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
33.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.69, Jaccard 0.58, H-bond role recall 0.30
Reason: no major geometry red flags detected
1 protein-contact clashes
37% of hydrophobic surface appears solvent-exposed (11/30 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 (-0.659 kcal/mol/HA)
✓ Good fit quality (FQ -6.79)
✓ Strong H-bond network (8 bonds)
✓ Good burial (63% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ Very high strain energy (33.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-25.046
kcal/mol
LE
-0.659
kcal/mol/HA
Fit Quality
-6.79
FQ (Leeson)
HAC
38
heavy atoms
MW
515
Da
LogP
5.18
cLogP
Interaction summary
HB 8
HY 12
PI 2
CLASH 1
⚠ Exposure 36%
Interaction summary
HB 8
HY 12
PI 2
CLASH 1
⚠ Exposure 36%
Partial hydrophobic solvent exposure
37% of hydrophobic surface appears solvent-exposed (11/30 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 30
Buried (contacted) 19
Exposed 11
LogP 5.18
H-bonds 8
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 3.485 | Score | -25.046 |
|---|---|---|---|
| Inter norm | -0.714 | Intra norm | 0.054 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 8 |
| Artifact reason | geometry warning; 16 clashes; 2 protein clashes; high strain Δ 32.4 | ||
| Residues |
ARG140
ARG144
HIS105
HIS141
MET101
TYR97
ARG116
ARG46
ASP13
CYS72
GLY73
HIS14
ILE15
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 | 11 | Native recall | 0.69 |
| Jaccard | 0.58 | RMSD | - |
| HB strict | 3 | Strict recall | 0.25 |
| HB same residue+role | 3 | HB role recall | 0.30 |
| HB same residue | 3 | HB residue recall | 0.30 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 242 | 1.2061003088206848 | -0.920315 | -32.7614 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 250 | 1.6503078268434284 | -0.702237 | -24.6212 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 292 | 1.731561596222887 | -0.706716 | -23.0589 | 7 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 245 | 1.977778943085613 | -0.84556 | -28.2026 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 192 | 3.4848070954252997 | -0.714249 | -25.0458 | 8 | 14 | 11 | 0.69 | 0.30 | - | no | Current |
| 288 | 4.208588974776811 | -0.511351 | -19.8728 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 211 | 4.5254155240912235 | -0.68483 | -25.2718 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 216 | 4.543538828410204 | -0.917323 | -30.6767 | 12 | 24 | 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
-25.046kcal/mol
Ligand efficiency (LE)
-0.6591kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.795
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
38HA
Physicochemical properties
Molecular weight
514.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.18
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
138.50kcal/mol
Minimised FF energy
105.55kcal/mol
SASA & burial
✓ computed
SASA (unbound)
863.8Ų
Total solvent-accessible surface area of free ligand
BSA total
545.5Ų
Buried surface area upon binding
BSA apolar
456.6Ų
Hydrophobic contacts buried
BSA polar
88.8Ų
Polar contacts buried
Fraction buried
63.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2403.0Ų
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
790.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)