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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
9.9 kcal/mol
Protein clashes
3
Internal clashes
4
Native overlap
contact recall 0.86, Jaccard 0.82, H-bond role recall 0.20
Reason: no major geometry red flags detected
3 protein-contact clashes
4 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.977 kcal/mol/HA)
✓ Good fit quality (FQ -9.52)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (98%)
✗ Moderate strain (9.9 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Internal clashes (9)
Score
-30.298
kcal/mol
LE
-0.977
kcal/mol/HA
Fit Quality
-9.52
FQ (Leeson)
HAC
31
heavy atoms
MW
559
Da
LogP
6.72
cLogP
Interaction summary
HB 2
HY 24
PI 3
CLASH 4
Interaction summary
HB 2
HY 24
PI 3
CLASH 4
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 | 0.800 | Score | -30.298 |
|---|---|---|---|
| Inter norm | -0.934 | Intra norm | -0.044 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 2 |
| Artifact reason | geometry warning; 9 clashes; 4 protein contact clashes; 1 severe cofactor-context clash | ||
| Residues |
ALA10
ASP22
GLN36
GLU31
GLY21
ILE61
ILE8
LEU23
LEU28
NAP201
PHE32
PHE35
PRO62
SER60
THR137
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 | 18 | Native recall | 0.86 |
| Jaccard | 0.82 | RMSD | - |
| HB strict | 1 | Strict recall | 0.20 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 664 | 0.8004369919995663 | -0.933844 | -30.298 | 2 | 19 | 18 | 0.86 | 0.20 | - | no | Current |
| 675 | 0.9663918242020272 | -0.695012 | -17.6101 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 662 | 2.0882393819561376 | -0.939599 | -24.7443 | 3 | 21 | 18 | 0.86 | 0.60 | - | no | Open |
| 670 | 2.1198155062657644 | -0.77114 | -20.2531 | 3 | 19 | 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
-30.298kcal/mol
Ligand efficiency (LE)
-0.9774kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.522
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
558.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.72
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
9.87kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
61.39kcal/mol
Minimised FF energy
51.52kcal/mol
SASA & burial
✓ computed
SASA (unbound)
685.4Ų
Total solvent-accessible surface area of free ligand
BSA total
631.0Ų
Buried surface area upon binding
BSA apolar
620.1Ų
Hydrophobic contacts buried
BSA polar
10.9Ų
Polar contacts buried
Fraction buried
92.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
98.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1706.2Ų
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
645.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)