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
19.0 kcal/mol
Protein clashes
0
Internal clashes
4
Native overlap
contact recall 0.62, Jaccard 0.54, H-bond role recall 0.20
Reason: no major geometry red flags detected
4 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.870 kcal/mol/HA)
✓ Good fit quality (FQ -8.01)
✓ Good H-bonds (4 bonds)
✓ Deep burial (84% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ Moderate strain (19.0 kcal/mol)
✗ Geometry warnings
Score
-22.608
kcal/mol
LE
-0.870
kcal/mol/HA
Fit Quality
-8.01
FQ (Leeson)
HAC
26
heavy atoms
MW
350
Da
LogP
2.45
cLogP
Interaction summary
HB 4
HY 16
PI 2
CLASH 0
Interaction summary
HB 4
HY 16
PI 2
CLASH 0
| Final rank | 1.122 | Score | -22.608 |
|---|---|---|---|
| Inter norm | -0.984 | Intra norm | 0.115 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 4 |
| Artifact reason | geometry warning; 4 clashes; 1 protein clash; 1 cofactor-context clash | ||
| Residues |
ALA10
ASP22
GLY21
ILE61
ILE8
LEU23
NAP201
PHE35
PRO26
PRO27
SER60
THR57
TRP25
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 | 13 | Native recall | 0.62 |
| Jaccard | 0.54 | RMSD | - |
| HB strict | 1 | Strict recall | 0.20 |
| 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
No clash · clashes detected for this pose.
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 232 | 0.22512664578509115 | -0.982056 | -23.3495 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 203 | 0.6142823023382752 | -1.00213 | -23.6948 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 285 | 1.1222800013457437 | -0.984396 | -22.608 | 4 | 16 | 13 | 0.62 | 0.20 | - | no | Current |
| 238 | 1.9179388927226144 | -1.20382 | -29.2649 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 234 | 2.1949120016563737 | -1.18622 | -28.0822 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 341 | 2.442548170009624 | -0.972273 | -22.0173 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 213 | 2.9637696841486436 | -1.24057 | -28.6769 | 16 | 24 | 0 | 0.00 | 0.00 | - | no | Open |
| 167 | 3.258232707517787 | -1.05416 | -24.6519 | 12 | 18 | 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
-22.608kcal/mol
Ligand efficiency (LE)
-0.8695kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.011
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
350.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.45
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.03kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
44.62kcal/mol
Minimised FF energy
25.59kcal/mol
SASA & burial
✓ computed
SASA (unbound)
634.0Ų
Total solvent-accessible surface area of free ligand
BSA total
531.1Ų
Buried surface area upon binding
BSA apolar
431.6Ų
Hydrophobic contacts buried
BSA polar
99.5Ų
Polar contacts buried
Fraction buried
83.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1598.4Ų
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
614.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)