# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 05:53:30 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: 2-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](OCC(O)=O)[C@H](O)[C@@H](O)[C@@H]1O
#
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
 9YW  9YW  '2-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyethanoic acid'  D-saccharide  29  16  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9YW
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
 9YW  C10  C  C      0   0.364  -3.4034   0.2787  -0.4122
 9YW  C01  C  CH2    0  -0.160   1.4773  -2.6493   0.2155
 9YW  C02  C  CH1    0  -0.008   1.0133  -1.2246  -0.0050
 9YW  C03  C  CH1    0   0.032   2.1675  -0.3107  -0.4155
 9YW  C04  C  CH1    0  -0.010   1.7032   1.1405  -0.4601
 9YW  C05  C  CH1    0  -0.014   1.0434   1.5180   0.8596
 9YW  C06  C  CH1    0   0.250  -0.0765   0.5271   1.1844
 9YW  C09  C  CH2    0  -0.290  -2.2585  -0.0612   0.5533
 9YW  O07  O  O2     0  -0.507   0.4504  -0.7745   1.2147
 9YW  O08  O  O2     0  -0.484  -1.0927   0.6799   0.2601
 9YW  O11  O  OC    -1  -0.630  -4.4536  -0.3598  -0.1951
 9YW  O12  O  O      0  -0.598  -3.2012   1.1267  -1.2944
 9YW  O13  O  OH1    0  -0.668   0.5847   2.8417   0.7571
 9YW  O14  O  OH1    0  -0.676   2.8409   1.9315  -0.7229
 9YW  O15  O  OH1    0  -0.674   2.6380  -0.7395  -1.6704
 9YW  O16  O  OH1    0  -0.669   0.3551  -3.4565   0.4848
 9YW  H1   H  HCH2   0   0.210   2.0079  -2.9842  -0.6818
 9YW  H2   H  HCH2   0   0.193   2.1996  -2.6663   1.0438
 9YW  H4   H  HCH1   0   0.207   2.9591  -0.3919   0.3481
 9YW  H5   H  HCH1   0   0.219   0.9659   1.2432  -1.2699
 9YW  H6   H  HCH1   0   0.223   1.7928   1.4211   1.6581
 9YW  H7   H  HCH1   0   0.223  -0.4484   0.6990   2.2064
 9YW  H8   H  HCH2   0   0.209  -2.5919   0.1433   1.5819
 9YW  H9   H  HCH2   0   0.215  -2.0664  -1.1402   0.5012
 9YW  H11  H  HOH1   0   0.457   0.4009   3.1755   1.6402
 9YW  H12  H  HOH1   0   0.455   2.5507   2.8307  -0.9042
 9YW  H13  H  HOH1   0   0.453   3.3605  -0.1596  -1.9326
 9YW  H14  H  HOH1   0   0.455   0.6562  -4.3673   0.5475
 9YW  H3   H  HCH1   0   0.225   0.2597  -1.2232  -0.8059

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
 9YW  O12  C10  deloc   1.240  0.020  1.240
 9YW  C10  O11  deloc   1.248  0.020  1.248
 9YW  C10  C09  single  1.536  0.020  1.536
 9YW  C09  O08  single  1.412  0.020  1.412
 9YW  O08  C06  single  1.382  0.020  1.382
 9YW  O07  C02  single  1.417  0.020  1.417
 9YW  O07  C06  single  1.405  0.020  1.405
 9YW  C02  C01  single  1.514  0.020  1.514
 9YW  C02  C03  single  1.528  0.020  1.528
 9YW  C01  O16  single  1.408  0.020  1.408
 9YW  C06  C05  single  1.530  0.020  1.530
 9YW  O15  C03  single  1.407  0.020  1.407
 9YW  C03  C04  single  1.524  0.020  1.524
 9YW  C04  C05  single  1.523  0.020  1.523
 9YW  C04  O14  single  1.410  0.020  1.410
 9YW  C05  O13  single  1.405  0.020  1.405
