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
Reject
SASA cached
Likely artefact or unreliable pose
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
20.8 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.94, Jaccard 0.79, H-bond role recall 0.40
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
64% of hydrophobic surface is solvent-exposed (16/25 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
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.743 kcal/mol/HA)
✓ Good fit quality (FQ -7.49)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ High strain energy (20.8 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (11)
✗ Many internal clashes (10)
Score
-25.995
kcal/mol
LE
-0.743
kcal/mol/HA
Fit Quality
-7.49
FQ (Leeson)
HAC
35
heavy atoms
MW
512
Da
LogP
4.13
cLogP
Interaction summary
HB 11
HY 6
PI 3
CLASH 3
⚠ Exposure 64%
Interaction summary
HB 11
HY 6
PI 3
CLASH 3
⚠ Exposure 64%
Solvent-exposed hydrophobic surface — desolvation penalty likely
64% of hydrophobic surface is solvent-exposed (16/25 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 25
Buried (contacted) 9
Exposed 16
LogP 4.13
H-bonds 11
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (4/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 2.101 | Score | -25.995 |
|---|---|---|---|
| Inter norm | -0.777 | Intra norm | 0.035 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 11 |
| Artifact reason | geometry warning; 10 clashes; 11 protein contact clashes; moderate strain Δ 20.8 | ||
| Residues |
ARG140
ARG144
ASN106
GLN104
HIS105
HIS141
MET101
ARG46
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
ILE76
MET78
SER74
TYR49
| ||
Protein summary
302 residues
| Protein target | T12 | Atoms | 4598 |
|---|---|---|---|
| Residues | 302 | Chains | 2 |
| Residue summary | ARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121 | ||
Receptor context
1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1
Excluded HETATM 0
Kept cofactors / ions
A:CSD72
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6FXS | Contacts | 16 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG140
ARG144
ASN106
HIS105
HIS141
ARG46
ASP13
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
ILE76
SER74
TYR49
| ||
| Current overlap | 15 | Native recall | 0.94 |
| Jaccard | 0.79 | RMSD | - |
| HB strict | 4 | Strict recall | 0.33 |
| HB same residue+role | 4 | HB role recall | 0.40 |
| HB same residue | 6 | HB residue recall | 0.60 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 403 | 1.8056888399198356 | -0.719953 | -20.1535 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 374 | 2.1013551352678435 | -0.777468 | -25.9952 | 11 | 18 | 15 | 0.94 | 0.40 | - | no | Current |
| 410 | 4.183505542941841 | -0.585981 | -16.2516 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 447 | 4.720481022983788 | -0.674248 | -21.8514 | 8 | 18 | 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
-25.995kcal/mol
Ligand efficiency (LE)
-0.7427kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.491
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
512.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.13
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.77kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
19.35kcal/mol
Minimised FF energy
-1.41kcal/mol
SASA & burial
✓ computed
SASA (unbound)
789.6Ų
Total solvent-accessible surface area of free ligand
BSA total
537.7Ų
Buried surface area upon binding
BSA apolar
399.4Ų
Hydrophobic contacts buried
BSA polar
138.3Ų
Polar contacts buried
Fraction buried
68.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2239.1Ų
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
2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
836.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)