# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 07:56:53 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: (2~{S},3~{S},4~{R},5~{S},6~{R})-2-methyl-6-propa-1,2-dienoxy-oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1O[C@@H](O[CH]=[C]=[CH2])[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
 KG1  KG1  (2~{S},3~{S},4~{R},5~{S},6~{R})-2-methyl-6-propa-1,2-dienoxy-oxane-3,4,5-triol  L-saccharide  28  14  .  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_KG1
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
 KG1  O4   O  OH1   0  -0.672  -2.8157  -0.8392   0.0977
 KG1  C4   C  CH1   0  -0.006  -1.7090  -0.6207  -0.7428
 KG1  C5   C  CH1   0   0.013  -0.4745  -1.4159  -0.3104
 KG1  C6   C  CH3   0  -0.709  -0.7240  -2.9073  -0.2301
 KG1  O5   O  O2    0  -0.489  -0.0238  -0.9945   0.9753
 KG1  C3   C  CH1   0   0.024  -1.3722   0.8637  -0.7132
 KG1  O3   O  OH1   0  -0.671  -2.5124   1.6002  -1.0733
 KG1  C2   C  CH1   0  -0.030  -0.8608   1.2517   0.6707
 KG1  O2   O  OH1   0  -0.668  -0.4927   2.6073   0.6383
 KG1  C1   C  CH1   0   0.230   0.3083   0.3505   1.0767
 KG1  O1   O  O2    0  -0.472   1.4078   0.6809   0.2624
 KG1  CM   C  C1    0  -0.069   2.5777   0.0806   0.6209
 KG1  C7   C  CSP   0   0.144   3.5031  -0.2083  -0.2525
 KG1  C8   C  C2    0  -0.665   4.4503  -0.4799  -1.1034
 KG1  H1   H  HOH1  0   0.457  -3.1443  -1.7309  -0.0495
 KG1  H2   H  HCH1  0   0.236  -1.9356  -0.9054  -1.7805
 KG1  H3   H  HCH1  0   0.226   0.3080  -1.2373  -1.0595
 KG1  H4   H  HCH3  0   0.239  -1.0713  -3.2820  -1.1934
 KG1  H5   H  HCH3  0   0.251   0.1944  -3.4390   0.0182
 KG1  H6   H  HCH3  0   0.230  -1.4695  -3.1596   0.5253
 KG1  H7   H  HCH1  0   0.222  -0.5647   1.0220  -1.4434
 KG1  H8   H  HOH1  0   0.449  -2.2731   2.5326  -1.0699
 KG1  H9   H  HCH1  0   0.240  -1.6607   1.0778   1.4012
 KG1  H10  H  HOH1  0   0.460  -0.4936   2.9519   1.5362
 KG1  H11  H  HCH1  0   0.249   0.5669   0.5130   2.1318
 KG1  H12  H  H     0   0.258   2.7309  -0.1123   1.6812
 KG1  H14  H  H     0   0.263   4.5258  -1.4522  -1.5786
 KG1  H13  H  H     0   0.262   5.2020   0.2543  -1.3734

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
 KG1  C6  C5   single  1.514  0.020  1.514
 KG1  C5  C4   single  1.531  0.020  1.531
 KG1  C5  O5   single  1.426  0.020  1.426
 KG1  C8  C7   double  1.302  0.020  1.302
 KG1  C7  CM   double  1.305  0.020  1.305
 KG1  C4  O4   single  1.407  0.020  1.407
 KG1  C4  C3   single  1.522  0.020  1.522
 KG1  CM  O1   single  1.363  0.020  1.363
 KG1  O5  C1   single  1.389  0.020  1.389
 KG1  O1  C1   single  1.408  0.020  1.408
 KG1  C3  O3   single  1.404  0.020  1.404
 KG1  C3  C2   single  1.526  0.020  1.526
 KG1  C1  C2   single  1.531  0.020  1.531
 KG1  C2  O2   single  1.405  0.020  1.405
 KG1  O4  H1   single  0.850  0.020  0.980
 KG1  C4  H2   single  0.970  0.020  1.090
