# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 15:22:42 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: (1~{S},3~{S},4~{S},5~{R})-3-(aminomethyl)-3,4,5-tris(oxidanyl)cyclohexane-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@@]1(O)C[C@H](C[C@@H](O)[C@@H]1O)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
 L9Z  L9Z  '(1~{S},3~{S},4~{S},5~{R})-3-(aminomethyl)-3,4,5-tris(oxidanyl)cyclohexane-1-carboxylic acid'  ligand  28  14  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L9Z
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
 L9Z  O16  O  O      0  -0.595  -17.5119  -1.4202  -14.6768
 L9Z  C14  C  C      0   0.423  -16.7302  -0.7140  -14.0095
 L9Z  O15  O  OC    -1  -0.617  -15.8915   0.0932  -14.4632
 L9Z  C5   C  CH1    0  -0.376  -16.7797  -0.8328  -12.4685
 L9Z  C6   C  CH2    0  -0.437  -15.4222  -1.2807  -11.9255
 L9Z  C1   C  CT     0   0.200  -15.3783  -1.3352  -10.3929
 L9Z  O28  O  OH1    0  -0.698  -15.5645  -0.0479   -9.8427
 L9Z  C21  C  CH2    0  -0.310  -14.0130  -1.8597   -9.9186
 L9Z  C4   C  CH2    0  -0.444  -17.8717  -1.7562  -11.9464
 L9Z  C3   C  CH1    0   0.061  -17.8690  -1.8038  -10.4288
 L9Z  O19  O  OH1    0  -0.677  -18.8783  -2.6975  -10.0025
 L9Z  C2   C  CH1    0   0.031  -16.5051  -2.2496   -9.9032
 L9Z  O17  O  OH1    0  -0.683  -16.5570  -2.2962   -8.4873
 L9Z  H2   H  HCH1   0   0.209  -16.9670   0.1763  -12.0805
 L9Z  H3   H  HCH2   0   0.206  -15.1890  -2.2764  -12.3231
 L9Z  H4   H  HCH2   0   0.227  -14.6413  -0.6088  -12.2888
 L9Z  H5   H  HOH1   0   0.430  -14.6665   0.3247   -9.8223
 L9Z  H6   H  HCH2   0   0.234  -14.0655  -2.0693   -8.8489
 L9Z  H7   H  HCH2   0   0.207  -13.7835  -2.8068  -10.4220
 L9Z  H9   H  HCH2   0   0.222  -18.8533  -1.4305  -12.2991
 L9Z  H10  H  HCH2   0   0.202  -17.7167  -2.7692  -12.3344
 L9Z  H11  H  HCH1   0   0.185  -18.0731  -0.7935  -10.0417
 L9Z  H12  H  HOH1   0   0.435  -18.8416  -2.7310   -9.0407
 L9Z  H13  H  HCH1   0   0.209  -16.3068  -3.2512  -10.3123
 L9Z  H14  H  HOH1   0   0.453  -16.3623  -3.1900   -8.1974
 L9Z  N1   N  NH2    0  -0.816  -13.0067  -0.8254  -10.1191
 L9Z  H8   H  HNH2   0   0.362  -12.2213  -0.9683   -9.5000
 L9Z  H15  H  HNH2   0   0.355  -12.6402  -0.8537  -11.0612

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
 L9Z  O16  C14  deloc   1.247  0.020  1.247
 L9Z  O15  C14  deloc   1.249  0.020  1.249
 L9Z  C14  C5   single  1.546  0.020  1.546
 L9Z  C5   C6   single  1.529  0.020  1.529
 L9Z  C5   C4   single  1.522  0.020  1.522
 L9Z  C6   C1   single  1.534  0.020  1.534
 L9Z  C4   C3   single  1.518  0.020  1.518
 L9Z  C1   C21  single  1.538  0.020  1.538
 L9Z  C1   O28  single  1.412  0.020  1.412
 L9Z  C1   C2   single  1.532  0.020  1.532
 L9Z  C3   C2   single  1.528  0.020  1.528
 L9Z  C3   O19  single  1.414  0.020  1.414
 L9Z  C2   O17  single  1.418  0.020  1.418
 L9Z  C5   H2   single  0.970  0.020  1.090
