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
18.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.76, Jaccard 0.73, H-bond role recall 0.40
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 (-1.183 kcal/mol/HA)
✓ Good fit quality (FQ -10.09)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ Moderate strain (18.4 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-24.848
kcal/mol
LE
-1.183
kcal/mol/HA
Fit Quality
-10.09
FQ (Leeson)
HAC
21
heavy atoms
MW
286
Da
LogP
2.28
cLogP
Interaction summary
HB 6
HY 14
PI 2
CLASH 3
Interaction summary
HB 6
HY 14
PI 2
CLASH 3
| Final rank | 2.866 | Score | -24.848 |
|---|---|---|---|
| Inter norm | -1.304 | Intra norm | 0.120 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 6 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes; 1 cofactor-context clash | ||
| Residues |
ALA10
ASP22
GLU31
GLY117
GLY21
ILE61
ILE8
LEU23
NAP201
PHE35
SER60
THR137
THR57
TYR122
TYR34
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 | 16 | Native recall | 0.76 |
| Jaccard | 0.73 | RMSD | - |
| HB strict | 2 | Strict recall | 0.40 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 432 | 1.222860932044016 | -1.53558 | -29.3424 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 507 | 2.8658798137281876 | -1.3035 | -24.8475 | 6 | 17 | 16 | 0.76 | 0.40 | - | no | Current |
| 464 | 2.896089366624946 | -1.21353 | -24.2204 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 473 | 2.991356188843517 | -1.35257 | -28.5222 | 12 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 447 | 3.4604292682728732 | -1.15154 | -23.9773 | 9 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 446 | 3.547725783304717 | -1.35351 | -28.2583 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 533 | 3.728277754062 | -1.13114 | -23.4955 | 8 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 418 | 3.7308293894761544 | -1.61054 | -34.097 | 11 | 12 | 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
-24.848kcal/mol
Ligand efficiency (LE)
-1.1832kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.092
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
286.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.28
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.43kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
95.66kcal/mol
Minimised FF energy
77.22kcal/mol
SASA & burial
✓ computed
SASA (unbound)
480.1Ų
Total solvent-accessible surface area of free ligand
BSA total
443.4Ų
Buried surface area upon binding
BSA apolar
308.5Ų
Hydrophobic contacts buried
BSA polar
134.9Ų
Polar contacts buried
Fraction buried
92.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1383.7Ų
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
630.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)