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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
9.3 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.81, Jaccard 0.74, H-bond role recall 0.20
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.141 kcal/mol/HA)
✓ Good fit quality (FQ -10.07)
✓ Deep burial (90% SASA buried)
✓ Lipophilic contacts well-matched (97%)
✗ Moderate strain (9.3 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-26.244
kcal/mol
LE
-1.141
kcal/mol/HA
Fit Quality
-10.07
FQ (Leeson)
HAC
23
heavy atoms
MW
528
Da
LogP
4.23
cLogP
Interaction summary
HB 2
HY 23
PI 1
CLASH 3
Interaction summary
HB 2
HY 23
PI 1
CLASH 3
| Final rank | 1.613 | Score | -26.244 |
|---|---|---|---|
| Inter norm | -1.163 | Intra norm | 0.022 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 2 |
| Artifact reason | geometry warning; 8 clashes; 1 protein clash; 1 severe cofactor-context clash | ||
| Residues |
ALA10
ASP22
GLU31
GLY117
ILE61
ILE8
LEU23
LEU68
NAP201
PHE32
PHE35
PRO27
SER60
THR137
THR57
TYR122
TYR34
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 | 17 | Native recall | 0.81 |
| Jaccard | 0.74 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 675 | 0.08932108552118626 | -1.53139 | -33.7137 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 671 | 1.4623494220460063 | -1.20535 | -27.015 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 670 | 1.4838971022548233 | -1.01085 | -19.596 | 1 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 660 | 1.5296363297884992 | -1.24398 | -27.7842 | 3 | 17 | 15 | 0.71 | 0.20 | - | no | Open |
| 659 | 1.6127658204479765 | -1.16325 | -26.2443 | 2 | 19 | 17 | 0.81 | 0.20 | - | no | Current |
| 668 | 1.813401811970726 | -1.08305 | -23.0344 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 673 | 2.618099765994593 | -1.24331 | -24.7088 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 677 | 2.650135671650861 | -0.972587 | -21.0295 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 659 | 2.7068022141827996 | -1.03337 | -23.1766 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 670 | 3.068566625982152 | -1.0102 | -22.9013 | 4 | 16 | 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
-26.244kcal/mol
Ligand efficiency (LE)
-1.1411kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.071
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
528.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.23
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
9.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
56.69kcal/mol
Minimised FF energy
47.42kcal/mol
SASA & burial
✓ computed
SASA (unbound)
589.1Ų
Total solvent-accessible surface area of free ligand
BSA total
530.8Ų
Buried surface area upon binding
BSA apolar
516.8Ų
Hydrophobic contacts buried
BSA polar
14.1Ų
Polar contacts buried
Fraction buried
90.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
97.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1612.9Ų
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
640.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)