# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:35:31 2022
#   Inital geometry file: a 64 line input string
#   Ligand name: (1S,2R,3S,4S,5S,6R)-2-amino-3,4,5,6-tetrahydroxycyclohexane-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1[C@H](O)[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
 L9D  L9D  '(1S,2R,3S,4S,5S,6R)-2-amino-3,4,5,6-tetrahydroxycyclohexane-1-carboxylic acid'  ligand  26  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 GRAND
;

data_comp_L9D
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
 L9D  C08  C  CH1    0   0.034   1.2289   1.5128  -0.2544
 L9D  C09  C  CH1    0  -0.122  -0.2757   1.4503   0.0195
 L9D  C11  C  CH1    0  -0.413  -0.8599   0.0978  -0.4250
 L9D  C12  C  CH1    0   0.067  -0.1496  -1.0471   0.2794
 L9D  C14  C  CH1    0  -0.004   1.3442  -0.9956  -0.0350
 L9D  C16  C  CH1    0   0.025   1.9436   0.3354   0.4009
 L9D  C18  C  C      0   0.435  -2.3901   0.0561  -0.2266
 L9D  N10  N  NH2    0  -0.822  -0.4817   1.6785   1.4440
 L9D  O13  O  OH1    0  -0.682  -0.7165  -2.2607  -0.1768
 L9D  O15  O  OH1    0  -0.688   2.0596  -2.0170   0.6429
 L9D  O17  O  OH1    0  -0.686   3.3121   0.4242   0.0589
 L9D  O19  O  OC    -1  -0.603  -3.0962   0.1632  -1.2465
 L9D  O20  O  O      0  -0.608  -2.8080  -0.0499   0.9489
 L9D  H1   H  HCH1   0   0.214   1.6171   2.4384   0.2009
 L9D  H3   H  HCH1   0   0.223  -0.7527   2.2274  -0.5976
 L9D  H4   H  HCH1   0   0.216  -0.6604   0.0102  -1.4978
 L9D  H5   H  HCH1   0   0.196  -0.2825  -0.9494   1.3646
 L9D  H6   H  HCH1   0   0.207   1.4738  -1.1054  -1.1209
 L9D  H7   H  HCH1   0   0.206   1.8086   0.4343   1.4864
 L9D  H8   H  HNH2   0   0.341  -0.4455   2.6706   1.6388
 L9D  H9   H  HNH2   0   0.351  -1.4082   1.3533   1.6928
 L9D  H11  H  HOH1   0   0.444  -0.4290  -2.9661   0.4104
 L9D  H12  H  HOH1   0   0.456   2.0823  -2.8014   0.0883
 L9D  H13  H  HOH1   0   0.448   3.7376  -0.3951   0.3346
 L9D  O1   O  OH1    0  -0.678   1.4323   1.5371  -1.6500
 L9D  H2   H  HOH1   0   0.446   2.3738   1.4115  -1.8110

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
 L9D  O20  C18  deloc   1.252  0.020  1.252
 L9D  O19  C18  deloc   1.245  0.020  1.245
 L9D  C18  C11  single  1.544  0.020  1.544
 L9D  O13  C12  single  1.415  0.020  1.415
 L9D  C11  C12  single  1.520  0.020  1.520
 L9D  C11  C09  single  1.539  0.020  1.539
 L9D  C12  C14  single  1.527  0.020  1.527
 L9D  C09  N10  single  1.457  0.020  1.457
 L9D  C09  C08  single  1.531  0.020  1.531
 L9D  C14  O15  single  1.419  0.020  1.419
 L9D  C14  C16  single  1.523  0.020  1.523
 L9D  C08  C16  single  1.525  0.020  1.525
 L9D  C16  O17  single  1.413  0.020  1.413
 L9D  C08  H1   single  0.970  0.020  1.090
 L9D  C09  H3   single  0.970  0.020  1.090
 L9D  C11  H4   single  0.970  0.020  1.090
 L9D  C12  H5   single  0.970  0.020  1.090
 L9D  C14  H6   single  0.970  0.020  1.090
 L9D  C16  H7   single  0.970  0.020  1.090
 L9D  N10  H8   single  0.890  0.020  1.040
 L9D  N10  H9   single  0.890  0.020  1.040
 L9D  O13  H11  single  0.850  0.020  0.980
 L9D  O15  H12  single  0.850  0.020  0.980
 L9D  O17  H13  single  0.850  0.020  0.980
 L9D  C08  O1   single  1.411  0.020  1.411
 L9D  O1   H2   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
 L9D  O1   C08  H1   110.09  3.000
 L9D  O1   C08  C16  111.76  3.000
 L9D  H1   C08  C16  107.81  3.000
 L9D  O1   C08  C09  108.63  3.000
 L9D  H1   C08  C09  107.85  3.000
 L9D  C16  C08  C09  110.62  3.000
 L9D  H3   C09  N10  112.09  3.000
 L9D  H3   C09  C11  107.09  3.000
 L9D  N10  C09  C11  111.49  3.000
 L9D  H3   C09  C08  107.26  3.000
 L9D  N10  C09  C08  107.91  3.000
 L9D  C11  C09  C08  110.94  3.000
 L9D  H4   C11  C18  107.72  3.000
 L9D  H4   C11  C12  107.98  3.000
 L9D  C18  C11  C12  112.53  3.000
 L9D  H4   C11  C09  106.51  3.000
 L9D  C12  C11  C09  110.53  3.000
 L9D  C18  C11  C09  111.28  3.000
 L9D  H5   C12  O13  110.28  3.000
 L9D  H5   C12  C14  108.59  3.000
 L9D  O13  C12  C14  110.76  3.000
 L9D  H5   C12  C11  109.54  3.000
 L9D  C14  C12  C11  109.64  3.000
 L9D  O13  C12  C11  108.02  3.000
 L9D  H6   C14  O15  109.91  3.000
 L9D  H6   C14  C16  108.88  3.000
 L9D  O15  C14  C16  107.08  3.000
 L9D  H6   C14  C12  108.38  3.000
 L9D  C16  C14  C12  110.82  3.000
 L9D  O15  C14  C12  111.74  3.000
 L9D  H7   C16  O17  110.64  3.000
 L9D  H7   C16  C14  108.24  3.000
 L9D  O17  C16  C14  111.51  3.000
 L9D  H7   C16  C08  107.31  3.000
 L9D  O17  C16  C08  107.53  3.000
 L9D  C14  C16  C08  111.54  3.000
 L9D  O20  C18  O19  125.94  3.000
 L9D  O19  C18  C11  117.04  3.000
 L9D  O20  C18  C11  116.99  3.000
 L9D  H9   N10  H8   107.48  3.000
 L9D  H9   N10  C09  108.61  3.000
 L9D  H8   N10  C09  109.68  3.000
 L9D  H11  O13  C12  108.20  3.000
 L9D  H12  O15  C14  108.89  3.000
 L9D  H13  O17  C16  107.75  3.000
 L9D  H2   O1   C08  107.70  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
 L9D  chir_01  C08  C09  C16  O1   negativ
 L9D  chir_02  C09  N10  C08  C11  negativ
 L9D  chir_03  C11  C09  C12  C18  negativ
 L9D  chir_04  C12  O13  C11  C14  positiv
 L9D  chir_05  C14  O15  C12  C16  negativ
 L9D  chir_06  C16  O17  C14  C08  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
 L9D  plan-1  C11  0.020
 L9D  plan-1  C18  0.020
 L9D  plan-1  O19  0.020
 L9D  plan-1  O20  0.020

