# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 10:37:25 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: oxo{[(1S)-1-phenylethyl]amino}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(=O)C(O)=O)c1ccccc1
#
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
 E9J  E9J  'oxo{[(1S)-1-phenylethyl]amino}acetic acid'  ligand  24  14  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E9J
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
 E9J  C02  C  C      0   0.340   3.0253  -0.6814   0.3823
 E9J  C03  C  C      0   0.360   2.0218   0.5000   0.2157
 E9J  C05  C  CH1    0  -0.149  -0.3197   1.0270  -0.3342
 E9J  C06  C  CH3    0  -0.649  -0.2718   1.6328  -1.7363
 E9J  C07  C  CR6    0   0.138  -1.6265   0.3158  -0.0702
 E9J  C08  C  CR16   0  -0.323  -2.4564   0.7281   0.9672
 E9J  C09  C  CR16   0  -0.238  -3.6629   0.0841   1.2129
 E9J  C10  C  CR16   0  -0.268  -4.0505  -0.9900   0.4245
 E9J  C11  C  CR16   0  -0.239  -3.2269  -1.4124  -0.6120
 E9J  C12  C  CR16   0  -0.305  -2.0260  -0.7622  -0.8585
 E9J  N04  N  NH1    0  -0.619   0.7822   0.1103  -0.1068
 E9J  O01  O  O      0  -0.589   2.5688  -1.8174   0.1548
 E9J  O13  O  O      0  -0.505   2.3475   1.6683   0.3751
 E9J  O14  O  OC    -1  -0.577   4.1697  -0.3596   0.7211
 E9J  H1   H  HCH1   0   0.255  -0.2266   1.8399   0.3905
 E9J  H2   H  HCH3   0   0.232  -1.0855   2.3462  -1.8717
 E9J  H3   H  HCH3   0   0.240   0.6692   2.1608  -1.8893
 E9J  H4   H  HCH3   0   0.226  -0.3620   0.8642  -2.5048
 E9J  H5   H  HCR6   0   0.252  -2.1579   1.5644   1.5882
 E9J  H6   H  HCR6   0   0.256  -4.2978   0.4235   2.0213
 E9J  H7   H  HCR6   0   0.256  -4.9893  -1.4941   0.6143
 E9J  H8   H  HCR6   0   0.256  -3.5226  -2.2492  -1.2318
 E9J  H9   H  HCR6   0   0.257  -1.4033  -1.1008  -1.6791
 E9J  H10  H  HNH1   0   0.394   0.6471  -0.8819  -0.2297

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
 E9J  O01  C02  deloc     1.245  0.020  1.245
 E9J  O13  C03  double    1.223  0.020  1.223
 E9J  C02  C03  single    1.559  0.020  1.559
 E9J  C02  O14  deloc     1.236  0.020  1.236
 E9J  C03  N04  single    1.339  0.020  1.339
 E9J  N04  C05  single    1.451  0.020  1.451
 E9J  C05  C06  single    1.528  0.020  1.528
 E9J  C05  C07  single    1.511  0.020  1.511
 E9J  C07  C08  aromatic  1.391  0.020  1.391
 E9J  C07  C12  aromatic  1.394  0.020  1.394
 E9J  C08  C09  aromatic  1.390  0.020  1.390
 E9J  C12  C11  aromatic  1.388  0.020  1.388
 E9J  C09  C10  aromatic  1.388  0.020  1.388
 E9J  C11  C10  aromatic  1.390  0.020  1.390
 E9J  C05  H1   single    0.970  0.020  1.090
 E9J  C06  H2   single    0.970  0.020  1.090
 E9J  C06  H3   single    0.970  0.020  1.090
 E9J  C06  H4   single    0.970  0.020  1.090
 E9J  C08  H5   single    0.930  0.020  1.080
 E9J  C09  H6   single    0.930  0.020  1.080
 E9J  C10  H7   single    0.930  0.020  1.080
 E9J  C11  H8   single    0.930  0.020  1.080
 E9J  C12  H9   single    0.930  0.020  1.080
 E9J  N04  H10  single    0.860  0.020  1.020