 9YW  C01  H1   single  0.970  0.020  1.090
 9YW  C01  H2   single  0.970  0.020  1.090
 9YW  C02  H3   single  0.970  0.020  1.090
 9YW  C03  H4   single  0.970  0.020  1.090
 9YW  C04  H5   single  0.970  0.020  1.090
 9YW  C05  H6   single  0.970  0.020  1.090
 9YW  C06  H7   single  0.970  0.020  1.090
 9YW  C09  H8   single  0.970  0.020  1.090
 9YW  C09  H9   single  0.970  0.020  1.090
 9YW  O13  H11  single  0.850  0.020  0.980
 9YW  O14  H12  single  0.850  0.020  0.980
 9YW  O15  H13  single  0.850  0.020  0.980
 9YW  O16  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
 9YW  O12  C10  O11  127.64  3.000
 9YW  O11  C10  C09  113.87  3.000
 9YW  O12  C10  C09  118.49  3.000
 9YW  H2   C01  H1   107.12  3.000
 9YW  H2   C01  O16  111.76  3.000
 9YW  H1   C01  O16  111.57  3.000
 9YW  H2   C01  C02  109.00  3.000
 9YW  H1   C01  C02  108.48  3.000
 9YW  O16  C01  C02  108.84  3.000
 9YW  H3   C02  O07  110.75  3.000
 9YW  H3   C02  C03  108.73  3.000
 9YW  O07  C02  C03  109.96  3.000
 9YW  H3   C02  C01  108.50  3.000
 9YW  C03  C02  C01  111.73  3.000
 9YW  O07  C02  C01  107.17  3.000
 9YW  H4   C03  O15  110.80  3.000
 9YW  H4   C03  C04  107.99  3.000
 9YW  O15  C03  C04  111.46  3.000
 9YW  H4   C03  C02  108.18  3.000
 9YW  C04  C03  C02  110.31  3.000
 9YW  O15  C03  C02  108.05  3.000
 9YW  H5   C04  O14  110.56  3.000
 9YW  H5   C04  C05  108.93  3.000
 9YW  O14  C04  C05  111.84  3.000
 9YW  H5   C04  C03  108.33  3.000
 9YW  O14  C04  C03  107.08  3.000
 9YW  C05  C04  C03  110.04  3.000
 9YW  H6   C05  O13  111.02  3.000
 9YW  H6   C05  C06  106.72  3.000
 9YW  O13  C05  C06  112.75  3.000
 9YW  H6   C05  C04  108.20  3.000
 9YW  O13  C05  C04  108.17  3.000
 9YW  C06  C05  C04  109.91  3.000
 9YW  H7   C06  O08  110.80  3.000
 9YW  H7   C06  O07  104.55  3.000
 9YW  O08  C06  O07  113.12  3.000
 9YW  H7   C06  C05  110.07  3.000
 9YW  O07  C06  C05  109.28  3.000
 9YW  O08  C06  C05  108.94  3.000
 9YW  H9   C09  H8   106.27  3.000
 9YW  H9   C09  O08  111.21  3.000
 9YW  H8   C09  O08  110.28  3.000
 9YW  H9   C09  C10  108.56  3.000
 9YW  H8   C09  C10  108.70  3.000
 9YW  O08  C09  C10  111.64  3.000
 9YW  C06  O07  C02  115.14  3.000
 9YW  C09  O08  C06  114.21  3.000
 9YW  H11  O13  C05  108.80  3.000
 9YW  H12  O14  C04  108.42  3.000
 9YW  H13  O15  C03  108.07  3.000
 9YW  H14  O16  C01  107.81  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
 9YW  Var_01  H8   C09  O08  C06  52.23  30.0  1
 9YW  Var_02  O12  C10  C09  O08  -0.43  30.0  2

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
 9YW  chir_01  C02  O07  C01  C03  positiv
 9YW  chir_02  C03  O15  C02  C04  positiv
 9YW  chir_03  C04  O14  C05  C03  positiv
 9YW  chir_04  C05  O13  C04  C06  positiv
 9YW  chir_05  C06  O08  O07  C05  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
 9YW  plan-1  C10  0.020
 9YW  plan-1  C09  0.020
 9YW  plan-1  O11  0.020
 9YW  plan-1  O12  0.020

