# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 22:49:05 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: (6E)-2,6-dimethylocta-2,6-diene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C/C=C(C)/CCC=C(C)C
#
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
 650  650  (6E)-2,6-dimethylocta-2,6-diene  ligand  28  10  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_650
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
 650  C1   C  C     0   0.081   2.8126  -0.1398  -0.0958
 650  C2   C  C1    0  -0.257   1.7897   0.7042  -0.2538
 650  C3   C  CH2   0  -0.489   0.3820   0.3819  -0.6479
 650  C4   C  CH2   0  -0.480  -0.5849   0.5066   0.5410
 650  C5   C  C     0   0.115  -2.0282   0.3146   0.1531
 650  C6   C  CH3   0  -0.730  -2.6576   1.4732  -0.5629
 650  C7   C  C1    0  -0.284  -2.6563  -0.8274   0.4460
 650  C8   C  CH3   0  -0.713  -4.0648  -1.2173   0.1302
 650  C9   C  CH3   0  -0.704   4.1655   0.3578   0.3251
 650  C    C  CH3   0  -0.720   2.7378  -1.6229  -0.3069
 650  H1   H  H     0   0.220   1.9757   1.7566  -0.0489
 650  H2   H  HCH2  0   0.232   0.0732   1.0681  -1.4426
 650  H3   H  HCH2  0   0.235   0.2988  -0.6235  -1.0644
 650  H4   H  HCH2  0   0.234  -0.2982  -0.2272   1.2985
 650  H5   H  HCH2  0   0.225  -0.4566   1.4941   0.9981
 650  H6   H  HCH3  0   0.236  -2.6860   2.3525   0.0862
 650  H7   H  HCH3  0   0.235  -2.0777   1.7599  -1.4430
 650  H8   H  HCH3  0   0.240  -3.6742   1.2756  -0.8964
 650  H9   H  H     0   0.220  -2.0856  -1.5826   0.9818
 650  H10  H  HCH3  0   0.234  -4.0880  -2.1231  -0.4807
 650  H11  H  HCH3  0   0.234  -4.6175  -1.4494   1.0435
 650  H12  H  HCH3  0   0.234  -4.6178  -0.4463  -0.4033
 650  H13  H  HCH3  0   0.230   4.4923  -0.1303   1.2466
 650  H14  H  HCH3  0   0.230   4.9201   0.1266  -0.4314
 650  H15  H  HCH3  0   0.235   4.1736   1.4349   0.4905
 650  H16  H  HCH3  0   0.234   3.4483  -1.9400  -1.0747
 650  H17  H  HCH3  0   0.235   3.0188  -2.1515   0.6079
 650  H18  H  HCH3  0   0.239   1.7505  -1.9726  -0.6005

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
 650  C   C1   single  1.500  0.020  1.500
 650  C6  C5   single  1.500  0.020  1.500
 650  C3  C2   single  1.497  0.020  1.497
 650  C3  C4   single  1.537  0.020  1.537
 650  C5  C7   double  1.336  0.020  1.336
 650  C5  C4   single  1.507  0.020  1.507
 650  C1  C2   double  1.336  0.020  1.336
 650  C1  C9   single  1.502  0.020  1.502
 650  C8  C7   single  1.495  0.020  1.495
 650  C2  H1   single  0.930  0.020  1.080
 650  C3  H2   single  0.970  0.020  1.090
 650  C3  H3   single  0.970  0.020  1.090
 650  C4  H4   single  0.970  0.020  1.090
 650  C4  H5   single  0.970  0.020  1.090
 650  C6  H6   single  0.970  0.020  1.090
 650  C6  H7   single  0.970  0.020  1.090
 650  C6  H8   single  0.970  0.020  1.090
 650  C7  H9   single  0.930  0.020  1.080
