# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 18:47:06 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 2,5-dihydroxy-3-undecylcyclohexa-2,5-diene-1,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCC1=C(O)C(=O)C=C(O)C1=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
 EMJ  EMJ  2,5-dihydroxy-3-undecylcyclohexa-2,5-diene-1,4-dione  ligand  47  21  .  2021-08-08  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EMJ
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
 EMJ  C2   C  CR6   0   0.340  -4.0310  -1.2037  -0.4261
 EMJ  C3   C  CR6   0  -0.148  -3.4355   0.1180  -0.5692
 EMJ  C4   C  CR6   0   0.267  -4.0936   1.1763  -0.0573
 EMJ  C5   C  CR6   0   0.346  -5.4243   1.0536   0.6273
 EMJ  C6   C  CR16  0  -0.509  -6.0233  -0.2511   0.7426
 EMJ  C7   C  CR6   0   0.310  -5.3813  -1.3228   0.2439
 EMJ  O8   O  O     0  -0.418  -5.9329   2.0767   1.0519
 EMJ  O9   O  O     0  -0.372  -3.4946  -2.2171  -0.8211
 EMJ  O10  O  OH1   0  -0.583  -3.6104   2.4047  -0.1211
 EMJ  O11  O  OH1   0  -0.568  -5.8175  -2.5645   0.2733
 EMJ  C12  C  CH2   0  -0.475  -2.0959   0.2398  -1.2282
 EMJ  C13  C  CH2   0  -0.413  -0.9390   0.1618  -0.2285
 EMJ  C14  C  CH2   0  -0.418   0.4205   0.2123  -0.9130
 EMJ  C15  C  CH2   0  -0.413   1.5857   0.1738   0.0678
 EMJ  C16  C  CH2   0  -0.412   2.9451   0.1481  -0.6198
 EMJ  C17  C  CH2   0  -0.412   4.1160   0.1209   0.3549
 EMJ  C18  C  CH2   0  -0.411   5.4700   0.0425  -0.3391
 EMJ  C19  C  CH2   0  -0.412   6.6469   0.0165   0.6285
 EMJ  C20  C  CH2   0  -0.406   7.9951  -0.0904  -0.0725
 EMJ  C21  C  CH2   0  -0.419   9.1791  -0.1063   0.8869
 EMJ  C22  C  CH3   0  -0.662  10.5161  -0.2341   0.1698
 EMJ  H1   H  HCR6  0   0.303  -6.9867  -0.3312   1.2316
 EMJ  H2   H  HOH1  0   0.480  -4.2463   3.0125   0.2935
 EMJ  H3   H  HOH1  0   0.494  -6.6811  -2.6186   0.7053
 EMJ  H4   H  HCH2  0   0.245  -1.9820  -0.5515  -1.9711
 EMJ  H5   H  HCH2  0   0.223  -1.0235   0.9835   0.4891
 EMJ  H6   H  HCH2  0   0.212   0.5048  -0.6301  -1.6085
 EMJ  H7   H  HCH2  0   0.212   0.4895   1.1185  -1.5251
 EMJ  H8   H  HCH2  0   0.209   1.5279   1.0412   0.7346
 EMJ  H9   H  HCH2  0   0.208   1.4901  -0.7086   0.7107
 EMJ  H10  H  HCH2  0   0.207   3.0008  -0.7286  -1.2751
 EMJ  H11  H  HCH2  0   0.207   3.0391   1.0206  -1.2760
 EMJ  H12  H  HCH2  0   0.207   4.0810   1.0128   0.9905
 EMJ  H13  H  HCH2  0   0.206   4.0055  -0.7352   1.0300
 EMJ  H14  H  HCH2  0   0.206   5.5012  -0.8534  -0.9695
 EMJ  H15  H  HCH2  0   0.206   5.5801   0.8938  -1.0204
 EMJ  H16  H  HCH2  0   0.206   6.6279   0.9197   1.2490
 EMJ  H17  H  HCH2  0   0.206   6.5297  -0.8264   1.3188
 EMJ  H18  H  HCH2  0   0.205   8.0141  -1.0002  -0.6837
 EMJ  H19  H  HCH2  0   0.206   8.1090   0.7448  -0.7728
 EMJ  H20  H  HCH2  0   0.210   9.1693   0.8076   1.4891
 EMJ  H21  H  HCH2  0   0.210   9.0610  -0.9347   1.5922
 EMJ  H22  H  HCH3  0   0.225  11.3520  -0.2370   0.8704
 EMJ  H23  H  HCH3  0   0.215  10.5651  -1.1600  -0.4069
 EMJ  H24  H  HCH3  0   0.215  10.6707   0.5929  -0.5264
 EMJ  H25  H  HCH2  0   0.245  -2.0377   1.1835  -1.7750
