# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 20:58:07 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 2-[(~{E})-[(~{E})-2-oxidanylidenehexadec-5-enylidene]amino]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCC\C=C\CCC(=O)C=NCC(O)=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
 T65  T65  '2-[(~{E})-[(~{E})-2-oxidanylidenehexadec-5-enylidene]amino]ethanoic acid'  ligand  52  22  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_T65
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
 T65  O2   O  OC    -1  -0.614  -8.9622  -3.0671   0.8382
 T65  C17  C  C      0   0.409  -8.2842  -2.0341   0.6920
 T65  O1   O  O      0  -0.594  -8.4296  -0.9380   1.2535
 T65  C16  C  CH2    0  -0.469  -7.0892  -2.1809  -0.2925
 T65  N    N  N      0  -0.270  -6.5034  -0.9145  -0.6259
 T65  C15  C  C1     0  -0.127  -5.3724  -0.6378  -0.1468
 T65  C14  C  C      0   0.356  -4.7273   0.6838  -0.4438
 T65  O    O  O      0  -0.388  -5.3032   1.5469  -1.0641
 T65  C13  C  CH2    0  -0.581  -3.3287   0.8272   0.0800
 T65  C12  C  CH2    0  -0.483  -2.6721   2.1726  -0.1978
 T65  C11  C  C1     0  -0.216  -1.2959   2.2354   0.3860
 T65  C10  C  C1     0  -0.207  -0.1814   2.4637  -0.3023
 T65  C9   C  CH2    0  -0.480   1.1918   2.5113   0.2895
 T65  C8   C  CH2    0  -0.415   2.1562   1.5247  -0.3698
 T65  C7   C  CH2    0  -0.414   3.5177   1.4889   0.3125
 T65  C    C  CH2    0  -0.412   4.5163   0.5713  -0.3820
 T65  C1   C  CH2    0  -0.412   5.8317   0.4349   0.3743
 T65  C2   C  CH2    0  -0.412   6.8531  -0.4400  -0.3415
 T65  C3   C  CH2    0  -0.412   8.1389  -0.6338   0.4527
 T65  C4   C  CH2    0  -0.406   9.1753  -1.4816  -0.2734
 T65  C5   C  CH2    0  -0.419  10.4498  -1.6999   0.5334
 T65  C6   C  CH3    0  -0.663  11.4806  -2.5392  -0.2086
 T65  H2   H  HCH2   0   0.218  -6.3661  -2.8744   0.1614
 T65  H3   H  HCH2   0   0.246  -7.4544  -2.6467  -1.2109
 T65  H4   H  H      0   0.231  -4.8052  -1.3296   0.4865
 T65  H5   H  HCH2   0   0.276  -3.3515   0.6181   1.1564
 T65  H6   H  HCH2   0   0.281  -2.7338   0.0098  -0.3460
 T65  H7   H  HCH2   0   0.242  -2.6306   2.3564  -1.2737
 T65  H8   H  HCH2   0   0.241  -3.2901   2.9655   0.2346
 T65  H9   H  H      0   0.230  -1.2244   2.0750   1.4607
 T65  H10  H  H      0   0.228  -0.2507   2.6210  -1.3777
 T65  H11  H  HCH2   0   0.226   1.6019   3.5220   0.1840
 T65  H12  H  HCH2   0   0.225   1.1335   2.3120   1.3639
 T65  H13  H  HCH2   0   0.215   1.7177   0.5217  -0.3558
 T65  H14  H  HCH2   0   0.212   2.2785   1.7894  -1.4255
 T65  H15  H  HCH2   0   0.209   3.9304   2.5026   0.3628
 T65  H16  H  HCH2   0   0.208   3.3868   1.1646   1.3508
 T65  H17  H  HCH2   0   0.207   4.0704  -0.4214  -0.5101
 T65  H18  H  HCH2   0   0.207   4.7106   0.9465  -1.3929
 T65  H19  H  HCH2   0   0.207   6.2627   1.4281   0.5442
 T65  H20  H  HCH2   0   0.206   5.6320   0.0192   1.3683
 T65  H21  H  HCH2   0   0.206   6.4087  -1.4188  -0.5541
 T65  H22  H  HCH2   0   0.206   7.0887   0.0022  -1.3160
 T65  H23  H  HCH2   0   0.206   8.5725   0.3444   0.6900
 T65  H24  H  HCH2   0   0.206   7.9008  -1.0989   1.4159
 T65  H25  H  HCH2   0   0.205   8.7372  -2.4536  -0.5277
 T65  H26  H  HCH2   0   0.206   9.4277  -1.0060  -1.2278
 T65  H27  H  HCH2   0   0.210  10.8842  -0.7293   0.7929
 T65  H28  H  HCH2   0   0.210  10.1973  -2.1817   1.4833
 T65  H29  H  HCH3   0   0.216  11.0830  -3.5267  -0.4503
 T65  H30  H  HCH3   0   0.216  11.7690  -2.0637  -1.1479
 T65  H31  H  HCH3   0   0.226  12.3863  -2.6821   0.3817

