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 high
Native strong
SASA done
Strain ΔE
17.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 1.00, Jaccard 0.84, H-bond role recall 0.30
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.816 kcal/mol/HA)
✓ Good fit quality (FQ -8.10)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (69% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Moderate strain (17.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-26.924
kcal/mol
LE
-0.816
kcal/mol/HA
Fit Quality
-8.10
FQ (Leeson)
HAC
33
heavy atoms
MW
451
Da
LogP
6.36
cLogP
Interaction summary
HB 7
HY 16
PI 4
CLASH 1
Interaction summary
HB 7
HY 16
PI 4
CLASH 1
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
| Final rank | 4.552 | Score | -26.924 |
|---|---|---|---|
| Inter norm | -0.853 | Intra norm | 0.038 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 7 |
| Artifact reason | geometry warning; 16 clashes; 3 protein clashes | ||
| Residues |
ARG140
ARG144
ASN106
HIS105
HIS141
MET101
TYR97
ARG116
ARG46
ASP13
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
ILE76
SER74
TYR49
| ||
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 | 16 | Native recall | 1.00 |
| Jaccard | 0.84 | RMSD | - |
| HB strict | 3 | Strict recall | 0.25 |
| HB same residue+role | 3 | HB role recall | 0.30 |
| HB same residue | 4 | HB residue recall | 0.40 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 634 | 0.7703295841755433 | -1.01228 | -30.485 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 619 | 0.9227104539675254 | -0.988832 | -29.8563 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 635 | 0.9872537622581262 | -0.909874 | -26.5051 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 624 | 1.3874062123717454 | -0.912299 | -28.609 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 623 | 2.5042832255124376 | -0.78944 | -24.6851 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 641 | 2.575160669811322 | -0.729551 | -19.9056 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 624 | 3.143187244987514 | -0.689014 | -19.0993 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 637 | 3.1469015228773753 | -0.653269 | -16.8113 | 4 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 623 | 3.788589440580992 | -0.75815 | -19.7132 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 633 | 4.551784139291988 | -0.853444 | -26.9236 | 7 | 19 | 16 | 1.00 | 0.30 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-26.924kcal/mol
Ligand efficiency (LE)
-0.8159kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.095
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
450.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.36
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.96kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
126.23kcal/mol
Minimised FF energy
109.27kcal/mol
SASA & burial
✓ computed
SASA (unbound)
739.2Ų
Total solvent-accessible surface area of free ligand
BSA total
511.6Ų
Buried surface area upon binding
BSA apolar
421.5Ų
Hydrophobic contacts buried
BSA polar
90.1Ų
Polar contacts buried
Fraction buried
69.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2307.0Ų
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
796.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)