# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 10:50:40 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: (2E)-dodec-2-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCC/C=C/C(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
 3X1  3X1  '(2E)-dodec-2-enoic acid  '  ligand  35  14  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3X1
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
 3X1  C1   C  C      0   0.386  -5.7721  -0.1964   0.2343
 3X1  C2   C  C1     0  -0.428  -4.4504   0.5342   0.2360
 3X1  C3   C  C1     0  -0.158  -3.4264   0.2280  -0.5572
 3X1  C4   C  CH2    0  -0.480  -2.1045   0.9232  -0.5693
 3X1  C5   C  CH2    0  -0.416  -0.9408  -0.0229  -0.2695
 3X1  C6   C  CH2    0  -0.413   0.4098   0.6816  -0.2945
 3X1  C8   C  CH2    0  -0.411   2.9311   0.4575  -0.0484
 3X1  O2   O  O      0  -0.609  -5.9123  -1.1513  -0.5573
 3X1  O1   O  OC    -1  -0.624  -6.6249   0.2271   1.0441
 3X1  C7   C  CH2    0  -0.412   1.5872  -0.2604  -0.0786
 3X1  C9   C  CH2    0  -0.412   4.1188  -0.4878   0.0820
 3X1  C10  C  CH2    0  -0.407   5.4577   0.2357   0.1556
 3X1  C11  C  CH2    0  -0.419   6.6519  -0.7079   0.2337
 3X1  C12  C  CH3    0  -0.662   7.9814   0.0290   0.3208
 3X1  H1   H  H      0   0.211  -4.3474   1.3596   0.9375
 3X1  H2   H  H      0   0.227  -3.5382  -0.6006  -1.2527
 3X1  H3   H  HCH2   0   0.227  -1.9395   1.3678  -1.5575
 3X1  H4   H  HCH2   0   0.225  -2.1067   1.7499   0.1476
 3X1  H5   H  HCH2   0   0.216  -1.0933  -0.4884   0.7095
 3X1  H6   H  HCH2   0   0.213  -0.9415  -0.8398  -0.9995
 3X1  H7   H  HCH2   0   0.208   0.5317   1.1965  -1.2540
 3X1  H8   H  HCH2   0   0.209   0.4222   1.4650   0.4716
 3X1  H9   H  HCH2   0   0.206   3.0445   1.0548  -0.9603
 3X1  H10  H  HCH2   0   0.207   2.9404   1.1719   0.7824
 3X1  H12  H  HCH2   0   0.207   1.4505  -0.8103   0.8592
 3X1  H13  H  HCH2   0   0.207   1.5961  -1.0155  -0.8727
 3X1  H14  H  HCH2   0   0.206   3.9943  -1.1104   0.9753
 3X1  H15  H  HCH2   0   0.206   4.1253  -1.1789  -0.7685
 3X1  H16  H  HCH2   0   0.205   5.5686   0.8857  -0.7200
 3X1  H17  H  HCH2   0   0.206   5.4639   0.9009   1.0266
 3X1  H18  H  HCH2   0   0.210   6.5384  -1.3645   1.1020
 3X1  H19  H  HCH2   0   0.210   6.6515  -1.3634  -0.6428
 3X1  H20  H  HCH3   0   0.225   8.8235  -0.6621   0.3726
 3X1  H21  H  HCH3   0   0.215   8.1334   0.6705  -0.5498
 3X1  H22  H  HCH3   0   0.215   8.0209   0.6651   1.2073

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
 3X1  C12  C11  single  1.523  0.020  1.523
 3X1  C11  C10  single  1.524  0.020  1.524
 3X1  C10  C9   single  1.524  0.020  1.524
 3X1  C9   C8   single  1.524  0.020  1.524
 3X1  C8   C7   single  1.524  0.020  1.524
 3X1  C7   C6   single  1.523  0.020  1.523
 3X1  C6   C5   single  1.524  0.020  1.524
 3X1  C5   C4   single  1.529  0.020  1.529
 3X1  C4   C3   single  1.494  0.020  1.494
 3X1  C2   C3   double  1.331  0.020  1.331
 3X1  C2   C1   single  1.510  0.020  1.510
 3X1  O2   C1   deloc   1.248  0.020  1.248
 3X1  C1   O1   deloc   1.250  0.020  1.250
 3X1  C2   H1   single  0.930  0.020  1.080
 3X1  C3   H2   single  0.930  0.020  1.080
 3X1  C4   H3   single  0.970  0.020  1.090
 3X1  C4   H4   single  0.970  0.020  1.090
 3X1  C5   H5   single  0.970  0.020  1.090
 3X1  C5   H6   single  0.970  0.020  1.090
 3X1  C6   H7   single  0.970  0.020  1.090
 3X1  C6   H8   single  0.970  0.020  1.090
 3X1  C8   H9   single  0.970  0.020  1.090
 3X1  C8   H10  single  0.970  0.020  1.090
 3X1  C7   H12  single  0.970  0.020  1.090
