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
24.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 1.00, Jaccard 0.94, H-bond role recall 0.50
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.209 kcal/mol/HA)
✓ Good fit quality (FQ -10.50)
✓ Strong H-bond network (13 bonds)
✓ Deep burial (83% SASA buried)
✓ Lipophilic contacts well-matched (67%)
✗ High strain energy (24.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-26.600
kcal/mol
LE
-1.209
kcal/mol/HA
Fit Quality
-10.50
FQ (Leeson)
HAC
22
heavy atoms
MW
302
Da
LogP
1.99
cLogP
Interaction summary
HB 13
HY 12
PI 4
CLASH 2
Interaction summary
HB 13
HY 12
PI 4
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 | 3.423 | Score | -26.600 |
|---|---|---|---|
| Inter norm | -1.367 | Intra norm | 0.158 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 13 |
| Artifact reason | geometry warning; 11 clashes; 2 protein clashes; moderate strain Δ 24.9 | ||
| Residues |
ARG140
ARG144
ASN106
HIS105
HIS141
ARG46
ASP13
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
ILE76
MET78
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 | 16 | Native recall | 1.00 |
| Jaccard | 0.94 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| HB same residue+role | 5 | HB role recall | 0.50 |
| HB same residue | 7 | HB residue recall | 0.70 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 559 | 0.7198418180090042 | -0.933488 | -20.4818 | 6 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 525 | 2.4172194168614993 | -1.48041 | -32.0363 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 512 | 2.545937422647049 | -1.61802 | -34.0323 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 567 | 2.9952729829901434 | -1.24945 | -25.8165 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 524 | 3.422947619134114 | -1.36673 | -26.6001 | 13 | 17 | 16 | 1.00 | 0.50 | - | no | Current |
| 550 | 3.750956682432338 | -1.21808 | -25.8403 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 582 | 4.472569139535506 | -1.15982 | -25.4195 | 9 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 529 | 4.491059808940537 | -1.52163 | -29.8977 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 541 | 5.152210004952779 | -1.44518 | -30.0794 | 11 | 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
-26.600kcal/mol
Ligand efficiency (LE)
-1.2091kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.497
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
302.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.99
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.85kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
105.79kcal/mol
Minimised FF energy
80.93kcal/mol
SASA & burial
✓ computed
SASA (unbound)
490.5Ų
Total solvent-accessible surface area of free ligand
BSA total
409.3Ų
Buried surface area upon binding
BSA apolar
275.8Ų
Hydrophobic contacts buried
BSA polar
133.6Ų
Polar contacts buried
Fraction buried
83.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
67.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2018.4Ų
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
760.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)