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
12.9 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.50, Jaccard 0.42, H-bond role recall 0.60
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Not classified (>100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low
Ames Clear
DILI Low
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.173 kcal/mol/HA)
✓ Good fit quality (FQ -10.01)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Moderate strain (12.9 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-24.644
kcal/mol
LE
-1.173
kcal/mol/HA
Fit Quality
-10.01
FQ (Leeson)
HAC
21
heavy atoms
MW
307
Da
LogP
1.71
cLogP
Final rank
3.2710
rank score
Inter norm
-1.271
normalised
Contacts
14
H-bonds 8
Interaction summary
HBD 4
HBA 2
HY 5
PI 2
CLASH 3
Interaction summary
HBD 4
HBA 2
HY 5
PI 2
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.
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 | 10 | Native recall | 0.50 |
| Jaccard | 0.42 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 418 | 1.706034983384381 | -1.42669 | -24.5139 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 388 | 2.3216341406732472 | -1.43894 | -27.529 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 451 | 3.2126587318185202 | -1.1889 | -20.8917 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 434 | 3.2709996425598846 | -1.27088 | -24.6443 | 8 | 14 | 10 | 0.50 | 0.60 | - | no | Current |
| 410 | 3.976349501105721 | -1.3018 | -24.3757 | 6 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 387 | 4.466629566632373 | -1.1529 | -22.7938 | 7 | 17 | 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
-24.644kcal/mol
Ligand efficiency (LE)
-1.1735kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.010
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
306.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.71
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
100.50kcal/mol
Minimised FF energy
87.55kcal/mol
SASA & burial
✓ computed
SASA (unbound)
510.0Ų
Total solvent-accessible surface area of free ligand
BSA total
444.0Ų
Buried surface area upon binding
BSA apolar
357.5Ų
Hydrophobic contacts buried
BSA polar
86.4Ų
Polar contacts buried
Fraction buried
87.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1417.9Ų
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
826.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)