Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
25.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.81, Jaccard 0.68, H-bond role recall 0.40
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.035 kcal/mol/HA)
✓ Good fit quality (FQ -9.77)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (78% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ High strain energy (25.5 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (9)
✗ Internal clashes (9)
Score
-28.988
kcal/mol
LE
-1.035
kcal/mol/HA
Fit Quality
-9.77
FQ (Leeson)
HAC
28
heavy atoms
MW
417
Da
LogP
2.68
cLogP
Final rank
1.4345
rank score
Inter norm
-1.032
normalised
Contacts
16
H-bonds 10
Interaction summary
HBA 7
PC 1
HY 5
PI 6
CLASH 2
Interaction summary
HBA 7
PC 1
HY 5
PI 6
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.
PC · Polar contacts (possible, no H geometry)
HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.
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: permissive.
| 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 | 13 | Native recall | 0.81 |
| Jaccard | 0.68 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| HB same residue+role | 4 | HB role recall | 0.40 |
| HB same residue | 4 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 621 | 1.4345497717291078 | -1.0318 | -28.9875 | 10 | 16 | 13 | 0.81 | 0.40 | - | no | Current |
| 624 | 1.9005361944032626 | -0.963332 | -23.5994 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 633 | 2.034066149755648 | -0.997448 | -27.4985 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 614 | 2.1205691892069596 | -1.06766 | -31.8052 | 5 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 617 | 2.21543994317517 | -0.943733 | -25.4581 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 636 | 2.2733624275643116 | -0.935816 | -24.4034 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 631 | 2.613527185358712 | -0.808865 | -21.8381 | 2 | 15 | 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
-28.988kcal/mol
Ligand efficiency (LE)
-1.0353kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.773
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
416.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.68
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.46kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
37.27kcal/mol
Minimised FF energy
11.81kcal/mol
SASA & burial
✓ computed
SASA (unbound)
632.9Ų
Total solvent-accessible surface area of free ligand
BSA total
491.1Ų
Buried surface area upon binding
BSA apolar
339.6Ų
Hydrophobic contacts buried
BSA polar
151.5Ų
Polar contacts buried
Fraction buried
77.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2152.7Ų
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
759.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)