# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 08:43:33 2021
#   Inital geometry file: a 105 line input string
#   Ligand name: methyl 3-[(~{E},3~{R},9~{R})-3,9-bis(oxidanyl)dec-4-enoyl]sulfanylpropanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)CCSC(=O)C[C@@H](O)\C=C\CCC[C@@H](C)O
#
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
 GY0  GY0  'methyl 3-[(~{E},3~{R},9~{R})-3,9-bis(oxidanyl)dec-4-enoyl]sulfanylpropanoate'  ligand  44  20  .  2022-03-18  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GY0
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
 GY0  C02  C  CH1   0   0.058  64.8829  76.5052  97.1485
 GY0  C03  C  CH2   0  -0.445  64.5532  77.8999  97.6620
 GY0  C04  C  CH2   0  -0.455  65.7640  78.7923  97.9246
 GY0  C05  C  CH2   0  -0.500  66.6673  79.0263  96.7088
 GY0  C06  C  C1    0  -0.184  65.9243  79.6294  95.5623
 GY0  C07  C  C1    0  -0.264  65.7842  79.0753  94.3625
 GY0  C08  C  CH1   0   0.013  65.0092  79.7031  93.2451
 GY0  C09  C  CH2   0  -0.572  65.9080  80.0033  92.0398
 GY0  C10  C  C     0   0.267  67.0536  80.9135  92.3988
 GY0  C12  C  CH2   0  -0.578  68.0986  83.3527  93.2287
 GY0  C13  C  CH2   0  -0.557  68.8295  83.8113  91.9792
 GY0  C14  C  CH3   0  -0.695  65.7513  75.7101  98.1118
 GY0  C17  C  C     0   0.603  70.0929  84.5641  92.3072
 GY0  C19  C  CH3   0  -0.426  72.0036  85.5750  91.3739
 GY0  O01  O  OH1   0  -0.678  63.6434  75.8522  96.9231
 GY0  O15  O  OH1   0  -0.663  64.0001  78.8395  92.7625
 GY0  O16  O  O     0  -0.378  68.2107  80.5823  92.3941
 GY0  O18  O  O2    0  -0.453  70.7888  84.8406  91.2143
 GY0  O20  O  O     0  -0.451  70.4345  84.8874  93.4172
 GY0  S11  S  S2    0   0.011  66.5250  82.5462  92.8415
 GY0  H1   H  HCH1  0   0.191  65.4244  76.6010  96.1964
 GY0  H2   H  HCH2  0   0.224  63.9808  77.8065  98.5913
 GY0  H3   H  HCH2  0   0.227  63.8939  78.3870  96.9372
 GY0  H4   H  HCH2  0   0.232  66.3669  78.3782  98.7362
 GY0  H5   H  HCH2  0   0.234  65.4043  79.7599  98.2853
 GY0  H6   H  HCH2  0   0.232  67.1481  78.0964  96.3939
 GY0  H7   H  HCH2  0   0.248  67.4758  79.6996  97.0105
 GY0  H8   H  H     0   0.237  65.4507  80.5912  95.7535
 GY0  H9   H  H     0   0.242  66.2464  78.1131  94.1486
 GY0  H10  H  HCH1  0   0.225  64.5717  80.6443  93.6055
 GY0  H11  H  HCH2  0   0.288  65.3114  80.4688  91.2501
 GY0  H12  H  HCH2  0   0.278  66.3241  79.0719  91.6508
 GY0  H13  H  HCH2  0   0.294  68.7013  82.6695  93.8259
 GY0  H14  H  HCH2  0   0.301  67.8318  84.1980  93.8622
 GY0  H15  H  HCH2  0   0.292  68.1880  84.4652  91.3817
 GY0  H16  H  HCH2  0   0.290  69.0802  82.9636  91.3389
 GY0  H17  H  HCH3  0   0.232  65.9542  74.7109  97.7204
 GY0  H18  H  HCH3  0   0.227  66.7153  76.1930  98.2731
 GY0  H19  H  HCH3  0   0.222  65.2626  75.6029  99.0826
 GY0  H20  H  HCH3  0   0.253  72.4133  85.6942  90.3753
 GY0  H21  H  HCH3  0   0.240  71.8209  86.5574  91.8087
