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
25.1 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.57, Jaccard 0.46, H-bond role recall 0.17
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.121 kcal/mol/HA)
✓ Good fit quality (FQ -9.56)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (88% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ High strain energy (25.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-23.533
kcal/mol
LE
-1.121
kcal/mol/HA
Fit Quality
-9.56
FQ (Leeson)
HAC
21
heavy atoms
MW
280
Da
LogP
2.76
cLogP
Interaction summary
HB 7
HY 24
PI 1
CLASH 4
Interaction summary
HB 7
HY 24
PI 1
CLASH 4
| Final rank | 2.899 | Score | -23.533 |
|---|---|---|---|
| Inter norm | -1.222 | Intra norm | 0.102 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 7 |
| Artifact reason | geometry warning; 7 clashes; 2 protein clashes; moderate strain Δ 25.1 | ||
| Residues |
NDP301
ALA32
ARG48
ASP52
ILE182
ILE45
MET53
PHE55
PHE56
PRO50
THR180
TRP47
TYR162
VAL156
VAL30
VAL31
VAL49
| ||
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 | 12 | Native recall | 0.57 |
| Jaccard | 0.46 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 416 | 1.6779642607557501 | -1.14471 | -22.4351 | 4 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 424 | 2.8992859618120224 | -1.22226 | -23.5331 | 7 | 17 | 12 | 0.57 | 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
-23.533kcal/mol
Ligand efficiency (LE)
-1.1206kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.559
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
280.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.76
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.10kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
71.25kcal/mol
Minimised FF energy
46.15kcal/mol
SASA & burial
✓ computed
SASA (unbound)
529.1Ų
Total solvent-accessible surface area of free ligand
BSA total
464.8Ų
Buried surface area upon binding
BSA apolar
390.9Ų
Hydrophobic contacts buried
BSA polar
73.9Ų
Polar contacts buried
Fraction buried
87.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
84.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3198.3Ų
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
4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1685.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)