# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 08:30:37 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: (2~{E})-3,7-dimethylocta-2,6-dienal
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)=CCC/C(C)=C/C=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
 GRQ  GRQ  (2~{E})-3,7-dimethylocta-2,6-dienal  ligand  27  11  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GRQ
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
 GRQ  C1   C  C     0   0.091  -3.1407  -0.2923   0.0922
 GRQ  C2   C  C1    0  -0.254  -2.2907   0.7362   0.0853
 GRQ  C3   C  CH2   0  -0.495  -0.8720   0.7089   0.5636
 GRQ  C4   C  CH2   0  -0.494   0.1156   0.6957  -0.6147
 GRQ  C5   C  C     0   0.166   1.5499   0.6615  -0.1791
 GRQ  C6   C  C1    0  -0.406   2.3084  -0.4111  -0.4762
 GRQ  C7   C  C1    0   0.140   3.7035  -0.5744  -0.1051
 GRQ  C8   C  CH3   0  -0.739   2.0149   1.8535   0.5980
 GRQ  C9   C  CH3   0  -0.737  -2.7737  -1.6567   0.6178
 GRQ  O    O  O     0  -0.421   4.3528  -1.5709  -0.3580
 GRQ  C    C  CH3   0  -0.719  -4.5437  -0.1482  -0.4178
 GRQ  H1   H  H     0   0.225  -2.6310   1.6851  -0.3226
 GRQ  H2   H  HCH2  0   0.246  -0.6895   1.5897   1.1853
 GRQ  H3   H  HCH2  0   0.245  -0.6858  -0.1598   1.1986
 GRQ  H4   H  HCH2  0   0.252  -0.1021  -0.1630  -1.2528
 GRQ  H5   H  HCH2  0   0.253  -0.0444   1.5931  -1.2223
 GRQ  H6   H  H     0   0.253   1.8657  -1.2331  -1.0300
 GRQ  H7   H  H     0   0.189   4.1732   0.2641   0.4335
 GRQ  H8   H  HCH3  0   0.265   1.6393   1.8033   1.6224
 GRQ  H9   H  HCH3  0   0.259   3.0953   1.9548   0.6537
 GRQ  H10  H  HCH3  0   0.256   1.6109   2.7675   0.1613
 GRQ  H11  H  HCH3  0   0.244  -2.7537  -1.6740   1.7100
 GRQ  H12  H  HCH3  0   0.243  -3.4995  -2.4064   0.3023
 GRQ  H13  H  HCH3  0   0.239  -1.7931  -1.9855   0.2720
 GRQ  H14  H  HCH3  0   0.234  -5.2687  -0.4107   0.3575
 GRQ  H15  H  HCH3  0   0.235  -4.7578   0.8670  -0.7510
 GRQ  H16  H  HCH3  0   0.234  -4.7278  -0.8283  -1.2534

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
 GRQ  C4  C5   single  1.499  0.020  1.499
 GRQ  C4  C3   single  1.538  0.020  1.538
 GRQ  C6  C5   double  1.347  0.020  1.347
 GRQ  C6  C7   single  1.453  0.020  1.453
 GRQ  C5  C8   single  1.497  0.020  1.497
 GRQ  C7  O    double  1.216  0.020  1.216
 GRQ  C2  C3   single  1.497  0.020  1.497
 GRQ  C2  C1   double  1.334  0.020  1.334
 GRQ  C   C1   single  1.500  0.020  1.500
 GRQ  C1  C9   single  1.508  0.020  1.508
 GRQ  C2  H1   single  0.930  0.020  1.080
 GRQ  C3  H2   single  0.970  0.020  1.090
 GRQ  C3  H3   single  0.970  0.020  1.090
 GRQ  C4  H4   single  0.970  0.020  1.090
 GRQ  C4  H5   single  0.970  0.020  1.090
 GRQ  C6  H6   single  0.930  0.020  1.080
 GRQ  C7  H7   single  0.930  0.020  1.080
 GRQ  C8  H8   single  0.970  0.020  1.090
