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
33.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.88, Jaccard 0.82, H-bond role recall 0.60
Reason: no major geometry red flags detected
2 protein-contact clashes
68% of hydrophobic surface is solvent-exposed (13/19 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.962 kcal/mol/HA)
✓ Good fit quality (FQ -9.08)
✓ Strong H-bond network (11 bonds)
✓ Good burial (63% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ Very high strain energy (33.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-26.939
kcal/mol
LE
-0.962
kcal/mol/HA
Fit Quality
-9.08
FQ (Leeson)
HAC
28
heavy atoms
MW
403
Da
LogP
2.61
cLogP
Interaction summary
HB 11
HY 2
PI 3
CLASH 2
⚠ Exposure 68%
Interaction summary
HB 11
HY 2
PI 3
CLASH 2
⚠ Exposure 68%
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
Solvent-exposed hydrophobic surface — desolvation penalty likely
68% of hydrophobic surface is solvent-exposed (13/19 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 19
Buried (contacted) 6
Exposed 13
LogP 2.61
H-bonds 11
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 3.250 | Score | -26.939 |
|---|---|---|---|
| Inter norm | -0.959 | Intra norm | -0.004 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 11 |
| Artifact reason | geometry warning; 10 clashes; 2 protein clashes; high strain Δ 33.4 | ||
| Residues |
ARG140
ARG144
ASN106
GLU138
HIS105
HIS141
ARG46
CYS72
GLY73
GLY75
GLY77
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 | 14 | Native recall | 0.88 |
| Jaccard | 0.82 | RMSD | - |
| HB strict | 8 | Strict recall | 0.67 |
| HB same residue+role | 6 | HB role recall | 0.60 |
| HB same residue | 6 | HB residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 591 | 2.575736968686273 | -1.17244 | -23.8569 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 595 | 2.65130882111342 | -1.28326 | -28.0046 | 7 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 619 | 3.05728268097349 | -0.912384 | -19.1381 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 601 | 3.2501329553842218 | -0.958986 | -26.9388 | 11 | 15 | 14 | 0.88 | 0.60 | - | no | Current |
| 592 | 4.161214079419215 | -0.790111 | -19.9052 | 7 | 11 | 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
-26.939kcal/mol
Ligand efficiency (LE)
-0.9621kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.083
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
403.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.61
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
30.68kcal/mol
Minimised FF energy
-2.76kcal/mol
SASA & burial
✓ computed
SASA (unbound)
682.8Ų
Total solvent-accessible surface area of free ligand
BSA total
431.7Ų
Buried surface area upon binding
BSA apolar
301.6Ų
Hydrophobic contacts buried
BSA polar
130.1Ų
Polar contacts buried
Fraction buried
63.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2196.1Ų
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
767.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)