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 high
Native strong
SASA done
Strain ΔE
9.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.90, Jaccard 0.86, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 protein-contact 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.
B — Bioaccumulative (BCF>2000)
Persistent
Yes
ADMET alerts (in-silico)
hERG High
Ames Clear
DILI Risk
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.883 kcal/mol/HA)
✓ Good fit quality (FQ -8.43)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (96%)
✗ Moderate strain (9.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-25.594
kcal/mol
LE
-0.883
kcal/mol/HA
Fit Quality
-8.43
FQ (Leeson)
HAC
29
heavy atoms
MW
530
Da
LogP
6.13
cLogP
Final rank
1.4915
rank score
Inter norm
-0.919
normalised
Contacts
19
H-bonds 3
Interaction summary
HBD 2
HY 8
PI 3
CLASH 2
Interaction summary
HBD 2
HY 8
PI 3
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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: 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 | 18 | Native recall | 0.90 |
| Jaccard | 0.86 | RMSD | - |
| HB strict | 1 | Strict recall | 0.14 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 673 | 0.7497194082801134 | -0.82269 | -17.2529 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 669 | 1.232737016346297 | -0.788014 | -20.274 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 674 | 1.4914675157547654 | -0.918953 | -25.5943 | 3 | 19 | 18 | 0.90 | 0.20 | - | no | Current |
| 670 | 1.6936239314371768 | -0.843158 | -22.4207 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 667 | 2.9645212209224328 | -0.899472 | -21.6515 | 3 | 16 | 1 | 0.05 | 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
-25.594kcal/mol
Ligand efficiency (LE)
-0.8826kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.425
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
530.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.13
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
9.00kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
44.27kcal/mol
Minimised FF energy
35.27kcal/mol
SASA & burial
✓ computed
SASA (unbound)
678.9Ų
Total solvent-accessible surface area of free ligand
BSA total
624.8Ų
Buried surface area upon binding
BSA apolar
596.7Ų
Hydrophobic contacts buried
BSA polar
28.0Ų
Polar contacts buried
Fraction buried
92.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
95.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1651.4Ų
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
820.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)