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
26.8 kcal/mol
Protein clashes
0
Internal clashes
1
Native overlap
contact recall 0.85, Jaccard 0.81, H-bond role recall 0.60
Reason: no major geometry red flags detected
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 Low
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.874 kcal/mol/HA)
✓ Good fit quality (FQ -8.43)
✓ Deep burial (91% SASA buried)
✓ Lipophilic contacts well-matched (90%)
✗ High strain energy (26.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-26.217
kcal/mol
LE
-0.874
kcal/mol/HA
Fit Quality
-8.43
FQ (Leeson)
HAC
30
heavy atoms
MW
408
Da
LogP
3.79
cLogP
Final rank
2.1518
rank score
Inter norm
-0.895
normalised
Contacts
18
H-bonds 5
Interaction summary
HBD 2
HY 10
PI 2
CLASH 1
Interaction summary
HBD 2
HY 10
PI 2
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 | 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 | 17 | Native recall | 0.85 |
| Jaccard | 0.81 | RMSD | - |
| HB strict | 3 | Strict recall | 0.43 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| HB same residue | 3 | HB residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 130 | 0.870373929008191 | -0.853403 | -23.6981 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 119 | 2.15175022324376 | -0.895312 | -26.2166 | 5 | 18 | 17 | 0.85 | 0.60 | - | no | Current |
| 88 | 2.1601832392393416 | -0.844229 | -25.4939 | 9 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 104 | 3.202378879495191 | -0.790226 | -23.2885 | 5 | 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
-26.217kcal/mol
Ligand efficiency (LE)
-0.8739kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.430
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
407.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.79
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.76kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-55.24kcal/mol
Minimised FF energy
-82.00kcal/mol
SASA & burial
✓ computed
SASA (unbound)
732.8Ų
Total solvent-accessible surface area of free ligand
BSA total
667.9Ų
Buried surface area upon binding
BSA apolar
603.3Ų
Hydrophobic contacts buried
BSA polar
64.5Ų
Polar contacts buried
Fraction buried
91.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
90.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1666.3Ų
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
1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
818.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)