# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 20:54:10 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  18  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  -0.808  -1.0823  -1.0651   1.4666
 8GL  C02  C  CT     0   0.242  -1.0265  -0.5122   0.1163
 8GL  O03  O  OH1    0  -0.707  -1.0687  -1.5744  -0.7985
 8GL  C04  C  CH2    0  -0.422   0.2677   0.2913  -0.0416
 8GL  C05  C  CH2    0  -0.583   1.5361  -0.5297   0.1159
 8GL  C06  C  C      0   0.408   2.8535   0.2551  -0.0071
 8GL  O07  O  O      0  -0.612   2.7926   1.4845  -0.2096
 8GL  O08  O  OC    -1  -0.638   3.9016  -0.4171   0.1118
 8GL  C09  C  C      0   0.396  -2.2503   0.4070  -0.1747
 8GL  O10  O  O      0  -0.615  -2.9841   0.0356  -1.1230
 8GL  O11  O  OC    -1  -0.594  -2.4096   1.4052   0.5450
 8GL  H1   H  HNH2   0   0.333  -1.0488  -0.3016   2.1317
 8GL  H2   H  HNH2   0   0.333  -1.9816  -1.5121   1.6133
 8GL  H4   H  HOH1   0   0.425  -1.8717  -1.3660  -1.3153
 8GL  H5   H  HCH2   0   0.203   0.2572   0.7654  -1.0283
 8GL  H6   H  HCH2   0   0.203   0.2611   1.1116   0.6800
 8GL  H7   H  HCH2   0   0.219   1.5325  -1.0384   1.0850
 8GL  H8   H  HCH2   0   0.216   1.5533  -1.3352  -0.6254

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  deloc   1.255  0.020  1.255
 8GL  O07  C06  deloc   1.247  0.020  1.247
 8GL  C09  O11  deloc   1.241  0.020  1.241
 8GL  C09  C02  single  1.558  0.020  1.558
 8GL  C04  C02  single  1.532  0.020  1.532
 8GL  C04  C05  single  1.519  0.020  1.519
 8GL  C06  C05  single  1.538  0.020  1.538
 8GL  C06  O08  deloc   1.251  0.020  1.251
 8GL  N01  C02  single  1.460  0.020  1.460
 8GL  C02  O03  single  1.402  0.020  1.402
 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

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   105.44  3.000
 8GL  H2   N01  C02  109.53  3.000
 8GL  H1   N01  C02  108.69  3.000
 8GL  C09  C02  C04  109.57  3.000
 8GL  C04  C02  O03  110.83  3.000
 8GL  C09  C02  O03  107.54  3.000
 8GL  O03  C02  N01  108.38  3.000
 8GL  C04  C02  N01  109.04  3.000
 8GL  C09  C02  N01  111.48  3.000
 8GL  H4   O03  C02  102.01  3.000
 8GL  H6   C04  H5   105.67  3.000
 8GL  H6   C04  C05  110.02  3.000
 8GL  H5   C04  C05  109.60  3.000
 8GL  H6   C04  C02  108.71  3.000
 8GL  H5   C04  C02  108.18  3.000
 8GL  C05  C04  C02  114.29  3.000
 8GL  H8   C05  H7   104.93  3.000
 8GL  H8   C05  C06  107.92  3.000
 8GL  H7   C05  C06  108.11  3.000
 8GL  H8   C05  C04  109.91  3.000
 8GL  H7   C05  C04  109.89  3.000
 8GL  C06  C05  C04  115.53  3.000
 8GL  O08  C06  O07  125.87  3.000
 8GL  O08  C06  C05  115.84  3.000
 8GL  O07  C06  C05  118.29  3.000
 8GL  O11  C09  O10  126.94  3.000
 8GL  O11  C09  C02  117.85  3.000
 8GL  O10  C09  C02  115.20  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  Var_01  C06  C05  C04  C02  -178.74  30.0  3
 8GL  Var_02  O07  C06  C05  C04     0.69  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-2  C02  0.020
 8GL  plan-2  C09  0.020
 8GL  plan-2  O10  0.020
 8GL  plan-2  O11  0.020

