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
14.8 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.60, Jaccard 0.50, H-bond role recall 0.60
Reason: no major geometry red flags detected
2 protein-contact clashes
80% of hydrophobic surface is solvent-exposed (24/30 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 (-0.639 kcal/mol/HA)
✓ Good fit quality (FQ -6.67)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ Moderate strain (14.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (18)
Score
-25.565
kcal/mol
LE
-0.639
kcal/mol/HA
Fit Quality
-6.67
FQ (Leeson)
HAC
40
heavy atoms
MW
538
Da
LogP
5.13
cLogP
Interaction summary
HB 8
HY 1
PI 0
CLASH 2
⚠ Exposure 80%
Interaction summary
HB 8
HY 1
PI 0
CLASH 2
⚠ Exposure 80%
Solvent-exposed hydrophobic surface — desolvation penalty likely
80% of hydrophobic surface is solvent-exposed (24/30 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 30
Buried (contacted) 6
Exposed 24
LogP 5.13
H-bonds 8
Exposed fragments:
phenyl (5/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)phenyl (6/6 atoms exposed)
| Final rank | 4.328 | Score | -25.565 |
|---|---|---|---|
| Inter norm | -0.664 | Intra norm | 0.025 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 8 |
| Artifact reason | geometry warning; 18 clashes; 2 protein clashes | ||
| Residues |
ARG22
ARG242
ARG337
ASP243
ASP385
GLU384
LEU339
PHE383
SER282
THR21
THR241
THR285
| ||
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
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 | 9 | Native recall | 0.60 |
| Jaccard | 0.50 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| HB same residue | 4 | HB residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 34 | 2.037464332345491 | -0.816862 | -31.8466 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 25 | 2.378437056644811 | -0.79296 | -25.1786 | 11 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 28 | 3.1939535201530846 | -0.720039 | -24.3367 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 12 | 3.2679598625087527 | -0.927293 | -34.1568 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 20 | 3.495100387591973 | -0.687709 | -25.9631 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 26 | 3.6318101855931193 | -0.794213 | -29.5742 | 8 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 25 | 3.6473712664434346 | -0.864399 | -31.0091 | 12 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 11 | 3.756350175949824 | -0.818637 | -30.0821 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 36 | 4.328059027755822 | -0.664103 | -25.5651 | 8 | 12 | 9 | 0.60 | 0.60 | - | no | Current |
| 13 | 4.367243655754057 | -0.718582 | -25.2048 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 30 | 4.3947619074725255 | -0.797581 | -32.0325 | 7 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 27 | 4.675590440132758 | -0.575435 | -21.4762 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 18 | 4.709489958919522 | -0.661154 | -21.8688 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 26 | 4.853888287172083 | -0.702973 | -26.167 | 8 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 25 | 5.0046255959625645 | -0.602508 | -21.2208 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 20 | 5.305300875417073 | -0.744562 | -26.4698 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 17 | 5.662829045447725 | -0.771959 | -29.8084 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 12 | 6.260876601403174 | -0.803018 | -30.5918 | 10 | 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
-25.565kcal/mol
Ligand efficiency (LE)
-0.6391kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.675
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
40HA
Physicochemical properties
Molecular weight
538.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.13
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.82kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
137.93kcal/mol
Minimised FF energy
123.10kcal/mol
SASA & burial
✓ computed
SASA (unbound)
792.0Ų
Total solvent-accessible surface area of free ligand
BSA total
542.5Ų
Buried surface area upon binding
BSA apolar
376.8Ų
Hydrophobic contacts buried
BSA polar
165.7Ų
Polar contacts buried
Fraction buried
68.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2455.9Ų
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
1432.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)