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
12.2 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.88, Jaccard 0.78, 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 (-1.226 kcal/mol/HA)
✓ Good fit quality (FQ -10.45)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (83% SASA buried)
✓ Lipophilic contacts well-matched (62%)
✗ Moderate strain (12.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-25.737
kcal/mol
LE
-1.226
kcal/mol/HA
Fit Quality
-10.45
FQ (Leeson)
HAC
21
heavy atoms
MW
301
Da
LogP
3.21
cLogP
Final rank
4.3246
rank score
Inter norm
-1.406
normalised
Contacts
16
H-bonds 10
Interaction summary
HBD 2
HBA 5
HY 3
PI 4
CLASH 5
Interaction summary
HBD 2
HBA 5
HY 3
PI 4
CLASH 5
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
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 | 14 | Native recall | 0.88 |
| Jaccard | 0.78 | RMSD | - |
| HB strict | 4 | Strict recall | 0.33 |
| HB same residue+role | 4 | HB role recall | 0.40 |
| HB same residue | 5 | HB residue recall | 0.50 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 551 | -0.10966209886901078 | -1.29964 | -25.3355 | 2 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 532 | 1.0046581056658084 | -1.50673 | -28.6964 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 558 | 1.8507984583927155 | -0.895968 | -16.1192 | 6 | 7 | 0 | 0.00 | 0.00 | - | no | Open |
| 548 | 2.3499413020302247 | -1.40164 | -21.5647 | 7 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 536 | 2.4750002428206046 | -1.35939 | -27.4286 | 11 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 542 | 2.63527126834114 | -1.20429 | -22.2029 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 545 | 2.800134034659489 | -1.54392 | -31.1493 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 541 | 3.544151329633376 | -1.50159 | -24.6005 | 12 | 18 | 5 | 0.31 | 0.30 | - | no | Open |
| 539 | 4.324614488326156 | -1.4057 | -25.737 | 10 | 16 | 14 | 0.88 | 0.40 | - | no | Current |
| 565 | 4.84275437333706 | -1.34595 | -23.6881 | 11 | 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
-25.737kcal/mol
Ligand efficiency (LE)
-1.2256kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.454
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
301.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.21
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.24kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
38.08kcal/mol
Minimised FF energy
25.84kcal/mol
SASA & burial
✓ computed
SASA (unbound)
529.8Ų
Total solvent-accessible surface area of free ligand
BSA total
437.6Ų
Buried surface area upon binding
BSA apolar
270.1Ų
Hydrophobic contacts buried
BSA polar
167.5Ų
Polar contacts buried
Fraction buried
82.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
61.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2044.6Ų
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
2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
768.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)