# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 01:30:35 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: (3S)-3-(benzyloxy)-L-aspartic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]([C@H](OCc1ccccc1)C(O)=O)C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 TB1  TB1  '(3S)-3-(benzyloxy)-L-aspartic acid'  ligand  28  17  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_TB1
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 TB1  C2   C  C1     0  -0.290   0.8850  -2.4814  -3.7552
 TB1  C5   C  C1     0  -0.245   1.1136  -3.4710  -4.6986
 TB1  C8   C  C1     0  -0.269   0.3862  -4.6569  -4.6614
 TB1  C6   C  C1     0  -0.243  -0.5713  -4.8436  -3.6754
 TB1  C3   C  C1     0  -0.318  -0.7977  -3.8499  -2.7284
 TB1  C1   C  C      0   0.060  -0.0775  -2.6621  -2.7614
 TB1  C4   C  CH2    0  -0.183  -0.3169  -1.5685  -1.7591
 TB1  O2   O  O2     0  -0.490   0.9058  -1.2243  -1.1663
 TB1  C11  C  CH1    0  -0.045   0.9434   0.0660  -0.6075
 TB1  C9   C  C      0   0.370   0.9039   1.2023  -1.6536
 TB1  O5   O  OC    -1  -0.614   0.5669   2.3186  -1.2079
 TB1  O1   O  O      0  -0.588   1.2505   0.9400  -2.8223
 TB1  C7   C  CH1    0  -0.239   2.2417   0.1623   0.2107
 TB1  C10  C  C      0   0.406   2.1814  -0.8643   1.3681
 TB1  O4   O  O      0  -0.602   3.0075  -1.7974   1.3621
 TB1  O3   O  OC    -1  -0.622   1.2897  -0.6694   2.2182
 TB1  N    N  NH2    0  -0.814   3.4554   0.0066  -0.5751
 TB1  H2   H  H      0   0.258   1.4445  -1.5539  -3.7790
 TB1  H5   H  H      0   0.250   1.8614  -3.3211  -5.4673
 TB1  H8   H  H      0   0.252   0.5689  -5.4301  -5.3966
 TB1  H6   H  H      0   0.251  -1.1381  -5.7651  -3.6359
 TB1  H3   H  H      0   0.247  -1.5407  -4.0053  -1.9545
 TB1  H41  H  HCH2   0   0.210  -0.7669  -0.7119  -2.2752
 TB1  H42  H  HCH2   0   0.208  -1.0454  -1.8961  -1.0031
 TB1  H11  H  HCH1   0   0.184   0.1055   0.2124   0.0889
 TB1  H7   H  HCH1   0   0.210   2.2308   1.1604   0.6657
 TB1  HN1  H  HNH2   0   0.329   3.2954   0.3057  -1.5295
 TB1  HN2  H  HNH2   0   0.327   3.6673  -0.9819  -0.6196

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 TB1  C2   C5   aromatic  1.386  0.020  1.386
 TB1  C2   C1   aromatic  1.395  0.020  1.395
 TB1  C2   H2   single    0.930  0.020  1.080
 TB1  C5   C8   aromatic  1.392  0.020  1.392
 TB1  C5   H5   single    0.930  0.020  1.080
 TB1  C8   C6   aromatic  1.387  0.020  1.387
 TB1  C8   H8   single    0.930  0.020  1.080
 TB1  C6   C3   aromatic  1.391  0.020  1.391
 TB1  C6   H6   single    0.930  0.020  1.080
 TB1  C3   C1   aromatic  1.389  0.020  1.389
 TB1  C3   H3   single    0.930  0.020  1.080
 TB1  C1   C4   single    1.503  0.020  1.503
 TB1  C4   O2   single    1.402  0.020  1.402
 TB1  C4   H41  single    0.970  0.020  1.090
 TB1  C4   H42  single    0.970  0.020  1.090
 TB1  O2   C11  single    1.407  0.020  1.407
 TB1  C11  C9   single    1.545  0.020  1.545
 TB1  C11  C7   single    1.538  0.020  1.538
 TB1  C11  H11  single    0.970  0.020  1.090
 TB1  C9   O1   deloc     1.247  0.020  1.247
 TB1  C9   O5   deloc     1.248  0.020  1.248
 TB1  C7   N    single    1.454  0.020  1.454
 TB1  C7   C10  single    1.548  0.020  1.548
 TB1  C7   H7   single    0.970  0.020  1.090
