# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 21:47:19 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  45  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 GRAND
;

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   0.524   7.3688  -0.4948  -0.0522
 9GE  O    O  O     0  -0.454   7.6807  -0.4855   1.1168
 9GE  CA   C  C1    0  -0.403   6.1004   0.0078  -0.6042
 9GE  C04  C  C1    0  -0.119   5.1674   0.5500   0.1789
 9GE  C05  C  CH2   0  -0.493   3.8584   1.0694  -0.3013
 9GE  C06  C  CH2   0  -0.422   2.6757   0.3552   0.3574
 9GE  O1   O  OH1   0  -0.604   8.1598  -0.9755  -1.0084
 9GE  H1   H  H     0   0.271   5.9482  -0.0746  -1.6746
 9GE  H2   H  H     0   0.265   5.3490   0.6162   1.2485
 9GE  H3   H  HCH2  0   0.249   3.7977   2.1374  -0.0649
 9GE  H4   H  HCH2  0   0.242   3.7894   0.9801  -1.3883
 9GE  H5   H  HCH2  0   0.225   2.7401  -0.7173   0.1502
 9GE  H6   H  HCH2  0   0.223   2.7422   0.4633   1.4446
 9GE  H8   H  HOH1  0   0.479   8.9856  -1.3024  -0.6220
 9GE  C1   C  CH2   0  -0.415   1.3375   0.8911  -0.1335
 9GE  C2   C  CH2   0  -0.414   0.1376   0.1842   0.4836
 9GE  C3   C  CH2   0  -0.412  -1.1903   0.7147  -0.0415
 9GE  C4   C  CH2   0  -0.413  -2.4067  -0.0245   0.5014
 9GE  C5   C  CH2   0  -0.409  -3.7206   0.5249  -0.0403
 9GE  C6   C  CH2   0  -0.418  -4.9427  -0.2854   0.3743
 9GE  C7   C  CH2   0  -0.397  -6.2475   0.3233  -0.1262
 9GE  C8   C  CH1   0  -0.231  -7.4986  -0.5169   0.1393
 9GE  C9   C  CH3   0  -0.651  -8.7578   0.3159  -0.0813
 9GE  C10  C  CH3   0  -0.656  -7.5347  -1.7657  -0.7368
 9GE  H7   H  HCH2  0   0.213   1.2763   1.9645   0.0763
 9GE  H9   H  HCH2  0   0.212   1.2891   0.7935  -1.2236
 9GE  H10  H  HCH2  0   0.208   0.2062  -0.8901   0.2797
 9GE  H11  H  HCH2  0   0.210   0.1707   0.2880   1.5736
 9GE  H12  H  HCH2  0   0.208  -1.2755   1.7810   0.1950
 9GE  H13  H  HCH2  0   0.206  -1.1944   0.6491  -1.1354
 9GE  H14  H  HCH2  0   0.206  -2.3241  -1.0874   0.2481
 9GE  H15  H  HCH2  0   0.207  -2.4112   0.0256   1.5957
 9GE  H16  H  HCH2  0   0.207  -3.8415   1.5645   0.2840
 9GE  H17  H  HCH2  0   0.205  -3.6713   0.5558  -1.1345
 9GE  H18  H  HCH2  0   0.210  -4.8277  -1.3082   0.0016
 9GE  H19  H  HCH2  0   0.207  -4.9792  -0.3649   1.4663
 9GE  H20  H  HCH2  0   0.212  -6.3717   1.3070   0.3401
 9GE  H21  H  HCH2  0   0.201  -6.1747   0.5115  -1.2046
 9GE  H22  H  HCH1  0   0.208  -7.4814  -0.8335   1.1893
 9GE  H23  H  HCH3  0   0.211  -8.7985   0.6946  -1.1057
 9GE  H24  H  HCH3  0   0.222  -9.6616  -0.2726   0.0876
 9GE  H25  H  HCH3  0   0.222  -8.7911   1.1759   0.5901
 9GE  H26  H  HCH3  0   0.211  -7.5704  -1.4898  -1.7942
 9GE  H27  H  HCH3  0   0.225  -6.6600  -2.4014  -0.5931
 9GE  H28  H  HCH3  0   0.224  -8.4160  -2.3738  -0.5254

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  1.531  0.020  1.531
 9GE  C05  C04  single  1.488  0.020  1.488
 9GE  C04  CA   double  1.333  0.020  1.333
 9GE  CA   C    single  1.472  0.020  1.472
 9GE  C    O    double  1.210  0.020  1.210
 9GE  C    O1   single  1.331  0.020  1.331
 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  O1   H8   single  0.850  0.020  0.980
 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   111.47  3.000
 9GE  O1   C    O    122.94  3.000
 9GE  CA   C    O    125.59  3.000
 9GE  H1   CA   C04  120.83  3.000
 9GE  H1   CA   C    117.73  3.000
 9GE  C04  CA   C    121.44  3.000
 9GE  H2   C04  C05  116.32  3.000
 9GE  H2   C04  CA   119.07  3.000
 9GE  C05  C04  CA   124.61  3.000
