# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 15:00:34 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: (~{E})-13-methyltetradec-2-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)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
 9GE  9GE  '(~{E})-13-methyltetradec-2-enoic acid'  ligand  44  17  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9GE
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
 9GE  C    C  C      0   0.386   7.4269  -0.5695  -0.1277
 9GE  O    O  O      0  -0.609   7.6712  -0.4663   1.0921
 9GE  CA   C  C1     0  -0.425   6.1063  -0.0394  -0.6337
 9GE  C04  C  C1     0  -0.158   5.1883   0.5403   0.1365
 9GE  C05  C  CH2    0  -0.481   3.8702   1.0597  -0.3366
 9GE  C06  C  CH2    0  -0.416   2.6861   0.3558   0.3282
 9GE  O1   O  OC    -1  -0.624   8.1730  -1.0762  -0.9932
 9GE  H1   H  H      0   0.211   5.9110  -0.1471  -1.6989
 9GE  H2   H  H      0   0.227   5.3905   0.6406   1.2005
 9GE  H3   H  HCH2   0   0.227   3.8023   2.1320  -0.1196
 9GE  H4   H  HCH2   0   0.225   3.7930   0.9565  -1.4230
 9GE  H5   H  HCH2   0   0.216   2.7481  -0.7190   0.1299
 9GE  H6   H  HCH2   0   0.214   2.7557   0.4696   1.4151
 9GE  C1   C  CH2    0  -0.413   1.3446   0.8876  -0.1586
 9GE  C2   C  CH2    0  -0.413   0.1456   0.1846   0.4649
 9GE  C3   C  CH2    0  -0.412  -1.1841   0.7119  -0.0588
 9GE  C4   C  CH2    0  -0.413  -2.3993  -0.0221   0.4939
 9GE  C5   C  CH2    0  -0.409  -3.7153   0.5290  -0.0409
 9GE  C6   C  CH2    0  -0.418  -4.9361  -0.2803   0.3790
 9GE  C7   C  CH2    0  -0.397  -6.2425   0.3278  -0.1179
 9GE  C8   C  CH1    0  -0.231  -7.4932  -0.5104   0.1556
 9GE  C9   C  CH3    0  -0.651  -8.7527   0.3223  -0.0635
 9GE  C10  C  CH3    0  -0.655  -7.5334  -1.7633  -0.7146
 9GE  H7   H  HCH2   0   0.209   1.2833   1.9623   0.0459
 9GE  H9   H  HCH2   0   0.208   1.2921   0.7861  -1.2485
 9GE  H10  H  HCH2   0   0.207   0.2133  -0.8909   0.2668
 9GE  H11  H  HCH2   0   0.208   0.1817   0.2936   1.5545
 9GE  H12  H  HCH2   0   0.207  -1.2674   1.7803   0.1692
 9GE  H13  H  HCH2   0   0.206  -1.1924   0.6377  -1.1522
 9GE  H14  H  HCH2   0   0.206  -2.3213  -1.0859   0.2424
 9GE  H15  H  HCH2   0   0.207  -2.3965   0.0300   1.5881
 9GE  H16  H  HCH2   0   0.207  -3.8340   1.5685   0.2846
 9GE  H17  H  HCH2   0   0.205  -3.6711   0.5608  -1.1353
 9GE  H18  H  HCH2   0   0.209  -4.8227  -1.3037   0.0072
 9GE  H19  H  HCH2   0   0.207  -4.9687  -0.3587   1.4712
 9GE  H20  H  HCH2   0   0.212  -6.3640   1.3134   0.3451
 9GE  H21  H  HCH2   0   0.201  -6.1738   0.5120  -1.1973
 9GE  H22  H  HCH1   0   0.208  -7.4722  -0.8224   1.2070
 9GE  H23  H  HCH3   0   0.211  -8.7967   0.6988  -1.0886
 9GE  H24  H  HCH3   0   0.222  -9.6560  -0.2655   0.1103
 9GE  H25  H  HCH3   0   0.222  -8.7832   1.1837   0.6063
 9GE  H26  H  HCH3   0   0.211  -7.5726  -1.4926  -1.7732
 9GE  H27  H  HCH3   0   0.224  -6.6587  -2.3990  -0.5707
