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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
55.5 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.88, Jaccard 0.39, H-bond role recall 0.00
Reason: strain 55.5 kcal/mol
strain ΔE 55.5 kcal/mol
3 protein-contact clashes
3 intramolecular clashes
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Daphnia EC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Algae IC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
Yes
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 (-0.527 kcal/mol/HA)
✓ Good fit quality (FQ -5.51)
✓ Good burial (61% SASA buried)
✓ Lipophilic contacts well-matched (93%)
✗ Extreme strain energy (55.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (23)
Score
-21.091
kcal/mol
LE
-0.527
kcal/mol/HA
Fit Quality
-5.51
FQ (Leeson)
HAC
40
heavy atoms
MW
650
Da
LogP
5.77
cLogP
Final rank
3.6904
rank score
Inter norm
-0.480
normalised
Contacts
17
H-bonds 3
Interaction summary
HBA 1
HY 5
PI 2
CLASH 3
Interaction summary
HBA 1
HY 5
PI 2
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 1.
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: strict.
| Name | 9IFH | Contacts | 8 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ASN402
GLU467
LEU399
PHE396
PRO398
SER394
SER470
THR397
| ||
| Current overlap | 7 | Native recall | 0.88 |
| Jaccard | 0.39 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
Protein summary
492 residues
| Protein target | T20 | Atoms | 7539 |
|---|---|---|---|
| Residues | 492 | 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:264; 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 30 | 2.8122849803695433 | -0.605681 | -21.2292 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 32 | 3.6904132075342484 | -0.479913 | -21.0909 | 3 | 17 | 7 | 0.88 | 0.00 | - | no | Current |
| 23 | 3.963480043409727 | -0.57271 | -23.4694 | 1 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 29 | 4.034277023512894 | -0.679794 | -27.5538 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 37 | 5.8925470979906365 | -0.565542 | -24.3824 | 5 | 25 | 0 | 0.00 | 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
-21.091kcal/mol
Ligand efficiency (LE)
-0.5273kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.507
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
40HA
Physicochemical properties
Molecular weight
650.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.77
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
55.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
141.29kcal/mol
Minimised FF energy
85.74kcal/mol
SASA & burial
✓ computed
SASA (unbound)
885.8Ų
Total solvent-accessible surface area of free ligand
BSA total
542.6Ų
Buried surface area upon binding
BSA apolar
507.1Ų
Hydrophobic contacts buried
BSA polar
35.6Ų
Polar contacts buried
Fraction buried
61.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
93.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3286.3Ų
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
4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1621.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)