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
17.2 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 1.00, Jaccard 0.89, H-bond role recall 0.70
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 (-1.322 kcal/mol/HA)
✓ Good fit quality (FQ -10.60)
✓ Strong H-bond network (14 bonds)
✓ Deep burial (89% SASA buried)
✓ Lipophilic contacts well-matched (68%)
✗ Moderate strain (17.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-23.802
kcal/mol
LE
-1.322
kcal/mol/HA
Fit Quality
-10.60
FQ (Leeson)
HAC
18
heavy atoms
MW
265
Da
LogP
0.45
cLogP
Interaction summary
HB 14
HY 6
PI 5
CLASH 3
Interaction summary
HB 14
HY 6
PI 5
CLASH 3
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 | 2.770 | Score | -23.802 |
|---|---|---|---|
| Inter norm | -1.517 | Intra norm | 0.195 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 14 |
| Artifact reason | geometry warning; 6 clashes; 2 protein clashes | ||
| Residues |
ARG140
ARG144
ASN106
HIS105
HIS141
MET101
ARG46
ASP13
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
ILE76
MET78
SER74
TYR49
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6FXS | Contacts | 16 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG140
ARG144
ASN106
HIS105
HIS141
ARG46
ASP13
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
ILE76
SER74
TYR49
| ||
| Current overlap | 16 | Native recall | 1.00 |
| Jaccard | 0.89 | RMSD | - |
| HB strict | 7 | Strict recall | 0.58 |
| HB same residue+role | 7 | HB role recall | 0.70 |
| HB same residue | 8 | HB residue recall | 0.80 |
Protein summary
302 residues
| Protein target | T12 | Atoms | 4598 |
|---|---|---|---|
| Residues | 302 | Chains | 2 |
| Residue summary | ARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121 | ||
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:CSD72
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 454 | -0.21749554397758344 | -1.75178 | -24.6391 | 12 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 480 | 2.44337014472352 | -1.42438 | -24.2473 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 465 | 2.7704179659118466 | -1.51719 | -23.8017 | 14 | 18 | 16 | 1.00 | 0.70 | - | no | Current |
| 466 | 4.00752394528947 | -1.47405 | -18.6377 | 16 | 17 | 5 | 0.31 | 0.30 | - | no | Open |
| 472 | 4.108278491893934 | -1.92763 | -25.3542 | 12 | 20 | 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
-23.802kcal/mol
Ligand efficiency (LE)
-1.3223kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.597
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
18HA
Physicochemical properties
Molecular weight
265.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.45
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.20kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-184.67kcal/mol
Minimised FF energy
-201.86kcal/mol
SASA & burial
✓ computed
SASA (unbound)
472.9Ų
Total solvent-accessible surface area of free ligand
BSA total
420.9Ų
Buried surface area upon binding
BSA apolar
285.9Ų
Hydrophobic contacts buried
BSA polar
135.0Ų
Polar contacts buried
Fraction buried
89.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
67.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2013.4Ų
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
2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
766.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)