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 mixed
SASA done
Strain ΔE
12.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.52, Jaccard 0.42, H-bond role recall 0.17
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.973 kcal/mol/HA)
✓ Good fit quality (FQ -9.19)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (83% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Moderate strain (12.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-27.247
kcal/mol
LE
-0.973
kcal/mol/HA
Fit Quality
-9.19
FQ (Leeson)
HAC
28
heavy atoms
MW
372
Da
LogP
5.11
cLogP
Interaction summary
HB 9
HY 24
PI 1
CLASH 1
Interaction summary
HB 9
HY 24
PI 1
CLASH 1
| Final rank | 3.178 | Score | -27.247 |
|---|---|---|---|
| Inter norm | -1.146 | Intra norm | 0.173 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 9 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes; 1 severe cofactor-context clash | ||
| Residues |
NDP301
ARG97
GLU43
ILE45
LEU94
LYS57
LYS90
LYS95
MET53
PHE56
PHE91
PRO88
PRO93
SER44
SER86
VAL87
| ||
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
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 | 11 | Native recall | 0.52 |
| Jaccard | 0.42 | RMSD | - |
| HB strict | 1 | Strict recall | 0.14 |
| HB same residue+role | 1 | HB role recall | 0.17 |
| HB same residue | 1 | HB residue recall | 0.17 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 385 | 1.2860520499306085 | -0.813745 | -15.6987 | 9 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 319 | 1.9323249343972482 | -1.23626 | -33.0227 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 345 | 2.215341088437669 | -1.04016 | -25.1848 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 346 | 3.1777867617016966 | -1.14625 | -27.2467 | 9 | 16 | 11 | 0.52 | 0.17 | - | no | Current |
| 338 | 3.2462078515503885 | -0.921637 | -21.1922 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 354 | 3.5510777675708924 | -0.838749 | -16.1268 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 455 | 3.653448925064978 | -0.888525 | -22.8681 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 339 | 3.8969988921781593 | -0.848867 | -11.9956 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-27.247kcal/mol
Ligand efficiency (LE)
-0.9731kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.186
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
372.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.11
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.70kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
82.39kcal/mol
Minimised FF energy
69.69kcal/mol
SASA & burial
✓ computed
SASA (unbound)
652.5Ų
Total solvent-accessible surface area of free ligand
BSA total
543.1Ų
Buried surface area upon binding
BSA apolar
421.8Ų
Hydrophobic contacts buried
BSA polar
121.3Ų
Polar contacts buried
Fraction buried
83.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3229.2Ų
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
1709.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)