# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 08:11:56 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: (2~{S})-2-azanyl-2-oxidanyl-pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@](O)(CCC(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
 8GL  8GL  '(2~{S})-2-azanyl-2-oxidanyl-pentanedioic acid'  ligand  20  11  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_8GL
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
 8GL  N01  N  NH2   0  -0.800  -1.0643  -1.0039   1.5024
 8GL  C02  C  CT    0   0.283  -1.0275  -0.5302   0.1464
 8GL  O03  O  OH1   0  -0.657  -1.0656  -1.6678  -0.6665
 8GL  C04  C  CH2   0  -0.468   0.2509   0.2950  -0.0820
 8GL  C05  C  CH2   0  -0.576   1.5091  -0.5330   0.1158
 8GL  C06  C  C     0   0.550   2.7646   0.2664  -0.0882
 8GL  O07  O  O     0  -0.446   2.8092   1.4360  -0.3794
 8GL  O08  O  OH1   0  -0.597   3.8540  -0.4749   0.0918
 8GL  C09  C  C     0   0.508  -2.2270   0.3671  -0.2256
 8GL  O10  O  O     0  -0.437  -2.8897   0.2166  -1.2219
 8GL  O11  O  OH1   0  -0.584  -2.4257   1.3309   0.6560
 8GL  H1   H  HNH2  0   0.362  -0.8807  -0.2608   2.1627
 8GL  H2   H  HNH2  0   0.362  -1.9639  -1.4055   1.7371
 8GL  H4   H  HOH1  0   0.449  -1.3607  -1.4149  -1.5489
 8GL  H5   H  HCH2  0   0.257   0.2304   0.7027  -1.0963
 8GL  H6   H  HCH2  0   0.254   0.2542   1.1521   0.5949
 8GL  H7   H  HCH2  0   0.286   1.5366  -0.9682   1.1178
 8GL  H8   H  HCH2  0   0.285   1.5286  -1.3790  -0.5759
 8GL  H9   H  HOH1  0   0.479   4.6463   0.0657  -0.0439
 8GL  H10  H  HOH1  0   0.489  -3.1634   1.8952   0.3783

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
 8GL  O10  C09  double  1.206  0.020  1.206
 8GL  O07  C06  double  1.206  0.020  1.206
 8GL  C09  O11  single  1.321  0.020  1.321
 8GL  C09  C02  single  1.543  0.020  1.543
 8GL  C04  C02  single  1.539  0.020  1.539
 8GL  C04  C05  single  1.519  0.020  1.519
 8GL  C06  C05  single  1.502  0.020  1.502
 8GL  C06  O08  single  1.330  0.020  1.330
 8GL  N01  C02  single  1.437  0.020  1.437
 8GL  C02  O03  single  1.399  0.020  1.399
 8GL  N01  H1   single  0.890  0.020  1.040
 8GL  N01  H2   single  0.890  0.020  1.040
 8GL  O03  H4   single  0.850  0.020  0.980
 8GL  C04  H5   single  0.970  0.020  1.090
 8GL  C04  H6   single  0.970  0.020  1.090
 8GL  C05  H7   single  0.970  0.020  1.090
 8GL  C05  H8   single  0.970  0.020  1.090
 8GL  O08  H9   single  0.850  0.020  0.980
 8GL  O11  H10  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
 8GL  H2   N01  H1   107.54  3.000
 8GL  H2   N01  C02  111.85  3.000
 8GL  H1   N01  C02  111.68  3.000
 8GL  C09  C02  C04  107.35  3.000
 8GL  C04  C02  O03  111.88  3.000
 8GL  C09  C02  O03  108.15  3.000
 8GL  O03  C02  N01  106.24  3.000
 8GL  C04  C02  N01  109.77  3.000
 8GL  C09  C02  N01  113.53  3.000
 8GL  H4   O03  C02  109.08  3.000
 8GL  H6   C04  H5   106.40  3.000
 8GL  H6   C04  C05  110.16  3.000
 8GL  H5   C04  C05  109.85  3.000
 8GL  H6   C04  C02  109.35  3.000
 8GL  H5   C04  C02  108.79  3.000
 8GL  C05  C04  C02  112.12  3.000
 8GL  H8   C05  H7   105.76  3.000
 8GL  H8   C05  C06  108.13  3.000
 8GL  H7   C05  C06  108.38  3.000
 8GL  H8   C05  C04  110.75  3.000
 8GL  H7   C05  C04  110.93  3.000
 8GL  C06  C05  C04  112.61  3.000
 8GL  O08  C06  O07  122.88  3.000
 8GL  O08  C06  C05  111.69  3.000
 8GL  O07  C06  C05  125.43  3.000
 8GL  H9   O08  C06  109.87  3.000
 8GL  O11  C09  O10  124.03  3.000
 8GL  O11  C09  C02  112.34  3.000
 8GL  O10  C09  C02  123.61  3.000
 8GL  H10  O11  C09  110.37  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
 8GL  CONST_01  H10  O11  C09  C02   180.00   0.0  0
 8GL  CONST_02  H9   O08  C06  C05   180.00   0.0  0
 8GL  Var_01    C06  C05  C04  C02  -179.30  30.0  3
 8GL  Var_02    O07  C06  C05  C04    -0.13  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
 8GL  chir_01  C02  C04  N01  O03  positiv

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
 8GL  plan-1  C05  0.020
 8GL  plan-1  C06  0.020
 8GL  plan-1  O07  0.020
 8GL  plan-1  O08  0.020
 8GL  plan-1  H9   0.020
 8GL  plan-2  C02  0.020
 8GL  plan-2  C09  0.020
 8GL  plan-2  O10  0.020
 8GL  plan-2  O11  0.020
 8GL  plan-2  H10  0.020

