# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 16:19:23 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCC1=C(C)C(=O)C(=C(OC)C1=O)OC
#
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
 DCQ  DCQ  2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione  ligand  53  23  .  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_DCQ
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
 DCQ  O2    O  O     0  -0.366    4.5213  -2.5414   0.0151
 DCQ  C2    C  CR6   0   0.352    3.9482  -1.4797  -0.1043
 DCQ  C3    C  CR6   0   0.196    4.6362  -0.2275   0.2999
 DCQ  O3    O  O2    0  -0.467    5.8868  -0.3323   0.7734
 DCQ  C3M   C  CH3   0  -0.414    5.9886  -0.6560   2.1600
 DCQ  C4    C  CR6   0   0.197    4.0234   0.9551   0.1610
 DCQ  O4    O  O2    0  -0.467    4.5764   2.1046   0.5762
 DCQ  C4M   C  CH3   0  -0.414    5.3041   2.8232  -0.4193
 DCQ  C5    C  CR6   0   0.340    2.6706   1.0341  -0.4477
 DCQ  O5    O  O     0  -0.366    2.1389   2.1167  -0.5705
 DCQ  C1    C  CR6   0  -0.098    2.5744  -1.4084  -0.6664
 DCQ  C1M   C  CH3   0  -0.723    1.9516  -2.7266  -0.9945
 DCQ  C6    C  CR6   0  -0.017    1.9871  -0.2162  -0.8732
 DCQ  C7    C  CH2   0  -0.523    0.6208  -0.0562  -1.4672
 DCQ  C8    C  CH2   0  -0.417   -0.4832  -0.0910  -0.4062
 DCQ  C9    C  CH2   0  -0.418   -1.8733   0.0113  -1.0196
 DCQ  C10   C  CH2   0  -0.414   -2.9861  -0.0115   0.0203
 DCQ  C11   C  CH2   0  -0.412   -4.3794   0.0353  -0.5944
 DCQ  C12   C  CH2   0  -0.412   -5.4969   0.0193   0.4409
 DCQ  C13   C  CH2   0  -0.411   -6.8888   0.0354  -0.1787
 DCQ  C14   C  CH2   0  -0.406   -8.0099   0.0227   0.8524
 DCQ  C15   C  CH2   0  -0.419   -9.4011   0.0281   0.2300
 DCQ  C16   C  CH3   0  -0.663  -10.5144   0.0157   1.2683
 DCQ  H3M   H  HCH3  0   0.248    7.0490  -0.7338   2.3868
 DCQ  H3MA  H  HCH3  0   0.232    5.5493   0.1295   2.7781
 DCQ  H3MB  H  HCH3  0   0.233    5.5074  -1.6069   2.3934
 DCQ  H4M   H  HCH3  0   0.232    6.1799   2.2605  -0.7472
 DCQ  H4MA  H  HCH3  0   0.232    4.6848   3.0585  -1.2865
 DCQ  H4MB  H  HCH3  0   0.248    5.6314   3.7525   0.0404
 DCQ  H1M   H  HCH3  0   0.261    2.0321  -3.4117  -0.1510
 DCQ  H1MA  H  HCH3  0   0.256    0.8991  -2.6332  -1.2457
 DCQ  H1MB  H  HCH3  0   0.263    2.4603  -3.1984  -1.8373
 DCQ  H7    H  HCH2  0   0.258    0.5660   0.8879  -2.0112
 DCQ  H7A   H  HCH2  0   0.254    0.4453  -0.8414  -2.2038
 DCQ  H8    H  HCH2  0   0.225   -0.4070  -1.0191   0.1697
 DCQ  H8A   H  HCH2  0   0.229   -0.3327   0.7256   0.3058
 DCQ  H9    H  HCH2  0   0.214   -1.9450   0.9301  -1.6119
 DCQ  H9A   H  HCH2  0   0.213   -2.0168  -0.8152  -1.7241
 DCQ  H10   H  HCH2  0   0.209   -2.8920  -0.9145   0.6339
