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
29.8 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 1.00, Jaccard 1.00, H-bond role recall 0.80
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 (-1.540 kcal/mol/HA)
✓ Good fit quality (FQ -12.62)
✓ Strong H-bond network (16 bonds)
✓ Deep burial (84% SASA buried)
✓ Lipophilic contacts well-matched (64%)
✗ High strain energy (29.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-29.255
kcal/mol
LE
-1.540
kcal/mol/HA
Fit Quality
-12.62
FQ (Leeson)
HAC
19
heavy atoms
MW
281
Da
LogP
1.69
cLogP
Interaction summary
HB 16
HY 5
PI 4
CLASH 4
Interaction summary
HB 16
HY 5
PI 4
CLASH 4
| Final rank | 3.365 | Score | -29.255 |
|---|---|---|---|
| Inter norm | -1.669 | Intra norm | 0.129 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 16 |
| Artifact reason | geometry warning; 6 clashes; 2 protein clashes; moderate strain Δ 29.8 | ||
| Residues |
ARG140
ARG144
ASN106
HIS105
HIS141
ARG46
ASP13
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
ILE76
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 | 16 | Native recall | 1.00 |
| Jaccard | 1.00 | RMSD | - |
| HB strict | 10 | Strict recall | 0.83 |
| HB same residue+role | 8 | HB role recall | 0.80 |
| HB same residue | 8 | HB residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 536 | -1.2117718742022974 | -2.27302 | -41.2505 | 13 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 543 | -0.4617272198664007 | -1.92622 | -35.1793 | 12 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 553 | 0.7901052041183204 | -1.64895 | -25.0906 | 5 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 574 | 1.9197835489469466 | -1.27997 | -22.0242 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 539 | 2.834875949212269 | -1.96567 | -32.6489 | 13 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 574 | 2.938359789590277 | -1.13258 | -19.6979 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 542 | 3.36456591187264 | -1.66906 | -29.2551 | 16 | 16 | 16 | 1.00 | 0.80 | - | no | Current |
| 544 | 3.597282871221922 | -1.55687 | -25.5432 | 13 | 14 | 5 | 0.31 | 0.30 | - | no | Open |
| 546 | 3.9655058659124927 | -1.52952 | -21.6706 | 9 | 11 | 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
-29.255kcal/mol
Ligand efficiency (LE)
-1.5397kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.621
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
280.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.69
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.79kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
113.74kcal/mol
Minimised FF energy
83.95kcal/mol
SASA & burial
✓ computed
SASA (unbound)
488.1Ų
Total solvent-accessible surface area of free ligand
BSA total
410.7Ų
Buried surface area upon binding
BSA apolar
261.2Ų
Hydrophobic contacts buried
BSA polar
149.4Ų
Polar contacts buried
Fraction buried
84.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
63.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2001.3Ų
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
792.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)