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
12.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.22, Jaccard 0.16, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 protein-contact clashes
47% of hydrophobic surface appears solvent-exposed (7/15 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.483 kcal/mol/HA)
✓ Good fit quality (FQ -12.65)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (97% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ Moderate strain (12.9 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-31.149
kcal/mol
LE
-1.483
kcal/mol/HA
Fit Quality
-12.65
FQ (Leeson)
HAC
21
heavy atoms
MW
301
Da
LogP
3.21
cLogP
Interaction summary
HB 11
HY 9
PI 0
CLASH 2
⚠ Exposure 46%
Interaction summary
HB 11
HY 9
PI 0
CLASH 2
⚠ Exposure 46%
Partial hydrophobic solvent exposure
47% of hydrophobic surface appears solvent-exposed (7/15 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 15
Buried (contacted) 8
Exposed 7
LogP 3.21
H-bonds 11
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 2.800 | Score | -31.149 |
|---|---|---|---|
| Inter norm | -1.544 | Intra norm | 0.061 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 11 |
| Artifact reason | geometry warning; 7 clashes; 2 protein clashes; 1 severe cofactor-context clash | ||
| Residues |
ARG287
ASP327
CYS52
CYS57
GLY56
ILE199
LEU334
LYS60
MET333
NDP800
PHE182
PHE203
SER162
SER178
THR335
THR51
VAL55
| ||
Protein summary
493 residues
| Protein target | T19 | Atoms | 7541 |
|---|---|---|---|
| Residues | 493 | Chains | 1 |
| Residue summary | VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:330; TYR:294; ASP:264; MET:221 | ||
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
C:NDP800
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 2WOV | Contacts | 27 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA284
ALA365
ARG222
ARG228
ARG287
ASN223
ASN254
GLN165
GLU202
GLY195
GLY196
GLY197
GLY286
ILE199
ILE285
LEU227
LEU334
LYS60
MET333
NDP800
PHE198
PHE367
PRO167
SER200
TYR221
VAL194
VAL366
| ||
| Current overlap | 6 | Native recall | 0.22 |
| Jaccard | 0.16 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.25 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 551 | -0.10966209886901078 | -1.29964 | -25.3355 | 2 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 532 | 1.0046581056658084 | -1.50673 | -28.6964 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 558 | 1.8507984583927155 | -0.895968 | -16.1192 | 6 | 7 | 0 | 0.00 | 0.00 | - | no | Open |
| 548 | 2.3499413020302247 | -1.40164 | -21.5647 | 7 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 536 | 2.4750002428206046 | -1.35939 | -27.4286 | 11 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 542 | 2.63527126834114 | -1.20429 | -22.2029 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 545 | 2.800134034659489 | -1.54392 | -31.1493 | 11 | 17 | 6 | 0.22 | 0.20 | - | no | Current |
| 541 | 3.544151329633376 | -1.50159 | -24.6005 | 12 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 539 | 4.324614488326156 | -1.4057 | -25.737 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 565 | 4.84275437333706 | -1.34595 | -23.6881 | 11 | 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
-31.149kcal/mol
Ligand efficiency (LE)
-1.4833kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.652
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
301.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.21
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.93kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
33.00kcal/mol
Minimised FF energy
20.07kcal/mol
SASA & burial
✓ computed
SASA (unbound)
488.4Ų
Total solvent-accessible surface area of free ligand
BSA total
473.1Ų
Buried surface area upon binding
BSA apolar
327.1Ų
Hydrophobic contacts buried
BSA polar
146.0Ų
Polar contacts buried
Fraction buried
96.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2930.7Ų
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
4064.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1471.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)