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 mixed
SASA done
Strain ΔE
9.4 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.52, Jaccard 0.42, H-bond role recall 0.00
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 (-1.536 kcal/mol/HA)
✓ Good fit quality (FQ -11.69)
✓ Good H-bonds (3 bonds)
✓ Deep burial (95% SASA buried)
✓ Lipophilic contacts well-matched (63%)
✗ Moderate strain (9.4 kcal/mol)
✗ Geometry warnings
Score
-24.580
kcal/mol
LE
-1.536
kcal/mol/HA
Fit Quality
-11.69
FQ (Leeson)
HAC
16
heavy atoms
MW
254
Da
LogP
1.80
cLogP
Final rank
2.2498
rank score
Inter norm
-1.616
normalised
Contacts
16
H-bonds 5
Interaction summary
HBD 2
HBA 1
HY 8
PI 1
CLASH 5
Interaction summary
HBD 2
HBA 1
HY 8
PI 1
CLASH 5
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
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 | 0.42 | 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 | -0.6860410761604958 | -1.57326 | -21.6586 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 513 | 0.923740226137635 | -1.55587 | -22.3636 | 11 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 493 | 2.2497935265458597 | -1.61594 | -24.5796 | 5 | 16 | 11 | 0.52 | 0.00 | - | no | Current |
| 467 | 2.89061770523603 | -2.02262 | -29.942 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 500 | 3.1916782193520294 | -1.74067 | -25.2459 | 7 | 13 | 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
-24.580kcal/mol
Ligand efficiency (LE)
-1.5362kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.693
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
16HA
Physicochemical properties
Molecular weight
254.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.80
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
9.41kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
44.75kcal/mol
Minimised FF energy
35.34kcal/mol
SASA & burial
✓ computed
SASA (unbound)
460.0Ų
Total solvent-accessible surface area of free ligand
BSA total
435.2Ų
Buried surface area upon binding
BSA apolar
272.9Ų
Hydrophobic contacts buried
BSA polar
162.3Ų
Polar contacts buried
Fraction buried
94.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
62.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3038.9Ų
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
1678.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)