# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 14:52:34 2020
#   Inital geometry file: a 45 line input string
#   Ligand name: (2Z)-2-methylbut-2-ene-1,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C/C(CO)=C/CO
#
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
 6OM  6OM  (2Z)-2-methylbut-2-ene-1,4-diol  ligand  17  7  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_6OM
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
 6OM  C1   C  C     0   0.080  -0.5237   0.4900  -0.0761
 6OM  C2   C  C1    0  -0.288   0.7612   0.5803   0.2744
 6OM  C3   C  CH2   0  -0.211   1.7744  -0.5136   0.3726
 6OM  C4   C  CH3   0  -0.703  -1.4156   1.6979  -0.0625
 6OM  C5   C  CH2   0  -0.221  -1.1964  -0.7809  -0.5128
 6OM  O1   O  OH1   0  -0.674   2.8293  -0.2290  -0.5291
 6OM  O2   O  OH1   0  -0.671  -2.2303  -1.0847   0.4039
 6OM  H1   H  H     0   0.235   1.1407   1.5633   0.5436
 6OM  H2   H  HCH2  0   0.209   2.1448  -0.5433   1.4057
 6OM  H3   H  HCH2  0   0.206   1.3318  -1.4949   0.1744
 6OM  H4   H  HCH3  0   0.242  -2.2093   1.5931   0.6789
 6OM  H5   H  HCH3  0   0.238  -0.8627   2.6086   0.1653
 6OM  H6   H  HCH3  0   0.232  -1.9059   1.8310  -1.0300
 6OM  H7   H  HOH1  0   0.453   3.5557  -0.8268  -0.3290
 6OM  H8   H  HOH1  0   0.456  -2.7980  -1.7461  -0.0013
 6OM  H9   H  HCH2  0   0.209  -1.6018  -0.6174  -1.5203
 6OM  H10  H  HCH2  0   0.209  -0.4824  -1.6062  -0.5942

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
 6OM  C2  C3   single  1.494  0.020  1.494
 6OM  C2  C1   double  1.335  0.020  1.335
 6OM  C3  O1   single  1.417  0.020  1.417
 6OM  C4  C1   single  1.502  0.020  1.502
 6OM  C1  C5   single  1.503  0.020  1.503
 6OM  C5  O2   single  1.415  0.020  1.415
 6OM  C2  H1   single  0.930  0.020  1.080
 6OM  C3  H2   single  0.970  0.020  1.090
 6OM  C3  H3   single  0.970  0.020  1.090
 6OM  C4  H4   single  0.970  0.020  1.090
 6OM  C4  H5   single  0.970  0.020  1.090
 6OM  C4  H6   single  0.970  0.020  1.090
 6OM  O1  H7   single  0.850  0.020  0.980
 6OM  O2  H8   single  0.850  0.020  0.980
 6OM  C5  H9   single  0.970  0.020  1.090
 6OM  C5  H10  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
 6OM  C5   C1  C4  114.65  3.000
 6OM  C5   C1  C2  124.36  3.000
 6OM  C4   C1  C2  120.99  3.000
 6OM  H1   C2  C3  114.13  3.000
 6OM  H1   C2  C1  117.52  3.000
 6OM  C3   C2  C1  128.35  3.000
 6OM  H3   C3  H2  106.41  3.000
 6OM  H3   C3  O1  111.46  3.000
 6OM  H2   C3  O1  110.68  3.000
 6OM  H3   C3  C2  111.73  3.000
 6OM  H2   C3  C2  108.09  3.000
 6OM  O1   C3  C2  108.43  3.000
 6OM  H6   C4  H5  108.12  3.000
 6OM  H6   C4  H4  106.68  3.000
 6OM  H5   C4  H4  107.90  3.000
 6OM  H6   C4  C1  110.88  3.000
 6OM  H5   C4  C1  111.89  3.000
 6OM  H4   C4  C1  111.16  3.000
 6OM  H10  C5  H9  106.55  3.000
 6OM  H10  C5  O2  111.29  3.000
 6OM  H9   C5  O2  110.89  3.000
 6OM  H10  C5  C1  111.55  3.000
 6OM  H9   C5  C1  107.81  3.000
 6OM  O2   C5  C1  108.69  3.000
 6OM  H7   O1  C3  107.76  3.000
 6OM  H8   O2  C5  107.83  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
 6OM  Var_01  C4  C1  C2  C3   177.34   0.0  2
 6OM  Var_02  O1  C3  C2  C1   119.56  30.0  3
 6OM  Var_03  O2  C5  C1  C2   117.99  30.0  3
 6OM  Var_04  H4  C4  C1  C2  -115.36  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
 6OM  plan-1  C1  0.020
 6OM  plan-1  C2  0.020
 6OM  plan-1  C3  0.020
 6OM  plan-1  C4  0.020
 6OM  plan-1  C5  0.020
 6OM  plan-1  H1  0.020

