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 medium
Native strong
SASA done
Strain ΔE
19.6 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.90, Jaccard 0.86, H-bond role recall 0.60
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.869 kcal/mol/HA)
✓ Good fit quality (FQ -8.20)
✓ Good H-bonds (4 bonds)
✓ Deep burial (93% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Moderate strain (19.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-24.324
kcal/mol
LE
-0.869
kcal/mol/HA
Fit Quality
-8.20
FQ (Leeson)
HAC
28
heavy atoms
MW
384
Da
LogP
4.16
cLogP
Interaction summary
HB 4
HY 24
PI 1
CLASH 3
Interaction summary
HB 4
HY 24
PI 1
CLASH 3
| Final rank | 2.918 | Score | -24.324 |
|---|---|---|---|
| Inter norm | -1.053 | Intra norm | 0.185 |
| Top1000 | no | Excluded | no |
| Contacts | 20 | H-bonds | 4 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes | ||
| Residues |
ALA10
ASN65
ASP22
GLN36
GLU31
GLY21
ILE115
ILE61
ILE8
LEU23
LEU68
NAP201
PHE32
PHE35
PRO62
SER60
THR57
TYR122
VAL116
VAL9
| ||
Protein summary
200 residues
| Protein target | T02 | 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 | 19 | Native recall | 0.90 |
| Jaccard | 0.86 | RMSD | - |
| HB strict | 3 | Strict recall | 0.60 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| HB same residue | 3 | HB residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 483 | 1.0853100332132994 | -1.15783 | -26.9741 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 533 | 1.3030885157662433 | -0.984884 | -24.6447 | 3 | 20 | 17 | 0.81 | 0.00 | - | no | Open |
| 539 | 1.3153312150478562 | -0.956507 | -24.115 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 468 | 1.4983376621522455 | -1.21454 | -29.8472 | 7 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 487 | 1.829623080713065 | -0.906153 | -22.6394 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 522 | 1.886285713477351 | -0.843689 | -17.4728 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 527 | 2.9175440723674373 | -1.05324 | -24.3241 | 4 | 20 | 19 | 0.90 | 0.60 | - | no | Current |
| 456 | 3.0916468248736995 | -1.03596 | -27.5073 | 4 | 16 | 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
-24.324kcal/mol
Ligand efficiency (LE)
-0.8687kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.201
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
384.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.16
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.61kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
98.00kcal/mol
Minimised FF energy
78.39kcal/mol
SASA & burial
✓ computed
SASA (unbound)
655.3Ų
Total solvent-accessible surface area of free ligand
BSA total
610.9Ų
Buried surface area upon binding
BSA apolar
480.9Ų
Hydrophobic contacts buried
BSA polar
130.0Ų
Polar contacts buried
Fraction buried
93.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1577.2Ų
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
615.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)