 9GE  H4   C05  H3   106.91  3.000
 9GE  H4   C05  C06  109.94  3.000
 9GE  H3   C05  C06  108.61  3.000
 9GE  H4   C05  C04  110.37  3.000
 9GE  H3   C05  C04  108.63  3.000
 9GE  C06  C05  C04  112.21  3.000
 9GE  C1   C06  H6   109.80  3.000
 9GE  C1   C06  H5   109.62  3.000
 9GE  H6   C06  H5   106.34  3.000
 9GE  C1   C06  C05  112.09  3.000
 9GE  H6   C06  C05  109.53  3.000
 9GE  H5   C06  C05  109.29  3.000
 9GE  H8   O1   C    110.00  3.000
 9GE  H9   C1   H7   105.98  3.000
 9GE  H9   C1   C2   109.08  3.000
 9GE  H7   C1   C2   109.46  3.000
 9GE  H9   C1   C06  109.16  3.000
 9GE  H7   C1   C06  109.41  3.000
 9GE  C2   C1   C06  113.47  3.000
 9GE  H11  C2   H10  106.03  3.000
 9GE  H11  C2   C3   109.65  3.000
 9GE  H10  C2   C3   109.38  3.000
 9GE  H11  C2   C1   109.59  3.000
 9GE  H10  C2   C1   109.29  3.000
 9GE  C3   C2   C1   112.67  3.000
 9GE  H13  C3   H12  105.87  3.000
 9GE  H13  C3   C4   108.88  3.000
 9GE  H12  C3   C4   109.47  3.000
 9GE  H13  C3   C2   109.06  3.000
 9GE  H12  C3   C2   109.41  3.000
 9GE  C4   C3   C2   113.84  3.000
 9GE  H15  C4   H14  105.99  3.000
 9GE  H15  C4   C5   109.57  3.000
 9GE  H14  C4   C5   109.43  3.000
 9GE  H15  C4   C3   109.70  3.000
 9GE  H14  C4   C3   109.16  3.000
 9GE  C5   C4   C3   112.76  3.000
 9GE  H17  C5   H16  105.89  3.000
 9GE  H17  C5   C6   108.83  3.000
 9GE  H16  C5   C6   109.60  3.000
 9GE  H17  C5   C4   109.05  3.000
 9GE  H16  C5   C4   109.39  3.000
 9GE  C6   C5   C4   113.77  3.000
 9GE  H19  C6   H18  105.97  3.000
 9GE  H19  C6   C7   109.13  3.000
 9GE  H18  C6   C7   110.56  3.000
 9GE  H19  C6   C5   109.67  3.000
 9GE  H18  C6   C5   108.66  3.000
 9GE  C7   C6   C5   112.63  3.000
 9GE  H21  C7   H20  105.78  3.000
 9GE  H21  C7   C8   108.60  3.000
 9GE  H20  C7   C8   109.05  3.000
 9GE  H21  C7   C6   109.54  3.000
 9GE  H20  C7   C6   108.41  3.000
 9GE  C8   C7   C6   115.06  3.000
 9GE  H22  C8   C10  108.29  3.000
 9GE  H22  C8   C9   108.00  3.000
 9GE  C10  C8   C9   110.13  3.000
 9GE  H22  C8   C7   108.16  3.000
 9GE  C10  C8   C7   111.66  3.000
 9GE  C9   C8   C7   110.48  3.000
 9GE  H25  C9   H24  107.72  3.000
 9GE  H25  C9   H23  107.59  3.000
 9GE  H24  C9   H23  107.52  3.000
 9GE  H25  C9   C8   111.49  3.000
 9GE  H24  C9   C8   111.51  3.000
 9GE  H23  C9   C8   110.82  3.000
 9GE  H28  C10  H27  107.30  3.000
 9GE  H28  C10  H26  107.55  3.000
 9GE  H27  C10  H26  107.50  3.000
 9GE  H28  C10  C8   111.33  3.000
 9GE  H27  C10  C8   112.48  3.000
 9GE  H26  C10  C8   110.46  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  CONST_01  H8   O1   C    O       0.00   0.0  0
 9GE  Var_01    C05  C04  CA   C    -179.49   0.0  2
 9GE  Var_02    C04  CA   C    O       0.89  30.0  2
 9GE  Var_03    C06  C05  C04  CA    120.70  30.0  1
 9GE  Var_04    C1   C06  C05  C04   179.86  30.0  1
 9GE  Var_05    C2   C1   C06  C05   178.95  30.0  3
 9GE  Var_06    C3   C2   C1   C06  -178.81  30.0  3
 9GE  Var_07    C4   C3   C2   C1    176.87  30.0  3
 9GE  Var_08    C5   C4   C3   C2   -179.95  30.0  3
 9GE  Var_09    C6   C5   C4   C3    174.09  30.0  3
 9GE  Var_10    C7   C6   C5   C4    177.30  30.0  3
 9GE  Var_11    C8   C7   C6   C5    174.23  30.0  3
 9GE  Var_12    C9   C8   C7   C6    166.09  30.0  3
 9GE  Var_13    H23  C9   C8   C7     59.31  30.0  3
 9GE  Var_14    H26  C10  C8   C7    -62.01  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-1  H8   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

