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
46.8 kcal/mol
Protein clashes
3
Internal clashes
4
Native overlap
contact recall 0.90, Jaccard 0.79, H-bond role recall 0.00
Reason: strain 46.8 kcal/mol
strain ΔE 46.8 kcal/mol
3 protein-contact clashes
4 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.513 kcal/mol/HA)
✓ Good fit quality (FQ -5.39)
✓ Good H-bonds (4 bonds)
✓ Deep burial (93% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ Extreme strain energy (46.8 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (6)
✗ Many internal clashes (16)
Score
-21.044
kcal/mol
LE
-0.513
kcal/mol/HA
Fit Quality
-5.39
FQ (Leeson)
HAC
41
heavy atoms
MW
559
Da
LogP
6.18
cLogP
Interaction summary
HB 4
HY 24
PI 3
CLASH 4
Interaction summary
HB 4
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 | 2.184 | Score | -21.044 |
|---|---|---|---|
| Inter norm | -0.680 | Intra norm | 0.166 |
| Top1000 | no | Excluded | no |
| Contacts | 22 | H-bonds | 4 |
| Artifact reason | geometry warning; 16 clashes; 6 protein contact clashes; 1 cofactor-context clash; high strain Δ 46.8 | ||
| Residues |
ALA10
ASN65
ASP22
GLU31
GLY21
ILE61
ILE8
LEU23
LEU28
LEU68
NAP201
PHE32
PHE35
PRO27
PRO62
SER60
THR137
THR57
TYR122
TYR34
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 | 19 | Native recall | 0.90 |
| Jaccard | 0.79 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 246 | 1.8978868650394465 | -0.592392 | -18.8585 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 305 | 2.1837762661457223 | -0.679556 | -21.0444 | 4 | 22 | 19 | 0.90 | 0.00 | - | no | Current |
| 227 | 2.84966926701502 | -0.632613 | -22.6906 | 12 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 186 | 3.375695172911135 | -0.680519 | -21.3821 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 204 | 3.967053383673706 | -0.639174 | -23.0484 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 214 | 5.088743032232535 | -0.858939 | -31.7132 | 14 | 27 | 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
-21.044kcal/mol
Ligand efficiency (LE)
-0.5133kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.393
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
41HA
Physicochemical properties
Molecular weight
558.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.18
Lipinski: ≤ 5
Rotatable bonds
12
Conformational strain (MMFF94s)
Strain energy (ΔE)
46.80kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
141.55kcal/mol
Minimised FF energy
94.75kcal/mol
SASA & burial
✓ computed
SASA (unbound)
824.0Ų
Total solvent-accessible surface area of free ligand
BSA total
763.4Ų
Buried surface area upon binding
BSA apolar
639.3Ų
Hydrophobic contacts buried
BSA polar
124.1Ų
Polar contacts buried
Fraction buried
92.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1770.2Ų
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
598.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)