 TB1  C10  O4   deloc     1.246  0.020  1.246
 TB1  C10  O3   deloc     1.247  0.020  1.247
 TB1  N    HN1  single    0.890  0.020  1.040
 TB1  N    HN2  single    0.890  0.020  1.040

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 TB1  H2   C2   C1   118.87  3.000
 TB1  H2   C2   C5   120.73  3.000
 TB1  C1   C2   C5   120.40  3.000
 TB1  H5   C5   C8   119.86  3.000
 TB1  H5   C5   C2   119.88  3.000
 TB1  C8   C5   C2   120.26  3.000
 TB1  H8   C8   C6   120.21  3.000
 TB1  H8   C8   C5   120.15  3.000
 TB1  C6   C8   C5   119.64  3.000
 TB1  H6   C6   C3   119.86  3.000
 TB1  H6   C6   C8   120.13  3.000
 TB1  C3   C6   C8   120.01  3.000
 TB1  H3   C3   C1   119.65  3.000
 TB1  H3   C3   C6   119.68  3.000
 TB1  C1   C3   C6   120.67  3.000
 TB1  C4   C1   C3   121.59  3.000
 TB1  C4   C1   C2   119.39  3.000
 TB1  C3   C1   C2   119.02  3.000
 TB1  H42  C4   H41  106.52  3.000
 TB1  H42  C4   O2   111.11  3.000
 TB1  H41  C4   O2   111.42  3.000
 TB1  H42  C4   C1   110.32  3.000
 TB1  H41  C4   C1   108.66  3.000
 TB1  O2   C4   C1   108.77  3.000
 TB1  C11  O2   C4   114.61  3.000
 TB1  H11  C11  C7   107.35  3.000
 TB1  H11  C11  C9   108.15  3.000
 TB1  C7   C11  C9   109.62  3.000
 TB1  H11  C11  O2   110.70  3.000
 TB1  C7   C11  O2   106.94  3.000
 TB1  C9   C11  O2   113.89  3.000
 TB1  O1   C9   O5   126.71  3.000
 TB1  O5   C9   C11  115.01  3.000
 TB1  O1   C9   C11  118.22  3.000
 TB1  H7   C7   N    109.26  3.000
 TB1  H7   C7   C10  107.03  3.000
 TB1  N    C7   C10  111.43  3.000
 TB1  H7   C7   C11  105.62  3.000
 TB1  C10  C7   C11  108.87  3.000
 TB1  N    C7   C11  114.24  3.000
 TB1  O3   C10  O4   126.45  3.000
 TB1  O3   C10  C7   115.71  3.000
 TB1  O4   C10  C7   117.84  3.000
 TB1  HN2  N    HN1  106.27  3.000
 TB1  HN2  N    C7   107.65  3.000
 TB1  HN1  N    C7   110.22  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 TB1  CONST_01  C6  C8  C5  C2    0.00   0.0  0
 TB1  CONST_02  C6  C3  C1  C2    0.00   0.0  0
 TB1  CONST_03  C3  C1  C2  C5    0.00   0.0  0
 TB1  CONST_04  C3  C6  C8  C5    0.00   0.0  0
 TB1  CONST_05  C1  C2  C5  C8    0.00   0.0  0
 TB1  CONST_06  C1  C3  C6  C8    0.00   0.0  0
 TB1  CONST_07  C4  C1  C2  C5  180.00   0.0  0
 TB1  CONST_08  C4  C1  C3  C6  180.00   0.0  0
 TB1  CONST_09  H8  C8  C5  C2  180.00   0.0  0
 TB1  CONST_10  H3  C3  C1  C2  180.00   0.0  0
 TB1  CONST_11  H6  C6  C8  C5  180.00   0.0  0
 TB1  CONST_12  H2  C2  C5  C8  180.00   0.0  0
 TB1  CONST_13  H5  C5  C8  C6  180.00   0.0  0
 TB1  Var_01    O2  C4  C1  C2  -53.54  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 TB1  chir_01  C11  O2  C9   C7   positiv
 TB1  chir_02  C7   N   C11  C10  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 TB1  plan-1  C2   0.020
 TB1  plan-1  C5   0.020
 TB1  plan-1  C8   0.020
 TB1  plan-1  C6   0.020
 TB1  plan-1  C3   0.020
 TB1  plan-1  C1   0.020
 TB1  plan-1  C4   0.020
 TB1  plan-1  H2   0.020
 TB1  plan-1  H5   0.020
 TB1  plan-1  H8   0.020
 TB1  plan-1  H6   0.020
 TB1  plan-1  H3   0.020
 TB1  plan-2  C11  0.020
 TB1  plan-2  C9   0.020
 TB1  plan-2  O5   0.020
 TB1  plan-2  O1   0.020
 TB1  plan-3  C7   0.020
 TB1  plan-3  C10  0.020
 TB1  plan-3  O4   0.020
 TB1  plan-3  O3   0.020