 DCQ  H10A  H  HCH2  0   0.209   -2.8607   0.8336   0.7060
 DCQ  H11   H  HCH2  0   0.207   -4.4730   0.9326  -1.2164
 DCQ  H11A  H  HCH2  0   0.207   -4.5026  -0.8156  -1.2736
 DCQ  H12   H  HCH2  0   0.206   -5.3928  -0.8689   1.0744
 DCQ  H12A  H  HCH2  0   0.207   -5.3857   0.8803   1.1095
 DCQ  H13   H  HCH2  0   0.206   -6.9920   0.9206  -0.8165
 DCQ  H13A  H  HCH2  0   0.206   -6.9985  -0.8284  -0.8440
 DCQ  H14   H  HCH2  0   0.205   -7.9043  -0.8595   1.4943
 DCQ  H14A  H  HCH2  0   0.206   -7.9056   0.8899   1.5143
 DCQ  H15   H  HCH2  0   0.210   -9.5058   0.9087  -0.4117
 DCQ  H15A  H  HCH2  0   0.210   -9.5042  -0.8391  -0.4301
 DCQ  H16   H  HCH3  0   0.216  -10.4522  -0.8717   1.9009
 DCQ  H16A  H  HCH3  0   0.216  -10.4537   0.8890   1.9202
 DCQ  H16B  H  HCH3  0   0.225  -11.5002   0.0198   0.8017

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
 DCQ  O2   C2    double  1.212  0.020  1.212
 DCQ  C2   C3    single  1.485  0.020  1.485
 DCQ  C2   C1    single  1.486  0.020  1.486
 DCQ  C3   O3    single  1.341  0.020  1.341
 DCQ  C3   C4    double  1.339  0.020  1.339
 DCQ  O3   C3M   single  1.428  0.020  1.428
 DCQ  C4   O4    single  1.341  0.020  1.341
 DCQ  C4   C5    single  1.485  0.020  1.485
 DCQ  O4   C4M   single  1.427  0.020  1.427
 DCQ  C5   O5    double  1.212  0.020  1.212
 DCQ  C5   C6    single  1.487  0.020  1.487
 DCQ  C1   C1M   single  1.494  0.020  1.494
 DCQ  C1   C6    double  1.345  0.020  1.345
 DCQ  C6   C7    single  1.498  0.020  1.498
 DCQ  C7   C8    single  1.532  0.020  1.532
 DCQ  C8   C9    single  1.523  0.020  1.523
 DCQ  C9   C10   single  1.523  0.020  1.523
 DCQ  C10  C11   single  1.524  0.020  1.524
 DCQ  C11  C12   single  1.523  0.020  1.523
 DCQ  C12  C13   single  1.524  0.020  1.524
 DCQ  C13  C14   single  1.523  0.020  1.523
 DCQ  C14  C15   single  1.524  0.020  1.524
 DCQ  C15  C16   single  1.522  0.020  1.522
 DCQ  C3M  H3M   single  0.970  0.020  1.090
 DCQ  C3M  H3MA  single  0.970  0.020  1.090
 DCQ  C3M  H3MB  single  0.970  0.020  1.090
 DCQ  C4M  H4M   single  0.970  0.020  1.090
 DCQ  C4M  H4MA  single  0.970  0.020  1.090
 DCQ  C4M  H4MB  single  0.970  0.020  1.090
 DCQ  C1M  H1M   single  0.970  0.020  1.090
 DCQ  C1M  H1MA  single  0.970  0.020  1.090
 DCQ  C1M  H1MB  single  0.970  0.020  1.090
 DCQ  C7   H7    single  0.970  0.020  1.090
 DCQ  C7   H7A   single  0.970  0.020  1.090
 DCQ  C8   H8    single  0.970  0.020  1.090
 DCQ  C8   H8A   single  0.970  0.020  1.090
 DCQ  C9   H9    single  0.970  0.020  1.090
 DCQ  C9   H9A   single  0.970  0.020  1.090
 DCQ  C10  H10   single  0.970  0.020  1.090
 DCQ  C10  H10A  single  0.970  0.020  1.090
