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
8.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.62, Jaccard 0.54, H-bond role recall 0.00
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.
Not B (BCF≤2000)
Persistent
Yes
ADMET alerts (in-silico)
hERG Medium
Ames Clear
DILI Low
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Low conformational strain (8.0 kcal/mol)
✓ Excellent LE (-0.870 kcal/mol/HA)
✓ Good fit quality (FQ -7.68)
✓ Deep burial (96% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-20.015
kcal/mol
LE
-0.870
kcal/mol/HA
Fit Quality
-7.68
FQ (Leeson)
HAC
23
heavy atoms
MW
312
Da
LogP
5.50
cLogP
Final rank
1.8962
rank score
Inter norm
-1.122
normalised
Contacts
16
H-bonds 1
Interaction summary
HBA 1
HY 10
PI 3
CLASH 2
Interaction summary
HBA 1
HY 10
PI 3
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. 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: permissive.
| Name | 3CL9 | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
NDP301
ALA32
ARG97
ASP52
GLY157
ILE45
LEU94
LYS57
MET53
PHE55
PHE56
PHE91
PRO88
SER86
THR180
THR83
TYR162
VAL156
VAL30
VAL31
VAL87
| ||
| Current overlap | 13 | Native recall | 0.62 |
| Jaccard | 0.54 | 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
511 residues
| Protein target | T09 | Atoms | 8170 |
|---|---|---|---|
| Residues | 511 | Chains | 2 |
| Residue summary | LEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224 | ||
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 198 | 1.0960749360608795 | -1.42576 | -34.336 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 181 | 1.8961524756756294 | -1.12199 | -20.0146 | 1 | 16 | 13 | 0.62 | 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
-20.015kcal/mol
Ligand efficiency (LE)
-0.8702kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.680
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
312.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.50
Lipinski: ≤ 5
Rotatable bonds
2
Conformational strain (MMFF94s)
Strain energy (ΔE)
8.00kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
64.59kcal/mol
Minimised FF energy
56.60kcal/mol
SASA & burial
✓ computed
SASA (unbound)
564.5Ų
Total solvent-accessible surface area of free ligand
BSA total
539.9Ų
Buried surface area upon binding
BSA apolar
431.1Ų
Hydrophobic contacts buried
BSA polar
108.8Ų
Polar contacts buried
Fraction buried
95.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3204.2Ų
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
4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1678.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)