# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 20 22:38:16 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: (2E,4E,6E)-octa-2,4,6-trienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C/C=C/C=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
 OTT  OTT  '(2E,4E,6E)-octa-2,4,6-trienoic acid'  ligand  20  10  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_OTT
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
 OTT  C1    C  C     0   0.525   3.2474   0.1587   0.0454
 OTT  C2    C  C1    0  -0.424   1.9629  -0.5345  -0.0810
 OTT  C3    C  C1    0  -0.168   0.8019   0.1323   0.0356
 OTT  C4    C  C1    0  -0.261  -0.4953  -0.4759  -0.0756
 OTT  C5    C  C1    0  -0.227  -1.6332   0.2370   0.0410
 OTT  C6    C  C1    0  -0.239  -2.9588  -0.3220  -0.0618
 OTT  C7    C  C1    0  -0.211  -4.0701   0.4164   0.0606
 OTT  C8    C  CH3   0  -0.713  -5.4584  -0.1067  -0.0410
 OTT  O11   O  O     0  -0.459   3.3901   1.3389   0.2803
 OTT  O12   O  OH1   0  -0.606   4.2754  -0.6705  -0.1302
 OTT  H2    H  H     0   0.274   1.9746  -1.6009  -0.2732
 OTT  H3    H  H     0   0.270   0.8260   1.2021   0.2231
 OTT  H4    H  H     0   0.258  -0.5442  -1.5452  -0.2582
 OTT  H5    H  H     0   0.262  -1.5632   1.3068   0.2221
 OTT  H6    H  H     0   0.250  -3.0398  -1.3898  -0.2466
 OTT  H7    H  H     0   0.253  -3.9664   1.4821   0.2480
 OTT  H8    H  HCH3  0   0.242  -5.4798  -1.1788  -0.2335
 OTT  H8A   H  HCH3  0   0.248  -6.0153   0.0891   0.8782
 OTT  H8B   H  HCH3  0   0.248  -6.0037   0.3979  -0.8420
 OTT  HO12  H  HOH1  0   0.479   5.1075  -0.1823  -0.0465

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
 OTT  C1   C2    single  1.465  0.020  1.465
 OTT  C1   O11   double  1.212  0.020  1.212
 OTT  C1   O12   single  1.332  0.020  1.332
 OTT  C2   C3    double  1.344  0.020  1.344
 OTT  C3   C4    single  1.437  0.020  1.437
 OTT  C4   C5    double  1.348  0.020  1.348
 OTT  C5   C6    single  1.442  0.020  1.442
 OTT  C6   C7    double  1.340  0.020  1.340
 OTT  C7   C8    single  1.487  0.020  1.487
 OTT  C2   H2    single  0.930  0.020  1.080
 OTT  C3   H3    single  0.930  0.020  1.080
 OTT  C4   H4    single  0.930  0.020  1.080
 OTT  C5   H5    single  0.930  0.020  1.080
 OTT  C6   H6    single  0.930  0.020  1.080
 OTT  C7   H7    single  0.930  0.020  1.080
 OTT  C8   H8    single  0.970  0.020  1.090
 OTT  C8   H8A   single  0.970  0.020  1.090
 OTT  C8   H8B   single  0.970  0.020  1.090
 OTT  O12  HO12  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
 OTT  O12   C1   O11  122.74  3.000
 OTT  O12   C1   C2   111.75  3.000
 OTT  O11   C1   C2   125.51  3.000
 OTT  H2    C2   C3   120.86  3.000
 OTT  H2    C2   C1   118.13  3.000
 OTT  C3    C2   C1   121.01  3.000
 OTT  H3    C3   C4   116.76  3.000
 OTT  H3    C3   C2   118.97  3.000
 OTT  C4    C3   C2   124.27  3.000
 OTT  H4    C4   C5   119.83  3.000
 OTT  H4    C4   C3   118.06  3.000
 OTT  C5    C4   C3   122.11  3.000
 OTT  H5    C5   C6   116.90  3.000
 OTT  H5    C5   C4   118.72  3.000
 OTT  C6    C5   C4   124.38  3.000
 OTT  H6    C6   C7   119.69  3.000
 OTT  H6    C6   C5   117.48  3.000
 OTT  C7    C6   C5   122.83  3.000
 OTT  H7    C7   C8   116.47  3.000
 OTT  H7    C7   C6   118.49  3.000
 OTT  C8    C7   C6   125.04  3.000
 OTT  H8B   C8   H8A  106.24  3.000
 OTT  H8B   C8   H8   108.37  3.000
 OTT  H8A   C8   H8   108.36  3.000
 OTT  H8B   C8   C7   110.70  3.000
 OTT  H8A   C8   C7   110.82  3.000
 OTT  H8    C8   C7   112.13  3.000
 OTT  HO12  O12  C1   109.74  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
 OTT  CONST_01  HO12  O12  C1  C2   180.00   0.0  0
 OTT  Var_01    C4    C3   C2  C1  -180.00   0.0  2
 OTT  Var_02    C6    C5   C4  C3  -179.99   0.0  2
 OTT  Var_03    C8    C7   C6  C5   179.78   0.0  2
 OTT  Var_04    C5    C4   C3  C2  -179.59  30.0  2
 OTT  Var_05    O11   C1   C2  C3     1.37  30.0  2
 OTT  Var_06    C7    C6   C5  C4   179.94  30.0  2
 OTT  Var_07    H8    C8   C7  C6    -0.21  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
 OTT  plan-1  C1    0.020
 OTT  plan-1  C2    0.020
 OTT  plan-1  O11   0.020
 OTT  plan-1  O12   0.020
 OTT  plan-1  HO12  0.020
 OTT  plan-2  C1    0.020
 OTT  plan-2  C2    0.020
 OTT  plan-2  C3    0.020
 OTT  plan-2  C4    0.020
 OTT  plan-2  H2    0.020
 OTT  plan-2  H3    0.020
 OTT  plan-3  C3    0.020
 OTT  plan-3  C4    0.020
 OTT  plan-3  C5    0.020
 OTT  plan-3  C6    0.020
 OTT  plan-3  H4    0.020
 OTT  plan-3  H5    0.020
 OTT  plan-4  C5    0.020
 OTT  plan-4  C6    0.020
 OTT  plan-4  C7    0.020
 OTT  plan-4  C8    0.020
 OTT  plan-4  H6    0.020
 OTT  plan-4  H7    0.020

