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
23.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.88, Jaccard 0.64, H-bond role recall 0.30
Reason: no major geometry red flags detected
2 protein-contact clashes
72% of hydrophobic surface is solvent-exposed (18/25 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 (-0.910 kcal/mol/HA)
✓ Good fit quality (FQ -9.03)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (71% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ High strain energy (23.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-30.030
kcal/mol
LE
-0.910
kcal/mol/HA
Fit Quality
-9.03
FQ (Leeson)
HAC
33
heavy atoms
MW
455
Da
LogP
2.76
cLogP
Interaction summary
HB 8
HY 5
PI 1
CLASH 2
⚠ Exposure 72%
Interaction summary
HB 8
HY 5
PI 1
CLASH 2
⚠ Exposure 72%
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
72% of hydrophobic surface is solvent-exposed (18/25 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 25
Buried (contacted) 7
Exposed 18
LogP 2.76
H-bonds 8
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (9 atoms exposed)
| Final rank | 3.764 | Score | -30.030 |
|---|---|---|---|
| Inter norm | -0.885 | Intra norm | -0.025 |
| Top1000 | no | Excluded | no |
| Contacts | 20 | H-bonds | 8 |
| Artifact reason | geometry warning; 13 clashes; 2 protein clashes; moderate strain Δ 23.2 | ||
| Residues |
ALA102
ARG140
ARG144
ASN106
GLN104
HIS105
HIS141
MET101
TYR97
ARG116
ARG46
CYS72
GLY73
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 | 14 | Native recall | 0.88 |
| Jaccard | 0.64 | RMSD | - |
| HB strict | 2 | Strict recall | 0.17 |
| HB same residue+role | 3 | HB role recall | 0.30 |
| HB same residue | 5 | HB residue recall | 0.50 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 296 | 1.2094497069229952 | -0.798718 | -24.0361 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 246 | 1.5777109956035995 | -1.02348 | -27.0051 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 217 | 2.907166553436376 | -0.828931 | -26.0142 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 272 | 2.937604839504376 | -0.709141 | -16.628 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 264 | 3.3766176770969594 | -0.963848 | -30.2461 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 195 | 3.764082353800593 | -0.885488 | -30.0305 | 8 | 20 | 14 | 0.88 | 0.30 | - | no | Current |
| 253 | 5.228683162267013 | -0.827143 | -20.3337 | 9 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 235 | 5.457047523773753 | -0.802528 | -20.4234 | 6 | 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
-30.030kcal/mol
Ligand efficiency (LE)
-0.9100kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.029
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
454.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.76
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.18kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
43.56kcal/mol
Minimised FF energy
20.38kcal/mol
SASA & burial
✓ computed
SASA (unbound)
733.9Ų
Total solvent-accessible surface area of free ligand
BSA total
520.9Ų
Buried surface area upon binding
BSA apolar
410.2Ų
Hydrophobic contacts buried
BSA polar
110.7Ų
Polar contacts buried
Fraction buried
71.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2278.5Ų
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
779.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)