# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 08:15:54 2022
#   Inital geometry file: a 156 line input string
#   Ligand name: S-[(2R)-2,3-dihydroxypropyl] (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenethioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC\C=C/C\C=C/C/C=C\C\C=C/CCCC(=O)SC[C@H](O)CO
#
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
 VPY  VPY  'S-[(2R)-2,3-dihydroxypropyl] (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenethioate'  ligand  65  27  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VPY
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
 VPY  S01  S  S2    0   0.014  -12.2184  6.2874   4.7590
 VPY  O01  O  OH1   0  -0.663   -9.4500  7.6309   4.4925
 VPY  O02  O  O     0  -0.381  -12.3187  5.9575   7.3694
 VPY  O03  O  OH1   0  -0.670   -7.3071  6.9744   6.2079
 VPY  C01  C  CH2   0  -0.429  -18.3711  8.4652  10.7697
 VPY  C02  C  CH2   0  -0.423  -17.1304  7.6201  10.5131
 VPY  C03  C  CH2   0  -0.494  -19.6833  7.7761  10.3982
 VPY  C04  C  CH2   0  -0.421  -15.8347  8.3846  10.7520
 VPY  C05  C  CH2   0  -0.428  -14.3395  8.3596   6.5947
 VPY  C06  C  C1    0  -0.207  -19.9311  6.5207  11.1794
 VPY  C07  C  CH3   0  -0.667  -14.5908  7.5491  10.4881
 VPY  C08  C  CH2   0  -0.514  -15.7614  8.8926   6.7935
 VPY  C09  C  CH2   0  -0.548  -14.3267  6.8411   6.3974
 VPY  C10  C  C1    0  -0.223  -20.5634  5.4231  10.7682
 VPY  C11  C  C1    0  -0.220  -16.6387  8.6872   5.5978
 VPY  C12  C  CH2   0  -0.546  -21.1944  5.1887   9.4255
 VPY  C13  C  CH1   0   0.036   -9.5518  6.6645   5.5098
 VPY  C14  C  C     0   0.263  -12.9197  6.3063   6.3853
 VPY  C15  C  CH2   0  -0.606  -10.5629  5.6250   5.0650
 VPY  C16  C  C1    0  -0.188  -17.6329  7.8101   5.4640
 VPY  C17  C  CH2   0  -0.592  -18.0936  6.8003   6.4750
 VPY  C18  C  CH2   0  -0.160   -8.2160  5.9867   5.7769
 VPY  C19  C  C1    0  -0.206  -20.8241  3.8478   8.8608
 VPY  C20  C  CH2   0  -0.562  -20.2740  4.5069   6.4643
 VPY  C21  C  C1    0  -0.192  -17.9514  5.4015   5.9472
 VPY  C22  C  C1    0  -0.208  -20.4440  3.5595   7.6181
 VPY  C23  C  C1    0  -0.213  -18.8718  4.4398   5.9320
 VPY  H37  H  HOH1  0   0.448   -8.7590  8.2534   4.7426
 VPY  H38  H  HOH1  0   0.458   -6.4174  6.6139   6.1632
 VPY  H01  H  HCH2  0   0.220  -18.2956  9.3982  10.2033
 VPY  H02  H  HCH2  0   0.213  -18.3996  8.7535  11.8259
 VPY  H04  H  HCH2  0   0.215  -17.1483  6.7273  11.1472
 VPY  H03  H  HCH2  0   0.218  -17.1484  7.2517   9.4815
 VPY  H06  H  HCH2  0   0.241  -20.5049  8.4781  10.5795
 VPY  H05  H  HCH2  0   0.235  -19.6974  7.5741   9.3234
