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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
27.0 kcal/mol
Protein clashes
0
Internal clashes
14
Native overlap
contact recall 0.57, Jaccard 0.50, H-bond role recall 0.17
Reason: 14 internal clashes
14 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.800 kcal/mol/HA)
✓ Good fit quality (FQ -8.07)
✓ Good H-bonds (4 bonds)
✓ Deep burial (79% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ High strain energy (27.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-28.003
kcal/mol
LE
-0.800
kcal/mol/HA
Fit Quality
-8.07
FQ (Leeson)
HAC
35
heavy atoms
MW
532
Da
LogP
3.60
cLogP
Final rank
2.8008
rank score
Inter norm
-0.767
normalised
Contacts
15
H-bonds 4
Interaction summary
HBA 4
HY 7
PI 2
CLASH 0
Interaction summary
HBA 4
HY 7
PI 2
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
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 | 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 | 0.50 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 481 | 1.9814764334454653 | -0.745404 | -27.8173 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 407 | 2.630855530796758 | -0.971801 | -34.7516 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 436 | 2.6890288080080516 | -0.609207 | -21.0021 | 2 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 420 | 2.800838731434333 | -0.767242 | -28.0025 | 4 | 15 | 12 | 0.57 | 0.17 | - | no | Current |
| 378 | 3.1271943614515645 | -0.922081 | -30.6509 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 442 | 3.302201812673812 | -0.782428 | -24.6025 | 4 | 17 | 1 | 0.05 | 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
-28.003kcal/mol
Ligand efficiency (LE)
-0.8001kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.070
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
532.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.60
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.96kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
58.36kcal/mol
Minimised FF energy
31.40kcal/mol
SASA & burial
✓ computed
SASA (unbound)
738.9Ų
Total solvent-accessible surface area of free ligand
BSA total
585.5Ų
Buried surface area upon binding
BSA apolar
401.9Ų
Hydrophobic contacts buried
BSA polar
183.7Ų
Polar contacts buried
Fraction buried
79.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3283.5Ų
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
1684.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)