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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
22.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.80, Jaccard 0.73, H-bond role recall 0.60
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.871 kcal/mol/HA)
✓ Good fit quality (FQ -8.71)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (86%)
✗ High strain energy (22.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-29.605
kcal/mol
LE
-0.871
kcal/mol/HA
Fit Quality
-8.71
FQ (Leeson)
HAC
34
heavy atoms
MW
469
Da
LogP
6.09
cLogP
Interaction summary
HB 6
HY 24
PI 0
CLASH 1
Interaction summary
HB 6
HY 24
PI 0
CLASH 1
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
| Final rank | 2.257 | Score | -29.605 |
|---|---|---|---|
| Inter norm | -0.850 | Intra norm | -0.020 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 6 |
| Artifact reason | geometry warning; 11 clashes; 1 protein clash; 1 cofactor-context clash; moderate strain Δ 22.9 | ||
| Residues |
ALA32
ARG97
ASP52
ILE45
LEU94
LYS57
LYS95
MET53
NDP301
PHE56
PHE91
PRO88
PRO93
TYR162
VAL156
VAL30
VAL31
VAL87
| ||
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 | 16 | Native recall | 0.80 |
| Jaccard | 0.73 | RMSD | - |
| HB strict | 3 | Strict recall | 0.43 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| HB same residue | 3 | HB residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 28 | 2.257322713487879 | -0.850289 | -29.6049 | 6 | 18 | 16 | 0.80 | 0.60 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-29.605kcal/mol
Ligand efficiency (LE)
-0.8707kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.712
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
468.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.09
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.89kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
43.41kcal/mol
Minimised FF energy
20.52kcal/mol
SASA & burial
✓ computed
SASA (unbound)
727.3Ų
Total solvent-accessible surface area of free ligand
BSA total
665.7Ų
Buried surface area upon binding
BSA apolar
572.9Ų
Hydrophobic contacts buried
BSA polar
92.8Ų
Polar contacts buried
Fraction buried
91.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
86.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1670.3Ų
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
784.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)