# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 10:48:17 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  30  16  .  2022-07-24  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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  -0.446   4.6083   0.5759   0.7937
 AE5  C02  C  C     0   0.550   3.8412   1.2972   0.2056
 AE5  O03  O  OH1   0  -0.598   4.1228   2.5619  -0.0945
 AE5  C04  C  CH2   0  -0.575   2.4716   0.9039  -0.2695
 AE5  C05  C  CH2   0  -0.432   2.1450  -0.5566  -0.0123
 AE5  C06  C  CH1   0  -0.205   0.7179  -0.8892  -0.4724
 AE5  N07  N  NH1   0  -0.585  -0.2453  -0.1095   0.2617
 AE5  C08  C  CH2   0  -0.270  -1.5727  -0.0784  -0.3163
 AE5  C09  C  CH1   0  -0.233  -2.4515   0.9266   0.4478
 AE5  N10  N  NH2   0  -0.787  -2.6390   0.6390   1.8516
 AE5  C11  C  C     0   0.544  -3.8044   1.0210  -0.2311
 AE5  O12  O  OH1   0  -0.595  -3.7131   1.5787  -1.4334
 AE5  O13  O  O     0  -0.435  -4.8394   0.6240   0.2382
 AE5  C14  C  C     0   0.535   0.4970  -2.3914  -0.3380
 AE5  O15  O  O     0  -0.437  -0.1077  -2.9075   0.5682
 AE5  O16  O  OH1   0  -0.590   1.0793  -3.0738  -1.3150
 AE5  H1   H  HOH1  0   0.479   5.0079   2.7893   0.2277
 AE5  H2   H  HCH2  0   0.288   1.7349   1.5483   0.2168
 AE5  H3   H  HCH2  0   0.278   2.4003   1.1291  -1.3383
 AE5  H4   H  HCH2  0   0.256   2.8556  -1.1942  -0.5404
 AE5  H5   H  HCH2  0   0.246   2.2421  -0.7876   1.0519
 AE5  H6   H  HCH1  0   0.272   0.6335  -0.6301  -1.5332
 AE5  H7   H  HNH1  0   0.342  -0.2866  -0.4396   1.2186
 AE5  H9   H  HCH2  0   0.241  -1.4777   0.2353  -1.3577
 AE5  H10  H  HCH2  0   0.210  -2.0761  -1.0577  -0.3235
 AE5  H11  H  HCH1  0   0.275  -1.9720   1.9070   0.3686
 AE5  H12  H  HNH2  0   0.348  -2.8860  -0.3319   1.9972
 AE5  H13  H  HNH2  0   0.360  -1.7842   0.8121   2.3623
 AE5  H15  H  HOH1  0   0.482  -4.5847   1.6026  -1.8562
 AE5  H16  H  HOH1  0   0.482   0.9640  -4.0262  -1.1752

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  double  1.205  0.020  1.205
 AE5  O16  C14  single  1.326  0.020  1.326
 AE5  C14  C06  single  1.524  0.020  1.524
 AE5  C06  N07  single  1.440  0.020  1.440
 AE5  C06  C05  single  1.536  0.020  1.536
 AE5  N10  C09  single  1.445  0.020  1.445
 AE5  N07  C08  single  1.448  0.020  1.448
 AE5  C09  C08  single  1.538  0.020  1.538
 AE5  C09  C11  single  1.517  0.020  1.517
 AE5  C04  C05  single  1.519  0.020  1.519
 AE5  C04  C02  single  1.502  0.020  1.502
 AE5  C11  O13  double  1.204  0.020  1.204
 AE5  C11  O12  single  1.328  0.020  1.328
 AE5  C02  O01  double  1.206  0.020  1.206
 AE5  C02  O03  single  1.330  0.020  1.330
 AE5  O03  H1   single  0.850  0.020  0.980
 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
 AE5  O12  H15  single  0.850  0.020  0.980
 AE5  O16  H16  single  0.850  0.020  0.980

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  111.76  3.000
 AE5  O03  C02  O01  122.96  3.000
 AE5  C04  C02  O01  125.28  3.000
 AE5  H1   O03  C02  109.98  3.000
 AE5  H3   C04  H2   105.62  3.000
 AE5  H3   C04  C05  110.44  3.000
 AE5  H2   C04  C05  110.29  3.000
 AE5  H3   C04  C02  108.33  3.000
 AE5  H2   C04  C02  108.63  3.000
 AE5  C05  C04  C02  113.23  3.000
 AE5  H5   C05  H4   106.85  3.000
 AE5  H5   C05  C06  109.17  3.000
 AE5  H4   C05  C06  109.49  3.000
 AE5  H5   C05  C04  110.43  3.000
 AE5  H4   C05  C04  109.87  3.000
 AE5  C06  C05  C04  110.94  3.000
 AE5  H6   C06  C14  107.90  3.000
 AE5  H6   C06  N07  108.30  3.000
 AE5  C14  C06  N07  113.06  3.000
 AE5  H6   C06  C05  108.09  3.000
 AE5  N07  C06  C05  110.58  3.000
 AE5  C14  C06  C05  108.77  3.000
 AE5  H7   N07  C08  110.28  3.000
 AE5  H7   N07  C06  109.41  3.000
 AE5  C08  N07  C06  114.91  3.000
 AE5  H10  C08  H9   106.80  3.000
 AE5  H10  C08  C09  108.85  3.000
 AE5  H9   C08  C09  109.62  3.000
 AE5  H10  C08  N07  113.74  3.000
 AE5  H9   C08  N07  107.89  3.000
 AE5  C09  C08  N07  109.85  3.000
 AE5  H11  C09  C11  107.62  3.000
 AE5  H11  C09  N10  107.78  3.000
 AE5  C11  C09  N10  109.36  3.000
 AE5  H11  C09  C08  107.40  3.000
 AE5  C11  C09  C08  109.15  3.000
 AE5  N10  C09  C08  115.25  3.000
 AE5  H13  N10  H12  107.33  3.000
 AE5  H13  N10  C09  110.31  3.000
 AE5  H12  N10  C09  111.23  3.000
 AE5  O13  C11  O12  123.39  3.000
 AE5  O12  C11  C09  111.71  3.000
 AE5  O13  C11  C09  124.89  3.000
 AE5  H15  O12  C11  110.09  3.000
 AE5  O16  C14  O15  123.62  3.000
 AE5  O16  C14  C06  112.24  3.000
 AE5  O15  C14  C06  124.12  3.000
 AE5  H16  O16  C14  110.30  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  CONST_01  H1   O03  C02  O01     0.00   0.0  0
 AE5  CONST_02  H16  O16  C14  C06   180.00   0.0  0
 AE5  CONST_03  H15  O12  C11  C09   180.00   0.0  0
 AE5  Var_01    C05  C04  C02  O01    -3.47  30.0  2
 AE5  Var_02    C06  C05  C04  C02   178.00  30.0  3
 AE5  Var_03    C09  C08  N07  C06  -172.55  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-1  H1   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-2  H15  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
 AE5  plan-3  H16  0.020

