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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native mixed
SASA done
Strain ΔE
33.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.38, Jaccard 0.31, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.643 kcal/mol/HA)
✓ Good fit quality (FQ -6.21)
✓ Good H-bonds (3 bonds)
✓ Deep burial (73% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ Very high strain energy (33.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-19.299
kcal/mol
LE
-0.643
kcal/mol/HA
Fit Quality
-6.21
FQ (Leeson)
HAC
30
heavy atoms
MW
407
Da
LogP
2.87
cLogP
Interaction summary
HB 3
HY 24
PI 2
CLASH 2
Interaction summary
HB 3
HY 24
PI 2
CLASH 2
| Final rank | 3.453 | Score | -19.299 |
|---|---|---|---|
| Inter norm | -0.915 | Intra norm | 0.271 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 3 |
| Artifact reason | geometry warning; 13 clashes; 2 protein clashes; high strain Δ 33.2 | ||
| Residues |
NDP301
ALA32
ARG48
ASP52
ILE45
MET53
PHE56
PRO50
THR54
TRP47
TYR162
VAL156
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 | 8 | Native recall | 0.38 |
| Jaccard | 0.31 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 333 | 0.8165892997804749 | -1.03679 | -23.7942 | 12 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 441 | 1.1685211136412954 | -0.880713 | -26.4243 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 356 | 1.6407871253580555 | -0.869268 | -22.1003 | 7 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 403 | 1.795979106920546 | -0.975825 | -28.8271 | 6 | 15 | 1 | 0.05 | 0.00 | - | no | Open |
| 383 | 3.452527861957111 | -0.914722 | -19.2993 | 3 | 13 | 8 | 0.38 | 0.00 | - | no | Current |
| 457 | 3.460735189732118 | -0.830068 | -17.489 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 391 | 3.50428813078884 | -0.797361 | -21.3187 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 352 | 3.756650634369295 | -1.01987 | -25.7771 | 9 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 318 | 4.326972274753828 | -1.10335 | -32.5603 | 12 | 23 | 0 | 0.00 | 0.00 | - | no | Open |
| 380 | 5.4593238784164 | -0.932728 | -21.1296 | 13 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 421 | 5.842856067255379 | -0.879322 | -23.9742 | 11 | 20 | 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
-19.299kcal/mol
Ligand efficiency (LE)
-0.6433kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.206
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
407.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.87
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.20kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
98.66kcal/mol
Minimised FF energy
65.45kcal/mol
SASA & burial
✓ computed
SASA (unbound)
666.4Ų
Total solvent-accessible surface area of free ligand
BSA total
486.9Ų
Buried surface area upon binding
BSA apolar
393.5Ų
Hydrophobic contacts buried
BSA polar
93.4Ų
Polar contacts buried
Fraction buried
73.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3227.3Ų
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
1708.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)