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
12.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.94, Jaccard 0.94, H-bond role recall 0.60
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.133 kcal/mol/HA)
✓ Good fit quality (FQ -9.84)
✓ Strong H-bond network (12 bonds)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (73%)
✗ Moderate strain (12.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-24.934
kcal/mol
LE
-1.133
kcal/mol/HA
Fit Quality
-9.84
FQ (Leeson)
HAC
22
heavy atoms
MW
299
Da
LogP
2.74
cLogP
Interaction summary
HB 12
HY 8
PI 5
CLASH 1
Interaction summary
HB 12
HY 8
PI 5
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 | 1.799 | Score | -24.934 |
|---|---|---|---|
| Inter norm | -1.259 | Intra norm | 0.126 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 12 |
| Artifact reason | geometry warning; 6 clashes; 1 protein clash | ||
| Residues |
ARG140
ARG144
ASN106
HIS105
HIS141
ARG46
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
ILE76
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 | 15 | Native recall | 0.94 |
| Jaccard | 0.94 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| HB same residue+role | 6 | HB role recall | 0.60 |
| HB same residue | 6 | HB residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 221 | -0.5342035848569257 | -1.48191 | -28.3703 | 10 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 210 | 1.589293489537325 | -1.07316 | -17.7732 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 168 | 1.7994056093051762 | -1.25927 | -24.9338 | 12 | 15 | 15 | 0.94 | 0.60 | - | no | Current |
| 156 | 2.1823482137671677 | -1.33711 | -18.3838 | 9 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 244 | 2.632384898312331 | -1.30724 | -22.0766 | 8 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 224 | 3.05553725405528 | -1.31477 | -25.7881 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 214 | 3.1880861317190305 | -1.12817 | -19.3279 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 155 | 4.489595302255546 | -1.27909 | -22.1697 | 11 | 18 | 5 | 0.31 | 0.30 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.934kcal/mol
Ligand efficiency (LE)
-1.1334kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.840
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
299.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.74
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
45.73kcal/mol
Minimised FF energy
33.26kcal/mol
SASA & burial
✓ computed
SASA (unbound)
543.2Ų
Total solvent-accessible surface area of free ligand
BSA total
401.7Ų
Buried surface area upon binding
BSA apolar
291.6Ų
Hydrophobic contacts buried
BSA polar
110.1Ų
Polar contacts buried
Fraction buried
74.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2048.8Ų
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
838.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)