 DCQ  C11  H11   single  0.970  0.020  1.090
 DCQ  C11  H11A  single  0.970  0.020  1.090
 DCQ  C12  H12   single  0.970  0.020  1.090
 DCQ  C12  H12A  single  0.970  0.020  1.090
 DCQ  C13  H13   single  0.970  0.020  1.090
 DCQ  C13  H13A  single  0.970  0.020  1.090
 DCQ  C14  H14   single  0.970  0.020  1.090
 DCQ  C14  H14A  single  0.970  0.020  1.090
 DCQ  C15  H15   single  0.970  0.020  1.090
 DCQ  C15  H15A  single  0.970  0.020  1.090
 DCQ  C16  H16   single  0.970  0.020  1.090
 DCQ  C16  H16A  single  0.970  0.020  1.090
 DCQ  C16  H16B  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
 DCQ  C1    C2   C3    119.40  3.000
 DCQ  C1    C2   O2    121.08  3.000
 DCQ  C3    C2   O2    119.51  3.000
 DCQ  C4    C3   O3    122.16  3.000
 DCQ  C4    C3   C2    120.29  3.000
 DCQ  O3    C3   C2    117.53  3.000
 DCQ  C3M   O3   C3    115.29  3.000
 DCQ  H3MB  C3M  H3MA  109.18  3.000
 DCQ  H3MB  C3M  H3M   108.85  3.000
 DCQ  H3MA  C3M  H3M   109.02  3.000
 DCQ  H3MB  C3M  O3    111.96  3.000
 DCQ  H3MA  C3M  O3    110.98  3.000
 DCQ  H3M   C3M  O3    106.76  3.000
 DCQ  C5    C4   O4    117.17  3.000
 DCQ  C5    C4   C3    120.41  3.000
 DCQ  O4    C4   C3    122.41  3.000
 DCQ  C4M   O4   C4    115.20  3.000
 DCQ  H4MB  C4M  H4MA  108.82  3.000
 DCQ  H4MB  C4M  H4M   109.04  3.000
 DCQ  H4MA  C4M  H4M   109.13  3.000
 DCQ  H4MB  C4M  O4    106.80  3.000
 DCQ  H4MA  C4M  O4    111.93  3.000
 DCQ  H4M   C4M  O4    111.04  3.000
 DCQ  C6    C5   O5    121.34  3.000
 DCQ  C6    C5   C4    119.41  3.000
 DCQ  O5    C5   C4    119.23  3.000
 DCQ  C6    C1   C1M   124.48  3.000
 DCQ  C6    C1   C2    120.29  3.000
 DCQ  C1M   C1   C2    115.21  3.000
 DCQ  H1MB  C1M  H1MA  108.07  3.000
 DCQ  H1MB  C1M  H1M   106.95  3.000
 DCQ  H1MA  C1M  H1M   107.74  3.000
 DCQ  H1MB  C1M  C1    110.88  3.000
 DCQ  H1MA  C1M  C1    112.26  3.000
 DCQ  H1M   C1M  C1    110.73  3.000
 DCQ  C7    C6   C1    123.63  3.000
 DCQ  C7    C6   C5    116.28  3.000
 DCQ  C1    C6   C5    120.04  3.000
 DCQ  H7A   C7   H7    106.15  3.000
 DCQ  H7A   C7   C8    109.60  3.000
 DCQ  H7    C7   C8    109.20  3.000
 DCQ  H7A   C7   C6    109.73  3.000
 DCQ  H7    C7   C6    109.63  3.000
 DCQ  C8    C7   C6    112.35  3.000
 DCQ  H8A   C8   H8    106.31  3.000
 DCQ  H8A   C8   C9    109.73  3.000
 DCQ  H8    C8   C9    109.41  3.000
 DCQ  H8A   C8   C7    109.56  3.000
 DCQ  H8    C8   C7    109.48  3.000
 DCQ  C9    C8   C7    112.18  3.000
 DCQ  H9A   C9   H9    106.06  3.000
 DCQ  H9A   C9   C10   109.40  3.000
 DCQ  H9    C9   C10   109.50  3.000
 DCQ  H9A   C9   C8    109.14  3.000
 DCQ  H9    C9   C8    109.50  3.000
