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 medium
Native strong
SASA done
Strain ΔE
22.1 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.88, Jaccard 0.64, H-bond role recall 0.00
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
46% of hydrophobic surface appears solvent-exposed (12/26 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.582 kcal/mol/HA)
✓ Good fit quality (FQ -5.96)
✓ Good H-bonds (4 bonds)
✓ Good burial (46% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ High strain energy (22.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (18)
Score
-21.543
kcal/mol
LE
-0.582
kcal/mol/HA
Fit Quality
-5.96
FQ (Leeson)
HAC
37
heavy atoms
MW
552
Da
LogP
5.58
cLogP
Final rank
3.7874
rank score
Inter norm
-0.596
normalised
Contacts
10
H-bonds 5
Interaction summary
HBA 4
HY 2
PI 2
CLASH 5
Interaction summary
HBA 4
HY 2
PI 2
CLASH 5
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.
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 | 0.64 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 32 | 1.795447965694356 | -0.800955 | -26.2534 | 3 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 38 | 2.54254757633253 | -0.666768 | -25.3827 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 31 | 2.6391231269031694 | -0.938147 | -31.4622 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 36 | 2.7345757417426713 | -0.666731 | -24.4372 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 34 | 2.929079553686404 | -0.770344 | -25.7463 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 18 | 2.982167915445581 | -0.674628 | -22.067 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 39 | 3.0351032789602472 | -0.961909 | -34.6797 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 29 | 3.737872089519109 | -0.599555 | -19.0113 | 3 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 34 | 3.7874201864497987 | -0.595766 | -21.543 | 5 | 10 | 7 | 0.88 | 0.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-21.543kcal/mol
Ligand efficiency (LE)
-0.5822kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.961
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
552.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.58
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.14kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
59.14kcal/mol
Minimised FF energy
37.00kcal/mol
SASA & burial
✓ computed
SASA (unbound)
787.9Ų
Total solvent-accessible surface area of free ligand
BSA total
361.1Ų
Buried surface area upon binding
BSA apolar
302.1Ų
Hydrophobic contacts buried
BSA polar
58.9Ų
Polar contacts buried
Fraction buried
45.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3120.6Ų
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
4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1609.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)