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 strong
SASA done
Strain ΔE
15.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.57, Jaccard 0.46, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.115 kcal/mol/HA)
✓ Good fit quality (FQ -10.40)
✓ Good H-bonds (3 bonds)
✓ Deep burial (82% SASA buried)
✓ Lipophilic contacts well-matched (89%)
✗ Moderate strain (15.0 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Internal clashes (9)
Score
-30.099
kcal/mol
LE
-1.115
kcal/mol/HA
Fit Quality
-10.40
FQ (Leeson)
HAC
27
heavy atoms
MW
415
Da
LogP
5.34
cLogP
Interaction summary
HB 3
HY 24
PI 3
CLASH 1
Interaction summary
HB 3
HY 24
PI 3
CLASH 1
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
| Final rank | 0.611 | Score | -30.099 |
|---|---|---|---|
| Inter norm | -1.150 | Intra norm | 0.035 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 3 |
| Artifact reason | geometry warning; 9 clashes; 4 protein contact clashes | ||
| Residues |
ALA10
ARG29
ASN65
GLU31
ILE8
LEU23
LEU28
NAP201
PHE32
PHE35
PRO27
THR137
TRP25
TYR122
TYR34
VAL116
VAL9
| ||
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 | 12 | Native recall | 0.57 |
| Jaccard | 0.46 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 569 | 0.5131596875696631 | -1.1201 | -30.2913 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 578 | 0.6110929766522484 | -1.15007 | -30.0985 | 3 | 17 | 12 | 0.57 | 0.20 | - | no | Current |
| 572 | 2.276295995643403 | -1.07847 | -29.4348 | 7 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 578 | 2.3195254778524115 | -1.02963 | -28.1488 | 3 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 575 | 3.1058572745469006 | -1.01781 | -27.1998 | 7 | 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
-30.099kcal/mol
Ligand efficiency (LE)
-1.1148kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.400
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
415.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.34
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.01kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
57.83kcal/mol
Minimised FF energy
42.83kcal/mol
SASA & burial
✓ computed
SASA (unbound)
635.7Ų
Total solvent-accessible surface area of free ligand
BSA total
524.0Ų
Buried surface area upon binding
BSA apolar
464.4Ų
Hydrophobic contacts buried
BSA polar
59.7Ų
Polar contacts buried
Fraction buried
82.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
88.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1600.6Ų
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
644.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)