# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 07:33:56 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 2,3,5,6-tetramethylcyclohexa-2,5-diene-1,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(C)C(=O)C(=C(C)C1=O)C
#
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
 DQN  DQN  2,3,5,6-tetramethylcyclohexa-2,5-diene-1,4-dione  ligand  24  12  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DQN
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
 DQN  C1    C  CR6   0   0.385   1.4245   0.0056   0.0001
 DQN  O1    O  O     0  -0.380   2.6399  -0.0036  -0.0004
 DQN  C2    C  CR6   0  -0.042   0.6785   0.0136   1.2839
 DQN  C2M   C  CH3   0  -0.737   1.4632   0.0230   2.5562
 DQN  C3    C  CR6   0  -0.043  -0.6650   0.0096   1.2849
 DQN  C3M   C  CH3   0  -0.737  -1.4480   0.0156   2.5582
 DQN  C4    C  CR6   0   0.385  -1.4124  -0.0072   0.0020
 DQN  O4    O  O     0  -0.380  -2.6276  -0.0347   0.0025
 DQN  C5    C  CR6   0  -0.044  -0.6665   0.0086  -1.2817
 DQN  C5M   C  CH3   0  -0.736  -1.4513   0.0103  -2.5539
 DQN  C6    C  CR6   0  -0.042   0.6770   0.0100  -1.2827
 DQN  C6M   C  CH3   0  -0.739   1.4603   0.0142  -2.5559
 DQN  H2M1  H  HCH3  0   0.265   2.5343   0.0272   2.3775
 DQN  H2M2  H  HCH3  0   0.256   1.2194   0.9014   3.1571
 DQN  H2M3  H  HCH3  0   0.256   1.2281  -0.8514   3.1660
 DQN  H3M1  H  HCH3  0   0.265  -2.5189   0.0488   2.3811
 DQN  H3M2  H  HCH3  0   0.257  -1.2343  -0.8754   3.1521
 DQN  H3M3  H  HCH3  0   0.255  -1.1812   0.8764   3.1739
 DQN  H5M1  H  HCH3  0   0.264  -2.5194   0.0958  -2.3777
 DQN  H5M2  H  HCH3  0   0.254  -1.1470   0.8370  -3.1977
 DQN  H5M3  H  HCH3  0   0.259  -1.2778  -0.9083  -3.1186
 DQN  H6M1  H  HCH3  0   0.265   2.5315   0.0034  -2.3786
 DQN  H6M2  H  HCH3  0   0.257   1.2119  -0.8540  -3.1693
 DQN  H6M3  H  HCH3  0   0.256   1.2278   0.8987  -3.1524

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
 DQN  C1   O1    double  1.215  0.020  1.215
 DQN  C1   C2    single  1.485  0.020  1.485
 DQN  C1   C6    single  1.485  0.020  1.485
 DQN  C2   C2M   single  1.495  0.020  1.495
 DQN  C2   C3    double  1.343  0.020  1.343
 DQN  C2M  H2M1  single  0.970  0.020  1.090
 DQN  C2M  H2M2  single  0.970  0.020  1.090
 DQN  C2M  H2M3  single  0.970  0.020  1.090
 DQN  C3   C3M   single  1.495  0.020  1.495
 DQN  C3   C4    single  1.485  0.020  1.485
 DQN  C3M  H3M1  single  0.970  0.020  1.090
 DQN  C3M  H3M2  single  0.970  0.020  1.090
 DQN  C3M  H3M3  single  0.970  0.020  1.090
 DQN  C4   O4    double  1.215  0.020  1.215
 DQN  C4   C5    single  1.485  0.020  1.485
 DQN  C5   C5M   single  1.495  0.020  1.495
 DQN  C5   C6    double  1.343  0.020  1.343
 DQN  C5M  H5M1  single  0.970  0.020  1.090
 DQN  C5M  H5M2  single  0.970  0.020  1.090
 DQN  C5M  H5M3  single  0.970  0.020  1.090
 DQN  C6   C6M   single  1.495  0.020  1.495
 DQN  C6M  H6M1  single  0.970  0.020  1.090
 DQN  C6M  H6M2  single  0.970  0.020  1.090
 DQN  C6M  H6M3  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
 DQN  C6    C1   C2    119.61  3.000
 DQN  C6    C1   O1    120.20  3.000
 DQN  C2    C1   O1    120.19  3.000
 DQN  C3    C2   C2M   121.63  3.000
 DQN  C3    C2   C1    120.20  3.000
 DQN  C2M   C2   C1    118.17  3.000
 DQN  H2M3  C2M  H2M2  106.79  3.000
 DQN  H2M3  C2M  H2M1  107.90  3.000
 DQN  H2M2  C2M  H2M1  107.92  3.000
 DQN  H2M3  C2M  C2    110.94  3.000
 DQN  H2M2  C2M  C2    110.87  3.000
 DQN  H2M1  C2M  C2    112.20  3.000
 DQN  C4    C3   C3M   118.19  3.000
 DQN  C4    C3   C2    120.19  3.000
 DQN  C3M   C3   C2    121.63  3.000
 DQN  H3M3  C3M  H3M2  106.79  3.000
 DQN  H3M3  C3M  H3M1  107.99  3.000
 DQN  H3M2  C3M  H3M1  107.85  3.000
 DQN  H3M3  C3M  C3    110.84  3.000
 DQN  H3M2  C3M  C3    110.95  3.000
 DQN  H3M1  C3M  C3    112.20  3.000
 DQN  C5    C4   O4    120.19  3.000
 DQN  C5    C4   C3    119.60  3.000
 DQN  O4    C4   C3    120.20  3.000
 DQN  C6    C5   C5M   121.63  3.000
 DQN  C6    C5   C4    120.20  3.000
 DQN  C5M   C5   C4    118.17  3.000
 DQN  H5M3  C5M  H5M2  106.73  3.000
 DQN  H5M3  C5M  H5M1  107.84  3.000
 DQN  H5M2  C5M  H5M1  108.08  3.000
 DQN  H5M3  C5M  C5    110.84  3.000
 DQN  H5M2  C5M  C5    110.89  3.000
 DQN  H5M1  C5M  C5    112.24  3.000
 DQN  C6M   C6   C5    121.64  3.000
 DQN  C6M   C6   C1    118.17  3.000
 DQN  C5    C6   C1    120.19  3.000
 DQN  H6M3  C6M  H6M2  106.79  3.000
 DQN  H6M3  C6M  H6M1  107.89  3.000
 DQN  H6M2  C6M  H6M1  107.95  3.000
 DQN  H6M3  C6M  C6    110.86  3.000
 DQN  H6M2  C6M  C6    110.93  3.000
 DQN  H6M1  C6M  C6    112.20  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
 DQN  Var_01  H2M1  C2M  C2  C1    0.24  30.0  3
 DQN  Var_02  H6M1  C6M  C6  C1    0.57  30.0  3
 DQN  Var_03  H3M1  C3M  C3  C2  177.86  30.0  3
 DQN  Var_04  H5M1  C5M  C5  C4    5.51  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
 DQN  plan-1  C1   0.020
 DQN  plan-1  O1   0.020
 DQN  plan-1  C2   0.020
 DQN  plan-1  C2M  0.020
 DQN  plan-1  C3   0.020
 DQN  plan-1  C3M  0.020
 DQN  plan-1  C4   0.020
 DQN  plan-1  O4   0.020
 DQN  plan-1  C5   0.020
 DQN  plan-1  C5M  0.020
 DQN  plan-1  C6   0.020
 DQN  plan-1  C6M  0.020

