# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 00:06:53 2022
#   Inital geometry file: a 90 line input string
#   Ligand name: (3E,5E)-6,10-dimethylundeca-3,5,9-trien-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)=CCC\C(C)=C\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
 DXJ  DXJ  (3E,5E)-6,10-dimethylundeca-3,5,9-trien-2-one  ligand  34  14  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DXJ
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
 DXJ  C10  C  C1    0  -0.179   2.3378   0.2986  -0.1055
 DXJ  C13  C  CH3   0  -0.780   5.4846  -1.7902  -0.2029
 DXJ  C01  C  CH3   0  -0.719  -3.9232  -2.0299   0.5758
 DXJ  C02  C  C     0   0.082  -4.4454  -0.6940   0.1367
 DXJ  C03  C  C1    0  -0.257  -3.7400   0.4402   0.1424
 DXJ  C04  C  CH3   0  -0.706  -5.8721  -0.7153  -0.3311
 DXJ  C05  C  CH2   0  -0.492  -2.3135   0.6321   0.5526
 DXJ  C06  C  CH2   0  -0.490  -1.4118   0.8964  -0.6680
 DXJ  C07  C  C     0   0.121   0.0142   1.1656  -0.2829
 DXJ  C08  C  C1    0  -0.300   0.9421   0.2026  -0.4474
 DXJ  C09  C  CH3   0  -0.730   0.2856   2.5244   0.2788
 DXJ  C11  C  C1    0  -0.386   3.2187  -0.7013  -0.2920
 DXJ  C12  C  C     0   0.357   4.6384  -0.5766   0.0684
 DXJ  O14  O  O     0  -0.427   5.1049   0.4383   0.5556
 DXJ  H1   H  H     0   0.264   2.7044   1.2245   0.3248
 DXJ  H2   H  HCH3  0   0.263   5.4402  -2.0499  -1.2626
 DXJ  H3   H  HCH3  0   0.256   6.5217  -1.6284   0.0829
 DXJ  H4   H  HCH3  0   0.263   5.0925  -2.6507   0.3434
 DXJ  H5   H  HCH3  0   0.239  -2.8929  -2.0056   0.9245
 DXJ  H6   H  HCH3  0   0.235  -4.5403  -2.4354   1.3815
 DXJ  H7   H  HCH3  0   0.236  -3.9800  -2.7479  -0.2459
 DXJ  H8   H  H     0   0.224  -4.2333   1.3407  -0.2168
 DXJ  H9   H  HCH3  0   0.231  -6.5359  -1.0741   0.4603
 DXJ  H10  H  HCH3  0   0.236  -6.2201   0.2691  -0.6432
 DXJ  H11  H  HCH3  0   0.231  -5.9972  -1.4019  -1.1726
 DXJ  H12  H  HCH2  0   0.239  -2.2526   1.4817   1.2385
 DXJ  H13  H  HCH2  0   0.242  -1.9265  -0.2307   1.0959
 DXJ  H14  H  HCH2  0   0.248  -1.4669   0.0330  -1.3341
 DXJ  H15  H  HCH2  0   0.243  -1.8090   1.7532  -1.2220
 DXJ  H16  H  H     0   0.242   0.6206  -0.7416  -0.8780
 DXJ  H17  H  HCH3  0   0.251  -0.3861   2.7413   1.1117
 DXJ  H18  H  HCH3  0   0.252   1.3042   2.6630   0.6320
 DXJ  H19  H  HCH3  0   0.253   0.0871   3.2840  -0.4813
 DXJ  H20  H  H     0   0.257   2.8911  -1.6428  -0.7205

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
 DXJ  C04  C02  single  1.502  0.020  1.502
 DXJ  C01  C02  single  1.500  0.020  1.500
 DXJ  C02  C03  double  1.336  0.020  1.336
 DXJ  C03  C05  single  1.497  0.020  1.497
 DXJ  C05  C06  single  1.540  0.020  1.540
 DXJ  C09  C07  single  1.495  0.020  1.495
 DXJ  C06  C07  single  1.501  0.020  1.501
 DXJ  C07  C08  double  1.347  0.020  1.347
 DXJ  C08  C10  single  1.440  0.020  1.440
 DXJ  C10  C11  double  1.346  0.020  1.346
 DXJ  O14  C12  double  1.219  0.020  1.219
 DXJ  C11  C12  single  1.470  0.020  1.470
 DXJ  C12  C13  single  1.504  0.020  1.504
 DXJ  C10  H1   single  0.930  0.020  1.080
 DXJ  C13  H2   single  0.970  0.020  1.090
 DXJ  C13  H3   single  0.970  0.020  1.090
 DXJ  C13  H4   single  0.970  0.020  1.090
 DXJ  C01  H5   single  0.970  0.020  1.090
 DXJ  C01  H6   single  0.970  0.020  1.090
 DXJ  C01  H7   single  0.970  0.020  1.090
 DXJ  C03  H8   single  0.930  0.020  1.080
 DXJ  C04  H9   single  0.970  0.020  1.090
 DXJ  C04  H10  single  0.970  0.020  1.090
 DXJ  C04  H11  single  0.970  0.020  1.090
 DXJ  C05  H12  single  0.970  0.020  1.090
