# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 14:14:41 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: (2Z)-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
 GEY  GEY  '(2Z)-dodec-2-enoic acid  '  ligand  36  14  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GEY
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
 GEY  C1   C  C     0   0.511   5.2370   0.5088  -0.4499
 GEY  C2   C  C1    0  -0.390   4.7752  -0.8537  -0.1373
 GEY  C3   C  C1    0  -0.118   3.5879  -1.1876   0.3784
 GEY  C4   C  CH2   0  -0.502   2.4187  -0.3485   0.7627
 GEY  C5   C  CH2   0  -0.424   1.1430  -0.8240   0.0609
 GEY  C6   C  CH2   0  -0.414  -0.0966  -0.0808   0.5415
 GEY  C8   C  CH2   0  -0.412  -2.6193   0.1803   0.3433
 GEY  O2   O  O     0  -0.448   4.6317   1.5418  -0.2752
 GEY  O1   O  OH1   0  -0.604   6.4630   0.4809  -0.9726
 GEY  C7   C  CH2   0  -0.413  -1.3720  -0.5395  -0.1544
 GEY  C9   C  CH2   0  -0.412  -3.8963  -0.2787  -0.3498
 GEY  C10  C  CH2   0  -0.406  -5.1459   0.4273   0.1612
 GEY  C11  C  CH2   0  -0.419  -6.4256  -0.0406  -0.5210
 GEY  C12  C  CH3   0  -0.662  -7.6691   0.6639   0.0039
 GEY  H1   H  H     0   0.270   5.4804  -1.6481  -0.3494
 GEY  H2   H  H     0   0.263   3.4357  -2.2514   0.5414
 GEY  H4   H  HCH2  0   0.246   2.2792  -0.4615   1.8444
 GEY  H3   H  HCH2  0   0.256   2.5856   0.7079   0.5696
 GEY  H5   H  HCH2  0   0.225   1.2540  -0.6946  -1.0200
 GEY  H6   H  HCH2  0   0.220   1.0127  -1.8979   0.2303
 GEY  H7   H  HCH2  0   0.212  -0.2021  -0.2192   1.6231
 GEY  H8   H  HCH2  0   0.212   0.0367   0.9948   0.3839
 GEY  H9   H  HCH2  0   0.207  -2.7188   0.0268   1.4236
 GEY  H10  H  HCH2  0   0.207  -2.4978   1.2599   0.2015
 GEY  H11  H  HOH1  0   0.479   6.7567   1.3832  -1.1662
 GEY  H12  H  HCH2  0   0.209  -1.2717  -0.3882  -1.2347
 GEY  H13  H  HCH2  0   0.208  -1.4938  -1.6187  -0.0096
 GEY  H14  H  HCH2  0   0.207  -3.8028  -0.1154  -1.4292
 GEY  H15  H  HCH2  0   0.206  -4.0107  -1.3603  -0.2165
 GEY  H16  H  HCH2  0   0.205  -5.2342   0.2704   1.2422
 GEY  H17  H  HCH2  0   0.206  -5.0364   1.5087   0.0220
 GEY  H19  H  HCH2  0   0.210  -6.3406   0.1212  -1.6001
 GEY  H18  H  HCH2  0   0.210  -6.5317  -1.1215  -0.3855
 GEY  H20  H  HCH3  0   0.226  -8.5728   0.3065  -0.4912
 GEY  H21  H  HCH3  0   0.215  -7.7915   0.4993   1.0762
 GEY  H22  H  HCH3  0   0.215  -7.6089   1.7421  -0.1567

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
 GEY  O2   C1   double  1.210  0.020  1.210
 GEY  C1   C2   single  1.472  0.020  1.472
 GEY  C1   O1   single  1.333  0.020  1.333
 GEY  C2   C3   double  1.337  0.020  1.337
 GEY  C3   C4   single  1.490  0.020  1.490
 GEY  C4   C5   single  1.532  0.020  1.532
 GEY  C6   C5   single  1.523  0.020  1.523
 GEY  C6   C7   single  1.524  0.020  1.524
 GEY  C8   C7   single  1.524  0.020  1.524
 GEY  C8   C9   single  1.524  0.020  1.524
 GEY  C9   C10  single  1.523  0.020  1.523
 GEY  C10  C11  single  1.524  0.020  1.524
 GEY  C11  C12  single  1.523  0.020  1.523
 GEY  C2   H1   single  0.930  0.020  1.080
 GEY  C3   H2   single  0.930  0.020  1.080
 GEY  C4   H4   single  0.970  0.020  1.090
 GEY  C4   H3   single  0.970  0.020  1.090
 GEY  C5   H5   single  0.970  0.020  1.090
 GEY  C5   H6   single  0.970  0.020  1.090
 GEY  C6   H7   single  0.970  0.020  1.090
 GEY  C6   H8   single  0.970  0.020  1.090
 GEY  C8   H9   single  0.970  0.020  1.090
 GEY  C8   H10  single  0.970  0.020  1.090
 GEY  O1   H11  single  0.850  0.020  0.980
 GEY  C7   H12  single  0.970  0.020  1.090
 GEY  C7   H13  single  0.970  0.020  1.090
 GEY  C9   H14  single  0.970  0.020  1.090
