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
20.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.38, Jaccard 0.29, 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 (-0.874 kcal/mol/HA)
✓ Good fit quality (FQ -8.52)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ Moderate strain (20.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-27.106
kcal/mol
LE
-0.874
kcal/mol/HA
Fit Quality
-8.52
FQ (Leeson)
HAC
31
heavy atoms
MW
449
Da
LogP
0.91
cLogP
Interaction summary
HB 6
HY 24
PI 0
CLASH 2
Interaction summary
HB 6
HY 24
PI 0
CLASH 2
| Final rank | 3.205 | Score | -27.106 |
|---|---|---|---|
| Inter norm | -0.928 | Intra norm | 0.054 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 6 |
| Artifact reason | geometry warning; 8 clashes; 2 protein clashes | ||
| Residues |
ALA32
ARG48
ARG97
ASP52
ILE45
LEU94
LYS57
LYS95
MET53
PHE56
PRO50
THR54
THR60
TRP47
VAL49
| ||
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
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 | 8 | Native recall | 0.38 |
| Jaccard | 0.29 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 1 | HB role recall | 0.17 |
| HB same residue | 1 | HB residue recall | 0.17 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 653 | 2.722098138210943 | -0.699326 | -17.7051 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 643 | 2.950615041156466 | -0.809494 | -22.4875 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 629 | 3.204630439018359 | -0.928268 | -27.106 | 6 | 15 | 8 | 0.38 | 0.17 | - | no | Current |
| 653 | 3.7390617616469473 | -0.929142 | -28.3549 | 14 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 662 | 4.499574721337301 | -1.20282 | -33.9202 | 16 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 651 | 4.5950468675443386 | -0.839344 | -15.0638 | 11 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 644 | 4.7851696497644545 | -0.712218 | -21.0542 | 6 | 12 | 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
-27.106kcal/mol
Ligand efficiency (LE)
-0.8744kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.519
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
449.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.91
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
66.72kcal/mol
Minimised FF energy
46.77kcal/mol
SASA & burial
✓ computed
SASA (unbound)
740.0Ų
Total solvent-accessible surface area of free ligand
BSA total
597.8Ų
Buried surface area upon binding
BSA apolar
422.3Ų
Hydrophobic contacts buried
BSA polar
175.5Ų
Polar contacts buried
Fraction buried
80.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3271.0Ų
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
1685.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)