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
29.2 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.75, Jaccard 0.71, H-bond role recall 0.40
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
52% of hydrophobic surface appears solvent-exposed (11/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.855 kcal/mol/HA)
✓ Good fit quality (FQ -8.25)
✓ Strong H-bond network (11 bonds)
✓ Good burial (64% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ High strain energy (29.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-25.645
kcal/mol
LE
-0.855
kcal/mol/HA
Fit Quality
-8.25
FQ (Leeson)
HAC
30
heavy atoms
MW
407
Da
LogP
2.81
cLogP
Interaction summary
HB 11
HY 4
PI 3
CLASH 4
⚠ Exposure 52%
Interaction summary
HB 11
HY 4
PI 3
CLASH 4
⚠ Exposure 52%
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
Partial hydrophobic solvent exposure
52% of hydrophobic surface appears solvent-exposed (11/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 21
Buried (contacted) 10
Exposed 11
LogP 2.81
H-bonds 11
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 2.655 | Score | -25.645 |
|---|---|---|---|
| Inter norm | -0.913 | Intra norm | 0.058 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 11 |
| Artifact reason | geometry warning; 10 clashes; 1 protein clash; moderate strain Δ 29.2 | ||
| Residues |
ARG140
ARG144
GLU138
HIS105
HIS141
ARG46
ASP13
CYS72
GLY73
HIS14
ILE15
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 | 12 | Native recall | 0.75 |
| Jaccard | 0.71 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| HB same residue+role | 4 | HB role recall | 0.40 |
| HB same residue | 4 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 674 | 1.5512422205691607 | -0.815383 | -15.9701 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 677 | 1.9033930537677903 | -0.878225 | -23.603 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 675 | 2.654721176662184 | -0.913095 | -25.6445 | 11 | 13 | 12 | 0.75 | 0.40 | - | no | Current |
| 676 | 3.149937329405016 | -0.830862 | -22.5223 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 675 | 3.3963568365121724 | -1.1746 | -33.1207 | 13 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 676 | 4.467756620184489 | -1.09954 | -25.516 | 13 | 20 | 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
-25.645kcal/mol
Ligand efficiency (LE)
-0.8548kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.246
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
407.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.81
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.23kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
57.10kcal/mol
Minimised FF energy
27.87kcal/mol
SASA & burial
✓ computed
SASA (unbound)
689.8Ų
Total solvent-accessible surface area of free ligand
BSA total
441.4Ų
Buried surface area upon binding
BSA apolar
314.7Ų
Hydrophobic contacts buried
BSA polar
126.7Ų
Polar contacts buried
Fraction buried
64.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2196.2Ų
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
803.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)