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
54.4 kcal/mol
Protein clashes
7
Internal clashes
8
Native overlap
contact recall 0.81, Jaccard 0.71, H-bond role recall 0.60
Reason: 8 internal clashes, strain 54.4 kcal/mol
strain ΔE 54.4 kcal/mol
7 protein-contact clashes
8 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.712 kcal/mol/HA)
✓ Good fit quality (FQ -7.07)
✓ Good H-bonds (4 bonds)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (91%)
✗ Extreme strain energy (54.4 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (8)
✗ Many internal clashes (14)
Score
-23.506
kcal/mol
LE
-0.712
kcal/mol/HA
Fit Quality
-7.07
FQ (Leeson)
HAC
33
heavy atoms
MW
570
Da
LogP
5.87
cLogP
Interaction summary
HB 4
HY 24
PI 3
CLASH 8
Interaction summary
HB 4
HY 24
PI 3
CLASH 8
| Final rank | 2.005 | Score | -23.506 |
|---|---|---|---|
| Inter norm | -0.854 | Intra norm | 0.142 |
| Top1000 | no | Excluded | no |
| Contacts | 20 | H-bonds | 4 |
| Artifact reason | geometry warning; 14 clashes; 8 protein contact clashes; 1 cofactor-context clash; high strain Δ 54.4 | ||
| Residues |
ALA10
ASP22
GLN36
GLU31
ILE61
ILE8
LEU23
LEU28
NAP201
PHE32
PHE35
PRO62
SER60
THR137
THR57
TRP25
TYR122
TYR34
VAL116
VAL9
| ||
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
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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 673 | 1.460630730191666 | -0.813316 | -18.0703 | 3 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 671 | 1.5175650898083437 | -0.742418 | -22.6673 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 663 | 2.0045850519298334 | -0.854055 | -23.5055 | 4 | 20 | 17 | 0.81 | 0.60 | - | no | Current |
| 664 | 2.531186904045026 | -0.715777 | -14.365 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 676 | 2.8347073317741125 | -0.638957 | -16.7356 | 3 | 10 | 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
-23.506kcal/mol
Ligand efficiency (LE)
-0.7123kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.067
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
570.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.87
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
54.37kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
108.78kcal/mol
Minimised FF energy
54.41kcal/mol
SASA & burial
✓ computed
SASA (unbound)
748.7Ų
Total solvent-accessible surface area of free ligand
BSA total
686.0Ų
Buried surface area upon binding
BSA apolar
623.9Ų
Hydrophobic contacts buried
BSA polar
62.1Ų
Polar contacts buried
Fraction buried
91.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
90.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1725.9Ų
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
619.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)