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
34.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.86, Jaccard 0.82, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.761 kcal/mol/HA)
✓ Good fit quality (FQ -7.62)
✓ Good H-bonds (4 bonds)
✓ Deep burial (88% SASA buried)
✓ Lipophilic contacts well-matched (88%)
✗ Very high strain energy (34.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-25.891
kcal/mol
LE
-0.761
kcal/mol/HA
Fit Quality
-7.62
FQ (Leeson)
HAC
34
heavy atoms
MW
489
Da
LogP
2.38
cLogP
Interaction summary
HB 4
HY 24
PI 1
CLASH 2
Interaction summary
HB 4
HY 24
PI 1
CLASH 2
| Final rank | 2.872 | Score | -25.891 |
|---|---|---|---|
| Inter norm | -0.853 | Intra norm | 0.092 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 4 |
| Artifact reason | geometry warning; 15 clashes; 1 protein clash; high strain Δ 34.9 | ||
| Residues |
ALA10
ASP22
GLN36
GLU31
GLY117
GLY21
ILE61
ILE8
LEU23
LEU68
NAP201
PHE32
PHE35
PRO27
SER60
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 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 299 | 1.270277674689491 | -0.790782 | -24.7584 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 271 | 1.4905750210783255 | -0.6785 | -19.7342 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 241 | 2.70855588526072 | -0.732684 | -25.8713 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 318 | 2.871521513199985 | -0.85308 | -25.8906 | 4 | 19 | 18 | 0.86 | 0.20 | - | no | Current |
| 201 | 3.5286327739905885 | -0.910439 | -24.7912 | 13 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 378 | 3.547138483489836 | -0.690767 | -21.3722 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 351 | 4.3080426726830545 | -0.782028 | -25.3532 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 178 | 4.807072804978598 | -0.807497 | -25.9908 | 6 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 298 | 5.138774342532221 | -0.552763 | -15.3157 | 8 | 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
-25.891kcal/mol
Ligand efficiency (LE)
-0.7615kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.619
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
488.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.38
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
34.91kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
118.97kcal/mol
Minimised FF energy
84.06kcal/mol
SASA & burial
✓ computed
SASA (unbound)
761.4Ų
Total solvent-accessible surface area of free ligand
BSA total
670.5Ų
Buried surface area upon binding
BSA apolar
591.4Ų
Hydrophobic contacts buried
BSA polar
79.1Ų
Polar contacts buried
Fraction buried
88.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
88.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1729.0Ų
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
604.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)