# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 22:15:43 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: (2Z)-9-oxodec-2-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)CCCCC\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
 9OD  9OD  '(2Z)-9-oxodec-2-enoic acid'  ligand  29  13  .  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_9OD
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
 9OD  O9    O  O     0  -0.409   4.8312  -0.8110   1.1241
 9OD  C9    C  C     0   0.392   4.7375   0.0926   0.3231
 9OD  C10   C  CH3   0  -0.767   5.9270   0.9105  -0.1028
 9OD  C8    C  CH2   0  -0.556   3.4231   0.4735  -0.3090
 9OD  C7    C  CH2   0  -0.416   2.2232  -0.3389   0.1486
 9OD  C6    C  CH2   0  -0.416   0.9372   0.1113  -0.5343
 9OD  C5    C  CH2   0  -0.425  -0.2708  -0.7165  -0.1167
 9OD  C4    C  CH2   0  -0.502  -1.5612  -0.2480  -0.7945
 9OD  C3    C  C1    0  -0.118  -2.6984  -1.1546  -0.4714
 9OD  C2    C  C1    0  -0.390  -3.9135  -0.8945   0.0216
 9OD  C1    C  C     0   0.512  -4.4470   0.4342   0.3636
 9OD  OE1   O  OH1   0  -0.604  -5.6678   0.3306   0.8889
 9OD  OE2   O  O     0  -0.448  -3.8982   1.5010   0.2074
 9OD  H10   H  HCH3  0   0.257   6.8425   0.5643   0.3722
 9OD  H10A  H  HCH3  0   0.262   6.0463   0.8674  -1.1869
 9OD  H10B  H  HCH3  0   0.263   5.7689   1.9606   0.1511
 9OD  H8    H  HCH2  0   0.262   3.2640   1.5416  -0.1205
 9OD  H8A   H  HCH2  0   0.263   3.5457   0.4006  -1.3960
 9OD  H7    H  HCH2  0   0.222   2.3909  -1.3992  -0.0594
 9OD  H7A   H  HCH2  0   0.223   2.1082  -0.2511   1.2324
 9OD  H6    H  HCH2  0   0.217   0.7552   1.1675  -0.3092
 9OD  H6A   H  HCH2  0   0.216   1.0579   0.0479  -1.6212
 9OD  H5    H  HCH2  0   0.221  -0.0930  -1.7694  -0.3588
 9OD  H5A   H  HCH2  0   0.226  -0.3938  -0.6670   0.9695
 9OD  H4    H  HCH2  0   0.257  -1.7709   0.7867  -0.5362
 9OD  H4A   H  HCH2  0   0.247  -1.4139  -0.2848  -1.8806
 9OD  H3    H  H     0   0.263  -2.4915  -2.2041  -0.6644
 9OD  H2    H  H     0   0.270  -4.5841  -1.7281   0.1909
 9OD  HOE1  H  HOH1  0   0.479  -6.0086   1.2119   1.1011

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
 9OD  O9   C9    double  1.211  0.020  1.211
 9OD  C9   C10   single  1.505  0.020  1.505
 9OD  C9   C8    single  1.507  0.020  1.507
 9OD  C8   C7    single  1.520  0.020  1.520
 9OD  C7   C6    single  1.524  0.020  1.524
 9OD  C6   C5    single  1.523  0.020  1.523
 9OD  C5   C4    single  1.531  0.020  1.531
 9OD  C4   C3    single  1.490  0.020  1.490
 9OD  C3   C2    double  1.337  0.020  1.337
 9OD  C2   C1    single  1.472  0.020  1.472
 9OD  C1   OE1   single  1.333  0.020  1.333
 9OD  C1   OE2   double  1.210  0.020  1.210
 9OD  C10  H10   single  0.970  0.020  1.090
 9OD  C10  H10A  single  0.970  0.020  1.090
 9OD  C10  H10B  single  0.970  0.020  1.090
 9OD  C8   H8    single  0.970  0.020  1.090
 9OD  C8   H8A   single  0.970  0.020  1.090
 9OD  C7   H7    single  0.970  0.020  1.090
 9OD  C7   H7A   single  0.970  0.020  1.090
 9OD  C6   H6    single  0.970  0.020  1.090
 9OD  C6   H6A   single  0.970  0.020  1.090
 9OD  C5   H5    single  0.970  0.020  1.090
