -22.6394 | 2 | 19 | 0 | 0.00 | - | - | no | Open |
| 522 | 1.886285713477351 | -0.843689 | -17.4728 | 3 | 15 | 0 | 0.00 | - | - | no | Open |
| 527 | 2.9175440723674373 | -1.05324 | -24.3241 | 4 | 20 | 0 | 0.00 | - | - | no | Open |
| 456 | 3.0916468248736995 | -1.03596 | -27.5073 | 4 | 16 | 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
-24.115kcal/mol
Ligand efficiency (LE)
-0.8612kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.130
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
384.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.16
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.06kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
103.21kcal/mol
Minimised FF energy
80.15kcal/mol
SASA & burial
✓ computed
SASA (unbound)
648.3Ų
Total solvent-accessible surface area of free ligand
BSA total
515.1Ų
Buried surface area upon binding
BSA apolar
410.0Ų
Hydrophobic contacts buried
BSA polar
105.1Ų
Polar contacts buried
Fraction buried
79.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3127.6Ų
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
1470.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)