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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
19.8 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.75, Jaccard 0.71, H-bond role recall 0.20
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular 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 Medium
Ames Clear
DILI Risk
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.957 kcal/mol/HA)
✓ Good fit quality (FQ -8.82)
✓ Good H-bonds (3 bonds)
✓ Deep burial (95% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Moderate strain (19.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-24.893
kcal/mol
LE
-0.957
kcal/mol/HA
Fit Quality
-8.82
FQ (Leeson)
HAC
26
heavy atoms
MW
382
Da
LogP
4.39
cLogP
Final rank
2.3291
rank score
Inter norm
-1.030
normalised
Contacts
16
H-bonds 3
Interaction summary
HBA 3
HY 9
PI 2
CLASH 4
Interaction summary
HBA 3
HY 9
PI 2
CLASH 4
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 | 3CL9 | Contacts | 20 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA32
ARG97
ASP52
ILE45
LEU94
LYS57
MET53
NDP301
PHE56
PHE91
PRO88
SER86
THR180
THR54
THR83
TYR162
VAL156
VAL30
VAL31
VAL87
| ||
| Current overlap | 15 | Native recall | 0.75 |
| Jaccard | 0.71 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
Protein summary
225 residues
| Protein target | T03 | Atoms | 3428 |
|---|---|---|---|
| Residues | 225 | Chains | 2 |
| Residue summary | LEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; NDP:74 | ||
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:NDP301
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 460 | 0.21507696682715546 | -1.23452 | -33.4222 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 422 | 0.45573710994041605 | -1.10353 | -26.9054 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 436 | 0.7156346003874801 | -0.91303 | -21.1257 | 2 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 510 | 1.0989410030589426 | -0.985425 | -25.1023 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 481 | 2.3291296682478277 | -1.03004 | -24.893 | 3 | 16 | 15 | 0.75 | 0.20 | - | no | Current |
| 453 | 2.381181812744746 | -1.00414 | -25.1506 | 2 | 11 | 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
-24.893kcal/mol
Ligand efficiency (LE)
-0.9574kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.821
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
382.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.39
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.77kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-19.36kcal/mol
Minimised FF energy
-39.13kcal/mol
SASA & burial
✓ computed
SASA (unbound)
641.8Ų
Total solvent-accessible surface area of free ligand
BSA total
609.8Ų
Buried surface area upon binding
BSA apolar
456.1Ų
Hydrophobic contacts buried
BSA polar
153.7Ų
Polar contacts buried
Fraction buried
95.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1489.1Ų
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
1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
807.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)