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
 T65  C2   C3   single  1.524  0.020  1.524
 T65  C2   C1   single  1.524  0.020  1.524
 T65  C5   C4   single  1.524  0.020  1.524
 T65  C5   C6   single  1.522  0.020  1.522
 T65  C7   C    single  1.524  0.020  1.524
 T65  C7   C8   single  1.523  0.020  1.523
 T65  C3   C4   single  1.523  0.020  1.523
 T65  C    C1   single  1.523  0.020  1.523
 T65  C8   C9   single  1.529  0.020  1.529
 T65  C9   C10  single  1.496  0.020  1.496
 T65  C10  C11  double  1.330  0.020  1.330
 T65  C11  C12  single  1.496  0.020  1.496
 T65  C12  C13  single  1.523  0.020  1.523
 T65  C13  C14  single  1.500  0.020  1.500
 T65  C14  C15  single  1.500  0.020  1.500
 T65  C14  O    double  1.209  0.020  1.209
 T65  C15  N    double  1.259  0.020  1.259
 T65  N    C16  single  1.435  0.020  1.435
 T65  C16  C17  single  1.555  0.020  1.555
 T65  C17  O1   deloc   1.240  0.020  1.240
 T65  C17  O2   deloc   1.244  0.020  1.244
 T65  C16  H2   single  0.970  0.020  1.090
 T65  C16  H3   single  0.970  0.020  1.090
 T65  C15  H4   single  0.930  0.020  1.080
 T65  C13  H5   single  0.970  0.020  1.090
 T65  C13  H6   single  0.970  0.020  1.090
 T65  C12  H7   single  0.970  0.020  1.090
 T65  C12  H8   single  0.970  0.020  1.090
 T65  C11  H9   single  0.930  0.020  1.080
 T65  C10  H10  single  0.930  0.020  1.080
 T65  C9   H11  single  0.970  0.020  1.090
 T65  C9   H12  single  0.970  0.020  1.090
 T65  C8   H13  single  0.970  0.020  1.090
 T65  C8   H14  single  0.970  0.020  1.090
 T65  C7   H15  single  0.970  0.020  1.090
 T65  C7   H16  single  0.970  0.020  1.090
 T65  C    H17  single  0.970  0.020  1.090
 T65  C    H18  single  0.970  0.020  1.090
 T65  C1   H19  single  0.970  0.020  1.090
 T65  C1   H20  single  0.970  0.020  1.090
 T65  C2   H21  single  0.970  0.020  1.090
 T65  C2   H22  single  0.970  0.020  1.090
 T65  C3   H23  single  0.970  0.020  1.090
 T65  C3   H24  single  0.970  0.020  1.090
 T65  C4   H25  single  0.970  0.020  1.090
 T65  C4   H26  single  0.970  0.020  1.090
 T65  C5   H27  single  0.970  0.020  1.090
 T65  C5   H28  single  0.970  0.020  1.090
 T65  C6   H29  single  0.970  0.020  1.090
 T65  C6   H30  single  0.970  0.020  1.090
 T65  C6   H31  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
 T65  C16  C17  O1   117.40  3.000
 T65  O1   C17  O2   128.08  3.000
 T65  C16  C17  O2   114.50  3.000
 T65  H3   C16  H2   107.32  3.000
 T65  H3   C16  N    108.51  3.000
 T65  H2   C16  N    112.58  3.000
 T65  H3   C16  C17  108.39  3.000
 T65  H2   C16  C17  107.66  3.000
 T65  N    C16  C17  112.19  3.000
 T65  C15  N    C16  118.19  3.000
 T65  H4   C15  C14  116.61  3.000
 T65  H4   C15  N    123.09  3.000
 T65  C14  C15  N    120.30  3.000
 T65  C13  C14  O    123.71  3.000
 T65  O    C14  C15  121.71  3.000
 T65  C13  C14  C15  114.58  3.000
 T65  H6   C13  H5   104.49  3.000
 T65  H6   C13  C12  110.71  3.000
 T65  H5   C13  C12  110.88  3.000
 T65  H6   C13  C14  107.38  3.000
 T65  H5   C13  C14  107.76  3.000
 T65  C12  C13  C14  115.01  3.000
 T65  H8   C12  H7   106.78  3.000
 T65  H8   C12  C11  109.56  3.000
 T65  H7   C12  C11  110.02  3.000
 T65  H8   C12  C13  108.94  3.000
 T65  H7   C12  C13  110.17  3.000
 T65  C11  C12  C13  111.26  3.000
 T65  H9   C11  C10  118.76  3.000
 T65  H9   C11  C12  116.06  3.000
 T65  C10  C11  C12  125.18  3.000
 T65  H10  C10  C9   116.39  3.000
 T65  H10  C10  C11  118.85  3.000
 T65  C9   C10  C11  124.75  3.000
