Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject
SASA cached
Likely artefact or unreliable pose
Binding strong
Geometry medium
Native mixed
SASA done
Strain ΔE
39.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.50, Jaccard 0.29
Reason: no major geometry red flags detected
1 protein-contact clashes
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Daphnia EC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Algae IC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG High
Ames Clear
DILI Risk
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.695 kcal/mol/HA)
✓ Good fit quality (FQ -6.89)
✓ Good H-bonds (4 bonds)
✓ Deep burial (66% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Very high strain energy (39.4 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (5)
✗ Many internal clashes (17)
Score
-22.931
kcal/mol
LE
-0.695
kcal/mol/HA
Fit Quality
-6.89
FQ (Leeson)
HAC
33
heavy atoms
MW
548
Da
LogP
4.56
cLogP
Final rank
1.9929
rank score
Inter norm
-0.742
normalised
Contacts
15
H-bonds 4
Interaction summary
HBD 1
HBA 3
HY 8
PI 0
CLASH 1
Interaction summary
HBD 1
HBA 3
HY 8
PI 0
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| 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 | - |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 593 | 0.912154842006513 | -0.775127 | -24.8327 | 2 | 17 | 0 | 0.00 | - | - | no | Open |
| 608 | 1.215222881182832 | -0.778051 | -22.7537 | 4 | 19 | 0 | 0.00 | - | - | no | Open |
| 605 | 1.9928994056526665 | -0.742342 | -22.9307 | 4 | 15 | 6 | 0.50 | - | - | no | Current |
| 601 | 2.51145667632488 | -0.848909 | -17.9326 | 3 | 17 | 0 | 0.00 | - | - | no | Open |
| 624 | 3.0107378610278723 | -1.0098 | -30.9262 | 13 | 25 | 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
-22.931kcal/mol
Ligand efficiency (LE)
-0.6949kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.894
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
548.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.56
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
39.43kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
85.23kcal/mol
Minimised FF energy
45.80kcal/mol
SASA & burial
✓ computed
SASA (unbound)
726.2Ų
Total solvent-accessible surface area of free ligand
BSA total
475.5Ų
Buried surface area upon binding
BSA apolar
357.6Ų
Hydrophobic contacts buried
BSA polar
117.9Ų
Polar contacts buried
Fraction buried
65.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3140.1Ų
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
1464.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)