Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
56.9 kcal/mol
Protein clashes
11
Internal clashes
11
Native overlap
contact recall 0.85, Jaccard 0.71, H-bond role recall 0.20
Reason: 11 protein-contact clashes, 11 internal clashes, strain 56.9 kcal/mol
strain ΔE 56.9 kcal/mol
11 protein-contact clashes
11 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Good LE (-0.330 kcal/mol/HA)
✓ Good fit quality (FQ -3.50)
✓ Good H-bonds (3 bonds)
✓ Deep burial (88% SASA buried)
✓ Lipophilic contacts well-matched (85%)
✗ Extreme strain energy (56.9 kcal/mol)
✗ Geometry warnings
✗ Severe protein-contact clashes (15)
✗ Many internal clashes (21)
Score
-14.167
kcal/mol
LE
-0.330
kcal/mol/HA
Fit Quality
-3.50
FQ (Leeson)
HAC
43
heavy atoms
MW
600
Da
LogP
5.27
cLogP
Interaction summary
HB 3
HY 24
PI 4
CLASH 11
Interaction summary
HB 3
HY 24
PI 4
CLASH 11
| Final rank | 4.101 | Score | -14.167 |
|---|---|---|---|
| Inter norm | -0.636 | Intra norm | 0.307 |
| Top1000 | no | Excluded | no |
| Contacts | 21 | H-bonds | 3 |
| Artifact reason | geometry warning; 21 clashes; 15 protein contact clashes; high strain Δ 56.8 | ||
| Residues |
ALA32
ARG97
ASP52
ILE45
LEU94
LYS57
LYS95
MET53
NDP301
PHE55
PHE56
PHE91
PRO93
THR180
THR54
TYR162
TYR178
VAL156
VAL30
VAL31
VAL87
| ||
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
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 | 17 | Native recall | 0.85 |
| Jaccard | 0.71 | 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 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 62 | 1.5867119734264483 | -0.597913 | -22.3579 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 63 | 1.9444565982844864 | -0.440864 | -16.2628 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 54 | 2.0122605666535036 | -0.586495 | -22.6203 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 66 | 4.100793611636282 | -0.636299 | -14.1672 | 3 | 21 | 17 | 0.85 | 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
-14.167kcal/mol
Ligand efficiency (LE)
-0.3295kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-3.502
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
43HA
Physicochemical properties
Molecular weight
599.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.27
Lipinski: ≤ 5
Rotatable bonds
13
Conformational strain (MMFF94s)
Strain energy (ΔE)
56.88kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
109.20kcal/mol
Minimised FF energy
52.32kcal/mol
SASA & burial
✓ computed
SASA (unbound)
910.4Ų
Total solvent-accessible surface area of free ligand
BSA total
804.6Ų
Buried surface area upon binding
BSA apolar
680.4Ų
Hydrophobic contacts buried
BSA polar
124.2Ų
Polar contacts buried
Fraction buried
88.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
84.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1803.5Ų
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
799.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)