 GRQ  C8  H9   single  0.970  0.020  1.090
 GRQ  C8  H10  single  0.970  0.020  1.090
 GRQ  C9  H11  single  0.970  0.020  1.090
 GRQ  C9  H12  single  0.970  0.020  1.090
 GRQ  C9  H13  single  0.970  0.020  1.090
 GRQ  C   H14  single  0.970  0.020  1.090
 GRQ  C   H15  single  0.970  0.020  1.090
 GRQ  C   H16  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
 GRQ  C    C1  C9   115.68  3.000
 GRQ  C9   C1  C2   122.98  3.000
 GRQ  C    C1  C2   121.34  3.000
 GRQ  H1   C2  C3   115.61  3.000
 GRQ  H1   C2  C1   118.37  3.000
 GRQ  C3   C2  C1   126.00  3.000
 GRQ  H3   C3  H2   106.37  3.000
 GRQ  H3   C3  C4   109.23  3.000
 GRQ  H2   C3  C4   109.60  3.000
 GRQ  H3   C3  C2   111.21  3.000
 GRQ  H2   C3  C2   108.97  3.000
 GRQ  C4   C3  C2   111.34  3.000
 GRQ  H5   C4  H4   106.92  3.000
 GRQ  H5   C4  C5   108.64  3.000
 GRQ  H4   C4  C5   110.03  3.000
 GRQ  H5   C4  C3   108.92  3.000
 GRQ  H4   C4  C3   109.06  3.000
 GRQ  C5   C4  C3   113.08  3.000
 GRQ  C8   C5  C6   125.01  3.000
 GRQ  C8   C5  C4   115.45  3.000
 GRQ  C6   C5  C4   119.52  3.000
 GRQ  H6   C6  C7   115.90  3.000
 GRQ  H6   C6  C5   119.07  3.000
 GRQ  C7   C6  C5   125.02  3.000
 GRQ  H7   C7  O    119.84  3.000
 GRQ  H7   C7  C6   116.67  3.000
 GRQ  O    C7  C6   123.49  3.000
 GRQ  H10  C8  H9   108.10  3.000
 GRQ  H10  C8  H8   106.66  3.000
 GRQ  H9   C8  H8   107.35  3.000
 GRQ  H10  C8  C5   110.15  3.000
 GRQ  H9   C8  C5   114.18  3.000
 GRQ  H8   C8  C5   110.09  3.000
 GRQ  H13  C9  H12  107.43  3.000
 GRQ  H13  C9  H11  107.21  3.000
 GRQ  H12  C9  H11  106.89  3.000
 GRQ  H13  C9  C1   112.42  3.000
 GRQ  H12  C9  C1   111.07  3.000
 GRQ  H11  C9  C1   111.55  3.000
 GRQ  H16  C   H15  108.23  3.000
 GRQ  H16  C   H14  106.32  3.000
 GRQ  H15  C   H14  108.07  3.000
 GRQ  H16  C   C1   110.96  3.000
 GRQ  H15  C   C1   112.17  3.000
 GRQ  H14  C   C1   110.86  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
 GRQ  Var_01  C    C1  C2  C3  -179.83   0.0  2
 GRQ  Var_02  C7   C6  C5  C4  -179.49   0.0  2
 GRQ  Var_03  C4   C3  C2  C1   104.82  30.0  3
 GRQ  Var_04  C5   C4  C3  C2  -179.72  30.0  1
 GRQ  Var_05  C6   C5  C4  C3   115.48  30.0  3
 GRQ  Var_06  O    C7  C6  C5   178.01  30.0  2
 GRQ  Var_07  H14  C   C1  C2  -122.25  30.0  3
 GRQ  Var_08  H11  C9  C1  C2    75.59  30.0  3
 GRQ  Var_09  H8   C8  C5  C4    76.15  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
 GRQ  plan-1  C4  0.020
 GRQ  plan-1  C5  0.020
 GRQ  plan-1  C6  0.020
 GRQ  plan-1  C7  0.020
 GRQ  plan-1  C8  0.020
 GRQ  plan-1  H6  0.020
 GRQ  plan-2  C6  0.020
 GRQ  plan-2  C7  0.020
 GRQ  plan-2  O   0.020
 GRQ  plan-2  H7  0.020
 GRQ  plan-3  C1  0.020
 GRQ  plan-3  C2  0.020
 GRQ  plan-3  C3  0.020
 GRQ  plan-3  C9  0.020
 GRQ  plan-3  C   0.020
 GRQ  plan-3  H1  0.020

