# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 14:53:30 2022
#   Inital geometry file: a 47 line input string
#   Ligand name: (2Z)-2-methylbut-2-enedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=C/C(O)=O)/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
 CIZ  CIZ  '(2Z)-2-methylbut-2-enedioic acid'  ligand  13  9  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_CIZ
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
 CIZ  O4  O  O      0  -0.561   1.7291  -0.9956   1.0300
 CIZ  C5  C  C      0   0.344   1.3485  -0.5424  -0.0646
 CIZ  O3  O  OC    -1  -0.816   1.5612  -1.0019  -1.1993
 CIZ  C3  C  C      0   0.159   0.7069   0.8301  -0.0100
 CIZ  C4  C  CH3    0  -0.769   1.7107   1.9469  -0.0585
 CIZ  C2  C  C1     0  -0.472  -0.6075   1.0614   0.0682
 CIZ  C1  C  C      0   0.378  -1.6629  -0.0126   0.1128
 CIZ  O1  O  OC    -1  -0.681  -2.8514   0.4014   0.1505
 CIZ  O2  O  O      0  -0.488  -1.2810  -1.2153   0.1486
 CIZ  H2  H  HCH3   0   0.252   2.3717   1.8366  -0.9179
 CIZ  H3  H  HCH3   0   0.248   1.2359   2.9338  -0.1088
 CIZ  H4  H  HCH3   0   0.213   2.3462   1.9233   0.8280
 CIZ  H5  H  H      0   0.193  -0.9559   2.0954   0.0850

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
 CIZ  O4  C5  deloc   1.244  0.020  1.244
 CIZ  O2  C1  deloc   1.262  0.020  1.262
 CIZ  C1  C2  single  1.506  0.020  1.506
 CIZ  C1  O1  deloc   1.259  0.020  1.259
 CIZ  C2  C3  double  1.337  0.020  1.337
 CIZ  C3  C4  single  1.502  0.020  1.502
 CIZ  C3  C5  single  1.516  0.020  1.516
 CIZ  C5  O3  deloc   1.243  0.020  1.243
 CIZ  C4  H2  single  0.970  0.020  1.090
 CIZ  C4  H3  single  0.970  0.020  1.090
 CIZ  C4  H4  single  0.970  0.020  1.090
 CIZ  C2  H5  single  0.930  0.020  1.080

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
 CIZ  C3  C5  O3  116.11  3.000
 CIZ  O3  C5  O4  128.05  3.000
 CIZ  C3  C5  O4  115.31  3.000
 CIZ  C2  C3  C4  122.01  3.000
 CIZ  C4  C3  C5  112.89  3.000
 CIZ  C2  C3  C5  125.09  3.000
 CIZ  H4  C4  H3  108.00  3.000
 CIZ  H4  C4  H2  106.57  3.000
 CIZ  H3  C4  H2  108.52  3.000
 CIZ  H4  C4  C3  110.29  3.000
 CIZ  H3  C4  C3  112.41  3.000
 CIZ  H2  C4  C3  110.82  3.000
 CIZ  H5  C2  C1  116.83  3.000
 CIZ  H5  C2  C3  118.61  3.000
 CIZ  C1  C2  C3  124.55  3.000
 CIZ  O2  C1  O1  126.72  3.000
 CIZ  O1  C1  C2  115.33  3.000
 CIZ  O2  C1  C2  117.91  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
 CIZ  Var_01  C1  C2  C3  C5   -0.07   0.0  2
 CIZ  Var_02  C2  C3  C5  O4  -95.16  30.0  2
 CIZ  Var_03  O2  C1  C2  C3    3.84  30.0  2
 CIZ  Var_04  H2  C4  C3  C5   53.26  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
 CIZ  plan-1  O4  0.020
 CIZ  plan-1  C5  0.020
 CIZ  plan-1  O3  0.020
 CIZ  plan-1  C3  0.020
 CIZ  plan-2  C2  0.020
 CIZ  plan-2  C1  0.020
 CIZ  plan-2  O1  0.020
 CIZ  plan-2  O2  0.020
 CIZ  plan-3  C5  0.020
 CIZ  plan-3  C3  0.020
 CIZ  plan-3  C4  0.020
 CIZ  plan-3  C2  0.020
 CIZ  plan-3  C1  0.020
 CIZ  plan-3  H5  0.020

