# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 12:41:16 2021
#   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  29  14  .  2022-03-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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  -0.438  -17.3774  -1.4980  -14.6975
 L9Z  C14  C  C     0   0.571  -16.7550  -0.7651  -13.9690
 L9Z  O15  O  OH1   0  -0.596  -15.9487   0.1880  -14.4259
 L9Z  C5   C  CH1   0  -0.400  -16.7802  -0.8070  -12.4608
 L9Z  C6   C  CH2   0  -0.451  -15.3931  -1.1780  -11.9155
 L9Z  C1   C  CT    0   0.196  -15.3629  -1.2307  -10.3893
 L9Z  O28  O  OH1   0  -0.680  -15.5907   0.0869   -9.9310
 L9Z  C21  C  CH2   0  -0.296  -14.0029  -1.7559   -9.9040
 L9Z  C4   C  CH2   0  -0.458  -17.8362  -1.7751  -11.9466
 L9Z  C3   C  CH1   0   0.067  -17.8460  -1.7846  -10.4290
 L9Z  O19  O  OH1   0  -0.678  -18.8310  -2.7014  -10.0033
 L9Z  C2   C  CH1   0   0.009  -16.4735  -2.1672   -9.8818
 L9Z  O17  O  OH1   0  -0.687  -16.5257  -2.1177   -8.4646
 L9Z  H1   H  HOH1  0   0.480  -15.9417   0.1779  -15.3945
 L9Z  H2   H  HCH1  0   0.283  -17.0215   0.2062  -12.1209
 L9Z  H3   H  HCH2  0   0.243  -15.1027  -2.1578  -12.3097
 L9Z  H4   H  HCH2  0   0.262  -14.6452  -0.4616  -12.2590
 L9Z  H5   H  HOH1  0   0.442  -15.6323   0.0637   -8.9683
 L9Z  H6   H  HCH2  0   0.231  -13.9876  -1.7117   -8.8120
 L9Z  H7   H  HCH2  0   0.197  -13.9355  -2.8221  -10.1673
 L9Z  H9   H  HCH2  0   0.253  -18.8255  -1.4953  -12.3152
 L9Z  H10  H  HCH2  0   0.231  -17.6275  -2.7850  -12.3148
 L9Z  H11  H  HCH1  0   0.198  -18.0875  -0.7727  -10.0716
 L9Z  H12  H  HOH1  0   0.444  -18.8648  -2.6675   -9.0418
 L9Z  H13  H  HCH1  0   0.221  -16.2423  -3.1850  -10.2233
 L9Z  H14  H  HOH1  0   0.462  -16.3071  -2.9815   -8.1079
 L9Z  N1   N  NH2   0  -0.801  -12.8897  -0.9656  -10.3984
 L9Z  H8   H  HNH2  0   0.351  -12.0568  -1.2099   -9.8791
 L9Z  H15  H  HNH2  0   0.345  -12.6885  -1.2130  -11.3586

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  double  1.206  0.020  1.206
 L9Z  O15  C14  single  1.329  0.020  1.329
 L9Z  C14  C5   single  1.509  0.020  1.509
 L9Z  C5   C6   single  1.536  0.020  1.536
 L9Z  C5   C4   single  1.522  0.020  1.522
 L9Z  C6   C1   single  1.527  0.020  1.527
 L9Z  C4   C3   single  1.518  0.020  1.518
 L9Z  C1   C21  single  1.537  0.020  1.537
 L9Z  C1   O28  single  1.413  0.020  1.413
 L9Z  C1   C2   single  1.539  0.020  1.539
 L9Z  C3   C2   single  1.526  0.020  1.526
 L9Z  C3   O19  single  1.411  0.020  1.411
 L9Z  C2   O17  single  1.419  0.020  1.419
 L9Z  O15  H1   single  0.850  0.020  0.980
 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  1.452  0.020  1.452
 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  111.93  3.000
 L9Z  C5   C14  O16  125.31  3.000
 L9Z  O15  C14  O16  122.75  3.000
 L9Z  H1   O15  C14  109.91  3.000
 L9Z  H2   C5   C4   109.31  3.000
 L9Z  H2   C5   C6   108.19  3.000
 L9Z  C4   C5   C6   110.67  3.000
 L9Z  H2   C5   C14  106.74  3.000
 L9Z  C4   C5   C14  111.53  3.000
 L9Z  C6   C5   C14  110.27  3.000
 L9Z  H4   C6   H3   106.99  3.000
 L9Z  H4   C6   C1   108.88  3.000
 L9Z  H3   C6   C1   108.88  3.000
 L9Z  H4   C6   C5   110.40  3.000
 L9Z  H3   C6   C5   109.13  3.000
 L9Z  C1   C6   C5   112.39  3.000
 L9Z  C2   C1   C21  109.06  3.000
 L9Z  C2   C1   O28  110.13  3.000
 L9Z  C21  C1   O28  111.03  3.000
 L9Z  C2   C1   C6   109.65  3.000
 L9Z  O28  C1   C6   106.78  3.000
 L9Z  C21  C1   C6   110.17  3.000
 L9Z  H5   O28  C1   107.96  3.000
 L9Z  N1   C21  H7   113.52  3.000
 L9Z  N1   C21  H6   107.91  3.000
 L9Z  H7   C21  H6   106.10  3.000
 L9Z  N1   C21  C1   112.64  3.000
 L9Z  H7   C21  C1   108.05  3.000
 L9Z  H6   C21  C1   108.31  3.000
 L9Z  H10  C4   H9   107.18  3.000
 L9Z  H10  C4   C3   109.37  3.000
 L9Z  H9   C4   C3   109.46  3.000
 L9Z  H10  C4   C5   109.93  3.000
 L9Z  H9   C4   C5   110.58  3.000
 L9Z  C3   C4   C5   110.26  3.000
 L9Z  H11  C3   C2   108.15  3.000
 L9Z  H11  C3   O19  110.26  3.000
 L9Z  C2   C3   O19  110.89  3.000
 L9Z  H11  C3   C4   108.70  3.000
 L9Z  O19  C3   C4   108.07  3.000
 L9Z  C2   C3   C4   110.75  3.000
 L9Z  H12  O19  C3   107.63  3.000
 L9Z  H13  C2   O17  110.53  3.000
 L9Z  H13  C2   C3   108.07  3.000
 L9Z  O17  C2   C3   108.43  3.000
 L9Z  H13  C2   C1   108.03  3.000
 L9Z  O17  C2   C1   109.55  3.000
 L9Z  C3   C2   C1   112.22  3.000
 L9Z  H14  O17  C2   109.35  3.000
 L9Z  H15  N1   H8   105.33  3.000
 L9Z  H15  N1   C21  110.03  3.000
 L9Z  H8   N1   C21  108.97  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  CONST_01  H1  O15  C14  C5  180.00   0.0  0
 L9Z  Var_01    H8  N1   C21  C1  166.42  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
 L9Z  plan-1  H1   0.020

