Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
14.5 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.65, Jaccard 0.59, H-bond role recall 0.20
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.837 kcal/mol/HA)
✓ Good fit quality (FQ -7.50)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ Moderate strain (14.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-20.082
kcal/mol
LE
-0.837
kcal/mol/HA
Fit Quality
-7.50
FQ (Leeson)
HAC
24
heavy atoms
MW
319
Da
LogP
2.54
cLogP
Interaction summary
HB 6
HY 24
PI 3
CLASH 5
Interaction summary
HB 6
HY 24
PI 3
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 | 2.069 | Score | -20.082 |
|---|---|---|---|
| Inter norm | -1.117 | Intra norm | 0.280 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 6 |
| Artifact reason | geometry warning; 7 clashes; 1 protein clash | ||
| Residues |
ALA32
ARG97
ASP52
ILE45
LEU94
LYS57
LYS95
MET53
NDP301
PHE56
PHE91
PRO93
TYR162
VAL30
VAL31
| ||
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 | 13 | Native recall | 0.65 |
| Jaccard | 0.59 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 123 | 0.1451304685743686 | -0.97239 | -17.5241 | 0 | 15 | 1 | 0.05 | 0.00 | - | no | Open |
| 432 | 1.5191133026187429 | -1.33258 | -31.4017 | 4 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 492 | 1.8540039960023957 | -0.91064 | -21.3878 | 5 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 490 | 2.0689198891758367 | -1.11677 | -20.0821 | 6 | 15 | 13 | 0.65 | 0.20 | - | no | Current |
| 135 | 2.8257868822054713 | -0.950388 | -21.5698 | 5 | 11 | 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
-20.082kcal/mol
Ligand efficiency (LE)
-0.8368kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.499
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
319.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.54
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
24.93kcal/mol
Minimised FF energy
10.39kcal/mol
SASA & burial
✓ computed
SASA (unbound)
591.6Ų
Total solvent-accessible surface area of free ligand
BSA total
545.4Ų
Buried surface area upon binding
BSA apolar
453.9Ų
Hydrophobic contacts buried
BSA polar
91.5Ų
Polar contacts buried
Fraction buried
92.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1495.8Ų
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
814.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)