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
16.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.52, Jaccard 0.46, H-bond role recall 0.50
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.144 kcal/mol/HA)
✓ Good fit quality (FQ -10.25)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (79% SASA buried)
✓ Lipophilic contacts well-matched (68%)
✗ Moderate strain (16.1 kcal/mol)
✗ Geometry warnings
Score
-27.449
kcal/mol
LE
-1.144
kcal/mol/HA
Fit Quality
-10.25
FQ (Leeson)
HAC
24
heavy atoms
MW
367
Da
LogP
3.19
cLogP
Interaction summary
HB 11
HY 21
PI 2
CLASH 2
Interaction summary
HB 11
HY 21
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 | 2.449 | Score | -27.449 |
|---|---|---|---|
| Inter norm | -1.175 | Intra norm | 0.031 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 11 |
| Artifact reason | geometry warning; 3 clashes; 2 protein clashes | ||
| Residues |
NDP301
ALA32
ARG48
ASP52
GLY157
ILE45
MET53
PHE56
TRP47
TYR162
VAL156
VAL30
VAL31
VAL49
| ||
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 | 11 | Native recall | 0.52 |
| Jaccard | 0.46 | RMSD | - |
| HB strict | 3 | Strict recall | 0.43 |
| HB same residue+role | 3 | HB role recall | 0.50 |
| HB same residue | 3 | HB residue recall | 0.50 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 250 | 0.33124369498846573 | -1.29643 | -23.0727 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 306 | 1.4980844275439626 | -1.16076 | -23.1033 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 302 | 2.3012365417379717 | -1.12079 | -20.9957 | 6 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 220 | 2.4491462354209257 | -1.17492 | -27.4486 | 11 | 14 | 11 | 0.52 | 0.50 | - | no | Current |
| 246 | 2.5415044901747534 | -1.09194 | -21.3662 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 304 | 3.2694936552292573 | -0.787157 | -13.9191 | 10 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 223 | 6.3559024232398045 | -1.30285 | -23.833 | 16 | 18 | 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
-27.449kcal/mol
Ligand efficiency (LE)
-1.1437kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.250
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
366.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.19
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.12kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
20.85kcal/mol
Minimised FF energy
4.72kcal/mol
SASA & burial
✓ computed
SASA (unbound)
639.3Ų
Total solvent-accessible surface area of free ligand
BSA total
504.1Ų
Buried surface area upon binding
BSA apolar
344.0Ų
Hydrophobic contacts buried
BSA polar
160.1Ų
Polar contacts buried
Fraction buried
78.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3185.1Ų
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
1660.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)