# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 03:09:13 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: (2~{R})-2-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O[C@H](CO)C(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
 9WN  9WN  '(2~{R})-2-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-propanoic acid'  D-saccharide  34  18  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9WN
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
 9WN  C10  C  CH2   0  -0.176  -2.2787  -1.1334  -1.4847
 9WN  C01  C  CH2   0  -0.159   2.3721  -2.3519   0.6466
 9WN  C02  C  CH1   0  -0.012   1.6824  -1.0976   0.1535
 9WN  C03  C  CH1   0   0.031   2.6749   0.0369  -0.0970
 9WN  C04  C  CH1   0  -0.012   1.9323   1.3261  -0.4283
 9WN  C05  C  CH1   0  -0.008   0.9061   1.6336   0.6537
 9WN  C06  C  CH1   0   0.238  -0.0054   0.4253   0.8731
 9WN  C09  C  CH1   0  -0.103  -1.8824  -0.6119  -0.1151
 9WN  C12  C  C     0   0.532  -3.0521   0.1114   0.5422
 9WN  O07  O  O2    0  -0.497   0.7524  -0.7139   1.1532
 9WN  O08  O  O2    0  -0.490  -0.8012   0.2662  -0.2608
 9WN  O11  O  OH1   0  -0.667  -2.8195  -0.0684  -2.2254
 9WN  O13  O  OH1   0  -0.593  -4.0704  -0.7131   0.7412
 9WN  O14  O  O     0  -0.428  -3.0533   1.2728   0.8527
 9WN  O15  O  OH1   0  -0.664   0.1990   2.7821   0.2685
 9WN  O16  O  OH1   0  -0.675   2.9011   2.3452  -0.5353
 9WN  O17  O  OH1   0  -0.673   3.5196  -0.3519  -1.1520
 9WN  O18  O  OH1   0  -0.667   1.4179  -3.3812   0.7527
 9WN  H1   H  HCH2  0   0.227  -1.3842  -1.5582  -1.9564
 9WN  H2   H  HCH2  0   0.221  -2.9922  -1.9530  -1.3541
 9WN  H3   H  HCH2  0   0.211   3.1683  -2.6098  -0.0599
 9WN  H4   H  HCH2  0   0.194   2.8534  -2.1383   1.6113
 9WN  H6   H  HCH1  0   0.210   3.2515   0.2024   0.8286
 9WN  H7   H  HCH1  0   0.221   1.4113   1.1874  -1.3867
 9WN  H8   H  HCH1  0   0.223   1.4424   1.7945   1.6008
 9WN  H9   H  HCH1  0   0.241  -0.6206   0.5778   1.7691
 9WN  H10  H  HCH1  0   0.280  -1.6184  -1.4813   0.5020
 9WN  H11  H  HOH1  0   0.463  -3.1714  -0.4188  -3.0487
 9WN  H12  H  HOH1  0   0.485  -4.8085  -0.2426   1.1574
 9WN  H13  H  HOH1  0   0.454  -0.4265   3.0116   0.9629
 9WN  H14  H  HOH1  0   0.457   2.4988   3.1088  -0.9601
 9WN  H15  H  HOH1  0   0.454   4.1285   0.3731  -1.3285
 9WN  H16  H  HOH1  0   0.455   1.8774  -4.1828   1.0177
 9WN  H5   H  HCH1  0   0.228   1.1654  -1.3301  -0.7885

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
 9WN  O14  C12  double  1.202  0.020  1.202
 9WN  C10  O11  single  1.405  0.020  1.405
 9WN  C10  C09  single  1.518  0.020  1.518
 9WN  C12  C09  single  1.524  0.020  1.524
 9WN  C12  O13  single  1.325  0.020  1.325
 9WN  C09  O08  single  1.400  0.020  1.400
 9WN  O08  C06  single  1.394  0.020  1.394
 9WN  C01  C02  single  1.514  0.020  1.514
 9WN  C01  O18  single  1.407  0.020  1.407
 9WN  O07  C02  single  1.418  0.020  1.418
 9WN  O07  C06  single  1.397  0.020  1.397
 9WN  C02  C03  single  1.528  0.020  1.528
 9WN  C06  C05  single  1.529  0.020  1.529
 9WN  O17  C03  single  1.406  0.020  1.406
 9WN  C03  C04  single  1.524  0.020  1.524
 9WN  C04  C05  single  1.523  0.020  1.523
 9WN  C04  O16  single  1.410  0.020  1.410
 9WN  C05  O15  single  1.403  0.020  1.403
 9WN  C10  H1   single  0.970  0.020  1.090
