# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 07:45:21 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  24  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  -0.454  -3.1497  -1.1525  -0.0650
 39Y  C8   C  C     0   0.525  -2.8923   0.0206   0.0813
 39Y  C9   C  C1    0  -0.401  -1.5829   0.6464  -0.1648
 39Y  C10  C  C1    0  -0.124  -0.5385  -0.0732  -0.5768
 39Y  C11  C  CH2   0  -0.483   0.8156   0.4872  -0.8382
 39Y  C12  C  CH1   0  -0.227   1.9025  -0.0678   0.0998
 39Y  C13  C  CH3   0  -0.671   2.0932  -1.5695  -0.0854
 39Y  C14  C  CH2   0  -0.407   3.2045   0.7044  -0.1262
 39Y  C15  C  CH3   0  -0.670   4.3188   0.3585   0.8530
 39Y  H14  H  H     0   0.271  -1.4952   1.7146  -0.0013
 39Y  H15  H  H     0   0.268  -0.6718  -1.1400  -0.7299
 39Y  H16  H  HCH2  0   0.243   1.0978   0.2552  -1.8721
 39Y  H17  H  HCH2  0   0.245   0.7853   1.5763  -0.7523
 39Y  H18  H  HCH1  0   0.222   1.5761   0.1186   1.1303
 39Y  H21  H  HCH3  0   0.233   1.1779  -2.1283   0.1118
 39Y  H19  H  HCH3  0   0.217   2.4073  -1.7947  -1.1076
 39Y  H20  H  HCH3  0   0.237   2.8546  -1.9622   0.5884
 39Y  H23  H  HCH2  0   0.211   3.5495   0.5313  -1.1516
 39Y  H22  H  HCH2  0   0.221   2.9924   1.7754  -0.0542
 39Y  H26  H  HCH3  0   0.217   3.9843   0.4685   1.8865
 39Y  H24  H  HCH3  0   0.222   4.6767  -0.6635   0.7280
 39Y  H25  H  HCH3  0   0.230   5.1752   1.0189   0.7120
 39Y  OXT  O  OH1   0  -0.604  -3.7906   0.9116   0.4936
 39Y  HXT  H  HOH1  0   0.479  -4.6422   0.4749   0.6426

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   double  1.210  0.020  1.210
 39Y  C8   C9   single  1.472  0.020  1.472
 39Y  C9   C10  double  1.334  0.020  1.334
 39Y  C10  C11  single  1.489  0.020  1.489
 39Y  C11  C12  single  1.539  0.020  1.539
 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  single  1.331  0.020  1.331
 39Y  OXT  HXT  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
 39Y  OXT  C8   C9   111.57  3.000
 39Y  OXT  C8   O    122.90  3.000
 39Y  C9   C8   O    125.54  3.000
 39Y  H14  C9   C10  120.99  3.000
 39Y  H14  C9   C8   117.75  3.000
 39Y  C10  C9   C8   121.26  3.000
 39Y  H15  C10  C11  117.18  3.000
 39Y  H15  C10  C9   118.52  3.000
 39Y  C11  C10  C9   124.30  3.000
 39Y  H17  C11  H16  106.98  3.000
 39Y  H17  C11  C12  109.33  3.000
 39Y  H16  C11  C12  108.45  3.000
 39Y  H17  C11  C10  109.64  3.000
 39Y  H16  C11  C10  108.67  3.000
 39Y  C12  C11  C10  113.55  3.000
 39Y  H18  C12  C14  107.82  3.000
 39Y  H18  C12  C13  108.58  3.000
 39Y  C14  C12  C13  111.88  3.000
 39Y  H18  C12  C11  107.52  3.000
 39Y  C14  C12  C11  109.19  3.000
 39Y  C13  C12  C11  111.67  3.000
 39Y  H20  C13  H19  107.65  3.000
 39Y  H20  C13  H21  106.86  3.000
 39Y  H19  C13  H21  107.75  3.000
 39Y  H20  C13  C12  111.53  3.000
 39Y  H19  C13  C12  110.63  3.000
 39Y  H21  C13  C12  112.19  3.000
 39Y  H22  C14  H23  106.10  3.000
 39Y  H22  C14  C15  108.77  3.000
 39Y  H23  C14  C15  109.59  3.000
 39Y  H22  C14  C12  108.62  3.000
 39Y  H23  C14  C12  109.05  3.000
 39Y  C15  C14  C12  114.38  3.000
 39Y  H25  C15  H24  107.16  3.000
 39Y  H25  C15  H26  107.58  3.000
 39Y  H24  C15  H26  107.67  3.000
 39Y  H25  C15  C14  110.72  3.000
 39Y  H24  C15  C14  112.30  3.000
 39Y  H26  C15  C14  111.19  3.000
 39Y  HXT  OXT  C8   109.83  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  CONST_01  HXT  OXT  C8   O       0.00   0.0  0
 39Y  Var_01    C11  C10  C9   C8   -179.62   0.0  2
 39Y  Var_02    C10  C9   C8   O      -0.49  30.0  2
 39Y  Var_03    C12  C11  C10  C9    116.19  30.0  3
 39Y  Var_04    H26  C15  C14  C12   -54.03  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-1  HXT  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

