# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 09:50:48 2022
#   Inital geometry file: a 79 line input string
#   Ligand name: (2S,3S,4R,5S,6R)-6-(hydroxymethyl)-5-methoxy-2-prop-2-enoxy-oxane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1[C@H](O)[C@H](O)[C@@H](OCC=C)O[C@@H]1CO
#
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
 G8Z  G8Z  (2S,3S,4R,5S,6R)-6-(hydroxymethyl)-5-methoxy-2-prop-2-enoxy-oxane-3,4-diol  D-saccharide  34  16  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G8Z
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
 G8Z  O6    O  OH1   0  -0.666  6.8441  -19.3806  10.7559
 G8Z  C6    C  CH2   0  -0.158  6.0607  -18.2473  10.4629
 G8Z  C5    C  CH1   0  -0.014  6.1282  -17.9835   8.9734
 G8Z  C4    C  CH1   0   0.037  5.4044  -16.6883   8.5860
 G8Z  O4    O  O2    0  -0.496  6.0985  -15.6042   9.1580
 G8Z  C7    C  CH3   0  -0.407  5.2936  -14.6895   9.8628
 G8Z  C3    C  CH1   0   0.029  5.3873  -16.5552   7.0663
 G8Z  O3    O  OH1   0  -0.663  4.6847  -15.3860   6.7293
 G8Z  C2    C  CH1   0  -0.030  4.7799  -17.8056   6.4297
 G8Z  O2    O  OH1   0  -0.666  3.4228  -17.8703   6.7904
 G8Z  O5    O  O2    0  -0.498  5.5412  -19.0999   8.3243
 G8Z  C1    C  CH1   0   0.243  5.5181  -19.0506   6.9304
 G8Z  O1    O  O2    0  -0.500  6.7902  -19.0405   6.3619
 G8Z  C8    C  CH2   0  -0.221  7.6615  -20.1036   6.7290
 G8Z  C9    C  C1    0  -0.220  7.0769  -21.4739   6.5630
 G8Z  C10   C  C2    0  -0.510  7.4536  -22.3182   5.6106
 G8Z  HO6   H  HOH1  0   0.454  6.8270  -19.5183  11.7071
 G8Z  H61   H  HCH2  0   0.195  5.0110  -18.3883  10.7563
 G8Z  H62   H  HCH2  0   0.209  6.4271  -17.3578  10.9868
 G8Z  H5    H  HCH1  0   0.224  7.1857  -17.8818   8.6880
 G8Z  H4    H  HCH1  0   0.224  4.3723  -16.7345   8.9607
 G8Z  H3    H  HCH1  0   0.218  6.4319  -16.4902   6.7306
 G8Z  H71C  H  HCH3  0   0.229  5.9470  -13.9059  10.2458
 G8Z  H72C  H  HCH3  0   0.212  4.5354  -14.2254   9.2262
 G8Z  H73C  H  HCH3  0   0.206  4.7864  -15.1564  10.7146
 G8Z  HO3   H  HOH1  0   0.450  4.8309  -15.2005   5.7961
 G8Z  H2    H  HCH1  0   0.231  4.8992  -17.7473   5.3380
 G8Z  HO2   H  HOH1  0   0.453  3.0044  -18.5801   6.2930
 G8Z  H1    H  HCH1  0   0.232  4.9621  -19.9494   6.6281
 G8Z  H81C  H  HCH2  0   0.242  8.5341  -19.9944   6.0835
 G8Z  H82C  H  HCH2  0   0.221  8.0034  -19.9769   7.7625
 G8Z  H9    H  H     0   0.257  6.3286  -21.7895   7.2834
 G8Z  H101  H  H     0   0.244  7.0302  -23.3113   5.5338
 G8Z  H102  H  H     0   0.241  8.2042  -22.0515   4.8756

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
 G8Z  O6   C6    single  1.408  0.020  1.408
 G8Z  C6   C5    single  1.514  0.020  1.514
 G8Z  C5   C4    single  1.533  0.020  1.533
 G8Z  C5   O5    single  1.418  0.020  1.418
 G8Z  C4   O4    single  1.409  0.020  1.409
 G8Z  C4   C3    single  1.526  0.020  1.526
 G8Z  O4   C7    single  1.408  0.020  1.408
 G8Z  C3   O3    single  1.405  0.020  1.405
 G8Z  C3   C2    single  1.529  0.020  1.529
 G8Z  C2   O2    single  1.406  0.020  1.406
 G8Z  C2   C1    single  1.532  0.020  1.532
 G8Z  O5   C1    single  1.395  0.020  1.395
 G8Z  C1   O1    single  1.393  0.020  1.393
 G8Z  O1   C8    single  1.423  0.020  1.423
 G8Z  C8   C9    single  1.499  0.020  1.499
 G8Z  C9   C10   double  1.327  0.020  1.327
 G8Z  O6   HO6   single  0.850  0.020  0.980
 G8Z  C6   H61   single  0.970  0.020  1.090
 G8Z  C6   H62   single  0.970  0.020  1.090
 G8Z  C5   H5    single  0.970  0.020  1.090
 G8Z  C4   H4    single  0.970  0.020  1.090