 EMJ  H26  H  HCH2  0   0.222  -1.0188  -0.7632   0.3511

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
 EMJ  O8   C5   double  1.219  0.020  1.219
 EMJ  C5   C6   single  1.440  0.020  1.440
 EMJ  C5   C4   single  1.501  0.020  1.501
 EMJ  O10  C4   single  1.322  0.020  1.322
 EMJ  C6   C7   double  1.345  0.020  1.345
 EMJ  C4   C3   double  1.347  0.020  1.347
 EMJ  C7   O11  single  1.316  0.020  1.316
 EMJ  C7   C2   single  1.512  0.020  1.512
 EMJ  C3   C2   single  1.457  0.020  1.457
 EMJ  C3   C12  single  1.498  0.020  1.498
 EMJ  C2   O9   double  1.213  0.020  1.213
 EMJ  C12  C13  single  1.531  0.020  1.531
 EMJ  C13  C14  single  1.523  0.020  1.523
 EMJ  C14  C15  single  1.524  0.020  1.524
 EMJ  C15  C16  single  1.524  0.020  1.524
 EMJ  C16  C17  single  1.524  0.020  1.524
 EMJ  C17  C18  single  1.523  0.020  1.523
 EMJ  C18  C19  single  1.524  0.020  1.524
 EMJ  C19  C20  single  1.523  0.020  1.523
 EMJ  C20  C21  single  1.524  0.020  1.524
 EMJ  C21  C22  single  1.523  0.020  1.523
 EMJ  C6   H1   single  0.930  0.020  1.080
 EMJ  O10  H2   single  0.850  0.020  0.980
 EMJ  O11  H3   single  0.850  0.020  0.980
 EMJ  C12  H4   single  0.970  0.020  1.090
 EMJ  C13  H5   single  0.970  0.020  1.090
 EMJ  C14  H6   single  0.970  0.020  1.090
 EMJ  C14  H7   single  0.970  0.020  1.090
 EMJ  C15  H8   single  0.970  0.020  1.090
 EMJ  C15  H9   single  0.970  0.020  1.090
 EMJ  C16  H10  single  0.970  0.020  1.090
 EMJ  C16  H11  single  0.970  0.020  1.090
 EMJ  C17  H12  single  0.970  0.020  1.090
 EMJ  C17  H13  single  0.970  0.020  1.090
 EMJ  C18  H14  single  0.970  0.020  1.090
 EMJ  C18  H15  single  0.970  0.020  1.090
 EMJ  C19  H16  single  0.970  0.020  1.090
 EMJ  C19  H17  single  0.970  0.020  1.090
 EMJ  C20  H18  single  0.970  0.020  1.090
 EMJ  C20  H19  single  0.970  0.020  1.090
 EMJ  C21  H20  single  0.970  0.020  1.090
 EMJ  C21  H21  single  0.970  0.020  1.090
 EMJ  C22  H22  single  0.970  0.020  1.090
 EMJ  C22  H23  single  0.970  0.020  1.090
 EMJ  C22  H24  single  0.970  0.020  1.090
 EMJ  C12  H25  single  0.970  0.020  1.090
 EMJ  C13  H26  single  0.970  0.020  1.090

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
 EMJ  O9   C2   C7   118.26  3.000
 EMJ  O9   C2   C3   123.05  3.000
 EMJ  C7   C2   C3   118.69  3.000
 EMJ  C12  C3   C4   122.69  3.000
 EMJ  C12  C3   C2   118.85  3.000
 EMJ  C4   C3   C2   118.40  3.000
 EMJ  O10  C4   C5   114.96  3.000
 EMJ  O10  C4   C3   122.22  3.000
 EMJ  C5   C4   C3   122.82  3.000
 EMJ  O8   C5   C6   123.98  3.000
 EMJ  C6   C5   C4   118.63  3.000
 EMJ  O8   C5   C4   117.39  3.000
 EMJ  H1   C6   C7   122.20  3.000
 EMJ  H1   C6   C5   118.22  3.000
 EMJ  C7   C6   C5   119.58  3.000
 EMJ  O11  C7   C6   125.81  3.000
 EMJ  O11  C7   C2   112.34  3.000
 EMJ  C6   C7   C2   121.85  3.000
 EMJ  H2   O10  C4   108.74  3.000
 EMJ  H3   O11  C7   111.02  3.000
 EMJ  H25  C12  H4   106.26  3.000
 EMJ  H25  C12  C13  109.31  3.000
 EMJ  H4   C12  C13  109.18  3.000
 EMJ  H25  C12  C3   109.77  3.000