 T65  H12  C9   H11  106.41  3.000
 T65  H12  C9   C8   109.84  3.000
 T65  H11  C9   C8   108.51  3.000
 T65  H12  C9   C10  109.50  3.000
 T65  H11  C9   C10  109.55  3.000
 T65  C8   C9   C10  112.82  3.000
 T65  H14  C8   H13  106.17  3.000
 T65  H14  C8   C7   109.73  3.000
 T65  H13  C8   C7   109.32  3.000
 T65  H14  C8   C9   109.27  3.000
 T65  H13  C8   C9   109.45  3.000
 T65  C7   C8   C9   112.69  3.000
 T65  H16  C7   H15  105.98  3.000
 T65  H16  C7   C    109.39  3.000
 T65  H15  C7   C    109.34  3.000
 T65  H16  C7   C8   108.95  3.000
 T65  H15  C7   C8   109.60  3.000
 T65  C    C7   C8   113.32  3.000
 T65  H18  C    H17  105.94  3.000
 T65  H18  C    C1   109.61  3.000
 T65  H17  C    C1   109.16  3.000
 T65  H18  C    C7   109.30  3.000
 T65  H17  C    C7   109.40  3.000
 T65  C1   C    C7   113.18  3.000
 T65  H20  C1   H19  105.95  3.000
 T65  H20  C1   C2   109.30  3.000
 T65  H19  C1   C2   109.24  3.000
 T65  H20  C1   C    109.08  3.000
 T65  H19  C1   C    109.60  3.000
 T65  C2   C1   C    113.40  3.000
 T65  H22  C2   H21  105.97  3.000
 T65  H22  C2   C3   109.48  3.000
 T65  H21  C2   C3   109.26  3.000
 T65  H22  C2   C1   109.29  3.000
 T65  H21  C2   C1   109.40  3.000
 T65  C3   C2   C1   113.20  3.000
 T65  H24  C3   H23  105.93  3.000
 T65  H24  C3   C4   109.30  3.000
 T65  H23  C3   C4   109.32  3.000
 T65  H24  C3   C2   109.19  3.000
 T65  H23  C3   C2   109.46  3.000
 T65  C4   C3   C2   113.36  3.000
 T65  H26  C4   H25  105.95  3.000
 T65  H26  C4   C5   109.31  3.000
 T65  H25  C4   C5   109.27  3.000
 T65  H26  C4   C3   109.29  3.000
 T65  H25  C4   C3   109.41  3.000
 T65  C5   C4   C3   113.35  3.000
 T65  H28  C5   H27  106.03  3.000
 T65  H28  C5   C6   109.66  3.000
 T65  H27  C5   C6   109.61  3.000
 T65  H28  C5   C4   109.24  3.000
 T65  H27  C5   C4   109.29  3.000
 T65  C6   C5   C4   112.78  3.000
 T65  H31  C6   H30  107.66  3.000
 T65  H31  C6   H29  107.69  3.000
 T65  H30  C6   H29  107.45  3.000
 T65  H31  C6   C5   111.76  3.000
 T65  H30  C6   C5   110.99  3.000
 T65  H29  C6   C5   111.10  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
 T65  Var_01  C14  C15  N    C16  -178.86   0.0  2
 T65  Var_02  C9   C10  C11  C12  -179.37   0.0  2
 T65  Var_03  N    C16  C17  O2    168.65  30.0  2
 T65  Var_04  C13  C14  C15  N    -174.36  30.0  1
 T65  Var_05  C12  C13  C14  C15  -179.12  30.0  2
 T65  Var_06  C11  C12  C13  C14   178.71  30.0  2
 T65  Var_07  C10  C11  C12  C13   121.56  30.0  1
 T65  Var_08  C8   C9   C10  C11   123.68  30.0  1
 T65  Var_09  C7   C8   C9   C10  -175.04  30.0  2
 T65  Var_10  C    C7   C8   C9   -176.62  30.0  2
 T65  Var_11  C1   C    C7   C8   -174.55  30.0  3
 T65  Var_12  C2   C1   C    C7   -177.85  30.0  3
 T65  Var_13  C3   C2   C1   C    -176.94  30.0  1
 T65  Var_14  C4   C3   C2   C1   -178.68  30.0  3
 T65  Var_15  C5   C4   C3   C2   -178.78  30.0  3
 T65  Var_16  C6   C5   C4   C3   -179.54  30.0  1
 T65  Var_17  H29  C6   C5   C4    -59.88  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
 T65  plan-1  C15  0.020
 T65  plan-1  C14  0.020
 T65  plan-1  O    0.020
 T65  plan-1  C13  0.020
 T65  plan-2  O2   0.020
 T65  plan-2  C17  0.020
 T65  plan-2  O1   0.020
 T65  plan-2  C16  0.020
 T65  plan-3  C12  0.020
 T65  plan-3  C11  0.020
 T65  plan-3  C10  0.020
 T65  plan-3  C9   0.020
 T65  plan-3  H9   0.020
 T65  plan-3  H10  0.020
 T65  plan-4  C16  0.020
 T65  plan-4  N    0.020
 T65  plan-4  C15  0.020
 T65  plan-4  C14  0.020
 T65  plan-4  H4   0.020