 G8Z  C3   H3    single  0.970  0.020  1.090
 G8Z  C7   H71C  single  0.970  0.020  1.090
 G8Z  C7   H72C  single  0.970  0.020  1.090
 G8Z  C7   H73C  single  0.970  0.020  1.090
 G8Z  O3   HO3   single  0.850  0.020  0.980
 G8Z  C2   H2    single  0.970  0.020  1.090
 G8Z  O2   HO2   single  0.850  0.020  0.980
 G8Z  C1   H1    single  0.970  0.020  1.090
 G8Z  C8   H81C  single  0.970  0.020  1.090
 G8Z  C8   H82C  single  0.970  0.020  1.090
 G8Z  C9   H9    single  0.930  0.020  1.080
 G8Z  C10  H101  single  0.930  0.020  1.080
 G8Z  C10  H102  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
 G8Z  HO6   O6   C6    108.14  3.000
 G8Z  H62   C6   H61   107.22  3.000
 G8Z  H62   C6   C5    108.31  3.000
 G8Z  H61   C6   C5    109.12  3.000
 G8Z  H62   C6   O6    111.58  3.000
 G8Z  H61   C6   O6    111.86  3.000
 G8Z  C5    C6   O6    108.66  3.000
 G8Z  H5    C5   O5    110.60  3.000
 G8Z  H5    C5   C4    108.07  3.000
 G8Z  O5    C5   C4    110.72  3.000
 G8Z  H5    C5   C6    108.31  3.000
 G8Z  O5    C5   C6    107.13  3.000
 G8Z  C4    C5   C6    112.00  3.000
 G8Z  H4    C4   C3    109.44  3.000
 G8Z  H4    C4   O4    110.90  3.000
 G8Z  C3    C4   O4    110.05  3.000
 G8Z  H4    C4   C5    108.76  3.000
 G8Z  C3    C4   C5    109.31  3.000
 G8Z  O4    C4   C5    108.35  3.000
 G8Z  C7    O4   C4    114.94  3.000
 G8Z  H73C  C7   H72C  108.21  3.000
 G8Z  H73C  C7   H71C  108.10  3.000
 G8Z  H72C  C7   H71C  108.37  3.000
 G8Z  H73C  C7   O4    112.15  3.000
 G8Z  H72C  C7   O4    112.39  3.000
 G8Z  H71C  C7   O4    107.48  3.000
 G8Z  H3    C3   C2    107.39  3.000
 G8Z  H3    C3   O3    110.66  3.000
 G8Z  C2    C3   O3    112.46  3.000
 G8Z  H3    C3   C4    107.38  3.000
 G8Z  C2    C3   C4    110.35  3.000
 G8Z  O3    C3   C4    108.49  3.000
 G8Z  HO3   O3   C3    108.48  3.000
 G8Z  H2    C2   C1    108.38  3.000
 G8Z  H2    C2   O2    111.22  3.000
 G8Z  C1    C2   O2    110.12  3.000
 G8Z  H2    C2   C3    109.08  3.000
 G8Z  C1    C2   C3    109.71  3.000
 G8Z  O2    C2   C3    108.32  3.000
 G8Z  HO2   O2   C2    108.72  3.000
 G8Z  C1    O5   C5    115.87  3.000
 G8Z  H1    C1   O1    110.83  3.000
 G8Z  H1    C1   O5    104.73  3.000
 G8Z  O1    C1   O5    113.13  3.000
 G8Z  H1    C1   C2    109.33  3.000
 G8Z  O1    C1   C2    107.51  3.000
 G8Z  O5    C1   C2    111.30  3.000
 G8Z  C8    O1   C1    116.65  3.000
 G8Z  H82C  C8   H81C  107.28  3.000
 G8Z  H82C  C8   C9    109.38  3.000
 G8Z  H81C  C8   C9    109.75  3.000
 G8Z  H82C  C8   O1    110.37  3.000
 G8Z  H81C  C8   O1    105.21  3.000
 G8Z  C9    C8   O1    114.56  3.000
 G8Z  H9    C9   C10   119.13  3.000
 G8Z  H9    C9   C8    117.46  3.000
 G8Z  C10   C9   C8    123.39  3.000
 G8Z  H102  C10  H101  116.65  3.000
 G8Z  H102  C10  C9    121.77  3.000
 G8Z  H101  C10  C9    121.57  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
 G8Z  Var_01  C9    C8   O1  C1    51.70  30.0  3
 G8Z  Var_02  H71C  C7   O4  C4  -179.71  30.0  3
 G8Z  Var_03  C10   C9   C8  O1   108.05  30.0  3
 G8Z  Var_04  H101  C10  C9  C8   178.34   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
 G8Z  chir_01  C5  C6  C4  O5  positiv
 G8Z  chir_02  C4  O4  C3  C5  negativ
 G8Z  chir_03  C3  O3  C2  C4  positiv
 G8Z  chir_04  C2  O2  C3  C1  negativ
 G8Z  chir_05  C1  O5  O1  C2  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
 G8Z  plan-1  C8    0.020
 G8Z  plan-1  C9    0.020
 G8Z  plan-1  C10   0.020
 G8Z  plan-1  H9    0.020
 G8Z  plan-1  H101  0.020
 G8Z  plan-1  H102  0.020

