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 mixed
SASA done
Strain ΔE
5.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.52, Jaccard 0.44, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Low conformational strain (5.1 kcal/mol)
✓ Excellent LE (-1.103 kcal/mol/HA)
✓ Good fit quality (FQ -9.41)
✓ Good H-bonds (4 bonds)
✓ Deep burial (88% SASA buried)
✓ Lipophilic contacts well-matched (65%)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-23.160
kcal/mol
LE
-1.103
kcal/mol/HA
Fit Quality
-9.41
FQ (Leeson)
HAC
21
heavy atoms
MW
294
Da
LogP
3.30
cLogP
Interaction summary
HB 4
HY 24
PI 2
CLASH 2
Interaction summary
HB 4
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 | 1.339 | Score | -23.160 |
|---|---|---|---|
| Inter norm | -1.214 | Intra norm | 0.111 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 4 |
| Artifact reason | geometry warning; 6 clashes; 1 protein clash | ||
| Residues |
NDP301
ALA32
ARG48
ASP52
ILE45
MET53
PHE55
PHE56
PRO50
THR180
TRP47
TYR162
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 | 0.44 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 494 | 1.3391484112069343 | -1.21365 | -23.16 | 4 | 15 | 11 | 0.52 | 0.00 | - | no | Current |
| 479 | 2.0118790855175046 | -1.27636 | -26.3833 | 8 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 468 | 2.2302149066875736 | -1.41383 | -27.8598 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 488 | 4.480625061862758 | -1.28514 | -26.7794 | 11 | 16 | 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
-23.160kcal/mol
Ligand efficiency (LE)
-1.1029kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.407
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
294.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.30
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
5.14kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
16.12kcal/mol
Minimised FF energy
10.98kcal/mol
SASA & burial
✓ computed
SASA (unbound)
538.2Ų
Total solvent-accessible surface area of free ligand
BSA total
474.4Ų
Buried surface area upon binding
BSA apolar
307.8Ų
Hydrophobic contacts buried
BSA polar
166.6Ų
Polar contacts buried
Fraction buried
88.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
64.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3096.9Ų
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
1693.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)