 VPY  H08  H  HCH2  0   0.211  -15.8201  9.2728  10.1124
 VPY  H07  H  HCH2  0   0.214  -15.8182  8.7540  11.7821
 VPY  H10  H  HCH2  0   0.247  -13.7436  8.6213   7.4722
 VPY  H09  H  HCH2  0   0.240  -13.8711  8.8486   5.7368
 VPY  H11  H  H     0   0.228  -19.5697  6.5319  12.2053
 VPY  H14  H  HCH3  0   0.225  -13.6784  8.1187  10.6675
 VPY  H16  H  HCH3  0   0.217  -14.5626  6.6671  11.1307
 VPY  H15  H  HCH3  0   0.222  -14.5620  7.2012   9.4538
 VPY  H12  H  HCH2  0   0.250  -15.6956  9.9628   7.0062
 VPY  H13  H  HCH2  0   0.246  -16.1886  8.4304   7.6855
 VPY  H17  H  HCH2  0   0.271  -14.8416  6.5816   5.4700
 VPY  H18  H  HCH2  0   0.272  -14.8638  6.3578   7.2173
 VPY  H19  H  H     0   0.232  -20.6728  4.6059  11.4764
 VPY  H20  H  H     0   0.234  -16.4165  9.3265   4.7477
 VPY  H22  H  HCH2  0   0.247  -20.9601  5.9957   8.7307
 VPY  H23  H  HCH2  0   0.251  -22.2841  5.2156   9.5571
 VPY  H21  H  HCH1  0   0.217   -9.8984  7.1183   6.4494
 VPY  H25  H  HCH2  0   0.291  -10.6423  4.8244   5.8003
 VPY  H24  H  HCH2  0   0.292  -10.2534  5.1744   4.1195
 VPY  H26  H  H     0   0.238  -18.1707  7.7929   4.5203
 VPY  H28  H  HCH2  0   0.259  -17.5116  6.8872   7.3956
 VPY  H27  H  HCH2  0   0.252  -19.1308  7.0064   6.7517
 VPY  H29  H  HCH2  0   0.202   -7.8746  5.4943   4.8569
 VPY  H30  H  HCH2  0   0.198   -8.3567  5.2043   6.5337
 VPY  H31  H  H     0   0.234  -20.8934  3.0214   9.5637
 VPY  H33  H  HCH2  0   0.248  -20.5479  5.5236   6.7427
 VPY  H32  H  HCH2  0   0.252  -20.9655  4.2090   5.6679
 VPY  H34  H  H     0   0.239  -16.9712  5.1644   5.5427
 VPY  H35  H  H     0   0.235  -20.2215  2.5202   7.3919
 VPY  H36  H  H     0   0.236  -18.5830  3.4771   5.5193

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
 VPY  C15  S01  single  1.809  0.020  1.809
 VPY  C15  C13  single  1.517  0.020  1.517
 VPY  S01  C14  single  1.771  0.020  1.771
 VPY  C18  O03  single  1.410  0.020  1.410
 VPY  C18  C13  single  1.522  0.020  1.522
 VPY  O01  C13  single  1.407  0.020  1.407
 VPY  C16  C11  double  1.332  0.020  1.332
 VPY  C16  C17  single  1.501  0.020  1.501
 VPY  C14  C09  single  1.505  0.020  1.505
 VPY  C14  O02  double  1.205  0.020  1.205
 VPY  C11  C08  single  1.497  0.020  1.497
 VPY  C23  C21  double  1.331  0.020  1.331
 VPY  C23  C20  single  1.501  0.020  1.501
 VPY  C21  C17  single  1.502  0.020  1.502
 VPY  C09  C05  single  1.531  0.020  1.531
 VPY  C20  C22  single  1.503  0.020  1.503
 VPY  C05  C08  single  1.531  0.020  1.531
 VPY  C22  C19  double  1.331  0.020  1.331
 VPY  C19  C12  single  1.501  0.020  1.501
 VPY  C12  C10  single  1.502  0.020  1.502
