# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 09:27:20 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: 3-[(2~{S},3~{S},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-2-oxidanylidene-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](CC(=O)C(O)=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
 K5B  K5B  '3-[(2~{S},3~{S},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-2-oxidanylidene-propanoic acid'  D-saccharide  26  15  .  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_K5B
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
 K5B  O1'  O  O      0  -0.578   3.7060  -0.5091   0.9812
 K5B  C1   C  C      0   0.348   3.5118   0.2435   0.0113
 K5B  O1   O  OC    -1  -0.582   4.2749   1.0808  -0.4887
 K5B  C2   C  C      0   0.240   2.1190   0.1089  -0.6695
 K5B  O2   O  O      0  -0.396   1.9026   0.6384  -1.7339
 K5B  C3   C  CH2    0  -0.579   1.0839  -0.7238   0.0446
 K5B  C4   C  CR15   0   0.061  -0.2972  -0.6339  -0.5643
 K5B  O7   O  O      0  -0.511  -0.8290   0.6684  -0.3599
 K5B  C7   C  CR15   0   0.003  -2.2409   0.6118  -0.2345
 K5B  C8   C  CH2    0  -0.162  -2.6841   1.2210   1.0797
 K5B  O8   O  OH1    0  -0.672  -2.3139   2.5806   1.0930
 K5B  C6   C  CR15   0  -0.056  -2.6308  -0.8690  -0.3625
 K5B  O6   O  OH1    0  -0.676  -2.9301  -1.2353  -1.6893
 K5B  C5   C  CR15   0   0.007  -1.3335  -1.5846   0.0205
 K5B  O5   O  OH1    0  -0.666  -1.1734  -1.6655   1.4139
 K5B  H2   H  HCH2   0   0.273   1.4305  -1.7627   0.0200
 K5B  H3   H  HCH2   0   0.266   1.0683  -0.4523   1.1014
 K5B  H4   H  HCR5   0   0.218  -0.2306  -0.8485  -1.6390
 K5B  H5   H  HCR5   0   0.227  -2.7026   1.1878  -1.0495
 K5B  H6   H  HCH2   0   0.194  -3.7730   1.0985   1.1579
 K5B  H7   H  HCH2   0   0.200  -2.2353   0.6679   1.9131
 K5B  H8   H  HOH1   0   0.455  -2.6064   2.9589   1.9267
 K5B  H9   H  HCR5   0   0.239  -3.4568  -1.1322   0.3134
 K5B  H10  H  HOH1   0   0.454  -3.6697  -0.7025  -1.9977
 K5B  H11  H  HCR5   0   0.238  -1.2732  -2.5730  -0.4517
 K5B  H12  H  HOH1   0   0.456  -1.8641  -2.2363   1.7647

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
 K5B  O8  C8   single  1.409  0.020  1.409
 K5B  C8  C7   single  1.515  0.020  1.515
 K5B  C7  C6   single  1.537  0.020  1.537
 K5B  C7  O7   single  1.419  0.020  1.419
 K5B  C6  O6   single  1.409  0.020  1.409
 K5B  C6  C5   single  1.530  0.020  1.530
 K5B  O5  C5   single  1.405  0.020  1.405
 K5B  O7  C4   single  1.422  0.020  1.422
 K5B  C5  C4   single  1.523  0.020  1.523
 K5B  C4  C3   single  1.512  0.020  1.512
 K5B  C3  C2   single  1.508  0.020  1.508
 K5B  C2  O2   double  1.208  0.020  1.208
 K5B  C2  C1   single  1.556  0.020  1.556
 K5B  C1  O1'  deloc   1.243  0.020  1.243
 K5B  C1  O1   deloc   1.238  0.020  1.238
 K5B  C3  H2   single  0.970  0.020  1.090
 K5B  C3  H3   single  0.970  0.020  1.090
 K5B  C4  H4   single  0.970  0.020  1.090
 K5B  C7  H5   single  0.970  0.020  1.090
 K5B  C8  H6   single  0.970  0.020  1.090
 K5B  C8  H7   single  0.970  0.020  1.090
 K5B  O8  H8   single  0.850  0.020  0.980
 K5B  C6  H9   single  0.970  0.020  1.090
 K5B  O6  H10  single  0.850  0.020  0.980
 K5B  C5  H11  single  0.970  0.020  1.090
 K5B  O5  H12  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
 K5B  C2   C1  O1   115.68  3.000
 K5B  O1   C1  O1'  128.92  3.000
 K5B  C2   C1  O1'  115.40  3.000
 K5B  C3   C2  O2   122.42  3.000
 K5B  O2   C2  C1   120.51  3.000
 K5B  C3   C2  C1   117.06  3.000
 K5B  H3   C3  H2   105.20  3.000
 K5B  H3   C3  C4   111.23  3.000
 K5B  H2   C3  C4   109.65  3.000
 K5B  H3   C3  C2   109.33  3.000
 K5B  H2   C3  C2   107.21  3.000
 K5B  C4   C3  C2   113.79  3.000
 K5B  H4   C4  C5   107.17  3.000
 K5B  H4   C4  O7   110.03  3.000
 K5B  C5   C4  O7   105.20  3.000
 K5B  H4   C4  C3   109.10  3.000
 K5B  C5   C4  C3   115.45  3.000
 K5B  O7   C4  C3   109.77  3.000
 K5B  C7   O7  C4   110.40  3.000
 K5B  H5   C7  C6   109.67  3.000
 K5B  H5   C7  C8   108.03  3.000
 K5B  C6   C7  C8   112.68  3.000
 K5B  H5   C7  O7   109.36  3.000
 K5B  C6   C7  O7   106.47  3.000
 K5B  C8   C7  O7   110.60  3.000
 K5B  H7   C8  H6   107.18  3.000
 K5B  H7   C8  O8   111.84  3.000
 K5B  H6   C8  O8   111.55  3.000
 K5B  H7   C8  C7   109.69  3.000
 K5B  H6   C8  C7   107.88  3.000
 K5B  O8   C8  C7   108.62  3.000
 K5B  H8   O8  C8   107.94  3.000
 K5B  H9   C6  C5   111.79  3.000
 K5B  H9   C6  O6   110.93  3.000
 K5B  C5   C6  O6   107.12  3.000
 K5B  H9   C6  C7   111.72  3.000
 K5B  C5   C6  C7   102.40  3.000
 K5B  O6   C6  C7   112.51  3.000
 K5B  H10  O6  C6   108.74  3.000
 K5B  H11  C5  O5   111.64  3.000
 K5B  H11  C5  C6   111.11  3.000
 K5B  O5   C5  C6   111.82  3.000
 K5B  H11  C5  C4   111.08  3.000
 K5B  O5   C5  C4   109.83  3.000
 K5B  C6   C5  C4   100.88  3.000
 K5B  H12  O5  C5   108.29  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
 K5B  Var_01  C4  C3  C2  C1   171.11  30.0  2
 K5B  Var_02  C3  C2  C1  O1'   10.25  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
 K5B  chir_01  C4  O7  C5  C3  positiv
 K5B  chir_02  C7  O7  C8  C6  positiv
 K5B  chir_03  C6  O6  C7  C5  positiv
 K5B  chir_04  C5  O5  C6  C4  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
 K5B  plan-1  C1   0.020
 K5B  plan-1  C2   0.020
 K5B  plan-1  O2   0.020
 K5B  plan-1  C3   0.020
 K5B  plan-2  O1'  0.020
 K5B  plan-2  C1   0.020
 K5B  plan-2  O1   0.020
 K5B  plan-2  C2   0.020