 DCQ  C10   C9   C8    113.01  3.000
 DCQ  H10A  C10  H10   105.99  3.000
 DCQ  H10A  C10  C11   109.48  3.000
 DCQ  H10   C10  C11   109.26  3.000
 DCQ  H10A  C10  C9    109.40  3.000
 DCQ  H10   C10  C9    109.38  3.000
 DCQ  C11   C10  C9    113.09  3.000
 DCQ  H11A  C11  H11   105.93  3.000
 DCQ  H11A  C11  C12   109.31  3.000
 DCQ  H11   C11  C12   109.38  3.000
 DCQ  H11A  C11  C10   109.21  3.000
 DCQ  H11   C11  C10   109.41  3.000
 DCQ  C12   C11  C10   113.35  3.000
 DCQ  H12A  C12  H12   105.93  3.000
 DCQ  H12A  C12  C13   109.42  3.000
 DCQ  H12   C12  C13   109.30  3.000
 DCQ  H12A  C12  C11   109.39  3.000
 DCQ  H12   C12  C11   109.37  3.000
 DCQ  C13   C12  C11   113.18  3.000
 DCQ  H13A  C13  H13   105.90  3.000
 DCQ  H13A  C13  C14   109.31  3.000
 DCQ  H13   C13  C14   109.35  3.000
 DCQ  H13A  C13  C12   109.26  3.000
 DCQ  H13   C13  C12   109.35  3.000
 DCQ  C14   C13  C12   113.39  3.000
 DCQ  H14A  C14  H14   105.90  3.000
 DCQ  H14A  C14  C15   109.31  3.000
 DCQ  H14   C14  C15   109.27  3.000
 DCQ  H14A  C14  C13   109.40  3.000
 DCQ  H14   C14  C13   109.40  3.000
 DCQ  C15   C14  C13   113.29  3.000
 DCQ  H15A  C15  H15   105.95  3.000
 DCQ  H15A  C15  C16   109.63  3.000
 DCQ  H15   C15  C16   109.66  3.000
 DCQ  H15A  C15  C14   109.23  3.000
 DCQ  H15   C15  C14   109.24  3.000
 DCQ  C16   C15  C14   112.89  3.000
 DCQ  H16B  C16  H16A  107.63  3.000
 DCQ  H16B  C16  H16   107.61  3.000
 DCQ  H16A  C16  H16   107.52  3.000
 DCQ  H16B  C16  C15   111.66  3.000
 DCQ  H16A  C16  C15   111.11  3.000
 DCQ  H16   C16  C15   111.11  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
 DCQ  Var_01  C4   C3   O3   C3M    97.98  30.0  2
 DCQ  Var_02  C8   C7   C6   C5    -88.88  30.0  3
 DCQ  Var_03  H1M  C1M  C1   C2     50.17  30.0  3
 DCQ  Var_04  C9   C8   C7   C6   -177.52  30.0  3
 DCQ  Var_05  H3M  C3M  O3   C3    178.40  30.0  3
 DCQ  Var_06  H4M  C4M  O4   C4    -65.00  30.0  3
 DCQ  Var_07  C10  C9   C8   C7   -179.59  30.0  3
 DCQ  Var_08  C11  C10  C9   C8   -177.73  30.0  3
 DCQ  Var_09  C12  C11  C10  C9   -179.73  30.0  3
 DCQ  Var_10  C13  C12  C11  C10  -178.74  30.0  3
 DCQ  Var_11  C14  C13  C12  C11  -179.87  30.0  3
 DCQ  Var_12  C15  C14  C13  C12  -179.56  30.0  3
 DCQ  Var_13  C16  C15  C14  C13  -179.98  30.0  3
 DCQ  Var_14  H16  C16  C15  C14   -59.85  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
 DCQ  plan-1  O2   0.020
 DCQ  plan-1  C2   0.020
 DCQ  plan-1  C3   0.020
 DCQ  plan-1  O3   0.020
 DCQ  plan-1  C4   0.020
 DCQ  plan-1  O4   0.020
 DCQ  plan-1  C5   0.020
 DCQ  plan-1  O5   0.020
 DCQ  plan-1  C1   0.020
 DCQ  plan-1  C1M  0.020
 DCQ  plan-1  C6   0.020
 DCQ  plan-1  C7   0.020

