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
12.2 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.76, Jaccard 0.73, H-bond role recall 0.17
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.775 kcal/mol/HA)
✓ Good fit quality (FQ -7.40)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (89%)
✗ Moderate strain (12.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-22.477
kcal/mol
LE
-0.775
kcal/mol/HA
Fit Quality
-7.40
FQ (Leeson)
HAC
29
heavy atoms
MW
529
Da
LogP
7.16
cLogP
Final rank
1.8545
rank score
Inter norm
-0.921
normalised
Contacts
17
H-bonds 3
Interaction summary
HBD 2
HY 7
PI 2
CLASH 3
Interaction summary
HBD 2
HY 7
PI 2
CLASH 3
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 | 16 | Native recall | 0.76 |
| Jaccard | 0.73 | RMSD | - |
| HB strict | 1 | Strict recall | 0.14 |
| HB same residue+role | 1 | HB role recall | 0.17 |
| HB same residue | 1 | HB residue recall | 0.17 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 667 | 0.5690369790417854 | -0.980307 | -27.0928 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 666 | 1.6845879446949032 | -0.955644 | -24.0533 | 2 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 677 | 1.7350019367006875 | -0.725009 | -18.0466 | 2 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 667 | 1.8545339706584674 | -0.92052 | -22.4775 | 3 | 17 | 16 | 0.76 | 0.17 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-22.477kcal/mol
Ligand efficiency (LE)
-0.7751kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.399
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
529.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
7.16
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.24kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
64.72kcal/mol
Minimised FF energy
52.48kcal/mol
SASA & burial
✓ computed
SASA (unbound)
691.4Ų
Total solvent-accessible surface area of free ligand
BSA total
600.6Ų
Buried surface area upon binding
BSA apolar
532.6Ų
Hydrophobic contacts buried
BSA polar
68.0Ų
Polar contacts buried
Fraction buried
86.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
88.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3348.1Ų
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
1703.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)