# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 02:03:19 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: (1~{R},2~{R},3~{R},4~{S},6~{S})-6-azanyl-2,3,4-tris(oxidanyl)cyclohexane-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1C[C@H](O)[C@@H](O)[C@H](O)[C@@H]1C(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
 H62  H62  '(1~{R},2~{R},3~{R},4~{S},6~{S})-6-azanyl-2,3,4-tris(oxidanyl)cyclohexane-1-carboxylic acid'  ligand  25  13  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H62
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
 H62  O5   O  O      0  -0.599   2.7729  -0.4970  -0.7116
 H62  C7   C  C      0   0.439   2.1831   0.3306   0.0139
 H62  O4   O  OC    -1  -0.619   2.6727   1.3865   0.4630
 H62  C1   C  CH1    0  -0.401   0.7148   0.0481   0.4134
 H62  C6   C  CH1    0  -0.040   0.1768  -1.3177  -0.0094
 H62  N1   N  NH2    0  -0.821   0.9560  -2.3750   0.6301
 H62  C5   C  CH2    0  -0.477  -1.2763  -1.4656   0.4323
 H62  C4   C  CH1    0   0.016  -2.1900  -0.3675  -0.0905
 H62  O2   O  OH1    0  -0.671  -2.3663  -0.4238  -1.4907
 H62  C3   C  CH1    0  -0.005  -1.6369   1.0165   0.2590
 H62  O1   O  OH1    0  -0.677  -1.7327   1.2451   1.6490
 H62  C2   C  CH1    0   0.043  -0.1575   1.1912  -0.1026
 H62  O3   O  OH1    0  -0.670   0.0297   1.2788  -1.4982
 H62  H2   H  HCH1   0   0.223   0.6688   0.0864   1.5094
 H62  H3   H  HCH1   0   0.185   0.2158  -1.3853  -1.1049
 H62  H4   H  HNH2   0   0.329   0.6050  -3.2745   0.3212
 H62  H5   H  HNH2   0   0.339   1.9017  -2.3106   0.2742
 H62  H7   H  HCH2   0   0.230  -1.6692  -2.4409   0.1191
 H62  H8   H  HCH2   0   0.216  -1.3166  -1.4644   1.5259
 H62  H9   H  HCH1   0   0.206  -3.1684  -0.4687   0.4086
 H62  H10  H  HOH1   0   0.446  -2.6788  -1.3065  -1.7114
 H62  H11  H  HCH1   0   0.215  -2.2204   1.7725  -0.2923
 H62  H12  H  HOH1   0   0.451  -2.6600   1.2032   1.9023
 H62  H13  H  HCH1   0   0.203   0.1794   2.1168   0.3847
 H62  H14  H  HOH1   0   0.441  -0.5276   1.9855  -1.8381

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
 H62  O5  C7   deloc   1.249  0.020  1.249
 H62  C7  O4   deloc   1.248  0.020  1.248
 H62  C7  C1   single  1.548  0.020  1.548
 H62  C1  C2   single  1.528  0.020  1.528
 H62  C1  C6   single  1.528  0.020  1.528
 H62  C2  O3   single  1.411  0.020  1.411
 H62  C2  C3   single  1.533  0.020  1.533
 H62  N1  C6   single  1.461  0.020  1.461
 H62  C6  C5   single  1.526  0.020  1.526
 H62  O1  C3   single  1.412  0.020  1.412
 H62  C3  C4   single  1.531  0.020  1.531
 H62  C5  C4   single  1.521  0.020  1.521
 H62  C4  O2   single  1.412  0.020  1.412
 H62  C1  H2   single  0.970  0.020  1.090
 H62  C6  H3   single  0.970  0.020  1.090
 H62  N1  H4   single  0.890  0.020  1.040
 H62  N1  H5   single  0.890  0.020  1.040
 H62  C5  H7   single  0.970  0.020  1.090
 H62  C5  H8   single  0.970  0.020  1.090
 H62  C4  H9   single  0.970  0.020  1.090
 H62  O2  H10  single  0.850  0.020  0.980
 H62  C3  H11  single  0.970  0.020  1.090
 H62  O1  H12  single  0.850  0.020  0.980
 H62  C2  H13  single  0.970  0.020  1.090
 H62  O3  H14  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
 H62  C1   C7  O4  115.72  3.000
 H62  C1   C7  O5  118.50  3.000
 H62  O4   C7  O5  125.79  3.000
 H62  H2   C1  C2  106.69  3.000
 H62  H2   C1  C6  107.03  3.000
 H62  C2   C1  C6  111.99  3.000
 H62  H2   C1  C7  106.93  3.000
 H62  C6   C1  C7  115.21  3.000
 H62  C2   C1  C7  108.54  3.000
 H62  H3   C6  C5  108.45  3.000
 H62  H3   C6  N1  111.91  3.000
 H62  C5   C6  N1  108.12  3.000
 H62  H3   C6  C1  108.58  3.000
 H62  C5   C6  C1  109.99  3.000
 H62  N1   C6  C1  109.76  3.000
 H62  H5   N1  H4  105.83  3.000
 H62  H5   N1  C6  107.36  3.000
 H62  H4   N1  C6  108.92  3.000
 H62  H8   C5  H7  105.85  3.000
 H62  H8   C5  C4  108.70  3.000
 H62  H7   C5  C4  109.18  3.000
 H62  H8   C5  C6  108.92  3.000
 H62  H7   C5  C6  110.15  3.000
 H62  C4   C5  C6  113.73  3.000
 H62  H9   C4  C3  107.46  3.000
 H62  H9   C4  O2  109.52  3.000
 H62  C3   C4  O2  107.91  3.000
 H62  H9   C4  C5  108.12  3.000
 H62  O2   C4  C5  112.76  3.000
 H62  C3   C4  C5  110.93  3.000
 H62  H10  O2  C4  107.73  3.000
 H62  H11  C3  C2  108.34  3.000
 H62  H11  C3  O1  110.20  3.000
 H62  C2   C3  O1  106.21  3.000
 H62  H11  C3  C4  108.33  3.000
 H62  O1   C3  C4  110.28  3.000
 H62  C2   C3  C4  113.44  3.000
 H62  H12  O1  C3  108.51  3.000
 H62  H13  C2  O3  110.22  3.000
 H62  H13  C2  C3  106.69  3.000
 H62  O3   C2  C3  111.62  3.000
 H62  H13  C2  C1  107.79  3.000
 H62  C3   C2  C1  112.72  3.000
 H62  O3   C2  C1  107.75  3.000
 H62  H14  O3  C2  108.56  3.000

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
 H62  chir_01  C1  C7  C2  C6  negativ
 H62  chir_02  C6  N1  C5  C1  negativ
 H62  chir_03  C4  O2  C3  C5  positiv
 H62  chir_04  C3  O1  C4  C2  positiv
 H62  chir_05  C2  O3  C3  C1  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
 H62  plan-1  O5  0.020
 H62  plan-1  C7  0.020
 H62  plan-1  O4  0.020
 H62  plan-1  C1  0.020