 GY0  H22  H  HCH3  0   0.240  72.7177  85.0346  91.9947
 GY0  H23  H  HOH1  0   0.445  63.8296  74.9796  96.5632
 GY0  H24  H  HOH1  0   0.451  63.4248  78.6167  93.5017

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
 GY0  O15  C08  single  1.413  0.020  1.413
 GY0  C09  C10  single  1.507  0.020  1.507
 GY0  C09  C08  single  1.533  0.020  1.533
 GY0  O18  C19  single  1.428  0.020  1.428
 GY0  O18  C17  single  1.325  0.020  1.325
 GY0  O16  C10  double  1.204  0.020  1.204
 GY0  C10  S11  single  1.772  0.020  1.772
 GY0  C08  C07  single  1.498  0.020  1.498
 GY0  C13  C17  single  1.507  0.020  1.507
 GY0  C13  C12  single  1.518  0.020  1.518
 GY0  C17  O20  double  1.206  0.020  1.206
 GY0  C07  C06  double  1.329  0.020  1.329
 GY0  S11  C12  single  1.810  0.020  1.810
 GY0  C06  C05  single  1.493  0.020  1.493
 GY0  C05  C04  single  1.533  0.020  1.533
 GY0  C04  C03  single  1.527  0.020  1.527
 GY0  C03  C02  single  1.522  0.020  1.522
 GY0  O01  C02  single  1.419  0.020  1.419
 GY0  C02  C14  single  1.521  0.020  1.521
 GY0  C02  H1   single  0.970  0.020  1.090
 GY0  C03  H2   single  0.970  0.020  1.090
 GY0  C03  H3   single  0.970  0.020  1.090
 GY0  C04  H4   single  0.970  0.020  1.090
 GY0  C04  H5   single  0.970  0.020  1.090
 GY0  C05  H6   single  0.970  0.020  1.090
 GY0  C05  H7   single  0.970  0.020  1.090
 GY0  C06  H8   single  0.930  0.020  1.080
 GY0  C07  H9   single  0.930  0.020  1.080
 GY0  C08  H10  single  0.970  0.020  1.090
 GY0  C09  H11  single  0.970  0.020  1.090
 GY0  C09  H12  single  0.970  0.020  1.090
 GY0  C12  H13  single  0.970  0.020  1.090
 GY0  C12  H14  single  0.970  0.020  1.090
 GY0  C13  H15  single  0.970  0.020  1.090
 GY0  C13  H16  single  0.970  0.020  1.090
 GY0  C14  H17  single  0.970  0.020  1.090
 GY0  C14  H18  single  0.970  0.020  1.090
 GY0  C14  H19  single  0.970  0.020  1.090
 GY0  C19  H20  single  0.970  0.020  1.090
 GY0  C19  H21  single  0.970  0.020  1.090
 GY0  C19  H22  single  0.970  0.020  1.090
 GY0  O01  H23  single  0.850  0.020  0.980
 GY0  O15  H24  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
 GY0  H1   C02  O01  109.43  3.000
 GY0  H1   C02  C14  108.22  3.000
 GY0  O01  C02  C14  111.02  3.000
 GY0  H1   C02  C03  108.60  3.000
 GY0  C14  C02  C03  112.88  3.000
 GY0  O01  C02  C03  106.62  3.000
 GY0  H3   C03  H2   106.56  3.000
 GY0  H3   C03  C04  109.37  3.000
 GY0  H2   C03  C04  108.56  3.000
 GY0  H3   C03  C02  108.35  3.000
 GY0  H2   C03  C02  108.73  3.000
 GY0  C04  C03  C02  114.94  3.000
 GY0  H5   C04  H4   105.77  3.000
 GY0  H5   C04  C05  108.69  3.000
 GY0  H4   C04  C05  108.78  3.000
 GY0  H5   C04  C03  108.24  3.000
 GY0  H4   C04  C03  110.12  3.000
 GY0  C05  C04  C03  114.85  3.000
 GY0  H7   C05  H6   106.13  3.000
 GY0  H7   C05  C06  109.31  3.000
 GY0  H6   C05  C06  109.95  3.000
 GY0  H7   C05  C04  108.09  3.000
