# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 00:57:41 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: (2E)-3,7-dimethylocta-2,6-dienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)=CCC\C(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
 58X  58X  '(2E)-3,7-dimethylocta-2,6-dienoic acid'  ligand  27  12  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_58X
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
 58X  CAA  C  CH3    0  -0.706   4.9209   0.1438  -0.3501
 58X  CAB  C  C      0   0.087   3.5058   0.2948   0.1280
 58X  CAC  C  C1     0  -0.261   2.6669  -0.7444   0.1375
 58X  CAD  C  CH2    0  -0.494   1.2293  -0.7508   0.5597
 58X  CAE  C  CH2    0  -0.485   0.2832  -0.6691  -0.6481
 58X  CAF  C  CH3    0  -0.720   3.1442   1.6823   0.5680
 58X  CAG  C  C      0   0.162  -1.1732  -0.6762  -0.2641
 58X  CAH  C  C1     0  -0.471  -1.9313   0.3950  -0.5345
 58X  CAI  C  CH3    0  -0.733  -1.6390  -1.9336   0.4105
 58X  CAJ  C  C      0   0.383  -3.3936   0.6305  -0.2508
 58X  OAK  O  OC    -1  -0.627  -3.8753   1.6519  -0.7908
 58X  OAL  O  O      0  -0.602  -4.0162  -0.1673   0.4821
 58X  H1   H  HCH3   0   0.230   5.1253   0.8109  -1.1918
 58X  H2   H  HCH3   0   0.230   5.6302   0.4156   0.4364
 58X  H3   H  HCH3   0   0.235   5.1417  -0.8758  -0.6649
 58X  H4   H  H      0   0.221   3.0424  -1.6961  -0.2320
 58X  H5   H  HCH2   0   0.237   1.0299  -1.6695   1.1180
 58X  H6   H  HCH2   0   0.236   1.0081   0.0735   1.2409
 58X  H7   H  HCH2   0   0.233   0.5189   0.2357  -1.2128
 58X  H8   H  HCH2   0   0.228   0.4864  -1.5167  -1.3133
 58X  H9   H  HCH3   0   0.238   2.1195   1.7750   0.9221
 58X  H10  H  HCH3   0   0.234   3.8075   2.0216   1.3677
 58X  H11  H  HCH3   0   0.235   3.2726   2.3865  -0.2578
 58X  H12  H  H      0   0.199  -1.4400   1.2185  -1.0479
 58X  H13  H  HCH3   0   0.234  -1.3906  -1.9203   1.4752
 58X  H14  H  HCH3   0   0.255  -2.7117  -2.0702   0.3323
 58X  H15  H  HCH3   0   0.220  -1.1305  -2.8013  -0.0143

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
 58X  CAI  CAG  single  1.501  0.020  1.501
 58X  CAF  CAB  single  1.500  0.020  1.500
 58X  OAL  CAJ  deloc   1.250  0.020  1.250
 58X  CAG  CAE  single  1.506  0.020  1.506
 58X  CAG  CAH  double  1.340  0.020  1.340
 58X  CAB  CAC  double  1.336  0.020  1.336
 58X  CAB  CAA  single  1.501  0.020  1.501
 58X  CAE  CAD  single  1.536  0.020  1.536
 58X  CAD  CAC  single  1.498  0.020  1.498
 58X  CAJ  CAH  single  1.508  0.020  1.508
 58X  CAJ  OAK  deloc   1.252  0.020  1.252
 58X  CAA  H1   single  0.970  0.020  1.090
 58X  CAA  H2   single  0.970  0.020  1.090
 58X  CAA  H3   single  0.970  0.020  1.090
 58X  CAC  H4   single  0.930  0.020  1.080
 58X  CAD  H5   single  0.970  0.020  1.090
 58X  CAD  H6   single  0.970  0.020  1.090
 58X  CAE  H7   single  0.970  0.020  1.090
 58X  CAE  H8   single  0.970  0.020  1.090