 VPY  C03  C01  single  1.528  0.020  1.528
 VPY  C03  C06  single  1.499  0.020  1.499
 VPY  C02  C01  single  1.523  0.020  1.523
 VPY  C02  C04  single  1.523  0.020  1.523
 VPY  C10  C06  double  1.332  0.020  1.332
 VPY  C04  C07  single  1.522  0.020  1.522
 VPY  O01  H37  single  0.850  0.020  0.980
 VPY  O03  H38  single  0.850  0.020  0.980
 VPY  C01  H01  single  0.970  0.020  1.090
 VPY  C01  H02  single  0.970  0.020  1.090
 VPY  C02  H04  single  0.970  0.020  1.090
 VPY  C02  H03  single  0.970  0.020  1.090
 VPY  C03  H06  single  0.970  0.020  1.090
 VPY  C03  H05  single  0.970  0.020  1.090
 VPY  C04  H08  single  0.970  0.020  1.090
 VPY  C04  H07  single  0.970  0.020  1.090
 VPY  C05  H10  single  0.970  0.020  1.090
 VPY  C05  H09  single  0.970  0.020  1.090
 VPY  C06  H11  single  0.930  0.020  1.080
 VPY  C07  H14  single  0.970  0.020  1.090
 VPY  C07  H16  single  0.970  0.020  1.090
 VPY  C07  H15  single  0.970  0.020  1.090
 VPY  C08  H12  single  0.970  0.020  1.090
 VPY  C08  H13  single  0.970  0.020  1.090
 VPY  C09  H17  single  0.970  0.020  1.090
 VPY  C09  H18  single  0.970  0.020  1.090
 VPY  C10  H19  single  0.930  0.020  1.080
 VPY  C11  H20  single  0.930  0.020  1.080
 VPY  C12  H22  single  0.970  0.020  1.090
 VPY  C12  H23  single  0.970  0.020  1.090
 VPY  C13  H21  single  0.970  0.020  1.090
 VPY  C15  H25  single  0.970  0.020  1.090
 VPY  C15  H24  single  0.970  0.020  1.090
 VPY  C16  H26  single  0.930  0.020  1.080
 VPY  C17  H28  single  0.970  0.020  1.090
 VPY  C17  H27  single  0.970  0.020  1.090
 VPY  C18  H29  single  0.970  0.020  1.090
 VPY  C18  H30  single  0.970  0.020  1.090
 VPY  C19  H31  single  0.930  0.020  1.080
 VPY  C20  H33  single  0.970  0.020  1.090
 VPY  C20  H32  single  0.970  0.020  1.090
 VPY  C21  H34  single  0.930  0.020  1.080
 VPY  C22  H35  single  0.930  0.020  1.080
 VPY  C23  H36  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
 VPY  C15  S01  C14  102.18  3.000
 VPY  H37  O01  C13  107.94  3.000
 VPY  H38  O03  C18  108.66  3.000
 VPY  H02  C01  H01  106.06  3.000
 VPY  H02  C01  C03  109.32  3.000
 VPY  H01  C01  C03  108.54  3.000
 VPY  H02  C01  C02  109.25  3.000
 VPY  H01  C01  C02  109.25  3.000
 VPY  C03  C01  C02  114.11  3.000
 VPY  H03  C02  H04  105.71  3.000
 VPY  H03  C02  C04  109.29  3.000
 VPY  H04  C02  C04  109.40  3.000
 VPY  H03  C02  C01  109.38  3.000
 VPY  H04  C02  C01  109.97  3.000
 VPY  C04  C02  C01  112.84  3.000
 VPY  H05  C03  H06  105.74  3.000
 VPY  H05  C03  C06  110.81  3.000
 VPY  H06  C03  C06  109.05  3.000
 VPY  H05  C03  C01  109.47  3.000
