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
4.5 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.62, Jaccard 0.54, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Low conformational strain (4.5 kcal/mol)
✓ Excellent LE (-1.149 kcal/mol/HA)
✓ Good fit quality (FQ -10.14)
✓ Deep burial (93% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
✗ Many internal clashes (10)
Score
-26.431
kcal/mol
LE
-1.149
kcal/mol/HA
Fit Quality
-10.14
FQ (Leeson)
HAC
23
heavy atoms
MW
313
Da
LogP
4.92
cLogP
Interaction summary
HB 2
HY 23
PI 1
CLASH 2
Interaction summary
HB 2
HY 23
PI 1
CLASH 2
| Final rank | 0.422 | Score | -26.431 |
|---|---|---|---|
| Inter norm | -1.180 | Intra norm | 0.031 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 2 |
| Artifact reason | geometry warning; 10 clashes; 3 protein contact clashes; 1 cofactor-context clash | ||
| Residues |
ALA10
GLU31
ILE61
ILE8
LEU23
LEU28
NAP201
PHE32
PHE35
PRO27
SER60
THR57
TRP25
TYR122
VAL116
VAL9
| ||
Protein summary
200 residues
| Protein target | T01 | Atoms | 3128 |
|---|---|---|---|
| Residues | 200 | Chains | 2 |
| Residue summary | LYS:374; LEU:361; GLU:240; VAL:224; ARG:192; PHE:180; ILE:171; PRO:168; ASN:140; SER:132; TYR:126; GLN:119; ASP:108; MET:102; THR:98; GLY:91 | ||
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:NAP201
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 5SD8 | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA10
ASN65
ASP22
GLN36
GLU31
GLY117
GLY21
ILE61
ILE8
LEU23
LEU68
NAP201
PHE32
PHE35
PRO62
SER60
THR137
THR57
TYR122
VAL116
VAL9
| ||
| Current overlap | 13 | Native recall | 0.62 |
| Jaccard | 0.54 | RMSD | - |
| HB strict | 1 | Strict recall | 0.20 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 196 | -0.09129784545088215 | -1.41659 | -33.5409 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 276 | 0.4221779857226626 | -1.17972 | -26.4315 | 2 | 16 | 13 | 0.62 | 0.20 | - | no | Current |
| 234 | 1.3950006973288718 | -1.23773 | -27.9298 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 177 | 1.5110784718979842 | -1.28616 | -29.4076 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 303 | 1.7107350648349646 | -1.01387 | -22.7081 | 4 | 12 | 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
-26.431kcal/mol
Ligand efficiency (LE)
-1.1492kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.143
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
313.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.92
Lipinski: ≤ 5
Rotatable bonds
2
Conformational strain (MMFF94s)
Strain energy (ΔE)
4.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
59.05kcal/mol
Minimised FF energy
54.56kcal/mol
SASA & burial
✓ computed
SASA (unbound)
543.3Ų
Total solvent-accessible surface area of free ligand
BSA total
504.9Ų
Buried surface area upon binding
BSA apolar
404.1Ų
Hydrophobic contacts buried
BSA polar
100.8Ų
Polar contacts buried
Fraction buried
92.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1483.7Ų
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
1677.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
634.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)