 9WN  C10  H2   single  0.970  0.020  1.090
 9WN  C01  H3   single  0.970  0.020  1.090
 9WN  C01  H4   single  0.970  0.020  1.090
 9WN  C02  H5   single  0.970  0.020  1.090
 9WN  C03  H6   single  0.970  0.020  1.090
 9WN  C04  H7   single  0.970  0.020  1.090
 9WN  C05  H8   single  0.970  0.020  1.090
 9WN  C06  H9   single  0.970  0.020  1.090
 9WN  C09  H10  single  0.970  0.020  1.090
 9WN  O11  H11  single  0.850  0.020  0.980
 9WN  O13  H12  single  0.850  0.020  0.980
 9WN  O15  H13  single  0.850  0.020  0.980
 9WN  O16  H14  single  0.850  0.020  0.980
 9WN  O17  H15  single  0.850  0.020  0.980
 9WN  O18  H16  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
 9WN  H2   C10  H1   107.03  3.000
 9WN  H2   C10  O11  112.30  3.000
 9WN  H1   C10  O11  112.37  3.000
 9WN  H2   C10  C09  108.65  3.000
 9WN  H1   C10  C09  107.94  3.000
 9WN  O11  C10  C09  108.39  3.000
 9WN  H4   C01  H3   107.07  3.000
 9WN  H4   C01  O18  111.89  3.000
 9WN  H3   C01  O18  111.67  3.000
 9WN  H4   C01  C02  108.92  3.000
 9WN  H3   C01  C02  108.43  3.000
 9WN  O18  C01  C02  108.76  3.000
 9WN  H5   C02  O07  110.65  3.000
 9WN  H5   C02  C03  108.78  3.000
 9WN  O07  C02  C03  109.91  3.000
 9WN  H5   C02  C01  108.55  3.000
 9WN  C03  C02  C01  111.88  3.000
 9WN  O07  C02  C01  107.05  3.000
 9WN  H6   C03  O17  110.92  3.000
 9WN  H6   C03  C04  108.07  3.000
 9WN  O17  C03  C04  111.31  3.000
 9WN  H6   C03  C02  108.26  3.000
 9WN  C04  C03  C02  110.31  3.000
 9WN  O17  C03  C02  107.93  3.000
 9WN  H7   C04  O16  110.52  3.000
 9WN  H7   C04  C05  108.99  3.000
 9WN  O16  C04  C05  111.78  3.000
 9WN  H7   C04  C03  108.28  3.000
 9WN  O16  C04  C03  107.04  3.000
 9WN  C05  C04  C03  110.16  3.000
 9WN  H8   C05  O15  111.25  3.000
 9WN  H8   C05  C06  106.41  3.000
 9WN  O15  C05  C06  112.70  3.000
 9WN  H8   C05  C04  108.22  3.000
 9WN  O15  C05  C04  108.06  3.000
 9WN  C06  C05  C04  110.13  3.000
 9WN  H9   C06  O08  111.09  3.000
 9WN  H9   C06  O07  104.70  3.000
 9WN  O08  C06  O07  112.31  3.000
 9WN  H9   C06  C05  109.96  3.000
 9WN  O07  C06  C05  110.48  3.000
 9WN  O08  C06  C05  108.28  3.000
 9WN  H10  C09  O08  111.66  3.000
 9WN  H10  C09  C12  108.54  3.000
 9WN  O08  C09  C12  109.87  3.000
 9WN  H10  C09  C10  107.32  3.000
 9WN  O08  C09  C10  108.85  3.000
 9WN  C12  C09  C10  110.59  3.000
 9WN  O14  C12  O13  124.16  3.000
 9WN  O13  C12  C09  111.05  3.000
 9WN  O14  C12  C09  124.79  3.000
 9WN  C06  O07  C02  115.79  3.000
 9WN  C09  O08  C06  115.31  3.000
 9WN  H11  O11  C10  108.41  3.000
 9WN  H12  O13  C12  110.34  3.000
 9WN  H13  O15  C05  108.95  3.000
 9WN  H14  O16  C04  108.65  3.000
 9WN  H15  O17  C03  108.00  3.000
 9WN  H16  O18  C01  107.85  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
 9WN  CONST_01  H12  O13  C12  C09  180.00  0.0  0

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
 9WN  chir_01  C02  C01  O07  C03  negativ
 9WN  chir_02  C03  O17  C02  C04  positiv
 9WN  chir_03  C04  O16  C05  C03  positiv
 9WN  chir_04  C05  O15  C04  C06  positiv
 9WN  chir_05  C06  O07  O08  C05  positiv
 9WN  chir_06  C09  O08  C10  C12  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
 9WN  plan-1  C09  0.020
 9WN  plan-1  C12  0.020
 9WN  plan-1  O13  0.020
 9WN  plan-1  O14  0.020
 9WN  plan-1  H12  0.020

