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 mixed
SASA done
Strain ΔE
16.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.35, Jaccard 0.30, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact 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 (-1.376 kcal/mol/HA)
✓ Good fit quality (FQ -11.03)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (85% SASA buried)
✓ Lipophilic contacts well-matched (64%)
✗ Moderate strain (16.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-24.767
kcal/mol
LE
-1.376
kcal/mol/HA
Fit Quality
-11.03
FQ (Leeson)
HAC
18
heavy atoms
MW
239
Da
LogP
1.65
cLogP
Final rank
1.5601
rank score
Inter norm
-1.522
normalised
Contacts
10
H-bonds 9
Interaction summary
HBD 1
HBA 6
HY 4
PI 1
CLASH 1
Interaction summary
HBD 1
HBA 6
HY 4
PI 1
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.
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 | 7 | Native recall | 0.35 |
| Jaccard | 0.30 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 203 | 0.02298586351220657 | -1.67971 | -28.8514 | 15 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 251 | 1.5600773526096692 | -1.52238 | -24.7668 | 9 | 10 | 7 | 0.35 | 0.20 | - | no | Current |
| 188 | 1.7393808742889532 | -1.44821 | -22.7179 | 10 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 187 | 1.904926657786237 | -1.44932 | -22.6819 | 10 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 250 | 2.4269731504899124 | -1.49993 | -21.6071 | 8 | 11 | 7 | 0.35 | 0.20 | - | no | Open |
| 150 | 2.4426115785973534 | -1.57076 | -27.0378 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 216 | 2.8029469416296977 | -1.24059 | -22.5753 | 4 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 218 | 2.8355536290807954 | -1.23817 | -22.5435 | 4 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 233 | 2.9732723546361126 | -1.37125 | -23.1711 | 13 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 235 | 3.0500479868790227 | -1.36184 | -23.2406 | 13 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 199 | 3.16779643854898 | -1.63926 | -24.4936 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 196 | 3.2361515800595497 | -1.64127 | -28.1494 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 166 | 3.6401952695033035 | -1.42704 | -24.205 | 14 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 164 | 3.729628072049191 | -1.43686 | -24.3204 | 14 | 13 | 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
-24.767kcal/mol
Ligand efficiency (LE)
-1.3759kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.027
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
18HA
Physicochemical properties
Molecular weight
239.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.65
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.52kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
54.59kcal/mol
Minimised FF energy
38.07kcal/mol
SASA & burial
✓ computed
SASA (unbound)
468.7Ų
Total solvent-accessible surface area of free ligand
BSA total
398.9Ų
Buried surface area upon binding
BSA apolar
256.5Ų
Hydrophobic contacts buried
BSA polar
142.3Ų
Polar contacts buried
Fraction buried
85.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
64.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1272.3Ų
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
857.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)