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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
68.1 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.81, Jaccard 0.71, H-bond role recall 0.60
Reason: strain 68.1 kcal/mol
strain ΔE 68.1 kcal/mol
2 protein-contact clashes
3 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Good fit quality (FQ -2.06)
✓ Deep burial (82% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Extreme strain energy (68.1 kcal/mol)
✗ Low LE (-0.186 kcal/mol/HA)
✗ Geometry warnings
✗ Many internal clashes (20)
Score
-9.650
kcal/mol
LE
-0.186
kcal/mol/HA
Fit Quality
-2.06
FQ (Leeson)
HAC
52
heavy atoms
MW
737
Da
LogP
-0.86
cLogP
Final rank
4.1076
rank score
Inter norm
-0.497
normalised
Contacts
20
H-bonds 5
Interaction summary
HBD 1
HBA 1
HY 8
PI 1
CLASH 3
Interaction summary
HBD 1
HBA 1
HY 8
PI 1
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
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 | 17 | Native recall | 0.81 |
| Jaccard | 0.71 | RMSD | - |
| HB strict | 3 | Strict recall | 0.60 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| HB same residue | 3 | HB residue recall | 0.60 |
Protein summary
200 residues
| Protein target | T02 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 90 | 4.1075721636921525 | -0.497227 | -9.64966 | 5 | 20 | 17 | 0.81 | 0.60 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-9.650kcal/mol
Ligand efficiency (LE)
-0.1856kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-2.056
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
52HA
Physicochemical properties
Molecular weight
736.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.86
Lipinski: ≤ 5
Rotatable bonds
14
Conformational strain (MMFF94s)
Strain energy (ΔE)
68.11kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
227.72kcal/mol
Minimised FF energy
159.61kcal/mol
SASA & burial
✓ computed
SASA (unbound)
946.2Ų
Total solvent-accessible surface area of free ligand
BSA total
777.7Ų
Buried surface area upon binding
BSA apolar
615.4Ų
Hydrophobic contacts buried
BSA polar
162.3Ų
Polar contacts buried
Fraction buried
82.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1850.2Ų
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
1677.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
594.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)