 9OD  C5   H5A   single  0.970  0.020  1.090
 9OD  C4   H4    single  0.970  0.020  1.090
 9OD  C4   H4A   single  0.970  0.020  1.090
 9OD  C3   H3    single  0.930  0.020  1.080
 9OD  C2   H2    single  0.930  0.020  1.080
 9OD  OE1  HOE1  single  0.850  0.020  0.980

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
 9OD  C8    C9   C10   115.67  3.000
 9OD  C8    C9   O9    122.22  3.000
 9OD  C10   C9   O9    122.11  3.000
 9OD  H10B  C10  H10A  106.54  3.000
 9OD  H10B  C10  H10   109.06  3.000
 9OD  H10A  C10  H10   109.21  3.000
 9OD  H10B  C10  C9    110.02  3.000
 9OD  H10A  C10  C9    110.24  3.000
 9OD  H10   C10  C9    111.63  3.000
 9OD  H8A   C8   H8    104.57  3.000
 9OD  H8A   C8   C7    110.57  3.000
 9OD  H8    C8   C7    110.77  3.000
 9OD  H8A   C8   C9    107.55  3.000
 9OD  H8    C8   C9    107.49  3.000
 9OD  C7    C8   C9    115.29  3.000
 9OD  H7A   C7   H7    106.41  3.000
 9OD  H7A   C7   C6    109.37  3.000
 9OD  H7    C7   C6    109.31  3.000
 9OD  H7A   C7   C8    109.79  3.000
 9OD  H7    C7   C8    109.88  3.000
 9OD  C6    C7   C8    111.93  3.000
 9OD  H6A   C6   H6    106.14  3.000
 9OD  H6A   C6   C5    109.15  3.000
 9OD  H6    C6   C5    109.64  3.000
 9OD  H6A   C6   C7    109.54  3.000
 9OD  H6    C6   C7    109.46  3.000
 9OD  C5    C6   C7    112.70  3.000
 9OD  H5A   C5   H5    106.34  3.000
 9OD  H5A   C5   C4    109.32  3.000
 9OD  H5    C5   C4    109.47  3.000
 9OD  H5A   C5   C6    109.68  3.000
 9OD  H5    C5   C6    109.47  3.000
 9OD  C4    C5   C6    112.39  3.000
 9OD  H4A   C4   H4    107.05  3.000
 9OD  H4A   C4   C3    107.27  3.000
 9OD  H4    C4   C3    112.37  3.000
 9OD  H4A   C4   C5    108.36  3.000
 9OD  H4    C4   C5    110.41  3.000
 9OD  C3    C4   C5    111.17  3.000
 9OD  H3    C3   C2    115.24  3.000
 9OD  H3    C3   C4    113.81  3.000
 9OD  C2    C3   C4    130.95  3.000
 9OD  H2    C2   C1    115.72  3.000
 9OD  H2    C2   C3    118.07  3.000
 9OD  C1    C2   C3    126.21  3.000
 9OD  OE2   C1   OE1   122.34  3.000
 9OD  OE2   C1   C2    126.97  3.000
 9OD  OE1   C1   C2    110.69  3.000
 9OD  HOE1  OE1  C1    109.75  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
 9OD  CONST_01  HOE1  OE1  C1  C2   180.00   0.0  0
 9OD  Var_01    C1    C2   C3  C4     0.91   0.0  2
 9OD  Var_02    C7    C8   C9  O9     1.06  30.0  3
 9OD  Var_03    C6    C7   C8  C9   179.85  30.0  3
 9OD  Var_04    C5    C6   C7  C8   178.44  30.0  3
 9OD  Var_05    C4    C5   C6  C7   179.34  30.0  3
 9OD  Var_06    C3    C4   C5  C6   174.50  30.0  3
 9OD  Var_07    C2    C3   C4  C5   127.18  30.0  3
 9OD  Var_08    OE1   C1   C2  C3  -177.11  30.0  2
 9OD  Var_09    H10   C10  C9  O9     1.62  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
 9OD  plan-1  O9    0.020
 9OD  plan-1  C9    0.020
 9OD  plan-1  C10   0.020
 9OD  plan-1  C8    0.020
 9OD  plan-2  C2    0.020
 9OD  plan-2  C1    0.020
 9OD  plan-2  OE1   0.020
 9OD  plan-2  OE2   0.020
 9OD  plan-2  HOE1  0.020
 9OD  plan-3  C4    0.020
 9OD  plan-3  C3    0.020
 9OD  plan-3  C2    0.020
 9OD  plan-3  C1    0.020
 9OD  plan-3  H3    0.020
 9OD  plan-3  H2    0.020