 3X1  C7   H13  single  0.970  0.020  1.090
 3X1  C9   H14  single  0.970  0.020  1.090
 3X1  C9   H15  single  0.970  0.020  1.090
 3X1  C10  H16  single  0.970  0.020  1.090
 3X1  C10  H17  single  0.970  0.020  1.090
 3X1  C11  H18  single  0.970  0.020  1.090
 3X1  C11  H19  single  0.970  0.020  1.090
 3X1  C12  H20  single  0.970  0.020  1.090
 3X1  C12  H21  single  0.970  0.020  1.090
 3X1  C12  H22  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
 3X1  O1   C1   O2   126.40  3.000
 3X1  O1   C1   C2   115.62  3.000
 3X1  O2   C1   C2   117.98  3.000
 3X1  H1   C2   C3   119.07  3.000
 3X1  H1   C2   C1   116.78  3.000
 3X1  C3   C2   C1   124.15  3.000
 3X1  H2   C3   C4   116.13  3.000
 3X1  H2   C3   C2   118.51  3.000
 3X1  C4   C3   C2   125.36  3.000
 3X1  H4   C4   H3   106.53  3.000
 3X1  H4   C4   C5   109.90  3.000
 3X1  H3   C4   C5   108.24  3.000
 3X1  H4   C4   C3   110.15  3.000
 3X1  H3   C4   C3   109.24  3.000
 3X1  C5   C4   C3   112.58  3.000
 3X1  H6   C5   H5   106.18  3.000
 3X1  H6   C5   C6   109.55  3.000
 3X1  H5   C5   C6   109.56  3.000
 3X1  H6   C5   C4   109.28  3.000
 3X1  H5   C5   C4   109.41  3.000
 3X1  C6   C5   C4   112.66  3.000
 3X1  H8   C6   H7   105.97  3.000
 3X1  H8   C6   C7   109.53  3.000
 3X1  H7   C6   C7   109.19  3.000
 3X1  H8   C6   C5   109.22  3.000
 3X1  H7   C6   C5   109.28  3.000
 3X1  C7   C6   C5   113.38  3.000
 3X1  H10  C8   H9   105.94  3.000
 3X1  H10  C8   C9   109.45  3.000
 3X1  H9   C8   C9   109.19  3.000
 3X1  H10  C8   C7   109.25  3.000
 3X1  H9   C8   C7   109.36  3.000
 3X1  C9   C8   C7   113.39  3.000
 3X1  H13  C7   H12  105.99  3.000
 3X1  H13  C7   C8   109.38  3.000
 3X1  H12  C7   C8   109.24  3.000
 3X1  H13  C7   C6   109.25  3.000
 3X1  H12  C7   C6   109.59  3.000
 3X1  C8   C7   C6   113.15  3.000
 3X1  H15  C9   H14  105.97  3.000
 3X1  H15  C9   C10  109.38  3.000
 3X1  H14  C9   C10  109.28  3.000
 3X1  H15  C9   C8   109.24  3.000
 3X1  H14  C9   C8   109.49  3.000
 3X1  C10  C9   C8   113.24  3.000
 3X1  H17  C10  H16  105.92  3.000
 3X1  H17  C10  C11  109.31  3.000
 3X1  H16  C10  C11  109.20  3.000
 3X1  H17  C10  C9   109.37  3.000
 3X1  H16  C10  C9   109.38  3.000
 3X1  C11  C10  C9   113.39  3.000
 3X1  H19  C11  H18  106.02  3.000
 3X1  H19  C11  C12  109.64  3.000
 3X1  H18  C11  C12  109.61  3.000
 3X1  H19  C11  C10  109.24  3.000
 3X1  H18  C11  C10  109.32  3.000
 3X1  C12  C11  C10  112.80  3.000
 3X1  H22  C12  H21  107.46  3.000
 3X1  H22  C12  H20  107.62  3.000
 3X1  H21  C12  H20  107.62  3.000
 3X1  H22  C12  C11  111.10  3.000
 3X1  H21  C12  C11  111.12  3.000
 3X1  H20  C12  C11  111.73  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
 3X1  Var_01  C4   C3   C2   C1   -179.40   0.0  2
 3X1  Var_02  C5   C4   C3   C2    121.08  30.0  2
 3X1  Var_03  C6   C5   C4   C3    179.46  30.0  2
 3X1  Var_04  O2   C1   C2   C3      0.28  30.0  2
 3X1  Var_05  C7   C6   C5   C4   -176.63  30.0  1
 3X1  Var_06  C8   C7   C6   C5   -177.68  30.0  1
 3X1  Var_07  C9   C8   C7   C6   -176.48  30.0  1
 3X1  Var_08  C11  C10  C9   C8   -177.85  30.0  1
 3X1  Var_09  C10  C9   C8   C7   -178.20  30.0  1
 3X1  Var_10  C12  C11  C10  C9   -179.42  30.0  1
 3X1  Var_11  H20  C12  C11  C10  -179.82  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
 3X1  plan-1  C1  0.020
 3X1  plan-1  C2  0.020
 3X1  plan-1  O2  0.020
 3X1  plan-1  O1  0.020
 3X1  plan-2  C1  0.020
 3X1  plan-2  C2  0.020
 3X1  plan-2  C3  0.020
 3X1  plan-2  C4  0.020
 3X1  plan-2  H1  0.020
 3X1  plan-2  H2  0.020