 KG1  C5  H3   single  0.970  0.020  1.090
 KG1  C6  H4   single  0.970  0.020  1.090
 KG1  C6  H5   single  0.970  0.020  1.090
 KG1  C6  H6   single  0.970  0.020  1.090
 KG1  C3  H7   single  0.970  0.020  1.090
 KG1  O3  H8   single  0.850  0.020  0.980
 KG1  C2  H9   single  0.970  0.020  1.090
 KG1  O2  H10  single  0.850  0.020  0.980
 KG1  C1  H11  single  0.970  0.020  1.090
 KG1  CM  H12  single  0.930  0.020  1.080
 KG1  C8  H14  single  0.930  0.020  1.080
 KG1  C8  H13  single  0.930  0.020  1.080

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
 KG1  H1   O4  C4   108.75  3.000
 KG1  H2   C4  C3   108.44  3.000
 KG1  H2   C4  C5   107.35  3.000
 KG1  C3   C4  C5   108.82  3.000
 KG1  H2   C4  O4   111.19  3.000
 KG1  C3   C4  O4   108.30  3.000
 KG1  C5   C4  O4   112.64  3.000
 KG1  H3   C5  O5   109.99  3.000
 KG1  H3   C5  C6   108.29  3.000
 KG1  O5   C5  C6   107.18  3.000
 KG1  H3   C5  C4   107.31  3.000
 KG1  O5   C5  C4   110.86  3.000
 KG1  C6   C5  C4   113.19  3.000
 KG1  H6   C6  H5   107.77  3.000
 KG1  H6   C6  H4   108.34  3.000
 KG1  H5   C6  H4   107.58  3.000
 KG1  H6   C6  C5   112.15  3.000
 KG1  H5   C6  C5   110.71  3.000
 KG1  H4   C6  C5   110.12  3.000
 KG1  C1   O5  C5   115.31  3.000
 KG1  H7   C3  C2   108.63  3.000
 KG1  H7   C3  O3   110.51  3.000
 KG1  C2   C3  O3   111.80  3.000
 KG1  H7   C3  C4   106.85  3.000
 KG1  C2   C3  C4   109.86  3.000
 KG1  O3   C3  C4   109.07  3.000
 KG1  H8   O3  C3   107.78  3.000
 KG1  H9   C2  C1   106.67  3.000
 KG1  H9   C2  O2   111.06  3.000
 KG1  C1   C2  O2   111.96  3.000
 KG1  H9   C2  C3   108.62  3.000
 KG1  O2   C2  C3   108.20  3.000
 KG1  C1   C2  C3   110.29  3.000
 KG1  H10  O2  C2   108.90  3.000
 KG1  H11  C1  O1   109.70  3.000
 KG1  H11  C1  C2   110.33  3.000
 KG1  O1   C1  C2   107.75  3.000
 KG1  H11  C1  O5   105.65  3.000
 KG1  C2   C1  O5   111.59  3.000
 KG1  O1   C1  O5   111.83  3.000
 KG1  CM   O1  C1   114.52  3.000
 KG1  H12  CM  C7   120.86  3.000
 KG1  H12  CM  O1   117.07  3.000
 KG1  C7   CM  O1   122.02  3.000
 KG1  C8   C7  CM   178.43  3.000
 KG1  H13  C8  H14  116.70  3.000
 KG1  H13  C8  C7   121.71  3.000
 KG1  H14  C8  C7   121.59  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
 KG1  Var_01  C7   CM  O1  C1  150.17  30.0  1
 KG1  Var_02  H14  C8  C7  CM  137.97   0.0  2
 KG1  Var_03  H12  CM  C7  C8  -48.85   0.0  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
 KG1  chir_01  C4  C5  O4  C3  negativ
 KG1  chir_02  C5  O5  C4  C6  positiv
 KG1  chir_03  C3  O3  C4  C2  positiv
 KG1  chir_04  C2  O2  C3  C1  negativ
 KG1  chir_05  C1  O5  O1  C2  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
 KG1  plan-1  O1   0.020
 KG1  plan-1  CM   0.020
 KG1  plan-1  C7   0.020
 KG1  plan-1  C8   0.020
 KG1  plan-1  H12  0.020
 KG1  plan-1  H14  0.020
 KG1  plan-1  H13  0.020

