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 high
Native mixed
SASA done
Strain ΔE
18.3 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.52, Jaccard 0.46, H-bond role recall 0.00
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.855 kcal/mol/HA)
✓ Good fit quality (FQ -8.48)
✓ Good H-bonds (3 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (88%)
✗ Moderate strain (18.3 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-28.209
kcal/mol
LE
-0.855
kcal/mol/HA
Fit Quality
-8.48
FQ (Leeson)
HAC
33
heavy atoms
MW
587
Da
LogP
6.59
cLogP
Interaction summary
HB 3
HY 24
PI 2
CLASH 2
Interaction summary
HB 3
HY 24
PI 2
CLASH 2
| Final rank | 3.005 | Score | -28.209 |
|---|---|---|---|
| Inter norm | -0.800 | Intra norm | -0.055 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 3 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes; 1 cofactor-context clash | ||
| Residues |
ARG29
ASN65
ASP22
GLU31
ILE61
LEU23
LEU28
NAP201
PHE32
PHE35
PRO27
PRO62
SER60
THR57
| ||
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 | 11 | Native recall | 0.52 |
| Jaccard | 0.46 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
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 | 0.7365778015741843 | -0.722297 | -22.475 | 0 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 675 | 0.9222024432790271 | -0.780298 | -20.7138 | 1 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 675 | 1.3318990393087835 | -0.784455 | -23.5259 | 2 | 21 | 16 | 0.76 | 0.20 | - | no | Open |
| 673 | 1.8257988947562371 | -0.780003 | -25.6147 | 1 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 677 | 2.185754577570499 | -0.707577 | -22.2139 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 679 | 2.313050101027019 | -0.653709 | -21.3095 | 3 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 673 | 3.0051206271132003 | -0.799552 | -28.209 | 3 | 14 | 11 | 0.52 | 0.00 | - | no | Current |
| 674 | 3.2471955707314253 | -0.731831 | -19.575 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 668 | 3.304781108763105 | -0.829561 | -25.784 | 7 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 671 | 3.426665874948449 | -0.751822 | -23.221 | 6 | 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
-28.209kcal/mol
Ligand efficiency (LE)
-0.8548kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.481
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
587.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.59
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.28kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-6.83kcal/mol
Minimised FF energy
-25.10kcal/mol
SASA & burial
✓ computed
SASA (unbound)
738.5Ų
Total solvent-accessible surface area of free ligand
BSA total
590.0Ų
Buried surface area upon binding
BSA apolar
518.8Ų
Hydrophobic contacts buried
BSA polar
71.2Ų
Polar contacts buried
Fraction buried
79.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
87.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1647.8Ų
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
679.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)