# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 04:39:20 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: (2E,5S)-5-methylhept-2-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](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
 39Y  39Y  '(2E,5S)-5-methylhept-2-enoic acid'  ligand  23  10  .  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_39Y
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
 39Y  O    O  O      0  -0.609  -3.1250  -1.1865  -0.0658
 39Y  C8   C  C      0   0.387  -2.9661   0.0361   0.1306
 39Y  C9   C  C1     0  -0.425  -1.6043   0.6270  -0.1485
 39Y  C10  C  C1     0  -0.163  -0.5593  -0.0794  -0.5748
 39Y  C11  C  CH2    0  -0.470   0.7987   0.4810  -0.8479
 39Y  C12  C  CH1    0  -0.219   1.8977  -0.0568   0.0832
 39Y  C13  C  CH3    0  -0.669   2.0971  -1.5584  -0.0930
 39Y  C14  C  CH2    0  -0.405   3.1950   0.7199  -0.1529
 39Y  C15  C  CH3    0  -0.669   4.3210   0.3815   0.8158
 39Y  H14  H  H      0   0.210  -1.4920   1.6968   0.0153
 39Y  H15  H  H      0   0.230  -0.6967  -1.1453  -0.7343
 39Y  H16  H  HCH2   0   0.222   1.0843   0.2536  -1.8828
 39Y  H17  H  HCH2   0   0.229   0.7658   1.5715  -0.7656
 39Y  H18  H  HCH1   0   0.212   1.5767   0.1329   1.1153
 39Y  H21  H  HCH3   0   0.231   1.1812  -2.1173   0.1011
 39Y  H19  H  HCH3   0   0.212   2.4153  -1.7863  -1.1136
 39Y  H20  H  HCH3   0   0.232   2.8574  -1.9476   0.5846
 39Y  H23  H  HCH2   0   0.207   3.5324   0.5488  -1.1815
 39Y  H22  H  HCH2   0   0.217   2.9779   1.7901  -0.0798
 39Y  H26  H  HCH3   0   0.215   3.9946   0.4888   1.8523
 39Y  H24  H  HCH3   0   0.220   4.6835  -0.6388   0.6879
 39Y  H25  H  HCH3   0   0.228   5.1727   1.0467   0.6682
 39Y  OXT  O  OC    -1  -0.624  -3.8299   0.8402   0.5420

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
 39Y  O    C8   deloc   1.248  0.020  1.248
 39Y  C8   C9   single  1.510  0.020  1.510
 39Y  C9   C10  double  1.331  0.020  1.331
 39Y  C10  C11  single  1.494  0.020  1.494
 39Y  C11  C12  single  1.538  0.020  1.538
 39Y  C12  C13  single  1.525  0.020  1.525
 39Y  C12  C14  single  1.530  0.020  1.530
 39Y  C14  C15  single  1.523  0.020  1.523
 39Y  C9   H14  single  0.930  0.020  1.080
 39Y  C10  H15  single  0.930  0.020  1.080
 39Y  C11  H16  single  0.970  0.020  1.090
 39Y  C11  H17  single  0.970  0.020  1.090
 39Y  C12  H18  single  0.970  0.020  1.090
 39Y  C13  H21  single  0.970  0.020  1.090
 39Y  C13  H19  single  0.970  0.020  1.090
 39Y  C13  H20  single  0.970  0.020  1.090
 39Y  C14  H23  single  0.970  0.020  1.090
 39Y  C14  H22  single  0.970  0.020  1.090
 39Y  C15  H26  single  0.970  0.020  1.090
 39Y  C15  H24  single  0.970  0.020  1.090
 39Y  C15  H25  single  0.970  0.020  1.090
 39Y  C8   OXT  deloc   1.250  0.020  1.250

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
 39Y  OXT  C8   C9   115.61  3.000
 39Y  OXT  C8   O    126.43  3.000
 39Y  C9   C8   O    117.96  3.000
 39Y  H14  C9   C10  119.27  3.000
 39Y  H14  C9   C8   116.74  3.000
 39Y  C10  C9   C8   124.00  3.000
 39Y  H15  C10  C11  117.13  3.000
 39Y  H15  C10  C9   117.93  3.000
 39Y  C11  C10  C9   124.94  3.000
 39Y  H17  C11  H16  106.58  3.000
 39Y  H17  C11  C12  108.94  3.000
 39Y  H16  C11  C12  108.22  3.000
 39Y  H17  C11  C10  109.43  3.000
 39Y  H16  C11  C10  109.34  3.000
 39Y  C12  C11  C10  114.06  3.000
 39Y  H18  C12  C14  107.78  3.000
 39Y  H18  C12  C13  108.49  3.000
 39Y  C14  C12  C13  111.79  3.000
 39Y  H18  C12  C11  107.45  3.000
 39Y  C14  C12  C11  109.57  3.000
 39Y  C13  C12  C11  111.59  3.000
 39Y  H20  C13  H19  107.63  3.000
 39Y  H20  C13  H21  106.99  3.000
 39Y  H19  C13  H21  107.70  3.000
 39Y  H20  C13  C12  111.77  3.000
 39Y  H19  C13  C12  110.56  3.000
 39Y  H21  C13  C12  111.99  3.000
 39Y  H22  C14  H23  106.05  3.000
 39Y  H22  C14  C15  108.75  3.000
 39Y  H23  C14  C15  109.54  3.000
 39Y  H22  C14  C12  108.53  3.000
 39Y  H23  C14  C12  109.05  3.000
 39Y  C15  C14  C12  114.56  3.000
 39Y  H25  C15  H24  107.17  3.000
 39Y  H25  C15  H26  107.57  3.000
 39Y  H24  C15  H26  107.62  3.000
 39Y  H25  C15  C14  110.83  3.000
 39Y  H24  C15  C14  112.28  3.000
 39Y  H26  C15  C14  111.15  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
 39Y  Var_01  C11  C10  C9   C8   -179.54   0.0  2
 39Y  Var_02  C10  C9   C8   O      -0.88  30.0  2
 39Y  Var_03  C12  C11  C10  C9    115.24  30.0  3
 39Y  Var_04  H26  C15  C14  C12   -53.89  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 39Y  chir_01  C12  C11  C13  C14  negativ

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
 39Y  plan-1  O    0.020
 39Y  plan-1  C8   0.020
 39Y  plan-1  C9   0.020
 39Y  plan-1  OXT  0.020
 39Y  plan-2  C8   0.020
 39Y  plan-2  C9   0.020
 39Y  plan-2  C10  0.020
 39Y  plan-2  C11  0.020
 39Y  plan-2  H14  0.020
 39Y  plan-2  H15  0.020

