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
17.8 kcal/mol
Protein clashes
0
Internal clashes
16
Native overlap
contact recall 0.81, Jaccard 0.71, H-bond role recall 0.00
Reason: 16 internal clashes
16 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.785 kcal/mol/HA)
✓ Good fit quality (FQ -8.15)
✓ Deep burial (84% SASA buried)
✓ Lipophilic contacts well-matched (91%)
✗ Moderate strain (17.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-30.632
kcal/mol
LE
-0.785
kcal/mol/HA
Fit Quality
-8.15
FQ (Leeson)
HAC
39
heavy atoms
MW
516
Da
LogP
6.68
cLogP
Interaction summary
HB 1
HY 24
PI 3
CLASH 0
Interaction summary
HB 1
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 | 1.184 | Score | -30.632 |
|---|---|---|---|
| Inter norm | -0.680 | Intra norm | -0.106 |
| Top1000 | no | Excluded | no |
| Contacts | 20 | H-bonds | 1 |
| Artifact reason | geometry warning; 16 clashes; 1 protein contact clash | ||
| Residues |
NDP301
ALA32
ARG97
ASP52
ILE45
LEU94
LYS57
LYS95
MET53
PHE56
PHE91
PRO88
PRO93
SER44
SER86
TYR162
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 | 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 | 17 | Native recall | 0.81 |
| Jaccard | 0.71 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 641 | 0.9282376030735032 | -0.690797 | -29.8265 | 1 | 18 | 1 | 0.05 | 0.00 | - | no | Open |
| 625 | 1.1837622349404375 | -0.679704 | -30.6316 | 1 | 20 | 17 | 0.81 | 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
-30.632kcal/mol
Ligand efficiency (LE)
-0.7854kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.151
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
39HA
Physicochemical properties
Molecular weight
515.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.68
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.84kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
89.37kcal/mol
Minimised FF energy
71.53kcal/mol
SASA & burial
✓ computed
SASA (unbound)
846.7Ų
Total solvent-accessible surface area of free ligand
BSA total
715.8Ų
Buried surface area upon binding
BSA apolar
650.6Ų
Hydrophobic contacts buried
BSA polar
65.1Ų
Polar contacts buried
Fraction buried
84.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
90.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3552.1Ų
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
1653.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)