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
25.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.94, Jaccard 0.79, H-bond role recall 0.60
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.810 kcal/mol/HA)
✓ Good fit quality (FQ -8.03)
✓ Strong H-bond network (12 bonds)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ High strain energy (25.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-26.719
kcal/mol
LE
-0.810
kcal/mol/HA
Fit Quality
-8.03
FQ (Leeson)
HAC
33
heavy atoms
MW
452
Da
LogP
4.67
cLogP
Interaction summary
HB 12
HY 15
PI 4
CLASH 1
Interaction summary
HB 12
HY 15
PI 4
CLASH 1
| Final rank | 3.253 | Score | -26.719 |
|---|---|---|---|
| Inter norm | -0.901 | Intra norm | 0.091 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 12 |
| Artifact reason | geometry warning; 11 clashes; 2 protein clashes; moderate strain Δ 25.8 | ||
| Residues |
ARG140
ARG144
ASN106
HIS105
HIS141
ARG116
ARG46
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
ILE76
LEU44
PRO18
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 | 15 | Native recall | 0.94 |
| Jaccard | 0.79 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| HB same residue+role | 6 | HB role recall | 0.60 |
| HB same residue | 7 | HB residue recall | 0.70 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 322 | 1.3070478662876737 | -0.795495 | -22.1443 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 239 | 1.429353830046023 | -0.85087 | -24.9661 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 332 | 2.109182079251565 | -0.787785 | -21.1675 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 280 | 2.8384458484406365 | -0.771278 | -19.4611 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 207 | 2.994404326852969 | -0.879267 | -22.1427 | 11 | 17 | 5 | 0.31 | 0.30 | - | no | Open |
| 228 | 3.25287543334116 | -0.900912 | -26.7187 | 12 | 18 | 15 | 0.94 | 0.60 | - | no | Current |
| 315 | 3.7913116092188326 | -0.611091 | -14.3237 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 305 | 5.387160225431737 | -0.730767 | -19.8354 | 6 | 18 | 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
-26.719kcal/mol
Ligand efficiency (LE)
-0.8097kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.033
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
451.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.67
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.79kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
44.30kcal/mol
Minimised FF energy
18.51kcal/mol
SASA & burial
✓ computed
SASA (unbound)
771.3Ų
Total solvent-accessible surface area of free ligand
BSA total
568.3Ų
Buried surface area upon binding
BSA apolar
445.1Ų
Hydrophobic contacts buried
BSA polar
123.3Ų
Polar contacts buried
Fraction buried
73.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2325.0Ų
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
776.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)