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
19.5 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.62, Jaccard 0.54, H-bond role recall 0.17
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.103 kcal/mol/HA)
✓ Good fit quality (FQ -9.74)
✓ Good H-bonds (3 bonds)
✓ Deep burial (95% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ Moderate strain (19.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-25.373
kcal/mol
LE
-1.103
kcal/mol/HA
Fit Quality
-9.74
FQ (Leeson)
HAC
23
heavy atoms
MW
327
Da
LogP
3.02
cLogP
Interaction summary
HB 3
HY 24
PI 2
CLASH 3
Interaction summary
HB 3
HY 24
PI 2
CLASH 3
| Final rank | 1.696 | Score | -25.373 |
|---|---|---|---|
| Inter norm | -1.121 | Intra norm | 0.017 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 3 |
| Artifact reason | geometry warning; 8 clashes; 1 protein clash; 1 cofactor-context clash | ||
| Residues |
NDP301
ALA32
ARG48
ASP52
GLY157
ILE45
LEU94
MET53
PHE56
TRP47
TYR162
VAL156
VAL30
VAL31
VAL49
VAL87
| ||
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
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 | 0.54 | 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 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 387 | -0.09937709662755156 | -0.983193 | -22.0873 | 3 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 407 | 0.22908774884999727 | -1.06452 | -22.8285 | 1 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 479 | 1.2365209322926816 | -1.19068 | -24.6906 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 435 | 1.249777940317059 | -0.934744 | -18.4415 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 418 | 1.6960879108787925 | -1.1206 | -25.3729 | 3 | 16 | 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
-25.373kcal/mol
Ligand efficiency (LE)
-1.1032kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.736
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
327.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.02
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.53kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
33.95kcal/mol
Minimised FF energy
14.41kcal/mol
SASA & burial
✓ computed
SASA (unbound)
537.1Ų
Total solvent-accessible surface area of free ligand
BSA total
509.3Ų
Buried surface area upon binding
BSA apolar
389.5Ų
Hydrophobic contacts buried
BSA polar
119.8Ų
Polar contacts buried
Fraction buried
94.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3173.1Ų
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
1671.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)