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
20.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.62, Jaccard 0.54, H-bond role recall 0.33
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.057 kcal/mol/HA)
✓ Good fit quality (FQ -9.61)
✓ Good H-bonds (5 bonds)
✓ Deep burial (94% SASA buried)
✓ Lipophilic contacts well-matched (89%)
✗ High strain energy (20.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-26.421
kcal/mol
LE
-1.057
kcal/mol/HA
Fit Quality
-9.61
FQ (Leeson)
HAC
25
heavy atoms
MW
337
Da
LogP
2.15
cLogP
Interaction summary
HB 5
HY 24
PI 3
CLASH 2
Interaction summary
HB 5
HY 24
PI 3
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 | 2.111 | Score | -26.421 |
|---|---|---|---|
| Inter norm | -1.009 | Intra norm | -0.048 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 5 |
| Artifact reason | geometry warning; 10 clashes; 1 protein clash; moderate strain Δ 20.5 | ||
| Residues |
NDP301
ALA32
ARG48
ASP52
GLY157
ILE45
MET53
PHE56
THR83
TRP47
TYR162
VAL156
VAL30
VAL31
VAL49
VAL87
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 3CL9 | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
NDP301
ALA32
ARG97
ASP52
GLY157
ILE45
LEU94
LYS57
MET53
PHE55
PHE56
PHE91
PRO88
SER86
THR180
THR83
TYR162
VAL156
VAL30
VAL31
VAL87
| ||
| Current overlap | 13 | Native recall | 0.62 |
| Jaccard | 0.54 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 2 | HB role recall | 0.33 |
| HB same residue | 2 | HB residue recall | 0.33 |
Protein summary
511 residues
| Protein target | T09 | Atoms | 8170 |
|---|---|---|---|
| Residues | 511 | Chains | 2 |
| Residue summary | LEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224 | ||
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 183 | 1.7509119923625154 | -1.01084 | -26.5641 | 5 | 16 | 13 | 0.62 | 0.33 | - | no | Open |
| 182 | 2.1106047773675534 | -1.00926 | -26.421 | 5 | 16 | 13 | 0.62 | 0.33 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-26.421kcal/mol
Ligand efficiency (LE)
-1.0568kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.608
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
337.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.15
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.53kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
65.89kcal/mol
Minimised FF energy
45.36kcal/mol
SASA & burial
✓ computed
SASA (unbound)
590.2Ų
Total solvent-accessible surface area of free ligand
BSA total
552.0Ų
Buried surface area upon binding
BSA apolar
489.4Ų
Hydrophobic contacts buried
BSA polar
62.6Ų
Polar contacts buried
Fraction buried
93.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
88.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3286.4Ų
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
4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1669.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)