 EMJ  H4   C12  C3   109.51  3.000
 EMJ  C13  C12  C3   112.61  3.000
 EMJ  H26  C13  H5   106.36  3.000
 EMJ  H26  C13  C14  109.33  3.000
 EMJ  H5   C13  C14  109.80  3.000
 EMJ  H26  C13  C12  109.50  3.000
 EMJ  H5   C13  C12  109.36  3.000
 EMJ  C14  C13  C12  112.30  3.000
 EMJ  H7   C14  H6   106.05  3.000
 EMJ  H7   C14  C15  109.41  3.000
 EMJ  H6   C14  C15  109.29  3.000
 EMJ  H7   C14  C13  109.56  3.000
 EMJ  H6   C14  C13  109.18  3.000
 EMJ  C15  C14  C13  113.11  3.000
 EMJ  H9   C15  H8   106.01  3.000
 EMJ  H9   C15  C16  109.21  3.000
 EMJ  H8   C15  C16  109.58  3.000
 EMJ  H9   C15  C14  109.34  3.000
 EMJ  H8   C15  C14  109.35  3.000
 EMJ  C16  C15  C14  113.09  3.000
 EMJ  H11  C16  H10  105.94  3.000
 EMJ  H11  C16  C17  109.34  3.000
 EMJ  H10  C16  C17  109.21  3.000
 EMJ  H11  C16  C15  109.48  3.000
 EMJ  H10  C16  C15  109.19  3.000
 EMJ  C17  C16  C15  113.40  3.000
 EMJ  H13  C17  H12  105.98  3.000
 EMJ  H13  C17  C18  109.27  3.000
 EMJ  H12  C17  C18  109.54  3.000
 EMJ  H13  C17  C16  109.30  3.000
 EMJ  H12  C17  C16  109.39  3.000
 EMJ  C18  C17  C16  113.11  3.000
 EMJ  H15  C18  H14  105.93  3.000
 EMJ  H15  C18  C19  109.30  3.000
 EMJ  H14  C18  C19  109.23  3.000
 EMJ  H15  C18  C17  109.42  3.000
 EMJ  H14  C18  C17  109.23  3.000
 EMJ  C19  C18  C17  113.46  3.000
 EMJ  H17  C19  H16  105.99  3.000
 EMJ  H17  C19  C20  109.30  3.000
 EMJ  H16  C19  C20  109.50  3.000
 EMJ  H17  C19  C18  109.30  3.000
 EMJ  H16  C19  C18  109.39  3.000
 EMJ  C20  C19  C18  113.11  3.000
 EMJ  H19  C20  H18  105.93  3.000
 EMJ  H19  C20  C21  109.24  3.000
 EMJ  H18  C20  C21  109.20  3.000
 EMJ  H19  C20  C19  109.42  3.000
 EMJ  H18  C20  C19  109.28  3.000
 EMJ  C21  C20  C19  113.49  3.000
 EMJ  H21  C21  H20  106.05  3.000
 EMJ  H21  C21  C22  109.56  3.000
 EMJ  H20  C21  C22  109.69  3.000
 EMJ  H21  C21  C20  109.26  3.000
 EMJ  H20  C21  C20  109.31  3.000
 EMJ  C22  C21  C20  112.74  3.000
 EMJ  H24  C22  H23  107.41  3.000
 EMJ  H24  C22  H22  107.64  3.000
 EMJ  H23  C22  H22  107.61  3.000
 EMJ  H24  C22  C21  111.16  3.000
 EMJ  H23  C22  C21  111.05  3.000
 EMJ  H22  C22  C21  111.75  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
 EMJ  Var_01  C13  C12  C3   C2   -90.92  30.0  3
 EMJ  Var_02  C14  C13  C12  C3   176.97  30.0  3
 EMJ  Var_03  C15  C14  C13  C12  178.44  30.0  3
 EMJ  Var_04  C16  C15  C14  C13  176.88  30.0  3
 EMJ  Var_05  C17  C16  C15  C14  179.53  30.0  3
 EMJ  Var_06  C18  C17  C16  C15  177.84  30.0  3
 EMJ  Var_07  C19  C18  C17  C16  179.93  30.0  3
 EMJ  Var_08  C20  C19  C18  C17  178.83  30.0  3
 EMJ  Var_09  C21  C20  C19  C18  179.55  30.0  3
 EMJ  Var_10  C22  C21  C20  C19  179.16  30.0  3
 EMJ  Var_11  H22  C22  C21  C20  179.61  30.0  3

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
 EMJ  plan-1  C2   0.020
 EMJ  plan-1  C3   0.020
 EMJ  plan-1  C4   0.020
 EMJ  plan-1  C5   0.020
 EMJ  plan-1  C6   0.020
 EMJ  plan-1  C7   0.020
 EMJ  plan-1  O8   0.020
 EMJ  plan-1  O9   0.020
 EMJ  plan-1  O10  0.020
 EMJ  plan-1  O11  0.020
 EMJ  plan-1  C12  0.020
 EMJ  plan-1  H1   0.020