 VPY  H06  C03  C01  108.35  3.000
 VPY  C06  C03  C01  113.13  3.000
 VPY  H07  C04  H08  106.01  3.000
 VPY  H07  C04  C07  109.65  3.000
 VPY  H08  C04  C07  109.47  3.000
 VPY  H07  C04  C02  109.26  3.000
 VPY  H08  C04  C02  109.08  3.000
 VPY  C07  C04  C02  113.12  3.000
 VPY  H09  C05  H10  106.83  3.000
 VPY  H09  C05  C09  109.81  3.000
 VPY  H10  C05  C09  109.66  3.000
 VPY  H09  C05  C08  110.13  3.000
 VPY  H10  C05  C08  108.59  3.000
 VPY  C09  C05  C08  111.69  3.000
 VPY  H11  C06  C10  117.23  3.000
 VPY  H11  C06  C03  115.33  3.000
 VPY  C10  C06  C03  127.42  3.000
 VPY  H15  C07  H16  107.43  3.000
 VPY  H15  C07  H14  107.47  3.000
 VPY  H16  C07  H14  107.67  3.000
 VPY  H15  C07  C04  111.16  3.000
 VPY  H16  C07  C04  111.27  3.000
 VPY  H14  C07  C04  111.63  3.000
 VPY  H13  C08  H12  106.21  3.000
 VPY  H13  C08  C11  111.41  3.000
 VPY  H12  C08  C11  108.96  3.000
 VPY  H13  C08  C05  108.79  3.000
 VPY  H12  C08  C05  108.07  3.000
 VPY  C11  C08  C05  113.12  3.000
 VPY  H18  C09  H17  107.48  3.000
 VPY  H18  C09  C14  107.95  3.000
 VPY  H17  C09  C14  110.45  3.000
 VPY  H18  C09  C05  109.74  3.000
 VPY  H17  C09  C05  109.95  3.000
 VPY  C14  C09  C05  111.17  3.000
 VPY  H19  C10  C12  115.02  3.000
 VPY  H19  C10  C06  117.79  3.000
 VPY  C12  C10  C06  127.17  3.000
 VPY  H20  C11  C16  117.47  3.000
 VPY  H20  C11  C08  115.10  3.000
 VPY  C16  C11  C08  127.42  3.000
 VPY  H23  C12  H22  105.75  3.000
 VPY  H23  C12  C19  108.16  3.000
 VPY  H22  C12  C19  111.61  3.000
 VPY  H23  C12  C10  107.82  3.000
 VPY  H22  C12  C10  111.34  3.000
 VPY  C19  C12  C10  111.84  3.000
 VPY  H21  C13  C18  108.10  3.000
 VPY  H21  C13  C15  108.86  3.000
 VPY  C18  C13  C15  109.35  3.000
 VPY  H21  C13  O01  110.94  3.000
 VPY  C18  C13  O01  111.68  3.000
 VPY  C15  C13  O01  107.87  3.000
 VPY  C09  C14  O02  124.23  3.000
 VPY  O02  C14  S01  123.33  3.000
 VPY  C09  C14  S01  112.42  3.000
 VPY  H24  C15  H25  107.56  3.000
 VPY  H24  C15  C13  110.35  3.000
 VPY  H25  C15  C13  110.74  3.000
 VPY  H24  C15  S01  105.30  3.000
 VPY  H25  C15  S01  108.44  3.000
 VPY  C13  C15  S01  114.12  3.000
 VPY  H26  C16  C17  114.99  3.000
 VPY  H26  C16  C11  117.84  3.000
 VPY  C17  C16  C11  127.16  3.000
 VPY  H27  C17  H28  106.09  3.000
 VPY  H27  C17  C21  110.76  3.000
 VPY  H28  C17  C21  108.65  3.000
 VPY  H27  C17  C16  109.56  3.000
 VPY  H28  C17  C16  110.51  3.000
 VPY  C21  C17  C16  111.15  3.000
 VPY  H30  C18  H29  107.33  3.000
 VPY  H30  C18  C13  109.03  3.000
 VPY  H29  C18  C13  109.01  3.000
