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
13.3 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.30, Jaccard 0.25, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.139 kcal/mol/HA)
✓ Good fit quality (FQ -9.34)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (83% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Moderate strain (13.3 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-21.643
kcal/mol
LE
-1.139
kcal/mol/HA
Fit Quality
-9.34
FQ (Leeson)
HAC
19
heavy atoms
MW
279
Da
LogP
2.90
cLogP
Interaction summary
HB 9
HY 13
PI 2
CLASH 2
Interaction summary
HB 9
HY 13
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 | 3.322 | Score | -21.643 |
|---|---|---|---|
| Inter norm | -1.468 | Intra norm | 0.329 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 9 |
| Artifact reason | geometry warning; 8 clashes; 3 protein clashes | ||
| Residues |
ARG92
ARG97
LEU94
LYS57
LYS90
LYS95
MET53
PHE91
PRO93
THR54
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 3CL9 | Contacts | 20 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA32
ARG97
ASP52
ILE45
LEU94
LYS57
MET53
NDP301
PHE56
PHE91
PRO88
SER86
THR180
THR54
THR83
TYR162
VAL156
VAL30
VAL31
VAL87
| ||
| Current overlap | 6 | Native recall | 0.30 |
| Jaccard | 0.25 | RMSD | - |
| HB strict | 1 | Strict recall | 0.14 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
Protein summary
225 residues
| Protein target | T03 | Atoms | 3428 |
|---|---|---|---|
| Residues | 225 | Chains | 2 |
| Residue summary | LEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; NDP:74 | ||
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 380 | 1.2157029303091844 | -1.31937 | -22.3757 | 8 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 365 | 2.03476027107978 | -1.69221 | -27.2831 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 492 | 2.149058578081181 | -1.23753 | -21.0928 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 344 | 2.4482415740067793 | -1.45975 | -25.5076 | 10 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 368 | 2.7696457872585443 | -1.25917 | -21.824 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 377 | 3.074515803373726 | -1.38191 | -21.767 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 414 | 3.32166662867758 | -1.46812 | -21.6428 | 9 | 10 | 6 | 0.30 | 0.20 | - | no | Current |
| 395 | 3.6859088691304858 | -1.28583 | -23.0255 | 8 | 14 | 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
-21.643kcal/mol
Ligand efficiency (LE)
-1.1391kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.337
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
278.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.90
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.35kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
90.25kcal/mol
Minimised FF energy
76.90kcal/mol
SASA & burial
✓ computed
SASA (unbound)
485.9Ų
Total solvent-accessible surface area of free ligand
BSA total
402.8Ų
Buried surface area upon binding
BSA apolar
315.8Ų
Hydrophobic contacts buried
BSA polar
87.0Ų
Polar contacts buried
Fraction buried
82.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1354.9Ų
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
1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
854.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)