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
13.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.71, Jaccard 0.60, H-bond role recall 0.17
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.000 kcal/mol/HA)
✓ Good fit quality (FQ -9.22)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (87%)
✗ Moderate strain (13.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-26.009
kcal/mol
LE
-1.000
kcal/mol/HA
Fit Quality
-9.22
FQ (Leeson)
HAC
26
heavy atoms
MW
367
Da
LogP
3.69
cLogP
Interaction summary
HB 2
HY 24
PI 2
CLASH 2
Interaction summary
HB 2
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 | 2.052 | Score | -26.009 |
|---|---|---|---|
| Inter norm | -1.017 | Intra norm | 0.017 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 2 |
| Artifact reason | geometry warning; 9 clashes; 1 protein clash | ||
| Residues |
NDP301
ALA32
ARG48
ASP52
GLY157
ILE45
MET53
PHE56
PRO50
PRO88
SER86
THR83
TRP47
TYR162
VAL156
VAL30
VAL31
VAL49
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 | 15 | Native recall | 0.71 |
| Jaccard | 0.60 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 151 | 0.32172865327613354 | -1.26883 | -25.9434 | 11 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 120 | 1.4182620796154546 | -0.869502 | -18.8868 | 0 | 18 | 1 | 0.05 | 0.00 | - | no | Open |
| 159 | 1.6639623900139582 | -1.07838 | -24.547 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 115 | 2.052194704544698 | -1.01732 | -26.0095 | 2 | 19 | 15 | 0.71 | 0.17 | - | no | Current |
| 155 | 2.6074809669883345 | -0.786201 | -16.7503 | 5 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 98 | 2.6369590614426244 | -1.2378 | -24.8459 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 88 | 3.6279790838447203 | -1.06416 | -18.492 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 158 | 4.168810452369634 | -0.945702 | -19.3234 | 5 | 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
-26.009kcal/mol
Ligand efficiency (LE)
-1.0004kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.217
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
366.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.69
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.05kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
79.01kcal/mol
Minimised FF energy
65.97kcal/mol
SASA & burial
✓ computed
SASA (unbound)
602.8Ų
Total solvent-accessible surface area of free ligand
BSA total
553.4Ų
Buried surface area upon binding
BSA apolar
482.0Ų
Hydrophobic contacts buried
BSA polar
71.4Ų
Polar contacts buried
Fraction buried
91.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
87.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3280.8Ų
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
1674.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)