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
16.6 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.94, Jaccard 0.94, H-bond role recall 0.27
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
64% of hydrophobic surface is solvent-exposed (14/22 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 (-0.841 kcal/mol/HA)
✓ Good fit quality (FQ -8.03)
✓ Strong H-bond network (8 bonds)
✓ Good burial (62% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ Moderate strain (16.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-24.384
kcal/mol
LE
-0.841
kcal/mol/HA
Fit Quality
-8.03
FQ (Leeson)
HAC
29
heavy atoms
MW
394
Da
LogP
3.58
cLogP
Interaction summary
HB 8
HY 1
PI 2
CLASH 4
⚠ Exposure 63%
Interaction summary
HB 8
HY 1
PI 2
CLASH 4
⚠ Exposure 63%
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
64% of hydrophobic surface is solvent-exposed (14/22 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 22
Buried (contacted) 8
Exposed 14
LogP 3.58
H-bonds 8
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (6 atoms exposed)
| Final rank | 3.058 | Score | -24.384 |
|---|---|---|---|
| Inter norm | -0.960 | Intra norm | 0.119 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 8 |
| Artifact reason | geometry warning; 11 clashes; 1 protein clash | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
LEU101
THR74
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 | 16 | Native recall | 0.94 |
| Jaccard | 0.94 | RMSD | - |
| HB strict | 4 | Strict recall | 0.31 |
| HB same residue+role | 3 | HB role recall | 0.27 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 312 | 0.8434741199414115 | -0.884212 | -23.938 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 243 | 2.6316584663284126 | -1.17998 | -30.7694 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 212 | 2.677236637207304 | -0.918954 | -25.2154 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 178 | 3.0577852371865224 | -0.960144 | -24.3843 | 8 | 16 | 16 | 0.94 | 0.27 | - | no | Current |
| 231 | 3.191083703202013 | -0.951026 | -21.92 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 242 | 3.7953820652748878 | -0.950828 | -25.6278 | 13 | 14 | 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
-24.384kcal/mol
Ligand efficiency (LE)
-0.8408kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.026
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
394.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.58
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
104.78kcal/mol
Minimised FF energy
88.22kcal/mol
SASA & burial
✓ computed
SASA (unbound)
668.2Ų
Total solvent-accessible surface area of free ligand
BSA total
411.2Ų
Buried surface area upon binding
BSA apolar
315.7Ų
Hydrophobic contacts buried
BSA polar
95.5Ų
Polar contacts buried
Fraction buried
61.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2309.3Ų
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
678.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)