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 mixed
SASA done
Strain ΔE
29.9 kcal/mol
Protein clashes
4
Internal clashes
5
Native overlap
contact recall 0.43, Jaccard 0.35, H-bond role recall 0.00
Reason: no major geometry red flags detected
4 protein-contact clashes
5 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.030 kcal/mol/HA)
✓ Good fit quality (FQ -9.23)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (82% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ High strain energy (29.9 kcal/mol)
✗ Geometry warnings
Score
-24.731
kcal/mol
LE
-1.030
kcal/mol/HA
Fit Quality
-9.23
FQ (Leeson)
HAC
24
heavy atoms
MW
328
Da
LogP
1.00
cLogP
Interaction summary
HB 7
HY 16
PI 1
CLASH 5
Interaction summary
HB 7
HY 16
PI 1
CLASH 5
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 | 2.957 | Score | -24.731 |
|---|---|---|---|
| Inter norm | -1.101 | Intra norm | 0.070 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 7 |
| Artifact reason | geometry warning; 4 clashes; 2 protein clashes; 1 severe cofactor-context clash; moderate strain Δ 29.9 | ||
| Residues |
NDP301
ALA32
ARG48
ASP52
GLU43
ILE45
MET53
PHE56
PRO88
SER44
SER86
TRP47
VAL49
VAL87
| ||
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 | 9 | Native recall | 0.43 |
| Jaccard | 0.35 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 95 | 0.5934958991407334 | -1.01273 | -19.1573 | 3 | 16 | 1 | 0.05 | 0.00 | - | no | Open |
| 88 | 2.9567790800273532 | -1.10083 | -24.7311 | 7 | 14 | 9 | 0.43 | 0.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.731kcal/mol
Ligand efficiency (LE)
-1.0305kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.235
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
328.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.00
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.90kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-47.86kcal/mol
Minimised FF energy
-77.76kcal/mol
SASA & burial
✓ computed
SASA (unbound)
588.8Ų
Total solvent-accessible surface area of free ligand
BSA total
482.6Ų
Buried surface area upon binding
BSA apolar
397.0Ų
Hydrophobic contacts buried
BSA polar
85.6Ų
Polar contacts buried
Fraction buried
82.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3219.9Ų
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
4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1706.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)