# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 10:39:11 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  27  15  .  2023-02-15  2023-02-16
;
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  -0.404   3.9024  -0.7724   0.9037
 K5B  C1   C  C     0   0.486   3.5901   0.0849   0.1213
 K5B  O1   O  OH1   0  -0.570   4.3850   1.0127  -0.3615
 K5B  C2   C  C     0   0.297   2.1648   0.2091  -0.4449
 K5B  O2   O  O     0  -0.341   1.9232   1.0627  -1.2542
 K5B  C3   C  CH2   0  -0.603   1.1843  -0.8007   0.0686
 K5B  C4   C  CH1   0   0.031  -0.2237  -0.5632  -0.4247
 K5B  O7   O  O2    0  -0.499  -0.7430   0.6140   0.1596
 K5B  C7   C  CH1   0   0.011  -2.1239   0.6196  -0.1316
 K5B  C8   C  CH2   0  -0.171  -2.8701   1.4578   0.8758
 K5B  O8   O  OH1   0  -0.669  -2.4616   2.7988   0.7640
 K5B  C6   C  CH1   0  -0.045  -2.5702  -0.8633  -0.1271
 K5B  O6   O  OH1   0  -0.670  -3.2911  -1.2289  -1.2765
 K5B  C5   C  CH1   0   0.040  -1.2429  -1.6432  -0.0710
 K5B  O5   O  OH1   0  -0.671  -0.9653  -2.1377   1.2144
 K5B  H1   H  HOH1  0   0.494   5.2794   0.9149   0.0006
 K5B  H2   H  HCH2  0   0.304   1.5328  -1.7891  -0.2512
 K5B  H3   H  HCH2  0   0.295   1.2268  -0.8199   1.1602
 K5B  H4   H  HCH1  0   0.234  -0.2161  -0.4718  -1.5214
 K5B  H5   H  HCH1  0   0.220  -2.2920   1.0191  -1.1444
 K5B  H6   H  HCH2  0   0.203  -3.9443   1.3387   0.6779
 K5B  H7   H  HCH2  0   0.200  -2.6850   1.0543   1.8808
 K5B  H8   H  HOH1  0   0.457  -2.9273   3.3110   1.4309
 K5B  H9   H  HCH1  0   0.230  -3.1480  -1.0782   0.7832
 K5B  H10  H  HOH1  0   0.455  -4.1220  -0.7436  -1.2845
 K5B  H11  H  HCH1  0   0.233  -1.2385  -2.4406  -0.8236
 K5B  H12  H  HOH1  0   0.457  -1.6160  -2.8140   1.4270

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  1.406  0.020  1.406
 K5B  C8  C7   single  1.508  0.020  1.508
 K5B  C7  C6   single  1.549  0.020  1.549
 K5B  C7  O7   single  1.411  0.020  1.411
 K5B  C6  O6   single  1.405  0.020  1.405
 K5B  C6  C5   single  1.541  0.020  1.541
 K5B  O5  C5   single  1.405  0.020  1.405
 K5B  O7  C4   single  1.413  0.020  1.413
 K5B  C5  C4   single  1.526  0.020  1.526
 K5B  C4  C3   single  1.511  0.020  1.511
 K5B  C3  C2   single  1.498  0.020  1.498
 K5B  C2  O2   double  1.201  0.020  1.201
 K5B  C2  C1   single  1.539  0.020  1.539
 K5B  C1  O1'  double  1.202  0.020  1.202
 K5B  C1  O1   single  1.314  0.020  1.314
 K5B  O1  H1   single  0.850  0.020  0.980
 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   111.61  3.000
 K5B  O1   C1  O1'  125.86  3.000
 K5B  C2   C1  O1'  122.53  3.000
 K5B  H1   O1  C1   110.46  3.000
 K5B  C3   C2  O2   125.34  3.000
 K5B  O2   C2  C1   119.46  3.000
 K5B  C3   C2  C1   115.19  3.000
 K5B  H3   C3  H2   105.28  3.000
 K5B  H3   C3  C4   111.42  3.000
 K5B  H2   C3  C4   110.05  3.000
 K5B  H3   C3  C2   109.20  3.000
 K5B  H2   C3  C2   107.45  3.000
 K5B  C4   C3  C2   113.08  3.000
 K5B  H4   C4  C5   107.12  3.000
 K5B  H4   C4  O7   110.20  3.000
 K5B  C5   C4  O7   104.37  3.000
 K5B  H4   C4  C3   109.39  3.000
 K5B  C5   C4  C3   115.81  3.000
 K5B  O7   C4  C3   109.78  3.000
 K5B  C7   O7  C4   106.11  3.000
 K5B  H5   C7  C6   107.82  3.000
 K5B  H5   C7  C8   109.70  3.000
 K5B  C6   C7  C8   112.81  3.000
 K5B  H5   C7  O7   109.90  3.000
 K5B  C6   C7  O7   106.12  3.000
 K5B  C8   C7  O7   110.39  3.000
 K5B  H7   C8  H6   106.84  3.000
 K5B  H7   C8  O8   111.96  3.000
 K5B  H6   C8  O8   111.90  3.000
 K5B  H7   C8  C7   108.88  3.000
 K5B  H6   C8  C7   107.65  3.000
 K5B  O8   C8  C7   109.46  3.000
 K5B  H8   O8  C8   108.19  3.000
 K5B  H9   C6  C5   108.89  3.000
 K5B  H9   C6  O6   110.90  3.000
 K5B  C5   C6  O6   109.88  3.000
 K5B  H9   C6  C7   109.95  3.000
 K5B  C5   C6  C7   103.68  3.000
 K5B  O6   C6  C7   113.24  3.000
 K5B  H10  O6  C6   108.58  3.000
 K5B  H11  C5  O5   111.79  3.000
 K5B  H11  C5  C6   110.28  3.000
 K5B  O5   C5  C6   112.44  3.000
 K5B  H11  C5  C4   110.66  3.000
 K5B  O5   C5  C4   109.22  3.000
 K5B  C6   C5  C4   102.05  3.000
 K5B  H12  O5  C5   108.42  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  CONST_01  H1  O1  C1  O1'    0.00   0.0  0
 K5B  Var_01    C4  C3  C2  C1   175.04  30.0  2
 K5B  Var_02    C3  C2  C1  O1'    1.10  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
 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
 K5B  plan-2  H1   0.020

