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 mixed
SASA done
Strain ΔE
23.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.40, Jaccard 0.26, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
100% of hydrophobic surface is solvent-exposed (17/17 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.069 kcal/mol/HA)
✓ Good fit quality (FQ -9.85)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (67%)
✗ High strain energy (23.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-27.791
kcal/mol
LE
-1.069
kcal/mol/HA
Fit Quality
-9.85
FQ (Leeson)
HAC
26
heavy atoms
MW
364
Da
LogP
1.67
cLogP
Interaction summary
HB 9
HY 0
PI 0
CLASH 2
⚠ Exposure 100%
Interaction summary
HB 9
HY 0
PI 0
CLASH 2
⚠ Exposure 100%
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
No hy · hydrophobic contacts detected for this pose.
CLASH · Clashes
Solvent-exposed hydrophobic surface — desolvation penalty likely
100% of hydrophobic surface is solvent-exposed (17/17 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 17
Buried (contacted) 0
Exposed 17
LogP 1.67
H-bonds 9
Exposed fragments:
phenyl (4/5 atoms exposed)phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 3.262 | Score | -27.791 |
|---|---|---|---|
| Inter norm | -1.070 | Intra norm | 0.001 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 9 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes; moderate strain Δ 23.0 | ||
| Residues |
ALA283
ARG242
ARG50
ASP243
ASP385
ASP44
ASP47
GLU384
LYS51
PHE284
SER282
THR21
THR241
THR285
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 1NJJ | Contacts | 15 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG22
ARG242
ARG337
ARG342
ASP243
ASP385
GLN341
GLU384
LEU25
LEU339
LEU382
PRO340
PRO344
SER282
THR241
| ||
| Current overlap | 6 | Native recall | 0.40 |
| Jaccard | 0.26 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 1 | HB residue recall | 0.20 |
Protein summary
398 residues
| Protein target | T14 | Atoms | 6140 |
|---|---|---|---|
| Residues | 398 | Chains | 1 |
| Residue summary | VAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170 | ||
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:ORX602
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 522 | 2.261262159608891 | -0.956395 | -21.4623 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 532 | 2.445465122574451 | -0.93199 | -23.3803 | 13 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 500 | 2.521021803203339 | -1.41509 | -32.6993 | 6 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 517 | 2.5299445645219074 | -0.770281 | -19.8585 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 509 | 3.262137122905528 | -1.06992 | -27.791 | 9 | 14 | 6 | 0.40 | 0.00 | - | no | Current |
| 544 | 3.481530108671423 | -0.925088 | -22.453 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 497 | 4.064661269329177 | -1.16787 | -30.0605 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 551 | 4.1785443525306984 | -0.940747 | -23.0358 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 505 | 4.605833726720881 | -1.07502 | -27.6675 | 13 | 20 | 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
-27.791kcal/mol
Ligand efficiency (LE)
-1.0689kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.848
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
364.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.67
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.03kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
60.91kcal/mol
Minimised FF energy
37.89kcal/mol
SASA & burial
✓ computed
SASA (unbound)
583.0Ų
Total solvent-accessible surface area of free ligand
BSA total
440.9Ų
Buried surface area upon binding
BSA apolar
296.4Ų
Hydrophobic contacts buried
BSA polar
144.5Ų
Polar contacts buried
Fraction buried
75.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
67.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2343.5Ų
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
3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1411.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)