# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 28 16:52:31 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  30  17  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  CR16  0  -0.282   0.8269  -2.5411  -3.8351
 TB1  C5   C  CR16  0  -0.243   1.0443  -3.5879  -4.7176
 TB1  C8   C  CR16  0  -0.265   0.3933  -4.8035  -4.5355
 TB1  C6   C  CR16  0  -0.241  -0.4750  -4.9649  -3.4658
 TB1  C3   C  CR16  0  -0.312  -0.6865  -3.9160  -2.5781
 TB1  C1   C  CR6   0   0.067  -0.0434  -2.6971  -2.7567
 TB1  C4   C  CH2   0  -0.205  -0.2864  -1.5529  -1.8183
 TB1  O2   O  O2    0  -0.483   0.9588  -1.1126  -1.3112
 TB1  C11  C  CH1   0  -0.052   0.9094   0.0990  -0.6273
 TB1  C9   C  C     0   0.514   0.9298   1.2722  -1.5966
 TB1  O5   O  OH1   0  -0.591   0.7620   2.4187  -0.9535
 TB1  O1   O  O     0  -0.416   1.0922   1.1769  -2.7837
 TB1  C7   C  CH1   0  -0.256   2.1556   0.1535   0.2885
 TB1  C10  C  C     0   0.555   2.1485  -1.1058   1.1440
 TB1  O4   O  O     0  -0.425   3.0304  -1.9217   1.1705
 TB1  O3   O  OH1   0  -0.595   1.0426  -1.1923   1.8719
 TB1  N    N  NH2   0  -0.782   3.4209   0.2756  -0.3854
 TB1  H2   H  HCR6  0   0.252   1.3311  -1.5938  -3.9844
 TB1  H5   H  HCR6  0   0.256   1.7221  -3.4571  -5.5515
 TB1  H8   H  HCR6  0   0.256   0.5645  -5.6199  -5.2251
 TB1  H6   H  HCR6  0   0.256  -0.9839  -5.9084  -3.3155
 TB1  H3   H  HCR6  0   0.253  -1.3592  -4.0505  -1.7392
 TB1  H41  H  HCH2  0   0.231  -0.7979  -0.7444  -2.3531
 TB1  H42  H  HCH2  0   0.235  -0.9446  -1.8607  -0.9965
 TB1  H11  H  HCH1  0   0.274   0.0051   0.1866  -0.0091
 TB1  HO5  H  HOH1  0   0.488   0.8077   3.1653  -1.5703
 TB1  H7   H  HCH1  0   0.308   2.0417   1.0065   0.9635
 TB1  HO3  H  HOH1  0   0.485   1.0459  -2.0114   2.3900
 TB1  HN1  H  HNH2  0   0.366   3.5352   1.2029  -0.7708
 TB1  HN2  H  HNH2  0   0.354   3.5061  -0.3864  -1.1457

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  1.391  0.020  1.391
 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  1.390  0.020  1.390
 TB1  C6   H6   single    0.930  0.020  1.080
 TB1  C3   C1   aromatic  1.390  0.020  1.390
 TB1  C3   H3   single    0.930  0.020  1.080
 TB1  C1   C4   single    1.500  0.020  1.500
 TB1  C4   O2   single    1.415  0.020  1.415
 TB1  C4   H41  single    0.970  0.020  1.090
 TB1  C4   H42  single    0.970  0.020  1.090
 TB1  O2   C11  single    1.392  0.020  1.392
 TB1  C11  C9   single    1.522  0.020  1.522
 TB1  C11  C7   single    1.547  0.020  1.547
 TB1  C11  H11  single    0.970  0.020  1.090
 TB1  C9   O1   double    1.202  0.020  1.202
 TB1  C9   O5   single    1.325  0.020  1.325
 TB1  O5   HO5  single    0.850  0.020  0.980
 TB1  C7   N    single    1.439  0.020  1.439
 TB1  C7   C10  single    1.522  0.020  1.522
 TB1  C7   H7   single    0.970  0.020  1.090
 TB1  C10  O4   double    1.202  0.020  1.202
 TB1  C10  O3   single    1.327  0.020  1.327
 TB1  O3   HO3  single    0.850  0.020  0.980
 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   119.66  3.000
 TB1  H2   C2   C5   119.96  3.000
 TB1  C1   C2   C5   120.38  3.000
 TB1  H5   C5   C8   119.97  3.000
 TB1  H5   C5   C2   119.83  3.000
 TB1  C8   C5   C2   120.21  3.000
 TB1  H8   C8   C6   120.18  3.000
 TB1  H8   C8   C5   120.11  3.000
 TB1  C6   C8   C5   119.71  3.000
 TB1  H6   C6   C3   119.83  3.000
 TB1  H6   C6   C8   120.18  3.000
 TB1  C3   C6   C8   119.99  3.000
 TB1  H3   C3   C1   119.71  3.000
 TB1  H3   C3   C6   119.67  3.000
 TB1  C1   C3   C6   120.62  3.000
 TB1  C4   C1   C3   120.92  3.000
 TB1  C4   C1   C2   119.98  3.000
 TB1  C3   C1   C2   119.10  3.000
 TB1  H42  C4   H41  107.01  3.000
 TB1  H42  C4   O2   110.30  3.000
 TB1  H41  C4   O2   110.86  3.000
 TB1  H42  C4   C1   110.60  3.000
 TB1  H41  C4   C1   109.45  3.000
 TB1  O2   C4   C1   108.61  3.000
 TB1  C11  O2   C4   114.56  3.000
 TB1  H11  C11  C7   109.09  3.000
 TB1  H11  C11  C9   107.92  3.000
 TB1  C7   C11  C9   109.82  3.000
 TB1  H11  C11  O2   112.02  3.000
 TB1  C7   C11  O2   107.03  3.000
 TB1  C9   C11  O2   110.95  3.000
 TB1  O1   C9   O5   124.40  3.000
 TB1  O5   C9   C11  110.87  3.000
 TB1  O1   C9   C11  124.73  3.000
 TB1  HO5  O5   C9   110.58  3.000
 TB1  H7   C7   N    108.33  3.000
 TB1  H7   C7   C10  107.32  3.000
 TB1  N    C7   C10  109.73  3.000
 TB1  H7   C7   C11  107.99  3.000
 TB1  C10  C7   C11  107.44  3.000
 TB1  N    C7   C11  115.72  3.000
 TB1  O3   C10  O4   123.73  3.000
 TB1  O3   C10  C7   111.48  3.000
 TB1  O4   C10  C7   124.79  3.000
 TB1  HO3  O3   C10  110.21  3.000
 TB1  HN2  N    HN1  107.72  3.000
 TB1  HN2  N    C7   111.75  3.000
 TB1  HN1  N    C7   110.85  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  CONST_14  HO5  O5  C9   C11  180.00   0.0  0
 TB1  CONST_15  HO3  O3  C10  C7   180.00   0.0  0
 TB1  Var_01    O2   C4  C1   C2   -55.37  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-2  HO5  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
 TB1  plan-3  HO3  0.020