 58X  CAF  H9   single  0.970  0.020  1.090
 58X  CAF  H10  single  0.970  0.020  1.090
 58X  CAF  H11  single  0.970  0.020  1.090
 58X  CAH  H12  single  0.930  0.020  1.080
 58X  CAI  H13  single  0.970  0.020  1.090
 58X  CAI  H14  single  0.970  0.020  1.090
 58X  CAI  H15  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
 58X  H3   CAA  H2   108.00  3.000
 58X  H3   CAA  H1   108.10  3.000
 58X  H2   CAA  H1   106.31  3.000
 58X  H3   CAA  CAB  112.15  3.000
 58X  H2   CAA  CAB  110.94  3.000
 58X  H1   CAA  CAB  111.10  3.000
 58X  CAF  CAB  CAC  124.49  3.000
 58X  CAC  CAB  CAA  121.07  3.000
 58X  CAF  CAB  CAA  114.44  3.000
 58X  H4   CAC  CAD  115.04  3.000
 58X  H4   CAC  CAB  117.48  3.000
 58X  CAD  CAC  CAB  127.44  3.000
 58X  H6   CAD  H5   106.19  3.000
 58X  H6   CAD  CAE  108.99  3.000
 58X  H5   CAD  CAE  109.50  3.000
 58X  H6   CAD  CAC  111.53  3.000
 58X  H5   CAD  CAC  108.82  3.000
 58X  CAE  CAD  CAC  111.66  3.000
 58X  H8   CAE  H7   106.66  3.000
 58X  H8   CAE  CAG  109.28  3.000
 58X  H7   CAE  CAG  110.14  3.000
 58X  H8   CAE  CAD  108.76  3.000
 58X  H7   CAE  CAD  108.52  3.000
 58X  CAG  CAE  CAD  113.25  3.000
 58X  H11  CAF  H10  106.35  3.000
 58X  H11  CAF  H9   107.56  3.000
 58X  H10  CAF  H9   107.88  3.000
 58X  H11  CAF  CAB  110.25  3.000
 58X  H10  CAF  CAB  110.83  3.000
 58X  H9   CAF  CAB  113.66  3.000
 58X  CAI  CAG  CAH  125.79  3.000
 58X  CAH  CAG  CAE  119.46  3.000
 58X  CAI  CAG  CAE  114.75  3.000
 58X  H12  CAH  CAJ  114.11  3.000
 58X  H12  CAH  CAG  116.42  3.000
 58X  CAJ  CAH  CAG  129.46  3.000
 58X  H15  CAI  H14  109.43  3.000
 58X  H15  CAI  H13  106.42  3.000
 58X  H14  CAI  H13  107.25  3.000
 58X  H15  CAI  CAG  110.26  3.000
 58X  H14  CAI  CAG  112.34  3.000
 58X  H13  CAI  CAG  110.92  3.000
 58X  OAL  CAJ  OAK  125.61  3.000
 58X  OAK  CAJ  CAH  114.80  3.000
 58X  OAL  CAJ  CAH  119.59  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
 58X  Var_01  CAD  CAC  CAB  CAA  -178.89   0.0  2
 58X  Var_02  CAJ  CAH  CAG  CAE  -179.81   0.0  2
 58X  Var_03  CAE  CAD  CAC  CAB    99.00  30.0  1
 58X  Var_04  CAG  CAE  CAD  CAC   179.87  30.0  1
 58X  Var_05  CAI  CAG  CAE  CAD   -63.52  30.0  2
 58X  Var_06  OAL  CAJ  CAH  CAG    10.24  30.0  2
 58X  Var_07  H9   CAF  CAB  CAA  -179.37  30.0  3
 58X  Var_08  H1   CAA  CAB  CAC   121.02  30.0  3
 58X  Var_09  H13  CAI  CAG  CAE    81.80  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
 58X  plan-1  CAH  0.020
 58X  plan-1  CAJ  0.020
 58X  plan-1  OAK  0.020
 58X  plan-1  OAL  0.020
 58X  plan-2  CAE  0.020
 58X  plan-2  CAG  0.020
 58X  plan-2  CAH  0.020
 58X  plan-2  CAI  0.020
 58X  plan-2  CAJ  0.020
 58X  plan-2  H12  0.020
 58X  plan-3  CAA  0.020
 58X  plan-3  CAB  0.020
 58X  plan-3  CAC  0.020
 58X  plan-3  CAD  0.020
 58X  plan-3  CAF  0.020
 58X  plan-3  H4   0.020

