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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
16.8 kcal/mol
Protein clashes
0
Internal clashes
12
Native overlap
contact recall 0.88, Jaccard 0.75, H-bond role recall 0.33
Reason: 12 internal clashes
12 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.200 kcal/mol/HA)
✓ Good fit quality (FQ -11.05)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (84% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ Moderate strain (16.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-31.189
kcal/mol
LE
-1.200
kcal/mol/HA
Fit Quality
-11.05
FQ (Leeson)
HAC
26
heavy atoms
MW
365
Da
LogP
2.13
cLogP
Interaction summary
HB 6
HY 17
PI 3
CLASH 0
Interaction summary
HB 6
HY 17
PI 3
CLASH 0
| Final rank | 3.109 | Score | -31.189 |
|---|---|---|---|
| Inter norm | -1.141 | Intra norm | -0.058 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 6 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes | ||
| Residues |
ARG17
ASP181
GLY225
HIS241
LEU188
LEU226
LEU229
MET233
NDP302
PHE113
PRO115
SER227
TYR114
TYR191
TYR194
VAL228
VAL230
ARG287
| ||
Protein summary
274 residues
| Protein target | T05 | Atoms | 4108 |
|---|---|---|---|
| Residues | 274 | Chains | 2 |
| Residue summary | LEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108 | ||
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:NDP302
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | ligand | Contacts | 17 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG17
GLY225
HIS241
LEU188
LEU226
LEU229
LYS198
MET233
NDP302
PHE113
PRO115
SER111
SER227
TYR191
TYR194
VAL230
ARG287
| ||
| Current overlap | 15 | Native recall | 0.88 |
| Jaccard | 0.75 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 2 | HB role recall | 0.33 |
| HB same residue | 3 | HB residue recall | 0.60 |
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
No clash · clashes detected for this pose.
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 581 | 1.000264785721566 | -0.918966 | -22.4821 | 5 | 11 | 11 | 0.65 | 0.17 | - | no | Open |
| 594 | 1.4646519661374353 | -0.944365 | -23.7072 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 578 | 2.564509005169744 | -0.753638 | -20.2448 | 5 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 591 | 3.000529114437112 | -1.19895 | -30.0875 | 13 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 560 | 3.1093396187805626 | -1.14147 | -31.1887 | 6 | 18 | 15 | 0.88 | 0.33 | - | no | Current |
| 567 | 3.516543969577786 | -0.922823 | -22.6476 | 6 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 574 | 3.8896490358075844 | -1.2635 | -33.1996 | 12 | 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
-31.189kcal/mol
Ligand efficiency (LE)
-1.1996kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.052
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
365.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.13
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.83kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
54.64kcal/mol
Minimised FF energy
37.81kcal/mol
SASA & burial
✓ computed
SASA (unbound)
577.4Ų
Total solvent-accessible surface area of free ligand
BSA total
486.5Ų
Buried surface area upon binding
BSA apolar
340.8Ų
Hydrophobic contacts buried
BSA polar
145.7Ų
Polar contacts buried
Fraction buried
84.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1577.2Ų
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
2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1031.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)