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
29.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.85, Jaccard 0.58
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. 1 — Very toxic (≤1 mg/L)
Algae IC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
Yes
ADMET alerts (in-silico)
hERG High
Ames Clear
DILI Risk
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.653 kcal/mol/HA)
✓ Good fit quality (FQ -6.47)
✓ Deep burial (70% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ High strain energy (29.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-21.537
kcal/mol
LE
-0.653
kcal/mol/HA
Fit Quality
-6.47
FQ (Leeson)
HAC
33
heavy atoms
MW
476
Da
LogP
4.69
cLogP
Final rank
2.7533
rank score
Inter norm
-0.694
normalised
Contacts
17
H-bonds 4
Interaction summary
HBD 2
HY 5
PI 4
CLASH 1
Interaction summary
HBD 2
HY 5
PI 4
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 2.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
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 | 13 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ASP116
GLU18
GLY112
ILE106
LEU17
MET113
SER109
THR117
THR335
TRP21
TYR110
VAL53
VAL58
| ||
| Current overlap | 11 | Native recall | 0.85 |
| Jaccard | 0.58 | 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 | T18 | Atoms | 7550 |
|---|---|---|---|
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 388 | 2.753265285932355 | -0.694431 | -21.5369 | 4 | 17 | 11 | 0.85 | - | - | no | Current |
| 480 | 2.8695446738657138 | -0.802467 | -9.36554 | 4 | 18 | 0 | 0.00 | - | - | no | Open |
| 379 | 2.8925673289428824 | -0.879413 | -26.0521 | 3 | 18 | 0 | 0.00 | - | - | no | Open |
| 355 | 4.690394542649569 | -0.728948 | -16.116 | 8 | 14 | 0 | 0.00 | - | - | no | Open |
| 349 | 4.975775818758638 | -0.940274 | -23.1449 | 11 | 24 | 0 | 0.00 | - | - | no | Open |
| 377 | 5.371363205795083 | -0.825457 | -20.8628 | 12 | 21 | 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
-21.537kcal/mol
Ligand efficiency (LE)
-0.6526kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.475
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
475.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.69
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.43kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
87.95kcal/mol
Minimised FF energy
58.52kcal/mol
SASA & burial
✓ computed
SASA (unbound)
702.7Ų
Total solvent-accessible surface area of free ligand
BSA total
488.6Ų
Buried surface area upon binding
BSA apolar
409.4Ų
Hydrophobic contacts buried
BSA polar
79.3Ų
Polar contacts buried
Fraction buried
69.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3132.3Ų
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
1521.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)