 DXJ  C05  H13  single  0.970  0.020  1.090
 DXJ  C06  H14  single  0.970  0.020  1.090
 DXJ  C06  H15  single  0.970  0.020  1.090
 DXJ  C08  H16  single  0.930  0.020  1.080
 DXJ  C09  H17  single  0.970  0.020  1.090
 DXJ  C09  H18  single  0.970  0.020  1.090
 DXJ  C09  H19  single  0.970  0.020  1.090
 DXJ  C11  H20  single  0.930  0.020  1.080

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
 DXJ  H1   C10  C11  117.90  3.000
 DXJ  H1   C10  C08  118.59  3.000
 DXJ  C11  C10  C08  123.51  3.000
 DXJ  H4   C13  H3   109.15  3.000
 DXJ  H4   C13  H2   106.46  3.000
 DXJ  H3   C13  H2   109.22  3.000
 DXJ  H4   C13  C12  110.09  3.000
 DXJ  H3   C13  C12  111.65  3.000
 DXJ  H2   C13  C12  110.12  3.000
 DXJ  H7   C01  H6   106.33  3.000
 DXJ  H7   C01  H5   107.75  3.000
 DXJ  H6   C01  H5   107.86  3.000
 DXJ  H7   C01  C02  110.30  3.000
 DXJ  H6   C01  C02  110.47  3.000
 DXJ  H5   C01  C02  113.80  3.000
 DXJ  C04  C02  C03  121.01  3.000
 DXJ  C03  C02  C01  124.83  3.000
 DXJ  C04  C02  C01  114.16  3.000
 DXJ  H8   C03  C05  114.62  3.000
 DXJ  H8   C03  C02  117.52  3.000
 DXJ  C05  C03  C02  127.84  3.000
 DXJ  H11  C04  H10  108.08  3.000
 DXJ  H11  C04  H9   106.35  3.000
 DXJ  H10  C04  H9   108.05  3.000
 DXJ  H11  C04  C02  110.94  3.000
 DXJ  H10  C04  C02  112.33  3.000
 DXJ  H9   C04  C02  110.85  3.000
 DXJ  H13  C05  H12  106.41  3.000
 DXJ  H13  C05  C06  108.83  3.000
 DXJ  H12  C05  C06  109.34  3.000
 DXJ  H13  C05  C03  111.92  3.000
 DXJ  H12  C05  C03  108.94  3.000
 DXJ  C06  C05  C03  111.27  3.000
 DXJ  H15  C06  H14  106.97  3.000
 DXJ  H15  C06  C07  109.51  3.000
 DXJ  H14  C06  C07  110.26  3.000
 DXJ  H15  C06  C05  108.84  3.000
 DXJ  H14  C06  C05  108.56  3.000
 DXJ  C07  C06  C05  112.55  3.000
 DXJ  C09  C07  C08  124.77  3.000
 DXJ  C08  C07  C06  119.64  3.000
 DXJ  C09  C07  C06  115.58  3.000
 DXJ  H16  C08  C07  117.76  3.000
 DXJ  H16  C08  C10  116.03  3.000
 DXJ  C07  C08  C10  126.22  3.000
 DXJ  H19  C09  H18  107.91  3.000
 DXJ  H19  C09  H17  106.30  3.000
 DXJ  H18  C09  H17  107.66  3.000
 DXJ  H19  C09  C07  109.72  3.000
 DXJ  H18  C09  C07  114.09  3.000
 DXJ  H17  C09  C07  110.82  3.000
 DXJ  H20  C11  C12  117.51  3.000
 DXJ  H20  C11  C10  120.12  3.000
 DXJ  C12  C11  C10  122.36  3.000
 DXJ  O14  C12  C11  122.57  3.000
 DXJ  C11  C12  C13  115.51  3.000
 DXJ  O14  C12  C13  121.92  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
 DXJ  Var_01  C09  C07  C08  C10     0.69   0.0  2
 DXJ  Var_02  C05  C03  C02  C01     0.97   0.0  2
 DXJ  Var_03  C12  C11  C10  C08  -179.90   0.0  2
 DXJ  Var_04  O14  C12  C11  C10    -0.10  30.0  2
 DXJ  Var_05  C06  C05  C03  C02   108.12  30.0  3
 DXJ  Var_06  C07  C06  C05  C03   176.95  30.0  3
 DXJ  Var_07  C11  C10  C08  C07   179.89  30.0  2
 DXJ  Var_08  H9   C04  C02  C01    59.05  30.0  3
 DXJ  Var_09  H5   C01  C02  C03     0.75  30.0  3
 DXJ  Var_10  H17  C09  C07  C06    53.07  30.0  3
 DXJ  Var_11  H2   C13  C12  C11    58.27  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
 DXJ  plan-1  C13  0.020
 DXJ  plan-1  C11  0.020
 DXJ  plan-1  C12  0.020
 DXJ  plan-1  O14  0.020
 DXJ  plan-2  C01  0.020
 DXJ  plan-2  C02  0.020
 DXJ  plan-2  C03  0.020
 DXJ  plan-2  C04  0.020
 DXJ  plan-2  C05  0.020
 DXJ  plan-2  H8   0.020
 DXJ  plan-3  C10  0.020
 DXJ  plan-3  C06  0.020
 DXJ  plan-3  C07  0.020
 DXJ  plan-3  C08  0.020
 DXJ  plan-3  C09  0.020
 DXJ  plan-3  H16  0.020
 DXJ  plan-4  C10  0.020
 DXJ  plan-4  C08  0.020
 DXJ  plan-4  C11  0.020
 DXJ  plan-4  C12  0.020
 DXJ  plan-4  H1   0.020
 DXJ  plan-4  H20  0.020

