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
23.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.55, Jaccard 0.46, H-bond role recall 0.80
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.081 kcal/mol/HA)
✓ Good fit quality (FQ -9.22)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ High strain energy (23.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-22.690
kcal/mol
LE
-1.081
kcal/mol/HA
Fit Quality
-9.22
FQ (Leeson)
HAC
21
heavy atoms
MW
286
Da
LogP
1.63
cLogP
Interaction summary
HB 7
HY 24
PI 1
CLASH 2
Interaction summary
HB 7
HY 24
PI 1
CLASH 2
| Final rank | 3.185 | Score | -22.690 |
|---|---|---|---|
| Inter norm | -1.264 | Intra norm | 0.183 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 7 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes; moderate strain Δ 23.1 | ||
| Residues |
ALA32
ARG48
ASP52
GLY157
ILE45
MET53
NDP301
PHE56
THR83
TRP47
TYR162
VAL156
VAL30
VAL31
VAL49
| ||
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 | 11 | Native recall | 0.55 |
| Jaccard | 0.46 | RMSD | - |
| HB strict | 4 | Strict recall | 0.57 |
| HB same residue+role | 4 | HB role recall | 0.80 |
| HB same residue | 4 | HB residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 50 | 1.3773557262025864 | -1.4831 | -21.2071 | 8 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 90 | 3.1848668360044043 | -1.26395 | -22.6897 | 7 | 15 | 11 | 0.55 | 0.80 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-22.690kcal/mol
Ligand efficiency (LE)
-1.0805kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.216
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
286.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.63
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.09kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
112.55kcal/mol
Minimised FF energy
89.45kcal/mol
SASA & burial
✓ computed
SASA (unbound)
531.2Ų
Total solvent-accessible surface area of free ligand
BSA total
462.2Ų
Buried surface area upon binding
BSA apolar
354.4Ų
Hydrophobic contacts buried
BSA polar
107.7Ų
Polar contacts buried
Fraction buried
87.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1404.5Ų
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
832.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)