 9GE  H28  H  HCH3   0   0.224  -8.4144  -2.3695  -0.4967

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
 9GE  C06  C05  single  1.530  0.020  1.530
 9GE  C05  C04  single  1.494  0.020  1.494
 9GE  C04  CA   double  1.331  0.020  1.331
 9GE  CA   C    single  1.510  0.020  1.510
 9GE  C    O    deloc   1.248  0.020  1.248
 9GE  C    O1   deloc   1.250  0.020  1.250
 9GE  CA   H1   single  0.930  0.020  1.080
 9GE  C04  H2   single  0.930  0.020  1.080
 9GE  C05  H3   single  0.970  0.020  1.090
 9GE  C05  H4   single  0.970  0.020  1.090
 9GE  C06  H5   single  0.970  0.020  1.090
 9GE  C06  H6   single  0.970  0.020  1.090
 9GE  C06  C1   single  1.523  0.020  1.523
 9GE  C1   C2   single  1.523  0.020  1.523
 9GE  C2   C3   single  1.523  0.020  1.523
 9GE  C3   C4   single  1.523  0.020  1.523
 9GE  C4   C5   single  1.524  0.020  1.524
 9GE  C5   C6   single  1.524  0.020  1.524
 9GE  C6   C7   single  1.524  0.020  1.524
 9GE  C7   C8   single  1.530  0.020  1.530
 9GE  C8   C9   single  1.526  0.020  1.526
 9GE  C8   C10  single  1.526  0.020  1.526
 9GE  C1   H7   single  0.970  0.020  1.090
 9GE  C1   H9   single  0.970  0.020  1.090
 9GE  C2   H10  single  0.970  0.020  1.090
 9GE  C2   H11  single  0.970  0.020  1.090
 9GE  C3   H12  single  0.970  0.020  1.090
 9GE  C3   H13  single  0.970  0.020  1.090
 9GE  C4   H14  single  0.970  0.020  1.090
 9GE  C4   H15  single  0.970  0.020  1.090
 9GE  C5   H16  single  0.970  0.020  1.090
 9GE  C5   H17  single  0.970  0.020  1.090
 9GE  C6   H18  single  0.970  0.020  1.090
 9GE  C6   H19  single  0.970  0.020  1.090
 9GE  C7   H20  single  0.970  0.020  1.090
 9GE  C7   H21  single  0.970  0.020  1.090
 9GE  C8   H22  single  0.970  0.020  1.090
 9GE  C9   H23  single  0.970  0.020  1.090
 9GE  C9   H24  single  0.970  0.020  1.090
 9GE  C9   H25  single  0.970  0.020  1.090
 9GE  C10  H26  single  0.970  0.020  1.090
 9GE  C10  H27  single  0.970  0.020  1.090
 9GE  C10  H28  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
 9GE  O1   C    CA   115.60  3.000
 9GE  O1   C    O    126.40  3.000
 9GE  CA   C    O    118.00  3.000
 9GE  H1   CA   C04  119.05  3.000
 9GE  H1   CA   C    116.75  3.000
 9GE  C04  CA   C    124.19  3.000
 9GE  H2   C04  C05  116.23  3.000
 9GE  H2   C04  CA   118.55  3.000
 9GE  C05  C04  CA   125.22  3.000
 9GE  H4   C05  H3   106.53  3.000
 9GE  H4   C05  C06  109.49  3.000
 9GE  H3   C05  C06  108.43  3.000
 9GE  H4   C05  C04  110.12  3.000
 9GE  H3   C05  C04  109.39  3.000
 9GE  C06  C05  C04  112.67  3.000
 9GE  C1   C06  H6   109.69  3.000
 9GE  C1   C06  H5   109.57  3.000
 9GE  H6   C06  H5   106.15  3.000
 9GE  C1   C06  C05  112.47  3.000
 9GE  H6   C06  C05  109.53  3.000
 9GE  H5   C06  C05  109.22  3.000
 9GE  H9   C1   H7   105.89  3.000
 9GE  H9   C1   C2   109.06  3.000
 9GE  H7   C1   C2   109.40  3.000
 9GE  H9   C1   C06  109.14  3.000
 9GE  H7   C1   C06  109.40  3.000
 9GE  C2   C1   C06  113.66  3.000
