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
28.0 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.71, Jaccard 0.67, H-bond role recall 0.36
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
62% of hydrophobic surface is solvent-exposed (10/16 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 (-0.889 kcal/mol/HA)
✓ Good fit quality (FQ -8.20)
✓ Strong H-bond network (11 bonds)
✓ Good burial (59% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ High strain energy (28.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-23.127
kcal/mol
LE
-0.889
kcal/mol/HA
Fit Quality
-8.20
FQ (Leeson)
HAC
26
heavy atoms
MW
398
Da
LogP
2.41
cLogP
Interaction summary
HB 11
HY 1
PI 1
CLASH 5
⚠ Exposure 62%
Interaction summary
HB 11
HY 1
PI 1
CLASH 5
⚠ Exposure 62%
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
62% of hydrophobic surface is solvent-exposed (10/16 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 16
Buried (contacted) 6
Exposed 10
LogP 2.41
H-bonds 11
Exposed fragments:
phenyl (4/6 atoms exposed)aliphatic chain/group (6 atoms exposed)
| Final rank | 5.154 | Score | -23.127 |
|---|---|---|---|
| Inter norm | -0.924 | Intra norm | 0.035 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 11 |
| Artifact reason | geometry warning; 6 clashes; 3 protein clashes; moderate strain Δ 28.0 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
HIS105
HIS14
HIS141
SER46
TYR49
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6FXW | Contacts | 17 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
LEU101
THR74
TYR49
| ||
| Current overlap | 12 | Native recall | 0.71 |
| Jaccard | 0.67 | RMSD | - |
| HB strict | 5 | Strict recall | 0.38 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 4 | HB residue recall | 0.36 |
Protein summary
155 residues
| Protein target | T10 | Atoms | 4590 |
|---|---|---|---|
| Residues | 155 | Chains | 1 |
| Residue summary | ILE:494; ARG:384; ALA:360; VAL:352; LEU:304; GLU:300; THR:280; MET:272; LYS:220; ASP:216; TYR:210; HIS:204; GLY:182; SER:176; GLN:170; ASN:140 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 338 | 2.1801465777957825 | -0.758294 | -18.4464 | 9 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 305 | 2.596552910981433 | -0.967078 | -23.6974 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 351 | 2.6551293991681417 | -1.12903 | -26.9003 | 9 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 358 | 3.5547396501747 | -1.09509 | -24.6491 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 375 | 3.929077751592255 | -1.028 | -24.1661 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 294 | 4.415045767776549 | -1.15916 | -29.2189 | 16 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 253 | 5.15382495728802 | -0.9244 | -23.1267 | 11 | 13 | 12 | 0.71 | 0.36 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.127kcal/mol
Ligand efficiency (LE)
-0.8895kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.195
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
397.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.41
Lipinski: ≤ 5
Rotatable bonds
11
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.04kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-93.85kcal/mol
Minimised FF energy
-121.89kcal/mol
SASA & burial
✓ computed
SASA (unbound)
637.1Ų
Total solvent-accessible surface area of free ligand
BSA total
378.5Ų
Buried surface area upon binding
BSA apolar
262.3Ų
Hydrophobic contacts buried
BSA polar
116.2Ų
Polar contacts buried
Fraction buried
59.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2237.2Ų
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
2417.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
655.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)