# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 11:33:17 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  19  10  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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   0.392   3.3772   0.0289  -0.0490
 OTT  C2   C  C1     0  -0.437   2.0044  -0.5935  -0.0064
 OTT  C3   C  C1     0  -0.204   0.8650   0.1110  -0.0250
 OTT  C4   C  C1     0  -0.255  -0.4539  -0.4769   0.0160
 OTT  C5   C  C1     0  -0.250  -1.5915   0.2416  -0.0020
 OTT  C6   C  C1     0  -0.219  -2.9157  -0.3374   0.0347
 OTT  C7   C  C1     0  -0.262  -4.0423   0.3857   0.0105
 OTT  C8   C  CH3    0  -0.707  -5.4241  -0.1889   0.0261
 OTT  O11  O  O      0  -0.605   3.4495   1.2711  -0.1457
 OTT  O12  O  OC    -1  -0.620   4.3352  -0.7709   0.0176
 OTT  H2   H  H      0   0.222   1.9535  -1.6785   0.0442
 OTT  H3   H  H      0   0.237   0.9208   1.1952  -0.0746
 OTT  H4   H  H      0   0.242  -0.5155  -1.5616   0.0611
 OTT  H5   H  H      0   0.245  -1.5290   1.3264  -0.0477
 OTT  H6   H  H      0   0.240  -2.9767  -1.4223   0.0868
 OTT  H7   H  H      0   0.248  -3.9575   1.4678  -0.0373
 OTT  H8   H  HCH3   0   0.247  -5.7027  -0.5790  -0.9560
 OTT  H8A  H  HCH3   0   0.243  -5.5143  -1.0132   0.7345
 OTT  H8B  H  HCH3   0   0.241  -6.1644   0.5646   0.2896

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  1.508  0.020  1.508
 OTT  C1  O11  deloc   1.248  0.020  1.248
 OTT  C1  O12  deloc   1.250  0.020  1.250
 OTT  C2  C3   double  1.340  0.020  1.340
 OTT  C3  C4   single  1.445  0.020  1.445
 OTT  C4  C5   double  1.346  0.020  1.346
 OTT  C5  C6   single  1.446  0.020  1.446
 OTT  C6  C7   double  1.339  0.020  1.339
 OTT  C7  C8   single  1.497  0.020  1.497
 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

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  126.63  3.000
 OTT  O12  C1  C2   115.61  3.000
 OTT  O11  C1  C2   117.76  3.000
 OTT  H2   C2  C3   119.05  3.000
 OTT  H2   C2  C1   117.11  3.000
 OTT  C3   C2  C1   123.83  3.000
 OTT  H3   C3  C4   117.01  3.000
 OTT  H3   C3  C2   118.79  3.000
 OTT  C4   C3  C2   124.20  3.000
 OTT  H4   C4  C5   119.03  3.000
 OTT  H4   C4  C3   117.32  3.000
 OTT  C5   C4  C3   123.65  3.000
 OTT  H5   C5  C6   116.95  3.000
 OTT  H5   C5  C4   118.98  3.000
 OTT  C6   C5  C4   124.07  3.000
 OTT  H6   C6  C7   119.49  3.000
 OTT  H6   C6  C5   116.87  3.000
 OTT  C7   C6  C5   123.64  3.000
 OTT  H7   C7  C8   117.06  3.000
 OTT  H7   C7  C6   118.23  3.000
 OTT  C8   C7  C6   124.70  3.000
 OTT  H8B  C8  H8A  108.04  3.000
 OTT  H8B  C8  H8   106.93  3.000
 OTT  H8A  C8  H8   107.02  3.000
 OTT  H8B  C8  C7   111.39  3.000
 OTT  H8A  C8  C7   111.93  3.000
 OTT  H8   C8  C7   111.29  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  Var_01  C4   C3  C2  C1  -179.97   0.0  2
 OTT  Var_02  C6   C5  C4  C3   179.81   0.0  2
 OTT  Var_03  C8   C7  C6  C5   179.01   0.0  2
 OTT  Var_04  C5   C4  C3  C2   179.94  30.0  2
 OTT  Var_05  O11  C1  C2  C3    -2.12  30.0  2
 OTT  Var_06  C7   C6  C5  C4  -179.70  30.0  2
 OTT  Var_07  H8   C8  C7  C6   -77.28  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-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

