Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
15.9 kcal/mol
Protein clashes
7
Internal clashes
7
Native overlap
contact recall 0.94, Jaccard 0.89, H-bond role recall 0.64
Reason: 7 internal clashes
7 protein-contact clashes
7 intramolecular clashes
50% of hydrophobic surface appears solvent-exposed (9/18 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.977 kcal/mol/HA)
✓ Good fit quality (FQ -9.00)
✓ Strong H-bond network (13 bonds)
✓ Deep burial (69% SASA buried)
✓ Lipophilic contacts well-matched (64%)
✗ Moderate strain (15.9 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-25.389
kcal/mol
LE
-0.977
kcal/mol/HA
Fit Quality
-9.00
FQ (Leeson)
HAC
26
heavy atoms
MW
390
Da
LogP
4.00
cLogP
Interaction summary
HB 13
HY 7
PI 2
CLASH 7
⚠ Exposure 50%
Interaction summary
HB 13
HY 7
PI 2
CLASH 7
⚠ Exposure 50%
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
50% of hydrophobic surface appears solvent-exposed (9/18 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 18
Buried (contacted) 9
Exposed 9
LogP 4.0
H-bonds 13
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 5.155 | Score | -25.389 |
|---|---|---|---|
| Inter norm | -1.069 | Intra norm | 0.093 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 13 |
| Artifact reason | geometry warning; 7 clashes; 3 protein clashes | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
MET78
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 | 8 | Strict recall | 0.62 |
| HB same residue+role | 7 | HB role recall | 0.64 |
| HB same residue | 10 | HB residue recall | 0.91 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 513 | -0.2908267176309925 | -1.19073 | -29.6003 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 530 | 1.8386052021954522 | -1.05981 | -26.1272 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 549 | 1.9584098801368803 | -1.07383 | -29.3381 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 560 | 2.428087883165567 | -0.799576 | -24.0181 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 552 | 2.7941902960594462 | -0.966006 | -17.0384 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 530 | 3.472283433281198 | -1.06233 | -28.3109 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 516 | 3.8612649837231396 | -1.20279 | -31.5508 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 526 | 4.287644089881446 | -1.23726 | -27.9603 | 10 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 530 | 5.1552079225695575 | -1.06931 | -25.3885 | 13 | 17 | 16 | 0.94 | 0.64 | - | no | Current |
| 550 | 5.633262955142708 | -1.10654 | -23.6606 | 16 | 15 | 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
-25.389kcal/mol
Ligand efficiency (LE)
-0.9765kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.997
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
389.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.00
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.86kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
42.53kcal/mol
Minimised FF energy
26.67kcal/mol
SASA & burial
✓ computed
SASA (unbound)
632.7Ų
Total solvent-accessible surface area of free ligand
BSA total
438.0Ų
Buried surface area upon binding
BSA apolar
278.6Ų
Hydrophobic contacts buried
BSA polar
159.4Ų
Polar contacts buried
Fraction buried
69.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
63.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2144.3Ų
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
746.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)