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 but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
19.2 kcal/mol
Protein clashes
3
Internal clashes
9
Native overlap
contact recall 0.60, Jaccard 0.57, H-bond role recall 0.20
Reason: 9 internal clashes
3 protein-contact clashes
9 intramolecular clashes
42% of hydrophobic surface appears solvent-exposed (10/24 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.752 kcal/mol/HA)
✓ Good fit quality (FQ -7.47)
✓ Deep burial (78% SASA buried)
✓ Lipophilic contacts well-matched (67%)
✗ Moderate strain (19.2 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
✗ Internal clashes (9)
Score
-24.831
kcal/mol
LE
-0.752
kcal/mol/HA
Fit Quality
-7.47
FQ (Leeson)
HAC
33
heavy atoms
MW
488
Da
LogP
5.57
cLogP
Final rank
0.6900
rank score
Inter norm
-0.912
normalised
Contacts
13
H-bonds 2
Interaction summary
HBA 2
HY 5
PI 2
CLASH 0
Interaction summary
HBA 2
HY 5
PI 2
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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
No clash · clashes detected for this pose.
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 | 12 | Native recall | 0.60 |
| Jaccard | 0.57 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 585 | 0.2569287082877208 | -0.794756 | -22.3755 | 0 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 580 | 0.6899638235943697 | -0.911895 | -24.8311 | 2 | 13 | 12 | 0.60 | 0.20 | - | no | Current |
| 570 | 0.774398796580156 | -0.808344 | -21.7394 | 3 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 587 | 1.684180210553361 | -0.748881 | -14.6809 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 566 | 1.8476754197172935 | -1.0664 | -31.6066 | 4 | 23 | 0 | 0.00 | 0.00 | - | no | Open |
| 593 | 2.3429760084794173 | -0.743852 | -21.1563 | 12 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 603 | 2.4614585551832606 | -0.716776 | -18.8166 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 559 | 3.860075508321798 | -0.916895 | -22.0869 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 588 | 3.908763500807694 | -0.968638 | -28.0781 | 9 | 22 | 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
-24.831kcal/mol
Ligand efficiency (LE)
-0.7525kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.466
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
487.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.57
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.19kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
17.86kcal/mol
Minimised FF energy
-1.33kcal/mol
SASA & burial
✓ computed
SASA (unbound)
737.2Ų
Total solvent-accessible surface area of free ligand
BSA total
575.4Ų
Buried surface area upon binding
BSA apolar
385.5Ų
Hydrophobic contacts buried
BSA polar
189.9Ų
Polar contacts buried
Fraction buried
78.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
67.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1516.8Ų
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
836.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)