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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
17.2 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.67, Jaccard 0.58, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.779 kcal/mol/HA)
✓ Good fit quality (FQ -7.51)
✓ Good H-bonds (5 bonds)
✓ Deep burial (85% SASA buried)
✓ Lipophilic contacts well-matched (91%)
✗ Moderate strain (17.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-23.361
kcal/mol
LE
-0.779
kcal/mol/HA
Fit Quality
-7.51
FQ (Leeson)
HAC
30
heavy atoms
MW
469
Da
LogP
1.84
cLogP
Interaction summary
HB 5
HY 21
PI 2
CLASH 1
Interaction summary
HB 5
HY 21
PI 2
CLASH 1
| Final rank | 3.260 | Score | -23.361 |
|---|---|---|---|
| Inter norm | -0.863 | Intra norm | 0.084 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 5 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes | ||
| Residues |
ALA10
ARG29
ASP22
GLU31
GLY21
ILE61
ILE8
LEU23
LEU28
NAP201
PHE32
PHE35
PRO27
PRO62
SER60
TYR122
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 | 0.58 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 38 | 0.23260735759199924 | -1.01266 | -27.1093 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 31 | 0.33909315474714397 | -1.06707 | -28.7784 | 8 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 48 | 2.77195229334679 | -0.656087 | -16.4804 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 57 | 3.2600899578704263 | -0.863046 | -23.3609 | 5 | 17 | 14 | 0.67 | 0.20 | - | no | Current |
| 48 | 3.590920701421034 | -0.79323 | -22.6395 | 3 | 17 | 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
-23.361kcal/mol
Ligand efficiency (LE)
-0.7787kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.512
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
469.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.84
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.18kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
194.26kcal/mol
Minimised FF energy
177.08kcal/mol
SASA & burial
✓ computed
SASA (unbound)
652.6Ų
Total solvent-accessible surface area of free ligand
BSA total
556.7Ų
Buried surface area upon binding
BSA apolar
506.0Ų
Hydrophobic contacts buried
BSA polar
50.7Ų
Polar contacts buried
Fraction buried
85.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
90.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1625.5Ų
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
646.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)