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
22.4 kcal/mol
Protein clashes
0
Internal clashes
1
Native overlap
contact recall 0.71, Jaccard 0.68, H-bond role recall 0.20
Reason: no major geometry red flags detected
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.083 kcal/mol/HA)
✓ Good fit quality (FQ -10.10)
✓ Good H-bonds (5 bonds)
✓ Deep burial (83% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ High strain energy (22.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-29.237
kcal/mol
LE
-1.083
kcal/mol/HA
Fit Quality
-10.10
FQ (Leeson)
HAC
27
heavy atoms
MW
363
Da
LogP
2.73
cLogP
Interaction summary
HB 5
HY 15
PI 1
CLASH 1
Interaction summary
HB 5
HY 15
PI 1
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 | 2.700 | Score | -29.237 |
|---|---|---|---|
| Inter norm | -1.085 | Intra norm | 0.003 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 5 |
| Artifact reason | geometry warning; 11 clashes; 2 protein clashes; 1 cofactor-context clash; moderate strain Δ 22.4 | ||
| Residues |
ALA10
ASP22
GLY117
GLY21
ILE61
ILE8
LEU23
NAP201
PHE35
PRO27
PRO62
SER60
THR57
TYR122
VAL116
VAL9
| ||
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 | 15 | Native recall | 0.71 |
| Jaccard | 0.68 | 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 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 92 | 1.0569874525188159 | -1.10517 | -24.005 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 104 | 1.46016853012659 | -0.985948 | -23.9799 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 95 | 1.6104257095050154 | -0.899281 | -27.1083 | 7 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 118 | 1.9879243078262165 | -0.764076 | -22.6199 | 4 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 150 | 2.5978360506406286 | -0.935679 | -26.7983 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 149 | 2.6998886413891503 | -1.08536 | -29.2372 | 5 | 16 | 15 | 0.71 | 0.20 | - | no | Current |
| 130 | 3.061999676869863 | -0.986049 | -19.8883 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 88 | 3.162065719758737 | -1.14272 | -35.6793 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 63 | 3.99786131386113 | -0.912238 | -24.5335 | 16 | 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
-29.237kcal/mol
Ligand efficiency (LE)
-1.0829kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.103
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
363.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.73
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.39kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
143.94kcal/mol
Minimised FF energy
121.54kcal/mol
SASA & burial
✓ computed
SASA (unbound)
634.5Ų
Total solvent-accessible surface area of free ligand
BSA total
528.3Ų
Buried surface area upon binding
BSA apolar
431.5Ų
Hydrophobic contacts buried
BSA polar
96.7Ų
Polar contacts buried
Fraction buried
83.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1569.5Ų
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
637.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)