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
37.5 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.85, Jaccard 0.68, H-bond role recall 0.80
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.962 kcal/mol/HA)
✓ Good fit quality (FQ -9.70)
✓ Strong H-bond network (13 bonds)
✓ Deep burial (91% SASA buried)
✓ Lipophilic contacts well-matched (73%)
✗ Very high strain energy (37.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-33.672
kcal/mol
LE
-0.962
kcal/mol/HA
Fit Quality
-9.70
FQ (Leeson)
HAC
35
heavy atoms
MW
480
Da
LogP
-0.01
cLogP
Interaction summary
HB 13
HY 24
PI 2
CLASH 3
Interaction summary
HB 13
HY 24
PI 2
CLASH 3
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
| Final rank | 3.282 | Score | -33.672 |
|---|---|---|---|
| Inter norm | -1.053 | Intra norm | 0.091 |
| Top1000 | no | Excluded | no |
| Contacts | 22 | H-bonds | 13 |
| Artifact reason | geometry warning; 15 clashes; 1 protein clash; high strain Δ 37.5 | ||
| Residues |
ALA32
ARG97
ASP52
ILE45
LEU179
LEU94
LYS57
LYS95
MET53
NDP301
PHE55
PHE56
PHE91
PRO93
THR180
THR83
TYR162
TYR178
VAL156
VAL30
VAL31
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 | 17 | Native recall | 0.85 |
| Jaccard | 0.68 | RMSD | - |
| HB strict | 5 | Strict recall | 0.71 |
| HB same residue+role | 4 | HB role recall | 0.80 |
| HB same residue | 4 | HB residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 16 | 0.9318185768716343 | -1.30717 | -37.5358 | 9 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 8 | 2.388499099499413 | -0.914871 | -29.2444 | 13 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 13 | 2.5152482222802455 | -1.00556 | -32.4774 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 16 | 3.282337965943439 | -1.05297 | -33.6719 | 13 | 22 | 17 | 0.85 | 0.80 | - | no | Current |
| 7 | 3.3491516125816614 | -0.614311 | -21.785 | 9 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 15 | 4.881715648797068 | -0.997797 | -30.3693 | 11 | 18 | 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
-33.672kcal/mol
Ligand efficiency (LE)
-0.9621kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.704
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
479.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.01
Lipinski: ≤ 5
Rotatable bonds
12
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.50kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
48.44kcal/mol
Minimised FF energy
10.94kcal/mol
SASA & burial
✓ computed
SASA (unbound)
744.6Ų
Total solvent-accessible surface area of free ligand
BSA total
680.8Ų
Buried surface area upon binding
BSA apolar
499.1Ų
Hydrophobic contacts buried
BSA polar
181.8Ų
Polar contacts buried
Fraction buried
91.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
73.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1574.9Ų
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
807.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)