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 mixed
SASA done
Strain ΔE
13.2 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.52, Jaccard 0.44, H-bond role recall 0.00
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.052 kcal/mol/HA)
✓ Good fit quality (FQ -9.43)
✓ Deep burial (85% SASA buried)
✓ Lipophilic contacts well-matched (67%)
✗ Moderate strain (13.2 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Internal clashes (6)
Score
-25.241
kcal/mol
LE
-1.052
kcal/mol/HA
Fit Quality
-9.43
FQ (Leeson)
HAC
24
heavy atoms
MW
354
Da
LogP
4.65
cLogP
Interaction summary
HB 2
HY 24
PI 3
CLASH 1
Interaction summary
HB 2
HY 24
PI 3
CLASH 1
| Final rank | 0.045 | Score | -25.241 |
|---|---|---|---|
| Inter norm | -1.090 | Intra norm | 0.039 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 2 |
| Artifact reason | geometry warning; 6 clashes; 2 protein contact clashes | ||
| Residues |
ALA10
ARG29
GLU31
ILE8
LEU23
LEU28
NAP201
PHE32
PHE35
PRO27
THR137
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 | 11 | Native recall | 0.52 |
| Jaccard | 0.44 | 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
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 389 | -0.18784752275886354 | -1.01592 | -23.8653 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 480 | 0.044810234807672045 | -1.09043 | -25.2406 | 2 | 15 | 11 | 0.52 | 0.00 | - | no | Current |
| 471 | 0.05669390183562073 | -1.09591 | -25.194 | 3 | 16 | 12 | 0.57 | 0.00 | - | no | Open |
| 419 | 0.2488068813182308 | -1.18196 | -27.8753 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 441 | 1.2946467321758754 | -1.18634 | -27.2383 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 383 | 2.0117884778778174 | -1.01577 | -22.8536 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 372 | 2.25182953308986 | -1.35937 | -32.3799 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 390 | 2.8542622317418695 | -1.17081 | -26.8659 | 9 | 15 | 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
-25.241kcal/mol
Ligand efficiency (LE)
-1.0517kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.425
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
354.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.65
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.22kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
17.25kcal/mol
Minimised FF energy
4.03kcal/mol
SASA & burial
✓ computed
SASA (unbound)
592.1Ų
Total solvent-accessible surface area of free ligand
BSA total
503.8Ų
Buried surface area upon binding
BSA apolar
337.5Ų
Hydrophobic contacts buried
BSA polar
166.3Ų
Polar contacts buried
Fraction buried
85.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
67.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1497.2Ų
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
606.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)