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
1
Internal clashes
1
Native overlap
contact recall 0.81, Jaccard 0.77, H-bond role recall 0.33
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.780 kcal/mol/HA)
✓ Good fit quality (FQ -7.53)
✓ Deep burial (91% SASA buried)
✓ Lipophilic contacts well-matched (89%)
✗ Moderate strain (16.1 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Internal clashes (9)
Score
-23.406
kcal/mol
LE
-0.780
kcal/mol/HA
Fit Quality
-7.53
FQ (Leeson)
HAC
30
heavy atoms
MW
543
Da
LogP
6.80
cLogP
Interaction summary
HB 2
HY 24
PI 2
CLASH 1
Interaction summary
HB 2
HY 24
PI 2
CLASH 1
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 | 0.515 | Score | -23.406 |
|---|---|---|---|
| Inter norm | -0.894 | Intra norm | 0.114 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 2 |
| Artifact reason | geometry warning; 9 clashes; 2 protein contact clashes | ||
| Residues |
NDP301
ALA32
ARG97
GLY157
ILE45
LEU94
LYS57
MET53
PHE56
PHE91
PRO88
SER44
SER86
THR83
TYR162
VAL156
VAL31
VAL87
| ||
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 | 17 | Native recall | 0.81 |
| Jaccard | 0.77 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 2 | HB role recall | 0.33 |
| HB same residue | 2 | HB residue recall | 0.33 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 672 | 0.514679985666019 | -0.894442 | -23.4063 | 2 | 18 | 17 | 0.81 | 0.33 | - | no | Current |
| 678 | 0.8105169412196023 | -0.697208 | -16.6119 | 3 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 674 | 2.040126377083499 | -0.900631 | -24.1106 | 3 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 676 | 2.2112625099320904 | -0.894359 | -20.4876 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 672 | 2.23237953245765 | -0.881443 | -23.9855 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 674 | 2.7366679178174302 | -0.777686 | -22.0152 | 2 | 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
-23.406kcal/mol
Ligand efficiency (LE)
-0.7802kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.526
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
543.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.80
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.06kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
39.76kcal/mol
Minimised FF energy
23.70kcal/mol
SASA & burial
✓ computed
SASA (unbound)
690.4Ų
Total solvent-accessible surface area of free ligand
BSA total
628.9Ų
Buried surface area upon binding
BSA apolar
558.2Ų
Hydrophobic contacts buried
BSA polar
70.6Ų
Polar contacts buried
Fraction buried
91.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
88.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3379.0Ų
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
1657.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)