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 medium
Native strong
SASA done
Strain ΔE
22.6 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.94, Jaccard 0.79, H-bond role recall 0.40
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.028 kcal/mol/HA)
✓ Good fit quality (FQ -9.59)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (90%)
✗ High strain energy (22.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-27.755
kcal/mol
LE
-1.028
kcal/mol/HA
Fit Quality
-9.59
FQ (Leeson)
HAC
27
heavy atoms
MW
426
Da
LogP
3.34
cLogP
Interaction summary
HB 7
HY 11
PI 4
CLASH 4
Interaction summary
HB 7
HY 11
PI 4
CLASH 4
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 | 2.657 | Score | -27.755 |
|---|---|---|---|
| Inter norm | -1.164 | Intra norm | 0.136 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 7 |
| Artifact reason | geometry warning; 9 clashes; 1 protein clash; moderate strain Δ 22.6 | ||
| Residues |
ARG140
ARG144
ASN106
HIS105
HIS141
MET101
TYR97
ARG116
ARG46
ASP13
CYS72
GLY73
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 | 0.79 | RMSD | - |
| HB strict | 5 | Strict recall | 0.42 |
| HB same residue+role | 4 | HB role recall | 0.40 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 112 | 1.0237228161835357 | -0.921618 | -20.3586 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 112 | 1.1484773859344817 | -0.881947 | -22.294 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 107 | 1.5906811673286758 | -1.13802 | -30.2193 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 116 | 1.7368687972028278 | -0.939455 | -24.4564 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 125 | 1.8705548783515578 | -0.824677 | -19.122 | 4 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 111 | 1.9567266273999773 | -0.941489 | -19.4943 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 148 | 2.1545192277817584 | -0.83535 | -23.2836 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 134 | 2.3450479455114124 | -0.937703 | -23.0809 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 87 | 2.657445309836105 | -1.16369 | -27.7545 | 7 | 18 | 15 | 0.94 | 0.40 | - | no | Current |
| 91 | 2.796280609468839 | -1.05791 | -24.8275 | 7 | 12 | 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
-27.755kcal/mol
Ligand efficiency (LE)
-1.0279kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.590
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
426.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.34
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.61kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
19.00kcal/mol
Minimised FF energy
-3.62kcal/mol
SASA & burial
✓ computed
SASA (unbound)
632.5Ų
Total solvent-accessible surface area of free ligand
BSA total
504.3Ų
Buried surface area upon binding
BSA apolar
451.7Ų
Hydrophobic contacts buried
BSA polar
52.6Ų
Polar contacts buried
Fraction buried
79.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
89.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2242.5Ų
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
789.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)