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
22.3 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.88, Jaccard 0.70, H-bond role recall 0.50
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.618 kcal/mol/HA)
✓ Good fit quality (FQ -13.26)
✓ Strong H-bond network (13 bonds)
✓ Deep burial (91% SASA buried)
✓ Lipophilic contacts well-matched (65%)
✗ High strain energy (22.3 kcal/mol)
✗ Geometry warnings
Score
-30.744
kcal/mol
LE
-1.618
kcal/mol/HA
Fit Quality
-13.26
FQ (Leeson)
HAC
19
heavy atoms
MW
287
Da
LogP
-1.07
cLogP
Interaction summary
HB 13
HY 10
PI 3
CLASH 3
Interaction summary
HB 13
HY 10
PI 3
CLASH 3
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 | 3.546 | Score | -30.744 |
|---|---|---|---|
| Inter norm | -1.452 | Intra norm | -0.166 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 13 |
| Artifact reason | geometry warning; 4 clashes; 3 protein clashes; moderate strain Δ 22.3 | ||
| Residues |
ALA102
ARG144
ASN106
HIS105
HIS141
MET101
TYR97
ARG116
ASP13
CYS72
GLY73
GLY75
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 | 14 | Native recall | 0.88 |
| Jaccard | 0.70 | RMSD | - |
| HB strict | 5 | Strict recall | 0.42 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 176 | 2.1235620534942115 | -1.649 | -32.7179 | 12 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 173 | 2.2097958068481676 | -1.68052 | -33.3208 | 16 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 140 | 2.6837438727649325 | -1.50508 | -31.2958 | 16 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 216 | 2.7228918607595345 | -1.1931 | -22.3343 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 129 | 3.546185683732613 | -1.45232 | -30.7445 | 13 | 18 | 14 | 0.88 | 0.50 | - | no | Current |
| 122 | 4.021631400475942 | -1.49408 | -32.5526 | 12 | 15 | 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
-30.744kcal/mol
Ligand efficiency (LE)
-1.6181kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-13.263
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
286.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-1.07
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.32kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
103.19kcal/mol
Minimised FF energy
80.86kcal/mol
SASA & burial
✓ computed
SASA (unbound)
438.3Ų
Total solvent-accessible surface area of free ligand
BSA total
400.3Ų
Buried surface area upon binding
BSA apolar
260.0Ų
Hydrophobic contacts buried
BSA polar
140.3Ų
Polar contacts buried
Fraction buried
91.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
64.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1987.9Ų
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
760.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)