# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 11:43:36 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  28  12  .  2021-08-05  2021-08-05  
;
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   4.9614   0.0923  -0.3299
 58X  CAB  C  C     0   0.087   3.5442   0.3145   0.1114
 58X  CAC  C  C1    0  -0.262   2.6754  -0.6985   0.1630
 58X  CAD  C  CH2   0  -0.494   1.2351  -0.6464   0.5693
 58X  CAE  C  CH2   0  -0.506   0.3015  -0.7017  -0.6515
 58X  CAF  C  CH3   0  -0.720   3.2219   1.7340   0.4712
 58X  CAG  C  C     0   0.189  -1.1422  -0.7253  -0.2458
 58X  CAH  C  C1    0  -0.438  -1.8917   0.3715  -0.4431
 58X  CAI  C  CH3   0  -0.724  -1.6254  -1.9984   0.3830
 58X  CAJ  C  C     0   0.519  -3.3019   0.5046  -0.0726
 58X  OAK  O  OH1   0  -0.610  -3.7753   1.7081  -0.4067
 58X  OAL  O  O     0  -0.456  -3.9909  -0.3337   0.4657
 58X  H1   H  HCH3  0   0.231   5.2052   0.7103  -1.1980
 58X  H2   H  HCH3  0   0.232   5.6639   0.3782   0.4575
 58X  H3   H  HCH3  0   0.236   5.1518  -0.9484  -0.5906
 58X  H4   H  H     0   0.225   3.0286  -1.6800  -0.1450
 58X  H5   H  HCH2  0   0.245   1.0234  -1.4931   1.2290
 58X  H6   H  HCH2  0   0.245   1.0091   0.2521   1.1454
 58X  H7   H  HCH2  0   0.250   0.5071   0.1552  -1.2958
 58X  H8   H  HCH2  0   0.252   0.5236  -1.6030  -1.2319
 58X  H9   H  HCH3  0   0.239   2.1924   1.8821   0.7901
 58X  H10  H  HCH3  0   0.236   3.8756   2.0876   1.2725
 58X  H11  H  HCH3  0   0.237   3.3999   2.3915  -0.3835
 58X  H12  H  H     0   0.259  -1.4369   1.2363  -0.9124
 58X  H13  H  HCH3  0   0.256  -1.9642  -1.8420   1.4069
 58X  H14  H  HCH3  0   0.260  -2.4686  -2.4149  -0.1672
 58X  H15  H  HCH3  0   0.242  -0.8339  -2.7457   0.4006
 58X  H16  H  HOH1  0   0.477  -4.7077   1.7728  -0.1536

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  1.500  0.020  1.500
 58X  CAF  CAB  single  1.499  0.020  1.499
 58X  OAL  CAJ  double  1.211  0.020  1.211
 58X  CAG  CAE  single  1.500  0.020  1.500
 58X  CAG  CAH  double  1.343  0.020  1.343
 58X  CAB  CAC  double  1.335  0.020  1.335
 58X  CAB  CAA  single  1.501  0.020  1.501
 58X  CAE  CAD  single  1.538  0.020  1.538
 58X  CAD  CAC  single  1.497  0.020  1.497
 58X  CAJ  CAH  single  1.464  0.020  1.464
 58X  CAJ  OAK  single  1.336  0.020  1.336
 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
 58X  OAK  H16  single  0.850  0.020  0.980

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   108.05  3.000
 58X  H3   CAA  H1   108.12  3.000
 58X  H2   CAA  H1   106.31  3.000
 58X  H3   CAA  CAB  112.13  3.000
 58X  H2   CAA  CAB  110.87  3.000
 58X  H1   CAA  CAB  111.12  3.000
 58X  CAF  CAB  CAC  124.68  3.000
 58X  CAC  CAB  CAA  120.88  3.000
 58X  CAF  CAB  CAA  114.44  3.000
 58X  H4   CAC  CAD  114.87  3.000
 58X  H4   CAC  CAB  117.54  3.000
 58X  CAD  CAC  CAB  127.58  3.000
 58X  H6   CAD  H5   106.19  3.000
 58X  H6   CAD  CAE  108.84  3.000
 58X  H5   CAD  CAE  109.47  3.000
 58X  H6   CAD  CAC  111.79  3.000
 58X  H5   CAD  CAC  108.84  3.000
 58X  CAE  CAD  CAC  111.55  3.000
 58X  H8   CAE  H7   107.17  3.000
 58X  H8   CAE  CAG  109.01  3.000
 58X  H7   CAE  CAG  110.69  3.000
 58X  H8   CAE  CAD  109.10  3.000
 58X  H7   CAE  CAD  109.02  3.000
 58X  CAG  CAE  CAD  111.73  3.000
 58X  H11  CAF  H10  106.34  3.000
 58X  H11  CAF  H9   107.55  3.000
 58X  H10  CAF  H9   107.88  3.000
 58X  H11  CAF  CAB  110.29  3.000
 58X  H10  CAF  CAB  110.71  3.000
 58X  H9   CAF  CAB  113.74  3.000
 58X  CAI  CAG  CAH  125.10  3.000
 58X  CAH  CAG  CAE  118.98  3.000
 58X  CAI  CAG  CAE  115.91  3.000
 58X  H12  CAH  CAJ  116.18  3.000
 58X  H12  CAH  CAG  118.75  3.000
 58X  CAJ  CAH  CAG  125.07  3.000
 58X  H15  CAI  H14  107.96  3.000
 58X  H15  CAI  H13  108.02  3.000
 58X  H14  CAI  H13  106.78  3.000
 58X  H15  CAI  CAG  110.80  3.000
 58X  H14  CAI  CAG  111.23  3.000
 58X  H13  CAI  CAG  111.85  3.000
 58X  OAL  CAJ  OAK  122.21  3.000
 58X  OAK  CAJ  CAH  111.10  3.000
 58X  OAL  CAJ  CAH  126.69  3.000
 58X  H16  OAK  CAJ  109.65  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  CONST_01  H16  OAK  CAJ  CAH   180.00   0.0  0
 58X  Var_01    CAD  CAC  CAB  CAA  -179.58   0.0  2
 58X  Var_02    CAJ  CAH  CAG  CAE  -178.63   0.0  2
 58X  Var_03    CAE  CAD  CAC  CAB   103.14  30.0  1
 58X  Var_04    CAG  CAE  CAD  CAC   176.89  30.0  1
 58X  Var_05    CAI  CAG  CAE  CAD   -71.26  30.0  2
 58X  Var_06    OAL  CAJ  CAH  CAG     0.54  30.0  2
 58X  Var_07    H9   CAF  CAB  CAA  -179.95  30.0  3
 58X  Var_08    H1   CAA  CAB  CAC   121.61  30.0  3
 58X  Var_09    H13  CAI  CAG  CAE   117.73  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-1  H16  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