 VPY  H30  C18  O03  111.79  3.000
 VPY  H29  C18  O03  111.71  3.000
 VPY  C13  C18  O03  107.91  3.000
 VPY  H31  C19  C22  117.20  3.000
 VPY  H31  C19  C12  114.84  3.000
 VPY  C22  C19  C12  127.95  3.000
 VPY  H32  C20  H33  106.31  3.000
 VPY  H32  C20  C23  108.63  3.000
 VPY  H33  C20  C23  111.55  3.000
 VPY  H32  C20  C22  108.37  3.000
 VPY  H33  C20  C22  111.34  3.000
 VPY  C23  C20  C22  110.47  3.000
 VPY  H34  C21  C23  117.50  3.000
 VPY  H34  C21  C17  114.80  3.000
 VPY  C23  C21  C17  127.69  3.000
 VPY  H35  C22  C20  114.84  3.000
 VPY  H35  C22  C19  117.39  3.000
 VPY  C20  C22  C19  127.78  3.000
 VPY  H36  C23  C21  117.43  3.000
 VPY  H36  C23  C20  114.99  3.000
 VPY  C21  C23  C20  127.54  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
 VPY  Var_01  C12  C10  C06  C03    -0.79   0.0  2
 VPY  Var_02  C17  C16  C11  C08    -1.21   0.0  2
 VPY  Var_03  C20  C22  C19  C12     0.72   0.0  2
 VPY  Var_04  C20  C23  C21  C17    -1.32   0.0  2
 VPY  Var_05  C05  C09  C14  S01   -89.64  30.0  3
 VPY  Var_06  C10  C06  C03  C01  -147.47  30.0  3
 VPY  Var_07  C07  C04  C02  C01  -179.60  30.0  3
 VPY  Var_08  C06  C03  C01  C02    61.33  30.0  1
 VPY  Var_09  C04  C02  C01  C03   173.87  30.0  1
 VPY  Var_10  C16  C11  C08  C05   106.88  30.0  1
 VPY  Var_11  C19  C12  C10  C06   133.63  30.0  2
 VPY  Var_12  C14  C09  C05  C08  -172.50  30.0  2
 VPY  Var_13  C11  C08  C05  C09   -63.66  30.0  3
 VPY  Var_14  C22  C19  C12  C10  -135.23  30.0  1
 VPY  Var_15  C21  C17  C16  C11  -118.95  30.0  3
 VPY  Var_16  C23  C21  C17  C16  -129.53  30.0  1
 VPY  Var_17  C23  C20  C22  C19   122.07  30.0  2
 VPY  Var_18  C22  C20  C23  C21  -114.82  30.0  3
 VPY  Var_19  H14  C07  C04  C02  -179.93  30.0  3
 VPY  Var_20  H25  C15  S01  C14    40.30  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
 VPY  chir_01  C13  C15  C18  O01  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
 VPY  plan-1  C08  0.020
 VPY  plan-1  C11  0.020
 VPY  plan-1  C16  0.020
 VPY  plan-1  C17  0.020
 VPY  plan-1  H20  0.020
 VPY  plan-1  H26  0.020
 VPY  plan-2  S01  0.020
 VPY  plan-2  O02  0.020
 VPY  plan-2  C09  0.020
 VPY  plan-2  C14  0.020
 VPY  plan-3  C17  0.020
 VPY  plan-3  C20  0.020
 VPY  plan-3  C21  0.020
 VPY  plan-3  C23  0.020
 VPY  plan-3  H34  0.020
 VPY  plan-3  H36  0.020
 VPY  plan-4  C12  0.020
 VPY  plan-4  C19  0.020
 VPY  plan-4  C20  0.020
 VPY  plan-4  C22  0.020
 VPY  plan-4  H31  0.020
 VPY  plan-4  H35  0.020
 VPY  plan-5  C03  0.020
 VPY  plan-5  C06  0.020
 VPY  plan-5  C10  0.020
 VPY  plan-5  C12  0.020
 VPY  plan-5  H11  0.020
 VPY  plan-5  H19  0.020