 650  C8  H10  single  0.970  0.020  1.090
 650  C8  H11  single  0.970  0.020  1.090
 650  C8  H12  single  0.970  0.020  1.090
 650  C9  H13  single  0.970  0.020  1.090
 650  C9  H14  single  0.970  0.020  1.090
 650  C9  H15  single  0.970  0.020  1.090
 650  C   H16  single  0.970  0.020  1.090
 650  C   H17  single  0.970  0.020  1.090
 650  C   H18  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
 650  C    C1  C9   114.33  3.000
 650  C9   C1  C2   120.91  3.000
 650  C    C1  C2   124.76  3.000
 650  H1   C2  C3   114.74  3.000
 650  H1   C2  C1   117.26  3.000
 650  C3   C2  C1   127.97  3.000
 650  H3   C3  H2   106.20  3.000
 650  H3   C3  C4   108.77  3.000
 650  H2   C3  C4   109.46  3.000
 650  H3   C3  C2   111.74  3.000
 650  H2   C3  C2   108.75  3.000
 650  C4   C3  C2   111.74  3.000
 650  H5   C4  H4   106.57  3.000
 650  H5   C4  C5   109.54  3.000
 650  H4   C4  C5   110.13  3.000
 650  H5   C4  C3   108.78  3.000
 650  H4   C4  C3   108.45  3.000
 650  C5   C4  C3   113.14  3.000
 650  C7   C5  C6   124.58  3.000
 650  C7   C5  C4   120.19  3.000
 650  C6   C5  C4   115.23  3.000
 650  H8   C6  H7   107.26  3.000
 650  H8   C6  H6   107.68  3.000
 650  H7   C6  H6   106.33  3.000
 650  H8   C6  C5   113.45  3.000
 650  H7   C6  C5   111.38  3.000
 650  H6   C6  C5   110.40  3.000
 650  H9   C7  C8   114.66  3.000
 650  H9   C7  C5   117.06  3.000
 650  C8   C7  C5   128.29  3.000
 650  H12  C8  H11  107.65  3.000
 650  H12  C8  H10  107.60  3.000
 650  H11  C8  H10  106.29  3.000
 650  H12  C8  C7   113.41  3.000
 650  H11  C8  C7   110.82  3.000
 650  H10  C8  C7   110.74  3.000
 650  H15  C9  H14  108.00  3.000
 650  H15  C9  H13  108.13  3.000
 650  H14  C9  H13  106.41  3.000
 650  H15  C9  C1   112.14  3.000
 650  H14  C9  C1   110.97  3.000
 650  H13  C9  C1   110.96  3.000
 650  H18  C   H17  107.68  3.000
 650  H18  C   H16  107.88  3.000
 650  H17  C   H16  106.28  3.000
 650  H18  C   C1   113.65  3.000
 650  H17  C   C1   110.34  3.000
 650  H16  C   C1   110.69  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
 650  Var_01  C    C1  C2  C3     0.70   0.0  2
 650  Var_02  C8   C7  C5  C4  -178.90   0.0  2
 650  Var_03  C4   C3  C2  C1   106.96  30.0  1
 650  Var_04  C5   C4  C3  C2   174.64  30.0  3
 650  Var_05  C6   C5  C4  C3   -75.37  30.0  2
 650  Var_06  H16  C   C1  C2   121.07  30.0  3
 650  Var_07  H13  C9  C1  C2   122.23  30.0  3
 650  Var_08  H6   C6  C5  C4   -63.45  30.0  3
 650  Var_09  H10  C8  C7  C5   120.86  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
 650  plan-1  C4  0.020
 650  plan-1  C5  0.020
 650  plan-1  C6  0.020
 650  plan-1  C7  0.020
 650  plan-1  C8  0.020
 650  plan-1  H9  0.020
 650  plan-2  C1  0.020
 650  plan-2  C2  0.020
 650  plan-2  C3  0.020
 650  plan-2  C9  0.020
 650  plan-2  C   0.020
 650  plan-2  H1  0.020

