Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
20.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.67, Jaccard 0.56, H-bond role recall 0.40
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.767 kcal/mol/HA)
✓ Good fit quality (FQ -7.40)
✓ Good H-bonds (4 bonds)
✓ Deep burial (89% SASA buried)
✓ Lipophilic contacts well-matched (90%)
✗ High strain energy (20.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-23.017
kcal/mol
LE
-0.767
kcal/mol/HA
Fit Quality
-7.40
FQ (Leeson)
HAC
30
heavy atoms
MW
408
Da
LogP
4.84
cLogP
Interaction summary
HB 4
HY 24
PI 3
CLASH 2
Interaction summary
HB 4
HY 24
PI 3
CLASH 2
| Final rank | 2.671 | Score | -23.017 |
|---|---|---|---|
| Inter norm | -0.868 | Intra norm | 0.101 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 4 |
| Artifact reason | geometry warning; 13 clashes; 1 protein clash; moderate strain Δ 20.2 | ||
| Residues |
ARG29
GLU31
GLY117
ILE61
ILE8
LEU23
LEU28
LEU68
NAP201
PHE32
PHE35
PRO27
SER60
THR57
TRP25
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 | 14 | Native recall | 0.67 |
| Jaccard | 0.56 | RMSD | - |
| HB strict | 1 | Strict recall | 0.20 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 87 | 2.671195977857273 | -0.868004 | -23.0165 | 4 | 18 | 14 | 0.67 | 0.40 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.017kcal/mol
Ligand efficiency (LE)
-0.7672kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.401
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
408.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.84
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.24kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
105.22kcal/mol
Minimised FF energy
84.98kcal/mol
SASA & burial
✓ computed
SASA (unbound)
700.7Ų
Total solvent-accessible surface area of free ligand
BSA total
621.0Ų
Buried surface area upon binding
BSA apolar
559.0Ų
Hydrophobic contacts buried
BSA polar
62.0Ų
Polar contacts buried
Fraction buried
88.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
90.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1711.0Ų
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
593.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)