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
29.9 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.94, Jaccard 0.89, H-bond role recall 0.55
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
53% of hydrophobic surface appears solvent-exposed (10/19 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 (-0.724 kcal/mol/HA)
✓ Good fit quality (FQ -6.67)
✓ Strong H-bond network (13 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (67%)
✗ High strain energy (29.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-18.832
kcal/mol
LE
-0.724
kcal/mol/HA
Fit Quality
-6.67
FQ (Leeson)
HAC
26
heavy atoms
MW
366
Da
LogP
4.37
cLogP
Interaction summary
HB 13
HY 6
PI 3
CLASH 3
⚠ Exposure 52%
Interaction summary
HB 13
HY 6
PI 3
CLASH 3
⚠ Exposure 52%
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
Partial hydrophobic solvent exposure
53% of hydrophobic surface appears solvent-exposed (10/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 19
Buried (contacted) 9
Exposed 10
LogP 4.37
H-bonds 13
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 2.337 | Score | -18.832 |
|---|---|---|---|
| Inter norm | -1.146 | Intra norm | 0.422 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 13 |
| Artifact reason | geometry warning; 10 clashes; 1 protein clash; moderate strain Δ 29.9 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
SER46
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 | 0.89 | RMSD | - |
| HB strict | 6 | Strict recall | 0.46 |
| HB same residue+role | 6 | HB role recall | 0.55 |
| HB same residue | 9 | HB residue recall | 0.82 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 566 | 1.241895999707433 | -0.864578 | -18.0317 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 538 | 2.3367169218121906 | -1.146 | -18.8322 | 13 | 17 | 16 | 0.94 | 0.55 | - | no | Current |
| 544 | 3.9129939104118683 | -1.0791 | -22.6874 | 12 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 532 | 4.5147354506759125 | -1.17 | -28.2284 | 12 | 15 | 5 | 0.29 | 0.18 | - | no | Open |
| 562 | 5.044498045614265 | -0.930602 | -23.1365 | 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
-18.832kcal/mol
Ligand efficiency (LE)
-0.7243kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.673
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
366.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.37
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.88kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
76.07kcal/mol
Minimised FF energy
46.19kcal/mol
SASA & burial
✓ computed
SASA (unbound)
628.7Ų
Total solvent-accessible surface area of free ligand
BSA total
426.8Ų
Buried surface area upon binding
BSA apolar
284.5Ų
Hydrophobic contacts buried
BSA polar
142.3Ų
Polar contacts buried
Fraction buried
67.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
66.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2199.8Ų
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
684.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)