 GEY  C9   H15  single  0.970  0.020  1.090
 GEY  C10  H16  single  0.970  0.020  1.090
 GEY  C10  H17  single  0.970  0.020  1.090
 GEY  C11  H19  single  0.970  0.020  1.090
 GEY  C11  H18  single  0.970  0.020  1.090
 GEY  C12  H20  single  0.970  0.020  1.090
 GEY  C12  H21  single  0.970  0.020  1.090
 GEY  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
 GEY  O1   C1   O2   122.31  3.000
 GEY  O1   C1   C2   110.63  3.000
 GEY  O2   C1   C2   127.05  3.000
 GEY  H1   C2   C3   118.07  3.000
 GEY  H1   C2   C1   115.66  3.000
 GEY  C3   C2   C1   126.27  3.000
 GEY  H2   C3   C4   113.75  3.000
 GEY  H2   C3   C2   115.25  3.000
 GEY  C4   C3   C2   130.99  3.000
 GEY  H3   C4   H4   107.15  3.000
 GEY  H3   C4   C5   110.39  3.000
 GEY  H4   C4   C5   108.31  3.000
 GEY  H3   C4   C3   112.40  3.000
 GEY  H4   C4   C3   107.23  3.000
 GEY  C5   C4   C3   111.14  3.000
 GEY  H6   C5   H5   106.31  3.000
 GEY  H6   C5   C6   109.44  3.000
 GEY  H5   C5   C6   109.66  3.000
 GEY  H6   C5   C4   109.44  3.000
 GEY  H5   C5   C4   109.35  3.000
 GEY  C6   C5   C4   112.45  3.000
 GEY  H8   C6   H7   106.12  3.000
 GEY  H8   C6   C7   109.38  3.000
 GEY  H7   C6   C7   109.41  3.000
 GEY  H8   C6   C5   109.55  3.000
 GEY  H7   C6   C5   109.16  3.000
 GEY  C7   C6   C5   112.98  3.000
 GEY  H10  C8   H9   106.00  3.000
 GEY  H10  C8   C9   109.32  3.000
 GEY  H9   C8   C9   109.28  3.000
 GEY  H10  C8   C7   109.42  3.000
 GEY  H9   C8   C7   109.28  3.000
 GEY  C9   C8   C7   113.28  3.000
 GEY  H11  O1   C1   109.75  3.000
 GEY  H13  C7   H12  106.05  3.000
 GEY  H13  C7   C8   109.34  3.000
 GEY  H12  C7   C8   109.38  3.000
 GEY  H13  C7   C6   109.22  3.000
 GEY  H12  C7   C6   109.40  3.000
 GEY  C8   C7   C6   113.20  3.000
 GEY  H15  C9   H14  106.01  3.000
 GEY  H15  C9   C10  109.32  3.000
 GEY  H14  C9   C10  109.35  3.000
 GEY  H15  C9   C8   109.24  3.000
 GEY  H14  C9   C8   109.37  3.000
 GEY  C10  C9   C8   113.28  3.000
 GEY  H17  C10  H16  105.94  3.000
 GEY  H17  C10  C11  109.27  3.000
 GEY  H16  C10  C11  109.27  3.000
 GEY  H17  C10  C9   109.43  3.000
 GEY  H16  C10  C9   109.31  3.000
 GEY  C11  C10  C9   113.36  3.000
 GEY  H18  C11  H19  105.99  3.000
 GEY  H18  C11  C12  109.58  3.000
 GEY  H19  C11  C12  109.57  3.000
 GEY  H18  C11  C10  109.22  3.000
 GEY  H19  C11  C10  109.32  3.000
 GEY  C12  C11  C10  112.93  3.000
 GEY  H22  C12  H21  107.43  3.000
 GEY  H22  C12  H20  107.62  3.000
 GEY  H21  C12  H20  107.67  3.000
 GEY  H22  C12  C11  111.17  3.000
 GEY  H21  C12  C11  111.12  3.000
 GEY  H20  C12  C11  111.63  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
 GEY  CONST_01  H11  O1   C1   C2    180.00   0.0  0
 GEY  Var_01    C4   C3   C2   C1      0.82   0.0  2
 GEY  Var_02    C5   C4   C3   C2    125.01  30.0  3
 GEY  Var_03    O2   C1   C2   C3      1.15  30.0  2
 GEY  Var_04    C6   C5   C4   C3    174.04  30.0  3
 GEY  Var_05    C7   C6   C5   C4    179.70  30.0  1
 GEY  Var_06    C8   C7   C6   C5    178.80  30.0  3
 GEY  Var_07    C9   C8   C7   C6   -179.90  30.0  1
 GEY  Var_08    C11  C10  C9   C8   -179.42  30.0  3
 GEY  Var_09    C10  C9   C8   C7    179.21  30.0  3
 GEY  Var_10    C12  C11  C10  C9    179.59  30.0  3
 GEY  Var_11    H20  C12  C11  C10  -179.43  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
 GEY  plan-1  C1   0.020
 GEY  plan-1  C2   0.020
 GEY  plan-1  O2   0.020
 GEY  plan-1  O1   0.020
 GEY  plan-1  H11  0.020
 GEY  plan-2  C1   0.020
 GEY  plan-2  C2   0.020
 GEY  plan-2  C3   0.020
 GEY  plan-2  C4   0.020
 GEY  plan-2  H1   0.020
 GEY  plan-2  H2   0.020

