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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
17.2 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.76, Jaccard 0.67, H-bond role recall 0.00
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.819 kcal/mol/HA)
✓ Good fit quality (FQ -8.26)
✓ Good H-bonds (3 bonds)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Moderate strain (17.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-28.672
kcal/mol
LE
-0.819
kcal/mol/HA
Fit Quality
-8.26
FQ (Leeson)
HAC
35
heavy atoms
MW
491
Da
LogP
3.33
cLogP
Interaction summary
HB 3
HY 24
PI 1
CLASH 3
Interaction summary
HB 3
HY 24
PI 1
CLASH 3
| Final rank | 3.267 | Score | -28.672 |
|---|---|---|---|
| Inter norm | -0.816 | Intra norm | -0.003 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 3 |
| Artifact reason | geometry warning; 15 clashes; 1 protein clash | ||
| Residues |
ALA10
ARG29
ASP22
GLU31
ILE61
ILE8
LEU23
LEU28
NAP201
PHE32
PHE35
PRO27
PRO62
SER60
THR137
THR57
TYR122
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 | 16 | Native recall | 0.76 |
| Jaccard | 0.67 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 56 | 1.141485241918407 | -0.716303 | -22.4125 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 72 | 2.8975975898799016 | -0.86444 | -22.4337 | 11 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 115 | 3.2669415162115714 | -0.815922 | -28.6717 | 3 | 19 | 16 | 0.76 | 0.00 | - | no | Current |
| 108 | 3.806235438234106 | -0.795357 | -26.5783 | 4 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 66 | 5.077675768715562 | -0.959199 | -30.87 | 8 | 20 | 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
-28.672kcal/mol
Ligand efficiency (LE)
-0.8192kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.263
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
490.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.33
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.18kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
44.26kcal/mol
Minimised FF energy
27.08kcal/mol
SASA & burial
✓ computed
SASA (unbound)
793.7Ų
Total solvent-accessible surface area of free ligand
BSA total
691.7Ų
Buried surface area upon binding
BSA apolar
542.7Ų
Hydrophobic contacts buried
BSA polar
149.1Ų
Polar contacts buried
Fraction buried
87.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1680.0Ų
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
606.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)