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
17.8 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.94, Jaccard 0.79, 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 (-0.896 kcal/mol/HA)
✓ Good fit quality (FQ -8.55)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ Moderate strain (17.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-25.987
kcal/mol
LE
-0.896
kcal/mol/HA
Fit Quality
-8.55
FQ (Leeson)
HAC
29
heavy atoms
MW
438
Da
LogP
2.22
cLogP
Interaction summary
HB 10
HY 6
PI 3
CLASH 2
Interaction summary
HB 10
HY 6
PI 3
CLASH 2
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 | 3.625 | Score | -25.987 |
|---|---|---|---|
| Inter norm | -0.928 | Intra norm | 0.032 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 10 |
| Artifact reason | geometry warning; 11 clashes; 2 protein clashes | ||
| 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 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 447 | 0.888337325445654 | -1.10697 | -31.2652 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 472 | 1.2275006668163393 | -1.04442 | -32.2197 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 454 | 2.2280732915593453 | -0.941058 | -30.4346 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 499 | 2.367404496171376 | -0.901446 | -20.999 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 456 | 3.454633655970856 | -0.895192 | -23.5284 | 9 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 429 | 3.6248530924080415 | -0.927639 | -25.9872 | 10 | 18 | 15 | 0.94 | 0.40 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.987kcal/mol
Ligand efficiency (LE)
-0.8961kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.554
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
437.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.22
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.81kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
79.10kcal/mol
Minimised FF energy
61.29kcal/mol
SASA & burial
✓ computed
SASA (unbound)
667.3Ų
Total solvent-accessible surface area of free ligand
BSA total
506.1Ų
Buried surface area upon binding
BSA apolar
376.5Ų
Hydrophobic contacts buried
BSA polar
129.6Ų
Polar contacts buried
Fraction buried
75.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2184.6Ų
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
772.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)