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
22.3 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.81, Jaccard 0.76, H-bond role recall 0.40
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
42% of hydrophobic surface appears solvent-exposed (8/19 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 (-0.967 kcal/mol/HA)
✓ Good fit quality (FQ -9.12)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ High strain energy (22.3 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-27.061
kcal/mol
LE
-0.967
kcal/mol/HA
Fit Quality
-9.12
FQ (Leeson)
HAC
28
heavy atoms
MW
416
Da
LogP
3.83
cLogP
Interaction summary
HB 7
HY 9
PI 3
CLASH 3
⚠ Exposure 42%
Interaction summary
HB 7
HY 9
PI 3
CLASH 3
⚠ Exposure 42%
Partial hydrophobic solvent exposure
42% of hydrophobic surface appears solvent-exposed (8/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 19
Buried (contacted) 11
Exposed 8
LogP 3.83
H-bonds 7
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (3/5 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 1.910 | Score | -27.061 |
|---|---|---|---|
| Inter norm | -1.069 | Intra norm | 0.102 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 7 |
| Artifact reason | geometry warning; 6 clashes; 1 protein clash; moderate strain Δ 22.3 | ||
| Residues |
ARG140
ARG144
ASN106
HIS105
HIS141
MET101
ARG46
ASP13
CYS72
GLY73
HIS14
ILE15
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 | 13 | Native recall | 0.81 |
| Jaccard | 0.76 | RMSD | - |
| HB strict | 5 | Strict recall | 0.42 |
| HB same residue+role | 4 | HB role recall | 0.40 |
| HB same residue | 4 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 500 | 0.48122871348213075 | -0.987448 | -17.9475 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 101 | 1.90974584426113 | -1.06854 | -27.0613 | 7 | 14 | 13 | 0.81 | 0.40 | - | no | Current |
| 82 | 2.385215210300992 | -0.913366 | -20.2078 | 14 | 14 | 5 | 0.31 | 0.20 | - | no | Open |
| 120 | 2.5639756970476455 | -0.948319 | -22.461 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 465 | 3.693939310354714 | -0.880271 | -20.0677 | 10 | 14 | 5 | 0.31 | 0.30 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-27.061kcal/mol
Ligand efficiency (LE)
-0.9665kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.124
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
415.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.83
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.35kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
7.37kcal/mol
Minimised FF energy
-14.97kcal/mol
SASA & burial
✓ computed
SASA (unbound)
681.6Ų
Total solvent-accessible surface area of free ligand
BSA total
507.0Ų
Buried surface area upon binding
BSA apolar
355.2Ų
Hydrophobic contacts buried
BSA polar
151.8Ų
Polar contacts buried
Fraction buried
74.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2160.2Ų
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
773.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)