# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 11:04:31 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: N-[(2S)-2-amino-2-carboxyethyl]-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CN[C@@H](CCC(O)=O)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
 AE5  AE5  'N-[(2S)-2-amino-2-carboxyethyl]-L-glutamic acid'  L-peptide  27  16  .  2022-07-24  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (side chain)
;

data_comp_AE5
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
 AE5  O01  O  O      0  -0.613   4.5772   0.6771   0.7675
 AE5  C02  C  C      0   0.405   3.8731   1.4518   0.0889
 AE5  O03  O  OC    -1  -0.638   4.1996   2.5999  -0.2855
 AE5  C04  C  CH2    0  -0.573   2.4703   0.9814  -0.3249
 AE5  C05  C  CH2    0  -0.406   2.1454  -0.4789  -0.0607
 AE5  C06  C  CH1    0  -0.194   0.7174  -0.8542  -0.4778
 AE5  N07  N  NH1    0  -0.592  -0.2467  -0.1049   0.3108
 AE5  C08  C  CH2    0  -0.259  -1.5565  -0.0077  -0.3055
 AE5  C09  C  CH1    0  -0.226  -2.4867   0.9298   0.4747
 AE5  N10  N  NH2    0  -0.796  -2.7396   0.5305   1.8502
 AE5  C11  C  C      0   0.398  -3.8042   1.0800  -0.3156
 AE5  O12  O  OC    -1  -0.624  -3.7218   1.6981  -1.3977
 AE5  O13  O  O      0  -0.607  -4.8283   0.5506   0.1581
 AE5  C14  C  C      0   0.396   0.5446  -2.3897  -0.3997
 AE5  O15  O  O      0  -0.608  -0.0919  -2.8466   0.5719
 AE5  O16  O  OC    -1  -0.625   1.0946  -3.0566  -1.3018
 AE5  H2   H  HCH2   0   0.222   1.7307   1.6085   0.1838
 AE5  H3   H  HCH2   0   0.204   2.3348   1.1975  -1.3912
 AE5  H4   H  HCH2   0   0.203   2.8472  -1.1175  -0.6022
 AE5  H5   H  HCH2   0   0.195   2.2810  -0.7091   1.0011
 AE5  H6   H  HCH1   0   0.194   0.5949  -0.5552  -1.5264
 AE5  H7   H  HNH1   0   0.316  -0.3459  -0.6147   1.1829
 AE5  H9   H  HCH2   0   0.204  -1.4281   0.3999  -1.3111
 AE5  H10  H  HCH2   0   0.172  -2.0506  -0.9875  -0.4233
 AE5  H11  H  HCH1   0   0.199  -1.9947   1.9096   0.5001
 AE5  H12  H  HNH2   0   0.325  -3.2963  -0.3148   1.8535
 AE5  H13  H  HNH2   0   0.329  -1.8689   0.3103   2.3179

