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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
27.5 kcal/mol
Protein clashes
0
Internal clashes
21
Native overlap
contact recall 0.70, Jaccard 0.61, H-bond role recall 0.20
Reason: 21 internal clashes
21 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.544 kcal/mol/HA)
✓ Good fit quality (FQ -5.79)
✓ Deep burial (82% SASA buried)
✓ Lipophilic contacts well-matched (96%)
✗ High strain energy (27.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (21)
Score
-23.412
kcal/mol
LE
-0.544
kcal/mol/HA
Fit Quality
-5.79
FQ (Leeson)
HAC
43
heavy atoms
MW
653
Da
LogP
8.74
cLogP
Interaction summary
HB 2
HY 24
PI 3
CLASH 0
Interaction summary
HB 2
HY 24
PI 3
CLASH 0
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
No clash · clashes detected for this pose.
| Final rank | 2.949 | Score | -23.412 |
|---|---|---|---|
| Inter norm | -0.669 | Intra norm | 0.125 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 2 |
| Artifact reason | geometry warning; 21 clashes; 1 protein clash; moderate strain Δ 27.3 | ||
| Residues |
ARG97
ILE45
LEU94
LYS57
LYS95
MET53
NDP301
PHE56
PHE91
PRO50
PRO88
SER44
SER86
THR54
THR83
VAL156
VAL87
| ||
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 | 14 | Native recall | 0.70 |
| Jaccard | 0.61 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 20 | 2.949487788862306 | -0.669496 | -23.4124 | 2 | 17 | 14 | 0.70 | 0.20 | - | no | Current |
| 23 | 3.3623200658043455 | -0.632471 | -23.1203 | 1 | 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
-23.412kcal/mol
Ligand efficiency (LE)
-0.5445kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.787
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
43HA
Physicochemical properties
Molecular weight
653.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
8.74
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.46kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
255.16kcal/mol
Minimised FF energy
227.70kcal/mol
SASA & burial
✓ computed
SASA (unbound)
938.2Ų
Total solvent-accessible surface area of free ligand
BSA total
766.0Ų
Buried surface area upon binding
BSA apolar
731.3Ų
Hydrophobic contacts buried
BSA polar
34.8Ų
Polar contacts buried
Fraction buried
81.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
95.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1858.2Ų
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
852.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)