# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 10:28:22 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: (2~{S},3~{R},4~{S},5~{S},6~{R})-2-[1,3-bis(oxidanyl)propan-2-yloxy]-6-(hydroxymethyl)oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC(CO)O[C@H]1O[C@H](CO)[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
 A0K  A0K  (2~{S},3~{R},4~{S},5~{S},6~{R})-2-[1,3-bis(oxidanyl)propan-2-yloxy]-6-(hydroxymethyl)oxane-3,4,5-triol  D-saccharide  35  17  .  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_A0K
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
 A0K  C10  C  CH2   0  -0.178  -3.2251  -1.3053   0.3437
 A0K  C01  C  CH2   0  -0.153   1.1977   2.7126   0.0196
 A0K  C02  C  CH1   0  -0.036   0.9616   1.2222   0.1257
 A0K  C03  C  CH1   0   0.042   2.2291   0.4309   0.4329
 A0K  C04  C  CH1   0  -0.007   1.8919  -1.0566   0.4389
 A0K  C05  C  CH1   0  -0.008   1.2150  -1.4445  -0.8711
 A0K  C06  C  CH1   0   0.245   0.0080  -0.5395  -1.1410
 A0K  C09  C  CH1   0   0.003  -2.3169  -0.5606  -0.6133
 A0K  C12  C  CH2   0  -0.196  -2.6624   0.9192  -0.8056
 A0K  O07  O  O2    0  -0.502   0.4278   0.7997  -1.1176
 A0K  O08  O  O2    0  -0.491  -0.9807  -0.8042  -0.2106
 A0K  O11  O  OH1   0  -0.662  -3.1489  -0.7735   1.6427
 A0K  O13  O  OH1   0  -0.690  -2.3975   1.7451   0.2959
 A0K  O15  O  OH1   0  -0.667   0.8643  -2.8019  -0.7958
 A0K  O16  O  OH1   0  -0.675   3.0955  -1.7621   0.6335
 A0K  O17  O  OH1   0  -0.673   2.7173   0.8593   1.6800
 A0K  O18  O  OH1   0  -0.670  -0.0458   3.3346  -0.2441
 A0K  H1   H  HCH2  0   0.194  -4.2435  -1.2455  -0.0632
 A0K  H2   H  HCH2  0   0.205  -2.9429  -2.3670   0.3245
 A0K  H3   H  HCH2  0   0.227   1.6308   3.0690   0.9570
 A0K  H4   H  HCH2  0   0.202   1.9203   2.9208  -0.7801
 A0K  H6   H  HCH1  0   0.210   2.9644   0.6201  -0.3660
 A0K  H7   H  HCH1  0   0.217   1.1930  -1.2426   1.2686
 A0K  H8   H  HCH1  0   0.225   1.9299  -1.2659  -1.6870
 A0K  H9   H  HCH1  0   0.232  -0.3618  -0.7083  -2.1624
 A0K  H10  H  HCH1  0   0.214  -2.4952  -1.0275  -1.5956
 A0K  H11  H  HCH2  0   0.213  -2.1548   1.2809  -1.7059
 A0K  H12  H  HCH2  0   0.205  -3.7347   0.9584  -1.0338
 A0K  H13  H  HOH1  0   0.452  -3.7378  -1.2882   2.2016
 A0K  H14  H  HOH1  0   0.458  -1.5871   2.2447   0.1235
 A0K  H15  H  HOH1  0   0.458   0.7072  -3.1322  -1.6854
 A0K  H16  H  HOH1  0   0.455   2.8873  -2.6958   0.7389
 A0K  H17  H  HOH1  0   0.455   3.5075   0.3498   1.8868
 A0K  H18  H  HOH1  0   0.469   0.0011   4.2572   0.0220
 A0K  H5   H  HCH1  0   0.231   0.2373   1.0460   0.9328

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
 A0K  O13  C12  single  1.402  0.020  1.402
 A0K  C10  O11  single  1.406  0.020  1.406
 A0K  C10  C09  single  1.515  0.020  1.515
 A0K  C12  C09  single  1.532  0.020  1.532
 A0K  C09  O08  single  1.417  0.020  1.417
 A0K  O08  C06  single  1.383  0.020  1.383
 A0K  C01  C02  single  1.513  0.020  1.513
 A0K  C01  O18  single  1.415  0.020  1.415
 A0K  C02  O07  single  1.418  0.020  1.418
 A0K  C02  C03  single  1.525  0.020  1.525
 A0K  O07  C06  single  1.404  0.020  1.404
 A0K  C06  C05  single  1.533  0.020  1.533
 A0K  O17  C03  single  1.406  0.020  1.406
 A0K  C03  C04  single  1.525  0.020  1.525
 A0K  C04  C05  single  1.525  0.020  1.525
 A0K  C04  O16  single  1.409  0.020  1.409
 A0K  C05  O15  single  1.404  0.020  1.404
 A0K  C10  H1   single  0.970  0.020  1.090