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
 E9J  O14  C02  O01  128.83  3.000
 E9J  O14  C02  C03  115.33  3.000
 E9J  O01  C02  C03  115.84  3.000
 E9J  O13  C03  N04  123.77  3.000
 E9J  N04  C03  C02  113.65  3.000
 E9J  O13  C03  C02  122.58  3.000
 E9J  H1   C05  N04  107.53  3.000
 E9J  H1   C05  C07  107.93  3.000
 E9J  N04  C05  C07  109.39  3.000
 E9J  H1   C05  C06  108.11  3.000
 E9J  C07  C05  C06  111.96  3.000
 E9J  N04  C05  C06  111.74  3.000
 E9J  H4   C06  H3   108.29  3.000
 E9J  H4   C06  H2   108.17  3.000
 E9J  H3   C06  H2   108.05  3.000
 E9J  H4   C06  C05  111.38  3.000
 E9J  H3   C06  C05  110.36  3.000
 E9J  H2   C06  C05  110.48  3.000
 E9J  C12  C07  C08  118.68  3.000
 E9J  C12  C07  C05  120.87  3.000
 E9J  C08  C07  C05  120.45  3.000
 E9J  H5   C08  C09  119.71  3.000
 E9J  H5   C08  C07  119.46  3.000
 E9J  C09  C08  C07  120.84  3.000
 E9J  H6   C09  C10  120.21  3.000
 E9J  H6   C09  C08  119.74  3.000
 E9J  C10  C09  C08  120.05  3.000
 E9J  H7   C10  C11  120.22  3.000
 E9J  H7   C10  C09  120.21  3.000
 E9J  C11  C10  C09  119.57  3.000
 E9J  H8   C11  C12  119.79  3.000
 E9J  H8   C11  C10  120.01  3.000
 E9J  C12  C11  C10  120.20  3.000
 E9J  H9   C12  C11  119.02  3.000
 E9J  H9   C12  C07  120.32  3.000
 E9J  C11  C12  C07  120.66  3.000
 E9J  H10  N04  C05  120.03  3.000
 E9J  H10  N04  C03  116.08  3.000
 E9J  C05  N04  C03  123.84  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
 E9J  CONST_01  C10  C09  C08  C07    0.00   0.0  0
 E9J  CONST_02  C10  C11  C12  C07    0.00   0.0  0
 E9J  CONST_03  C11  C12  C07  C08    0.00   0.0  0
 E9J  CONST_04  C11  C10  C09  C08    0.00   0.0  0
 E9J  CONST_05  C12  C07  C08  C09    0.00   0.0  0
 E9J  CONST_06  C12  C11  C10  C09    0.00   0.0  0
 E9J  CONST_07  C09  C08  C07  C05  180.00   0.0  0
 E9J  CONST_08  C11  C12  C07  C05  180.00   0.0  0
 E9J  CONST_09  H6   C09  C08  C07  180.00   0.0  0
 E9J  CONST_10  H8   C11  C12  C07  180.00   0.0  0
 E9J  CONST_11  H9   C12  C07  C08  180.00   0.0  0
 E9J  CONST_12  H7   C10  C09  C08  180.00   0.0  0
 E9J  CONST_13  H5   C08  C09  C10  180.00   0.0  0
 E9J  CONST_14  C05  N04  C03  C02  180.00   0.0  0
 E9J  CONST_15  O13  C03  N04  C05    0.00   0.0  0
 E9J  CONST_16  H10  N04  C03  C02    0.00   0.0  0
 E9J  Var_01    O01  C02  C03  N04    2.29  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
 E9J  chir_01  C05  N04  C06  C07  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
 E9J  plan-1  C05  0.020
 E9J  plan-1  C07  0.020
 E9J  plan-1  C08  0.020
 E9J  plan-1  C09  0.020
 E9J  plan-1  C10  0.020
 E9J  plan-1  C11  0.020
 E9J  plan-1  C12  0.020
 E9J  plan-1  H5   0.020
 E9J  plan-1  H6   0.020
 E9J  plan-1  H7   0.020
 E9J  plan-1  H8   0.020
 E9J  plan-1  H9   0.020
 E9J  plan-2  C02  0.020
 E9J  plan-2  C03  0.020
 E9J  plan-2  C05  0.020
 E9J  plan-2  N04  0.020
 E9J  plan-2  O13  0.020
 E9J  plan-2  H10  0.020
 E9J  plan-3  C02  0.020
 E9J  plan-3  C03  0.020
 E9J  plan-3  O01  0.020
 E9J  plan-3  O14  0.020

