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 high
Native strong
SASA done
Strain ΔE
16.6 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.65, Jaccard 0.59, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.898 kcal/mol/HA)
✓ Good fit quality (FQ -8.16)
✓ Good H-bonds (5 bonds)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Moderate strain (16.6 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Internal clashes (6)
Score
-22.455
kcal/mol
LE
-0.898
kcal/mol/HA
Fit Quality
-8.16
FQ (Leeson)
HAC
25
heavy atoms
MW
395
Da
LogP
3.17
cLogP
Interaction summary
HB 5
HY 24
PI 2
CLASH 2
Interaction summary
HB 5
HY 24
PI 2
CLASH 2
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 | 0.358 | Score | -22.455 |
|---|---|---|---|
| Inter norm | -1.106 | Intra norm | 0.208 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 5 |
| Artifact reason | geometry warning; 6 clashes; 4 protein contact clashes; 1 cofactor-context clash | ||
| Residues |
ALA32
ARG97
ASP52
LEU94
LYS57
LYS95
MET53
NDP301
PHE56
PHE91
PRO93
TYR162
VAL156
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 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 429 | 0.3580919713066338 | -1.10627 | -22.4548 | 5 | 15 | 13 | 0.65 | 0.20 | - | no | Current |
| 369 | 0.8369236842974171 | -1.2245 | -29.9994 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 349 | 2.44111177040875 | -1.12817 | -25.6437 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 416 | 2.596782112753742 | -0.83916 | -18.0269 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 383 | 3.432930616002931 | -1.59331 | -37.0484 | 12 | 21 | 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
-22.455kcal/mol
Ligand efficiency (LE)
-0.8982kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.165
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
394.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.17
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-71.49kcal/mol
Minimised FF energy
-88.07kcal/mol
SASA & burial
✓ computed
SASA (unbound)
630.1Ų
Total solvent-accessible surface area of free ligand
BSA total
580.6Ų
Buried surface area upon binding
BSA apolar
437.7Ų
Hydrophobic contacts buried
BSA polar
142.9Ų
Polar contacts buried
Fraction buried
92.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1479.3Ų
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
798.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)