 A0K  C10  H2   single  0.970  0.020  1.090
 A0K  C01  H3   single  0.970  0.020  1.090
 A0K  C01  H4   single  0.970  0.020  1.090
 A0K  C02  H5   single  0.970  0.020  1.090
 A0K  C03  H6   single  0.970  0.020  1.090
 A0K  C04  H7   single  0.970  0.020  1.090
 A0K  C05  H8   single  0.970  0.020  1.090
 A0K  C06  H9   single  0.970  0.020  1.090
 A0K  C09  H10  single  0.970  0.020  1.090
 A0K  C12  H11  single  0.970  0.020  1.090
 A0K  C12  H12  single  0.970  0.020  1.090
 A0K  O11  H13  single  0.850  0.020  0.980
 A0K  O13  H14  single  0.850  0.020  0.980
 A0K  O15  H15  single  0.850  0.020  0.980
 A0K  O16  H16  single  0.850  0.020  0.980
 A0K  O17  H17  single  0.850  0.020  0.980
 A0K  O18  H18  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
 A0K  H2   C10  H1   106.52  3.000
 A0K  H2   C10  O11  111.58  3.000
 A0K  H1   C10  O11  111.84  3.000
 A0K  H2   C10  C09  108.06  3.000
 A0K  H1   C10  C09  107.16  3.000
 A0K  O11  C10  C09  111.42  3.000
 A0K  H4   C01  H3   107.59  3.000
 A0K  H4   C01  O18  111.06  3.000
 A0K  H3   C01  O18  111.40  3.000
 A0K  H4   C01  C02  109.92  3.000
 A0K  H3   C01  C02  108.85  3.000
 A0K  O18  C01  C02  108.00  3.000
 A0K  H5   C02  O07  110.38  3.000
 A0K  H5   C02  C03  108.46  3.000
 A0K  O07  C02  C03  109.57  3.000
 A0K  H5   C02  C01  108.21  3.000
 A0K  C03  C02  C01  113.30  3.000
 A0K  O07  C02  C01  106.91  3.000
 A0K  H6   C03  O17  111.03  3.000
 A0K  H6   C03  C04  108.52  3.000
 A0K  O17  C03  C04  111.74  3.000
 A0K  H6   C03  C02  108.62  3.000
 A0K  C04  C03  C02  108.85  3.000
 A0K  O17  C03  C02  108.01  3.000
 A0K  H7   C04  O16  110.72  3.000
 A0K  H7   C04  C05  108.83  3.000
 A0K  O16  C04  C05  111.76  3.000
 A0K  H7   C04  C03  107.94  3.000
 A0K  O16  C04  C03  107.46  3.000
 A0K  C05  C04  C03  110.05  3.000
 A0K  H8   C05  O15  111.05  3.000
 A0K  H8   C05  C06  106.59  3.000
 A0K  O15  C05  C06  112.56  3.000
 A0K  H8   C05  C04  107.92  3.000
 A0K  O15  C05  C04  108.10  3.000
 A0K  C06  C05  C04  110.53  3.000
 A0K  H9   C06  O08  110.80  3.000
 A0K  H9   C06  O07  105.22  3.000
 A0K  O08  C06  O07  112.66  3.000
 A0K  H9   C06  C05  109.74  3.000
 A0K  O07  C06  C05  108.96  3.000
 A0K  O08  C06  C05  109.36  3.000
 A0K  H10  C09  O08  109.46  3.000
 A0K  H10  C09  C12  105.13  3.000
 A0K  O08  C09  C12  114.49  3.000
 A0K  H10  C09  C10  104.93  3.000
 A0K  O08  C09  C10  107.54  3.000
 A0K  C12  C09  C10  114.77  3.000
 A0K  H12  C12  H11  105.68  3.000
 A0K  H12  C12  O13  109.09  3.000
 A0K  H11  C12  O13  111.33  3.000
 A0K  H12  C12  C09  106.33  3.000
 A0K  H11  C12  C09  108.52  3.000
 A0K  O13  C12  C09  115.33  3.000
 A0K  C06  O07  C02  114.31  3.000
 A0K  C09  O08  C06  116.75  3.000
 A0K  H13  O11  C10  107.54  3.000
 A0K  H14  O13  C12  108.81  3.000
 A0K  H15  O15  C05  108.86  3.000
 A0K  H16  O16  C04  108.43  3.000
 A0K  H17  O17  C03  108.32  3.000
 A0K  H18  O18  C01  109.11  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
 A0K  Var_01  C12  C09  O08  C06  -68.74  30.0  1
 A0K  Var_02  O13  C12  C09  C10   70.59  30.0  1
 A0K  Var_03  O11  C10  C09  C12  -62.50  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
 A0K  chir_01  C02  C01  O07  C03  negativ
 A0K  chir_02  C03  O17  C02  C04  positiv
 A0K  chir_03  C04  O16  C05  C03  positiv
 A0K  chir_04  C05  O15  C04  C06  positiv
 A0K  chir_05  C06  O07  O08  C05  positiv

