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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
22.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.88, Jaccard 0.64, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
60% of hydrophobic surface is solvent-exposed (12/20 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
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 Low
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 -5.61)
✓ Good H-bonds (4 bonds)
✓ Good burial (49% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ High strain energy (22.9 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-17.454
kcal/mol
LE
-0.582
kcal/mol/HA
Fit Quality
-5.61
FQ (Leeson)
HAC
30
heavy atoms
MW
459
Da
LogP
4.59
cLogP
Final rank
2.4340
rank score
Inter norm
-0.660
normalised
Contacts
10
H-bonds 6
Interaction summary
HBD 2
HBA 2
HY 3
PI 1
CLASH 2
Interaction summary
HBD 2
HBA 2
HY 3
PI 1
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 396 | -0.11056417959593262 | -1.19533 | -34.8331 | 9 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 419 | 0.3271797508948459 | -0.839972 | -24.243 | 2 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 480 | 0.4575261200251558 | -0.989236 | -25.5218 | 1 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 388 | 1.3247621968802203 | -0.97422 | -27.5305 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 429 | 1.5682838105176942 | -0.894601 | -23.8867 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 452 | 1.7973468440035216 | -0.986403 | -22.7906 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 450 | 1.8532223899879046 | -0.707052 | -19.9579 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 442 | 2.056146307025179 | -0.886151 | -21.9132 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 402 | 2.1313085350777627 | -1.15443 | -29.8157 | 14 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 432 | 2.4339812204281435 | -0.65996 | -17.4537 | 6 | 10 | 7 | 0.88 | 0.00 | - | no | Current |
| 469 | 2.992470262134781 | -0.896028 | -22.0828 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 408 | 3.228580280103112 | -0.944403 | -24.0255 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 426 | 3.390641675980678 | -0.781192 | -18.2749 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 398 | 3.736159295282282 | -0.857475 | -20.4087 | 13 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 409 | 3.9602894299335802 | -0.833689 | -21.2615 | 10 | 15 | 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
-17.454kcal/mol
Ligand efficiency (LE)
-0.5818kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.612
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
458.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.59
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.86kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
32.03kcal/mol
Minimised FF energy
9.18kcal/mol
SASA & burial
✓ computed
SASA (unbound)
675.4Ų
Total solvent-accessible surface area of free ligand
BSA total
331.8Ų
Buried surface area upon binding
BSA apolar
239.5Ų
Hydrophobic contacts buried
BSA polar
92.3Ų
Polar contacts buried
Fraction buried
49.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3021.6Ų
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
1518.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)