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
18.5 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.75, Jaccard 0.63, H-bond role recall 0.40
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.419 kcal/mol/HA)
✓ Good fit quality (FQ -11.37)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (97% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ Moderate strain (18.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-25.545
kcal/mol
LE
-1.419
kcal/mol/HA
Fit Quality
-11.37
FQ (Leeson)
HAC
18
heavy atoms
MW
239
Da
LogP
2.01
cLogP
Interaction summary
HB 10
HY 13
PI 3
CLASH 5
Interaction summary
HB 10
HY 13
PI 3
CLASH 5
| Final rank | 2.260 | Score | -25.545 |
|---|---|---|---|
| Inter norm | -1.520 | Intra norm | 0.100 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 10 |
| Artifact reason | geometry warning; 7 clashes; 1 protein clash | ||
| Residues |
ARG144
ASN106
HIS105
HIS141
LEU145
MET101
ASP13
CYS72
GLY73
GLY77
ILE15
ILE76
MET78
SER74
TYR49
| ||
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
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 | 12 | Native recall | 0.75 |
| Jaccard | 0.63 | RMSD | - |
| HB strict | 3 | Strict recall | 0.25 |
| HB same residue+role | 4 | HB role recall | 0.40 |
| HB same residue | 5 | HB residue recall | 0.50 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 25 | -0.40648109881247935 | -1.41095 | -25.4015 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 31 | 0.9108405699533281 | -1.61043 | -29.861 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 32 | 1.5550531976658688 | -1.57572 | -27.2292 | 10 | 14 | 12 | 0.75 | 0.40 | - | no | Open |
| 95 | 1.5579141847049505 | -1.55021 | -29.6896 | 6 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 68 | 2.22640486292557 | -1.74451 | -29.6736 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 64 | 2.259681596132118 | -1.5196 | -25.5447 | 10 | 15 | 12 | 0.75 | 0.40 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.545kcal/mol
Ligand efficiency (LE)
-1.4191kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.373
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
18HA
Physicochemical properties
Molecular weight
239.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.01
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
48.10kcal/mol
Minimised FF energy
29.56kcal/mol
SASA & burial
✓ computed
SASA (unbound)
443.9Ų
Total solvent-accessible surface area of free ligand
BSA total
429.9Ų
Buried surface area upon binding
BSA apolar
362.1Ų
Hydrophobic contacts buried
BSA polar
67.8Ų
Polar contacts buried
Fraction buried
96.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
84.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2072.2Ų
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
2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
758.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)