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
14.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.52, Jaccard 0.44, H-bond role recall 0.40
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.259 kcal/mol/HA)
✓ Good fit quality (FQ -10.53)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (86% SASA buried)
✓ Lipophilic contacts well-matched (62%)
✗ Moderate strain (14.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-25.171
kcal/mol
LE
-1.259
kcal/mol/HA
Fit Quality
-10.53
FQ (Leeson)
HAC
20
heavy atoms
MW
313
Da
LogP
0.40
cLogP
Interaction summary
HB 6
HY 17
PI 2
CLASH 1
Interaction summary
HB 6
HY 17
PI 2
CLASH 1
| Final rank | 3.353 | Score | -25.171 |
|---|---|---|---|
| Inter norm | -1.357 | Intra norm | 0.099 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 6 |
| Artifact reason | geometry warning; 7 clashes; 3 protein clashes | ||
| Residues |
ALA10
ARG29
GLU31
GLY117
ILE8
LEU23
LEU28
NAP201
PHE32
PHE35
PRO27
THR57
TRP25
TYR122
VAL116
| ||
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 | 1 | Strict recall | 0.20 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 256 | 0.15772456433515986 | -1.39322 | -27.5062 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 326 | 1.7660606604934106 | -1.01819 | -19.6306 | 9 | 8 | 0 | 0.00 | 0.00 | - | no | Open |
| 277 | 1.8546395330541607 | -1.1627 | -22.7243 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 335 | 1.9539662524601658 | -1.4959 | -28.3343 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 298 | 2.257908716162415 | -1.0958 | -22.0596 | 7 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 400 | 2.419978712999776 | -1.28962 | -25.9234 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 274 | 2.725557170482087 | -1.20833 | -23.6186 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 372 | 2.95166993836523 | -1.43344 | -26.7737 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 256 | 3.0930541913905487 | -1.30737 | -26.3803 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 336 | 3.114127828859795 | -1.30283 | -25.5336 | 6 | 15 | 11 | 0.52 | 0.40 | - | no | Open |
| 348 | 3.3534428929750644 | -1.35737 | -25.171 | 6 | 15 | 11 | 0.52 | 0.40 | - | no | Current |
| 320 | 3.4590025533125908 | -1.2212 | -24.8485 | 8 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 230 | 3.7784047479922487 | -1.38875 | -26.8164 | 11 | 13 | 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
-25.171kcal/mol
Ligand efficiency (LE)
-1.2586kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.532
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
20HA
Physicochemical properties
Molecular weight
313.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.40
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.83kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-94.69kcal/mol
Minimised FF energy
-109.53kcal/mol
SASA & burial
✓ computed
SASA (unbound)
489.5Ų
Total solvent-accessible surface area of free ligand
BSA total
422.2Ų
Buried surface area upon binding
BSA apolar
262.4Ų
Hydrophobic contacts buried
BSA polar
159.8Ų
Polar contacts buried
Fraction buried
86.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
62.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1365.5Ų
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
600.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)