# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 07:05:03 2022
#   Inital geometry file: a 43 line input string
#   Ligand name: (~{Z})-2-oxidanylbut-2-enedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)/C=C(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
 Y3P  Y3P  '(~{Z})-2-oxidanylbut-2-enedioic acid'  ligand  11  9  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_Y3P
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
 Y3P  C1   C  C      0   0.366  24.7065  49.4604  35.5926
 Y3P  O1   O  OC    -1  -0.595  25.8320  49.1211  35.1891
 Y3P  C2   C  C      0   0.191  24.2045  50.8320  35.1233
 Y3P  O2   O  O      0  -0.589  23.9419  48.8204  36.3389
 Y3P  C3   C  C1     0  -0.616  23.0896  51.4130  35.6269
 Y3P  O3   O  OH1    0  -0.649  24.9398  51.4359  34.1984
 Y3P  C4   C  C      0   0.477  22.6521  52.7560  35.1770
 Y3P  O4   O  O      0  -0.652  23.3702  53.3049  34.2677
 Y3P  O5   O  OC    -1  -0.585  21.6476  53.2791  35.6814
 Y3P  HC3  H  H      0   0.207  22.5125  50.8912  36.3763
 Y3P  HO3  H  HOH1   0   0.445  24.4238  52.3225  34.0516

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
 Y3P  O3  C2   single  1.327  0.020  1.327
 Y3P  O4  C4   deloc   1.282  0.020  1.282
 Y3P  C2  C1   single  1.534  0.020  1.534
 Y3P  C2  C3   double  1.354  0.020  1.354
 Y3P  C4  C3   single  1.482  0.020  1.482
 Y3P  C4  O5   deloc   1.240  0.020  1.240
 Y3P  O2  C1   deloc   1.245  0.020  1.245
 Y3P  C1  O1   deloc   1.243  0.020  1.243
 Y3P  C3  HC3  single  0.930  0.020  1.080
 Y3P  O3  HO3  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
 Y3P  O2   C1  C2  116.22  3.000
 Y3P  O2   C1  O1  127.60  3.000
 Y3P  C2   C1  O1  116.17  3.000
 Y3P  O3   C2  C3  121.34  3.000
 Y3P  C3   C2  C1  122.63  3.000
 Y3P  O3   C2  C1  116.02  3.000
 Y3P  HC3  C3  C4  119.37  3.000
 Y3P  HC3  C3  C2  119.37  3.000
 Y3P  C4   C3  C2  121.25  3.000
 Y3P  HO3  O3  C2  102.25  3.000
 Y3P  O5   C4  O4  124.17  3.000
 Y3P  O5   C4  C3  119.86  3.000
 Y3P  O4   C4  C3  115.96  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
 Y3P  Var_01  C4  C3  C2  C1  178.35   0.0  2
 Y3P  Var_02  O3  C2  C1  O1    8.59  30.0  2
 Y3P  Var_03  O4  C4  C3  C2    1.76  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
 Y3P  plan-1  C1   0.020
 Y3P  plan-1  O1   0.020
 Y3P  plan-1  C2   0.020
 Y3P  plan-1  O2   0.020
 Y3P  plan-2  C3   0.020
 Y3P  plan-2  C4   0.020
 Y3P  plan-2  O4   0.020
 Y3P  plan-2  O5   0.020
 Y3P  plan-3  C1   0.020
 Y3P  plan-3  C2   0.020
 Y3P  plan-3  C3   0.020
 Y3P  plan-3  O3   0.020
 Y3P  plan-3  C4   0.020
 Y3P  plan-3  HC3  0.020