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
 AE5  O15  C14  deloc   1.248  0.020  1.248
 AE5  O16  C14  deloc   1.249  0.020  1.249
 AE5  C14  C06  single  1.547  0.020  1.547
 AE5  C06  N07  single  1.454  0.020  1.454
 AE5  C06  C05  single  1.534  0.020  1.534
 AE5  N10  C09  single  1.454  0.020  1.454
 AE5  N07  C08  single  1.451  0.020  1.451
 AE5  C09  C08  single  1.534  0.020  1.534
 AE5  C09  C11  single  1.544  0.020  1.544
 AE5  C04  C05  single  1.519  0.020  1.519
 AE5  C04  C02  single  1.536  0.020  1.536
 AE5  C11  O13  deloc   1.246  0.020  1.246
 AE5  C11  O12  deloc   1.249  0.020  1.249
 AE5  C02  O01  deloc   1.248  0.020  1.248
 AE5  C02  O03  deloc   1.251  0.020  1.251
 AE5  C04  H2   single  0.970  0.020  1.090
 AE5  C04  H3   single  0.970  0.020  1.090
 AE5  C05  H4   single  0.970  0.020  1.090
 AE5  C05  H5   single  0.970  0.020  1.090
 AE5  C06  H6   single  0.970  0.020  1.090
 AE5  N07  H7   single  0.890  0.020  1.040
 AE5  C08  H9   single  0.970  0.020  1.090
 AE5  C08  H10  single  0.970  0.020  1.090
 AE5  C09  H11  single  0.970  0.020  1.090
 AE5  N10  H12  single  0.890  0.020  1.040
 AE5  N10  H13  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
 AE5  C04  C02  O03  116.02  3.000
 AE5  O03  C02  O01  125.83  3.000
 AE5  C04  C02  O01  118.15  3.000
 AE5  H3   C04  H2   104.80  3.000
 AE5  H3   C04  C05  109.40  3.000
 AE5  H2   C04  C05  108.98  3.000
 AE5  H3   C04  C02  108.33  3.000
 AE5  H2   C04  C02  108.44  3.000
 AE5  C05  C04  C02  116.28  3.000
 AE5  H5   C05  H4   106.15  3.000
 AE5  H5   C05  C06  109.11  3.000
 AE5  H4   C05  C06  108.67  3.000
 AE5  H5   C05  C04  110.13  3.000
 AE5  H4   C05  C04  109.78  3.000
 AE5  C06  C05  C04  112.76  3.000
 AE5  H6   C06  C14  107.83  3.000
 AE5  H6   C06  N07  107.70  3.000
 AE5  C14  C06  N07  114.21  3.000
 AE5  H6   C06  C05  107.28  3.000
 AE5  N07  C06  C05  110.11  3.000
 AE5  C14  C06  C05  109.45  3.000
 AE5  H7   N07  C08  108.08  3.000
 AE5  H7   N07  C06  105.78  3.000
 AE5  C08  N07  C06  113.76  3.000
 AE5  H10  C08  H9   106.59  3.000
 AE5  H10  C08  C09  108.99  3.000
 AE5  H9   C08  C09  108.14  3.000
 AE5  H10  C08  N07  112.96  3.000
 AE5  H9   C08  N07  108.05  3.000
 AE5  C09  C08  N07  111.86  3.000
 AE5  H11  C09  C11  107.92  3.000
 AE5  H11  C09  N10  107.54  3.000
 AE5  C11  C09  N10  111.25  3.000
 AE5  H11  C09  C08  106.61  3.000
 AE5  C11  C09  C08  108.46  3.000
 AE5  N10  C09  C08  114.76  3.000
 AE5  H13  N10  H12  106.84  3.000
 AE5  H13  N10  C09  110.30  3.000
 AE5  H12  N10  C09  109.15  3.000
 AE5  O13  C11  O12  126.42  3.000
 AE5  O12  C11  C09  115.81  3.000
 AE5  O13  C11  C09  117.73  3.000
 AE5  O16  C14  O15  126.24  3.000
 AE5  O16  C14  C06  116.36  3.000
 AE5  O15  C14  C06  117.36  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
 AE5  Var_01  C05  C04  C02  O01    -9.56  30.0  2
 AE5  Var_02  C06  C05  C04  C02   178.84  30.0  3
 AE5  Var_03  C09  C08  N07  C06  -173.06  30.0  3

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
 AE5  chir_01  C06  C14  N07  C05  negativ
 AE5  chir_02  C09  N10  C08  C11  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
 AE5  plan-1  O01  0.020
 AE5  plan-1  C02  0.020
 AE5  plan-1  O03  0.020
 AE5  plan-1  C04  0.020
 AE5  plan-2  C09  0.020
 AE5  plan-2  C11  0.020
 AE5  plan-2  O12  0.020
 AE5  plan-2  O13  0.020
 AE5  plan-3  C06  0.020
 AE5  plan-3  C14  0.020
 AE5  plan-3  O15  0.020
 AE5  plan-3  O16  0.020

