# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 07:31:41 2022
#   Inital geometry file: a 47 line input string
#   Ligand name: (2E)-pent-2-enedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)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
 G9A  G9A  '(2E)-pent-2-enedioic acid'  ligand  13  9  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G9A
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
 G9A  O2  O  O      0  -0.603   2.2025  -1.1999   0.3941
 G9A  C4  C  C      0   0.417   2.4671  -0.0242   0.0808
 G9A  O1  O  OC    -1  -0.626   3.5594   0.5599   0.2232
 G9A  C1  C  CH2    0  -0.654   1.3388   0.8100  -0.5706
 G9A  C2  C  C1     0  -0.133  -0.0020   0.1634  -0.5378
 G9A  C3  C  C1     0  -0.432  -1.0855   0.6731   0.0463
 G9A  C5  C  C      0   0.383  -2.4363   0.0018   0.0586
 G9A  O4  O  O      0  -0.612  -2.5466  -1.1082  -0.5036
 G9A  O3  O  OC    -1  -0.629  -3.3495   0.6271   0.6419
 G9A  H2  H  HCH2   0   0.231   1.3019   1.7984  -0.1033
 G9A  H3  H  HCH2   0   0.238   1.6329   0.9868  -1.6131
 G9A  H4  H  H      0   0.218  -0.0951  -0.7934  -1.0420
 G9A  H5  H  H      0   0.203  -1.0109   1.6316   0.5568

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
 G9A  O4  C5  deloc   1.249  0.020  1.249
 G9A  C1  C2  single  1.489  0.020  1.489
 G9A  C1  C4  single  1.547  0.020  1.547
 G9A  C3  C2  double  1.332  0.020  1.332
 G9A  C3  C5  single  1.509  0.020  1.509
 G9A  C5  O3  deloc   1.251  0.020  1.251
 G9A  C4  O2  deloc   1.245  0.020  1.245
 G9A  C4  O1  deloc   1.247  0.020  1.247
 G9A  C1  H2  single  0.970  0.020  1.090
 G9A  C1  H3  single  0.970  0.020  1.090
 G9A  C2  H4  single  0.930  0.020  1.080
 G9A  C3  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
 G9A  C1  C4  O1  115.75  3.000
 G9A  O1  C4  O2  126.85  3.000
 G9A  C1  C4  O2  117.40  3.000
 G9A  H3  C1  H2  105.62  3.000
 G9A  H3  C1  C2  109.40  3.000
 G9A  H2  C1  C2  110.64  3.000
 G9A  H3  C1  C4  106.94  3.000
 G9A  H2  C1  C4  109.39  3.000
 G9A  C2  C1  C4  114.41  3.000
 G9A  H4  C2  C3  118.11  3.000
 G9A  H4  C2  C1  116.73  3.000
 G9A  C3  C2  C1  125.16  3.000
 G9A  H5  C3  C5  116.70  3.000
 G9A  H5  C3  C2  119.13  3.000
 G9A  C5  C3  C2  124.16  3.000
 G9A  O3  C5  O4  126.12  3.000
 G9A  O3  C5  C3  115.79  3.000
 G9A  O4  C5  C3  118.09  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
 G9A  Var_01  C5  C3  C2  C1  179.61   0.0  2
 G9A  Var_02  C2  C1  C4  O2    9.61  30.0  2
 G9A  Var_03  C3  C2  C1  C4  120.42  30.0  3
 G9A  Var_04  O4  C5  C3  C2    0.65  30.0  2

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
 G9A  plan-1  O2  0.020
 G9A  plan-1  C4  0.020
 G9A  plan-1  O1  0.020
 G9A  plan-1  C1  0.020
 G9A  plan-2  C3  0.020
 G9A  plan-2  C5  0.020
 G9A  plan-2  O4  0.020
 G9A  plan-2  O3  0.020
 G9A  plan-3  C1  0.020
 G9A  plan-3  C2  0.020
 G9A  plan-3  C3  0.020
 G9A  plan-3  C5  0.020
 G9A  plan-3  H4  0.020
 G9A  plan-3  H5  0.020