 GY0  H6   C05  C04  110.96  3.000
 GY0  C06  C05  C04  112.18  3.000
 GY0  H8   C06  C07  118.75  3.000
 GY0  H8   C06  C05  115.99  3.000
 GY0  C07  C06  C05  125.25  3.000
 GY0  H9   C07  C08  116.33  3.000
 GY0  H9   C07  C06  120.08  3.000
 GY0  C08  C07  C06  123.59  3.000
 GY0  H10  C08  O15  110.56  3.000
 GY0  H10  C08  C09  108.88  3.000
 GY0  O15  C08  C09  105.65  3.000
 GY0  H10  C08  C07  108.69  3.000
 GY0  C09  C08  C07  111.42  3.000
 GY0  O15  C08  C07  111.60  3.000
 GY0  H12  C09  H11  108.28  3.000
 GY0  H12  C09  C10  108.09  3.000
 GY0  H11  C09  C10  109.25  3.000
 GY0  H12  C09  C08  109.66  3.000
 GY0  H11  C09  C08  109.34  3.000
 GY0  C10  C09  C08  112.13  3.000
 GY0  S11  C10  O16  122.76  3.000
 GY0  S11  C10  C09  112.91  3.000
 GY0  O16  C10  C09  124.32  3.000
 GY0  H14  C12  H13  107.66  3.000
 GY0  H14  C12  S11  104.90  3.000
 GY0  H13  C12  S11  108.59  3.000
 GY0  H14  C12  C13  111.22  3.000
 GY0  H13  C12  C13  111.98  3.000
 GY0  S11  C12  C13  112.14  3.000
 GY0  H16  C13  H15  106.18  3.000
 GY0  H16  C13  C17  108.85  3.000
 GY0  H15  C13  C17  108.18  3.000
 GY0  H16  C13  C12  111.02  3.000
 GY0  H15  C13  C12  110.36  3.000
 GY0  C17  C13  C12  112.04  3.000
 GY0  H19  C14  H18  107.92  3.000
 GY0  H19  C14  H17  108.17  3.000
 GY0  H18  C14  H17  107.10  3.000
 GY0  H19  C14  C02  111.02  3.000
 GY0  H18  C14  C02  111.53  3.000
 GY0  H17  C14  C02  110.94  3.000
 GY0  O20  C17  O18  123.69  3.000
 GY0  O20  C17  C13  124.89  3.000
 GY0  O18  C17  C13  111.42  3.000
 GY0  H22  C19  H21  109.25  3.000
 GY0  H22  C19  H20  109.33  3.000
 GY0  H21  C19  H20  109.34  3.000
 GY0  H22  C19  O18  111.47  3.000
 GY0  H21  C19  O18  111.44  3.000
 GY0  H20  C19  O18  105.93  3.000
 GY0  H23  O01  C02  107.93  3.000
 GY0  H24  O15  C08  107.81  3.000
 GY0  C19  O18  C17  117.51  3.000
 GY0  C12  S11  C10  101.81  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
 GY0  Var_01  C08  C07  C06  C05   178.86   0.0  2
 GY0  Var_02  C05  C04  C03  C02    58.29  30.0  1
 GY0  Var_03  C06  C05  C04  C03    57.69  30.0  1
 GY0  Var_04  C07  C06  C05  C04  -119.51  30.0  1
 GY0  Var_05  O16  C10  C09  C08   113.12  30.0  3
 GY0  Var_06  C13  C12  S11  C10    80.61  30.0  3
 GY0  Var_07  O18  C17  C13  C12   173.67  30.0  3
 GY0  Var_08  S11  C12  C13  C17   176.15  30.0  3
 GY0  Var_09  H20  C19  O18  C17   179.99  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
 GY0  chir_01  C02  C03  O01  C14  positiv
 GY0  chir_02  C08  O15  C09  C07  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
 GY0  plan-1  C09  0.020
 GY0  plan-1  C10  0.020
 GY0  plan-1  O16  0.020
 GY0  plan-1  S11  0.020
 GY0  plan-2  C13  0.020
 GY0  plan-2  C17  0.020
 GY0  plan-2  O18  0.020
 GY0  plan-2  O20  0.020
 GY0  plan-3  C05  0.020
 GY0  plan-3  C06  0.020
 GY0  plan-3  C07  0.020
 GY0  plan-3  C08  0.020
 GY0  plan-3  H8   0.020
 GY0  plan-3  H9   0.020

