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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
60.8 kcal/mol
Protein clashes
0
Internal clashes
17
Native overlap
contact recall 0.67, Jaccard 0.61, H-bond role recall 0.00
Reason: 17 internal clashes, strain 60.8 kcal/mol
strain ΔE 60.8 kcal/mol
17 intramolecular clashes
35% of hydrophobic surface appears solvent-exposed (14/40 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.524 kcal/mol/HA)
✓ Good fit quality (FQ -5.60)
✓ Deep burial (78% SASA buried)
✓ Lipophilic contacts well-matched (100%)
✗ Extreme strain energy (60.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (17)
Score
-23.060
kcal/mol
LE
-0.524
kcal/mol/HA
Fit Quality
-5.60
FQ (Leeson)
HAC
44
heavy atoms
MW
585
Da
LogP
7.63
cLogP
Interaction summary
HB 2
HY 24
PI 1
CLASH 0
⚠ Exposure 35%
Interaction summary
HB 2
HY 24
PI 1
CLASH 0
⚠ Exposure 35%
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
35% of hydrophobic surface appears solvent-exposed (14/40 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 40
Buried (contacted) 26
Exposed 14
LogP 7.63
H-bonds 2
Exposed fragments:
phenyl (4/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (6 atoms exposed)
| Final rank | 1.598 | Score | -23.060 |
|---|---|---|---|
| Inter norm | -0.635 | Intra norm | 0.111 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 2 |
| Artifact reason | geometry warning; 17 clashes; 1 protein contact clash; 1 cofactor-context clash; high strain Δ 54.1 | ||
| Residues |
ASN65
GLU31
ILE61
ILE8
LEU23
LEU28
NAP201
PHE32
PHE35
PRO27
PRO62
SER60
THR57
TYR122
VAL116
VAL9
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 5SD8 | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA10
ASN65
ASP22
GLN36
GLU31
GLY117
GLY21
ILE61
ILE8
LEU23
LEU68
NAP201
PHE32
PHE35
PRO62
SER60
THR137
THR57
TYR122
VAL116
VAL9
| ||
| Current overlap | 14 | Native recall | 0.67 |
| Jaccard | 0.61 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
Protein summary
200 residues
| Protein target | T01 | Atoms | 3128 |
|---|---|---|---|
| Residues | 200 | Chains | 2 |
| Residue summary | LYS:374; LEU:361; GLU:240; VAL:224; ARG:192; PHE:180; ILE:171; PRO:168; ASN:140; SER:132; TYR:126; GLN:119; ASP:108; MET:102; THR:98; GLY:91 | ||
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:NAP201
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 298 | 1.5980247116679025 | -0.634928 | -23.0597 | 2 | 16 | 14 | 0.67 | 0.00 | - | no | Current |
| 278 | 1.754394841648101 | -0.579766 | -22.3914 | 2 | 18 | 16 | 0.76 | 0.00 | - | no | Open |
| 247 | 3.2222901339255166 | -0.475706 | -16.6641 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 335 | 4.130698106402877 | -0.539598 | -22.034 | 3 | 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
-23.060kcal/mol
Ligand efficiency (LE)
-0.5241kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.600
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
44HA
Physicochemical properties
Molecular weight
584.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
7.63
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
60.78kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
185.97kcal/mol
Minimised FF energy
125.19kcal/mol
SASA & burial
✓ computed
SASA (unbound)
902.0Ų
Total solvent-accessible surface area of free ligand
BSA total
704.7Ų
Buried surface area upon binding
BSA apolar
701.6Ų
Hydrophobic contacts buried
BSA polar
3.0Ų
Polar contacts buried
Fraction buried
78.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
99.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1940.7Ų
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
1677.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
635.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)