Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
10.5 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.62, Jaccard 0.50, H-bond role recall 0.17
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
36% of hydrophobic surface appears solvent-exposed (8/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
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 (-0.832 kcal/mol/HA)
✓ Good fit quality (FQ -8.02)
✓ Good H-bonds (5 bonds)
✓ Deep burial (79% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ Moderate strain (10.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-24.950
kcal/mol
LE
-0.832
kcal/mol/HA
Fit Quality
-8.02
FQ (Leeson)
HAC
30
heavy atoms
MW
420
Da
LogP
3.71
cLogP
Final rank
5.2394
rank score
Inter norm
-0.840
normalised
Contacts
18
H-bonds 9
Interaction summary
HBD 2
HBA 3
HY 8
PI 2
CLASH 4
Interaction summary
HBD 2
HBA 3
HY 8
PI 2
CLASH 4
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 | 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 | 0.50 | RMSD | - |
| HB strict | 1 | Strict recall | 0.14 |
| HB same residue+role | 1 | HB role recall | 0.17 |
| HB same residue | 1 | HB residue recall | 0.17 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 114 | 3.6092047519144113 | -0.980348 | -28.9132 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 124 | 3.6661153275384026 | -1.01311 | -30.2781 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 120 | 3.939630363477459 | -0.671014 | -19.9457 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 85 | 5.239444192633564 | -0.840368 | -24.9503 | 9 | 18 | 13 | 0.62 | 0.17 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.950kcal/mol
Ligand efficiency (LE)
-0.8317kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.023
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
419.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.71
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
10.51kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-68.90kcal/mol
Minimised FF energy
-79.40kcal/mol
SASA & burial
✓ computed
SASA (unbound)
684.5Ų
Total solvent-accessible surface area of free ligand
BSA total
542.7Ų
Buried surface area upon binding
BSA apolar
402.3Ų
Hydrophobic contacts buried
BSA polar
140.4Ų
Polar contacts buried
Fraction buried
79.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3271.2Ų
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
1693.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)