# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 18:07:50 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: (2~{S},3~{S},4~{S})-2,6-bis(azanyl)-3,4-bis(oxidanyl)hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC[C@H](O)[C@@H](O)[C@H](N)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
 LOH  LOH  '(2~{S},3~{S},4~{S})-2,6-bis(azanyl)-3,4-bis(oxidanyl)hexanoic acid'  ligand  25  12  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LOH
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
 LOH  NZ   N  NH2    0  -0.802  -4.4031  -0.4584  -0.8318
 LOH  CE   C  CH2    0  -0.268  -3.2004  -0.7380  -0.0570
 LOH  CD   C  CH2    0  -0.473  -2.0942   0.2425  -0.4194
 LOH  CG   C  CH1    0   0.015  -0.7739  -0.0384   0.2890
 LOH  CB   C  CH1    0   0.017   0.3444   0.8943  -0.1942
 LOH  CA   C  CH1    0  -0.211   1.7470   0.4935   0.3007
 LOH  N    N  NH2    0  -0.801   2.7918   1.4026  -0.1538
 LOH  C    C  C      0   0.399   2.0865  -0.9347  -0.1800
 LOH  O    O  O      0  -0.610   2.3843  -1.0407  -1.3883
 LOH  OH1  O  OH1    0  -0.674   0.0544   2.2425   0.1387
 LOH  OH2  O  OH1    0  -0.675  -0.9038   0.0125   1.7008
 LOH  O1   O  OC    -1  -0.609   2.0203  -1.8584   0.6527
 LOH  H1   H  HNH2   0   0.345  -5.1251  -1.1202  -0.5763
 LOH  H2   H  HNH2   0   0.336  -4.7671   0.4487  -0.5643
 LOH  H4   H  HCH2   0   0.191  -3.3700  -0.7178   1.0275
 LOH  H5   H  HCH2   0   0.211  -2.8696  -1.7526  -0.2984
 LOH  H6   H  HCH2   0   0.227  -1.9262   0.1961  -1.4992
 LOH  H7   H  HCH2   0   0.220  -2.4237   1.2656  -0.2014
 LOH  H8   H  HCH1   0   0.224  -0.4813  -1.0663   0.0546
 LOH  H9   H  HCH1   0   0.208   0.3612   0.8589  -1.2893
 LOH  H10  H  HCH1   0   0.197   1.7375   0.5028   1.3963
 LOH  H11  H  HNH2   0   0.326   2.8971   1.2814  -1.1545
 LOH  H12  H  HNH2   0   0.329   2.4958   2.3610  -0.0139
 LOH  H14  H  HOH1   0   0.437   0.1274   2.3375   1.0951
 LOH  H15  H  HOH1   0   0.442  -1.4743   0.7540   1.9271

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
 LOH  OH2  CG   single  1.419  0.020  1.419
 LOH  CE   NZ   single  1.458  0.020  1.458
 LOH  CE   CD   single  1.522  0.020  1.522
 LOH  CG   CD   single  1.524  0.020  1.524
 LOH  CG   CB   single  1.534  0.020  1.534
 LOH  OH1  CB   single  1.419  0.020  1.419
 LOH  CB   CA   single  1.540  0.020  1.540
 LOH  CA   N    single  1.458  0.020  1.458
 LOH  CA   C    single  1.545  0.020  1.545
 LOH  C    O    deloc   1.249  0.020  1.249
 LOH  C    O1   deloc   1.245  0.020  1.245
 LOH  NZ   H1   single  0.890  0.020  1.040
 LOH  NZ   H2   single  0.890  0.020  1.040
 LOH  CE   H4   single  0.970  0.020  1.090
 LOH  CE   H5   single  0.970  0.020  1.090
 LOH  CD   H6   single  0.970  0.020  1.090
 LOH  CD   H7   single  0.970  0.020  1.090
 LOH  CG   H8   single  0.970  0.020  1.090
 LOH  CB   H9   single  0.970  0.020  1.090
 LOH  CA   H10  single  0.970  0.020  1.090
 LOH  N    H11  single  0.890  0.020  1.040
 LOH  N    H12  single  0.890  0.020  1.040
 LOH  OH1  H14  single  0.850  0.020  0.980
 LOH  OH2  H15  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
 LOH  H2   NZ   H1   105.22  3.000
 LOH  H2   NZ   CE   109.14  3.000
 LOH  H1   NZ   CE   109.20  3.000
 LOH  H5   CE   H4   106.37  3.000
 LOH  H5   CE   CD   108.97  3.000
 LOH  H4   CE   CD   109.61  3.000
 LOH  H5   CE   NZ   108.06  3.000
 LOH  H4   CE   NZ   113.21  3.000
 LOH  CD   CE   NZ   110.46  3.000
 LOH  H7   CD   H6   106.38  3.000
 LOH  H7   CD   CG   109.86  3.000
 LOH  H6   CD   CG   108.54  3.000
 LOH  H7   CD   CE   109.59  3.000
 LOH  H6   CD   CE   108.63  3.000
 LOH  CG   CD   CE   113.59  3.000
 LOH  H8   CG   OH2  105.74  3.000
 LOH  H8   CG   CB   107.98  3.000
 LOH  OH2  CG   CB   110.99  3.000
 LOH  H8   CG   CD   107.77  3.000
 LOH  CB   CG   CD   111.90  3.000
 LOH  OH2  CG   CD   112.12  3.000
 LOH  H9   CB   OH1  105.56  3.000
 LOH  H9   CB   CA   107.38  3.000
 LOH  OH1  CB   CA   110.98  3.000
 LOH  H9   CB   CG   107.83  3.000
 LOH  CA   CB   CG   113.85  3.000
 LOH  OH1  CB   CG   110.78  3.000
 LOH  H10  CA   C    108.72  3.000
 LOH  H10  CA   N    108.23  3.000
 LOH  C    CA   N    108.79  3.000
 LOH  H10  CA   CB   108.13  3.000
 LOH  C    CA   CB   109.92  3.000
 LOH  N    CA   CB   112.96  3.000
 LOH  H12  N    H11  106.26  3.000
 LOH  H12  N    CA   109.73  3.000
 LOH  H11  N    CA   107.92  3.000
 LOH  O1   C    O    126.63  3.000
 LOH  O1   C    CA   117.77  3.000
 LOH  O    C    CA   115.59  3.000
 LOH  H14  OH1  CB   108.12  3.000
 LOH  H15  OH2  CG   108.41  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
 LOH  Var_01  CG  CD  CE  NZ  -176.49  30.0  3
 LOH  Var_02  H1  NZ  CE  CD   180.00  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
 LOH  chir_01  CG  OH2  CD  CB  negativ
 LOH  chir_02  CB  OH1  CG  CA  positiv
 LOH  chir_03  CA  N    CB  C   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
 LOH  plan-1  CA  0.020
 LOH  plan-1  C   0.020
 LOH  plan-1  O   0.020
 LOH  plan-1  O1  0.020

