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
39.8 kcal/mol
Protein clashes
0
Internal clashes
1
Native overlap
contact recall 0.62, Jaccard 0.57, H-bond role recall 0.00
Reason: no major geometry red flags detected
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.773 kcal/mol/HA)
✓ Good fit quality (FQ -7.53)
✓ Good H-bonds (3 bonds)
✓ Deep burial (89% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Very high strain energy (39.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-23.968
kcal/mol
LE
-0.773
kcal/mol/HA
Fit Quality
-7.53
FQ (Leeson)
HAC
31
heavy atoms
MW
459
Da
LogP
2.69
cLogP
Interaction summary
HB 3
HY 20
PI 0
CLASH 1
Interaction summary
HB 3
HY 20
PI 0
CLASH 1
| Final rank | 1.871 | Score | -23.968 |
|---|---|---|---|
| Inter norm | -0.873 | Intra norm | 0.100 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 3 |
| Artifact reason | geometry warning; 14 clashes; 1 protein clash; 1 severe cofactor-context clash; high strain Δ 39.8 | ||
| Residues |
ALA10
ASP22
GLN36
GLU31
GLY21
LEU23
NAP201
PHE32
PHE35
PRO27
SER60
THR57
TRP25
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 | 13 | Native recall | 0.62 |
| Jaccard | 0.57 | 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
No pi · π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 499 | 1.0099905898902652 | -1.00847 | -31.9657 | 3 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 544 | 1.8707408514739288 | -0.873227 | -23.9678 | 3 | 15 | 13 | 0.62 | 0.00 | - | no | Current |
| 496 | 2.170819513886973 | -0.869805 | -28.1543 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 510 | 2.353591927718863 | -1.04293 | -27.5315 | 10 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 493 | 3.5588482312512713 | -1.13358 | -35.258 | 7 | 22 | 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
-23.968kcal/mol
Ligand efficiency (LE)
-0.7732kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.532
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
458.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.69
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
39.78kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
29.11kcal/mol
Minimised FF energy
-10.66kcal/mol
SASA & burial
✓ computed
SASA (unbound)
678.7Ų
Total solvent-accessible surface area of free ligand
BSA total
604.4Ų
Buried surface area upon binding
BSA apolar
450.8Ų
Hydrophobic contacts buried
BSA polar
153.7Ų
Polar contacts buried
Fraction buried
89.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1574.1Ų
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
622.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)