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
24.6 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.50, Jaccard 0.37, H-bond role recall 0.20
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 (-0.564 kcal/mol/HA)
✓ Good fit quality (FQ -6.00)
✓ Deep burial (78% SASA buried)
✓ Lipophilic contacts well-matched (87%)
✗ High strain energy (24.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (25)
Score
-24.268
kcal/mol
LE
-0.564
kcal/mol/HA
Fit Quality
-6.00
FQ (Leeson)
HAC
43
heavy atoms
MW
610
Da
LogP
6.96
cLogP
Interaction summary
HB 2
HY 24
PI 2
CLASH 3
Interaction summary
HB 2
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 | 4.867 | Score | -24.268 |
|---|---|---|---|
| Inter norm | -0.619 | Intra norm | 0.055 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 2 |
| Artifact reason | geometry warning; 25 clashes; 2 protein clashes; moderate strain Δ 24.6 | ||
| Residues |
ARG48
ARG97
ILE45
LEU94
LYS57
LYS90
LYS95
MET53
PHE56
PHE91
PRO50
PRO88
PRO93
THR54
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 | 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 | 10 | Native recall | 0.50 |
| Jaccard | 0.37 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 57 | 2.324339219025657 | -0.568681 | -19.9326 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 56 | 3.2475930720691877 | -0.632778 | -22.8389 | 1 | 20 | 1 | 0.05 | 0.00 | - | no | Open |
| 73 | 3.3517337534061897 | -0.621376 | -25.2286 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 78 | 4.866861631561944 | -0.619025 | -24.2685 | 2 | 17 | 10 | 0.50 | 0.20 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.268kcal/mol
Ligand efficiency (LE)
-0.5644kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.998
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
43HA
Physicochemical properties
Molecular weight
609.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.96
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.64kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
104.83kcal/mol
Minimised FF energy
80.20kcal/mol
SASA & burial
✓ computed
SASA (unbound)
847.9Ų
Total solvent-accessible surface area of free ligand
BSA total
656.9Ų
Buried surface area upon binding
BSA apolar
573.0Ų
Hydrophobic contacts buried
BSA polar
83.8Ų
Polar contacts buried
Fraction buried
77.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
87.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1687.5Ų
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
1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
889.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)