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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
74.7 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.71, Jaccard 0.63, H-bond role recall 0.45
Reason: strain 74.7 kcal/mol
strain ΔE 74.7 kcal/mol
5 protein-contact clashes
5 intramolecular clashes
43% of hydrophobic surface appears solvent-exposed (10/23 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.572 kcal/mol/HA)
✓ Good fit quality (FQ -5.72)
✓ Strong H-bond network (15 bonds)
✓ Deep burial (67% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Extreme strain energy (74.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (18)
Score
-19.436
kcal/mol
LE
-0.572
kcal/mol/HA
Fit Quality
-5.72
FQ (Leeson)
HAC
34
heavy atoms
MW
481
Da
LogP
4.53
cLogP
Interaction summary
HB 15
HY 4
PI 2
CLASH 5
⚠ Exposure 43%
Interaction summary
HB 15
HY 4
PI 2
CLASH 5
⚠ Exposure 43%
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
43% of hydrophobic surface appears solvent-exposed (10/23 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 23
Buried (contacted) 13
Exposed 10
LogP 4.53
H-bonds 15
Exposed fragments:
phenyl (4/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 5.235 | Score | -19.436 |
|---|---|---|---|
| Inter norm | -0.742 | Intra norm | 0.170 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 15 |
| Artifact reason | geometry warning; 18 clashes; 2 protein clashes; high strain Δ 74.7 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
CYS72
GLY73
HIS105
HIS14
HIS141
LEU136
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 | 12 | Native recall | 0.71 |
| Jaccard | 0.63 | RMSD | - |
| HB strict | 6 | Strict recall | 0.46 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 6 | HB residue recall | 0.55 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 599 | 1.4196484638659015 | -0.939239 | -28.1464 | 11 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 613 | 2.5558035847312244 | -0.816482 | -25.0979 | 11 | 14 | 5 | 0.29 | 0.27 | - | no | Open |
| 621 | 4.119991031040839 | -0.563275 | -16.0134 | 4 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 623 | 5.234710793187857 | -0.741743 | -19.4364 | 15 | 14 | 12 | 0.71 | 0.45 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-19.436kcal/mol
Ligand efficiency (LE)
-0.5717kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.720
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
480.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.53
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
74.74kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
95.67kcal/mol
Minimised FF energy
20.93kcal/mol
SASA & burial
✓ computed
SASA (unbound)
721.3Ų
Total solvent-accessible surface area of free ligand
BSA total
482.2Ų
Buried surface area upon binding
BSA apolar
362.8Ų
Hydrophobic contacts buried
BSA polar
119.5Ų
Polar contacts buried
Fraction buried
66.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2305.4Ų
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
680.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)