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
14.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.35, Jaccard 0.30, 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 (-0.984 kcal/mol/HA)
✓ Good fit quality (FQ -8.82)
✓ Good H-bonds (4 bonds)
✓ Deep burial (73% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Moderate strain (14.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-23.613
kcal/mol
LE
-0.984
kcal/mol/HA
Fit Quality
-8.82
FQ (Leeson)
HAC
24
heavy atoms
MW
402
Da
LogP
4.42
cLogP
Interaction summary
HB 4
HY 18
PI 1
CLASH 2
Interaction summary
HB 4
HY 18
PI 1
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 | 2.995 | Score | -23.613 |
|---|---|---|---|
| Inter norm | -1.107 | Intra norm | 0.124 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 4 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes | ||
| Residues |
ARG97
LEU94
LYS57
LYS90
LYS95
MET53
PHE56
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 | 7 | Native recall | 0.35 |
| Jaccard | 0.30 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 29 | 0.13111952234188723 | -1.3806 | -31.136 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 30 | 0.7591190398503808 | -0.940797 | -16.8599 | 7 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 26 | 0.9544002616823256 | -1.29256 | -28.8045 | 8 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 19 | 1.1294901416468546 | -1.00522 | -19.339 | 1 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 12 | 1.7775808264988386 | -1.07097 | -24.5001 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 23 | 2.9951677238743564 | -1.10745 | -23.6127 | 4 | 10 | 7 | 0.35 | 0.20 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.613kcal/mol
Ligand efficiency (LE)
-0.9839kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.817
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
401.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.42
Lipinski: ≤ 5
Rotatable bonds
2
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.64kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
122.28kcal/mol
Minimised FF energy
107.64kcal/mol
SASA & burial
✓ computed
SASA (unbound)
536.7Ų
Total solvent-accessible surface area of free ligand
BSA total
391.2Ų
Buried surface area upon binding
BSA apolar
307.5Ų
Hydrophobic contacts buried
BSA polar
83.7Ų
Polar contacts buried
Fraction buried
72.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1323.3Ų
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
947.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)