Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
25.1 kcal/mol
Protein clashes
0
Internal clashes
18
Native overlap
contact recall 0.57, Jaccard 0.50, H-bond role recall 0.17
Reason: 18 internal clashes
18 intramolecular clashes
38% of hydrophobic surface appears solvent-exposed (11/29 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.642 kcal/mol/HA)
✓ Good fit quality (FQ -6.58)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ High strain energy (25.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (18)
Score
-23.764
kcal/mol
LE
-0.642
kcal/mol/HA
Fit Quality
-6.58
FQ (Leeson)
HAC
37
heavy atoms
MW
501
Da
LogP
4.88
cLogP
Interaction summary
HB 7
HY 24
PI 2
CLASH 0
⚠ Exposure 37%
Interaction summary
HB 7
HY 24
PI 2
CLASH 0
⚠ Exposure 37%
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
No clash · clashes detected for this pose.
Partial hydrophobic solvent exposure
38% of hydrophobic surface appears solvent-exposed (11/29 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 29
Buried (contacted) 18
Exposed 11
LogP 4.88
H-bonds 7
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 3.068 | Score | -23.764 |
|---|---|---|---|
| Inter norm | -0.707 | Intra norm | 0.064 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 7 |
| Artifact reason | geometry warning; 18 clashes; 1 protein clash; moderate strain Δ 22.9 | ||
| Residues |
NDP301
ARG97
LEU94
LYS57
LYS90
LYS95
MET53
PHE56
PHE91
PRO88
SER86
THR61
THR83
VAL156
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 | 12 | Native recall | 0.57 |
| Jaccard | 0.50 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 1 | HB role recall | 0.17 |
| HB same residue | 1 | HB residue recall | 0.17 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 268 | 2.630079909973411 | -0.658079 | -24.0081 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 213 | 3.0676599310111645 | -0.706539 | -23.7641 | 7 | 15 | 12 | 0.57 | 0.17 | - | no | Current |
| 266 | 3.1777508227757316 | -0.572857 | -16.3154 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 262 | 3.3128101503028407 | -0.84944 | -24.9796 | 11 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 244 | 3.630597105528765 | -1.02914 | -36.652 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 243 | 3.6890132466315455 | -0.792634 | -27.6005 | 12 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 273 | 5.027501237967726 | -0.728973 | -21.3679 | 7 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 232 | 5.4201557790674135 | -0.722783 | -24.5446 | 5 | 18 | 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
-23.764kcal/mol
Ligand efficiency (LE)
-0.6423kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.576
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
500.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.88
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.07kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
124.11kcal/mol
Minimised FF energy
99.04kcal/mol
SASA & burial
✓ computed
SASA (unbound)
824.5Ų
Total solvent-accessible surface area of free ligand
BSA total
592.4Ų
Buried surface area upon binding
BSA apolar
477.7Ų
Hydrophobic contacts buried
BSA polar
114.7Ų
Polar contacts buried
Fraction buried
71.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3397.3Ų
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
4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1710.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)