 L9Z  C6   H3   single  0.970  0.020  1.090
 L9Z  C6   H4   single  0.970  0.020  1.090
 L9Z  O28  H5   single  0.850  0.020  0.980
 L9Z  C21  H6   single  0.970  0.020  1.090
 L9Z  C21  H7   single  0.970  0.020  1.090
 L9Z  C4   H9   single  0.970  0.020  1.090
 L9Z  C4   H10  single  0.970  0.020  1.090
 L9Z  C3   H11  single  0.970  0.020  1.090
 L9Z  O19  H12  single  0.850  0.020  0.980
 L9Z  C2   H13  single  0.970  0.020  1.090
 L9Z  O17  H14  single  0.850  0.020  0.980
 L9Z  C21  N1   single  1.457  0.020  1.457
 L9Z  N1   H8   single  0.890  0.020  1.040
 L9Z  N1   H15  single  0.890  0.020  1.040

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
 L9Z  C5   C14  O15  115.66  3.000
 L9Z  C5   C14  O16  118.02  3.000
 L9Z  O15  C14  O16  126.32  3.000
 L9Z  H2   C5   C4   108.30  3.000
 L9Z  H2   C5   C6   107.18  3.000
 L9Z  C4   C5   C6   109.71  3.000
 L9Z  H2   C5   C14  106.69  3.000
 L9Z  C4   C5   C14  114.29  3.000
 L9Z  C6   C5   C14  110.36  3.000
 L9Z  H4   C6   H3   106.60  3.000
 L9Z  H4   C6   C1   109.49  3.000
 L9Z  H3   C6   C1   108.89  3.000
 L9Z  H4   C6   C5   109.66  3.000
 L9Z  H3   C6   C5   109.02  3.000
 L9Z  C1   C6   C5   112.99  3.000
 L9Z  C2   C1   C21  110.55  3.000
 L9Z  C2   C1   O28  108.82  3.000
 L9Z  C21  C1   O28  107.93  3.000
 L9Z  C2   C1   C6   108.63  3.000
 L9Z  O28  C1   C6   110.68  3.000
 L9Z  C21  C1   C6   110.22  3.000
 L9Z  H5   O28  C1   103.63  3.000
 L9Z  N1   C21  H7   113.91  3.000
 L9Z  N1   C21  H6   107.73  3.000
 L9Z  H7   C21  H6   107.10  3.000
 L9Z  N1   C21  C1   109.19  3.000
 L9Z  H7   C21  C1   109.81  3.000
 L9Z  H6   C21  C1   108.98  3.000
 L9Z  H10  C4   H9   106.76  3.000
 L9Z  H10  C4   C3   108.95  3.000
 L9Z  H9   C4   C3   109.49  3.000
 L9Z  H10  C4   C5   109.74  3.000
 L9Z  H9   C4   C5   110.66  3.000
 L9Z  C3   C4   C5   111.13  3.000
 L9Z  H11  C3   C2   108.20  3.000
 L9Z  H11  C3   O19  109.98  3.000
 L9Z  C2   C3   O19  110.43  3.000
 L9Z  H11  C3   C4   108.80  3.000
 L9Z  O19  C3   C4   108.65  3.000
 L9Z  C2   C3   C4   110.76  3.000
 L9Z  H12  O19  C3   107.21  3.000
 L9Z  H13  C2   O17  110.37  3.000
 L9Z  H13  C2   C3   107.38  3.000
 L9Z  O17  C2   C3   108.69  3.000
 L9Z  H13  C2   C1   106.99  3.000
 L9Z  O17  C2   C1   111.46  3.000
 L9Z  C3   C2   C1   111.87  3.000
 L9Z  H14  O17  C2   108.96  3.000
 L9Z  H15  N1   H8   106.57  3.000
 L9Z  H15  N1   C21  111.02  3.000
 L9Z  H8   N1   C21  110.63  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
 L9Z  Var_01  H8  N1  C21  C1  156.70  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
 L9Z  chir_01  C5  C14  C6   C4  positiv
 L9Z  chir_02  C1  C6   C21  C2  positiv
 L9Z  chir_03  C3  O19  C2   C4  negativ
 L9Z  chir_04  C2  O17  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
 L9Z  plan-1  O16  0.020
 L9Z  plan-1  C14  0.020
 L9Z  plan-1  O15  0.020
 L9Z  plan-1  C5   0.020