 9GE  H11  C2   H10  105.98  3.000
 9GE  H11  C2   C3   109.64  3.000
 9GE  H10  C2   C3   109.36  3.000
 9GE  H11  C2   C1   109.59  3.000
 9GE  H10  C2   C1   109.29  3.000
 9GE  C3   C2   C1   112.75  3.000
 9GE  H13  C3   H12  105.85  3.000
 9GE  H13  C3   C4   108.86  3.000
 9GE  H12  C3   C4   109.50  3.000
 9GE  H13  C3   C2   109.03  3.000
 9GE  H12  C3   C2   109.41  3.000
 9GE  C4   C3   C2   113.88  3.000
 9GE  H15  C4   H14  105.98  3.000
 9GE  H15  C4   C5   109.60  3.000
 9GE  H14  C4   C5   109.39  3.000
 9GE  H15  C4   C3   109.72  3.000
 9GE  H14  C4   C3   109.13  3.000
 9GE  C5   C4   C3   112.79  3.000
 9GE  H17  C5   H16  105.87  3.000
 9GE  H17  C5   C6   108.84  3.000
 9GE  H16  C5   C6   109.59  3.000
 9GE  H17  C5   C4   109.04  3.000
 9GE  H16  C5   C4   109.42  3.000
 9GE  C6   C5   C4   113.77  3.000
 9GE  H19  C6   H18  105.95  3.000
 9GE  H19  C6   C7   109.15  3.000
 9GE  H18  C6   C7   110.55  3.000
 9GE  H19  C6   C5   109.67  3.000
 9GE  H18  C6   C5   108.66  3.000
 9GE  C7   C6   C5   112.64  3.000
 9GE  H21  C7   H20  105.76  3.000
 9GE  H21  C7   C8   108.60  3.000
 9GE  H20  C7   C8   109.06  3.000
 9GE  H21  C7   C6   109.52  3.000
 9GE  H20  C7   C6   108.43  3.000
 9GE  C8   C7   C6   115.07  3.000
 9GE  H22  C8   C10  108.28  3.000
 9GE  H22  C8   C9   107.98  3.000
 9GE  C10  C8   C9   110.15  3.000
 9GE  H22  C8   C7   108.15  3.000
 9GE  C10  C8   C7   111.67  3.000
 9GE  C9   C8   C7   110.49  3.000
 9GE  H25  C9   H24  107.70  3.000
 9GE  H25  C9   H23  107.61  3.000
 9GE  H24  C9   H23  107.55  3.000
 9GE  H25  C9   C8   111.45  3.000
 9GE  H24  C9   C8   111.50  3.000
 9GE  H23  C9   C8   110.85  3.000
 9GE  H28  C10  H27  107.30  3.000
 9GE  H28  C10  H26  107.57  3.000
 9GE  H27  C10  H26  107.50  3.000
 9GE  H28  C10  C8   111.31  3.000
 9GE  H27  C10  C8   112.47  3.000
 9GE  H26  C10  C8   110.48  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
 9GE  Var_01  C05  C04  CA   C    -179.34   0.0  2
 9GE  Var_02  C04  CA   C    O       0.50  30.0  2
 9GE  Var_03  C06  C05  C04  CA    118.75  30.0  1
 9GE  Var_04  C1   C06  C05  C04  -179.94  30.0  1
 9GE  Var_05  C2   C1   C06  C05   178.78  30.0  3
 9GE  Var_06  C3   C2   C1   C06  -178.76  30.0  3
 9GE  Var_07  C4   C3   C2   C1    177.01  30.0  3
 9GE  Var_08  C5   C4   C3   C2    179.74  30.0  3
 9GE  Var_09  C6   C5   C4   C3    173.84  30.0  3
 9GE  Var_10  C7   C6   C5   C4    177.46  30.0  3
 9GE  Var_11  C8   C7   C6   C5    174.35  30.0  3
 9GE  Var_12  C9   C8   C7   C6    166.13  30.0  3
 9GE  Var_13  H23  C9   C8   C7     59.21  30.0  3
 9GE  Var_14  H26  C10  C8   C7    -62.02  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
 9GE  plan-1  C    0.020
 9GE  plan-1  O    0.020
 9GE  plan-1  CA   0.020
 9GE  plan-1  O1   0.020
 9GE  plan-2  C    0.020
 9GE  plan-2  CA   0.020
 9GE  plan-2  C04  0.020
 9GE  plan-2  C05  0.020
 9GE  plan-2  H1   0.020
 9GE  plan-2  H2   0.020

