# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 08:32:29 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCC(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
 GUA  GUA  'pentanedioic acid        '  ligand  17  9  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GUA
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
 GUA  C1   C  C     0   0.552   0.0473  -0.0121   2.5400
 GUA  C2   C  CH2   0  -0.581  -0.7374   0.0086   1.2576
 GUA  C3   C  CH2   0  -0.424   0.1361  -0.0060   0.0140
 GUA  C4   C  CH2   0  -0.581  -0.7236   0.0157  -1.2391
 GUA  C5   C  C     0   0.552   0.0744   0.0026  -2.5131
 GUA  O1   O  O     0  -0.444   1.2503  -0.0311   2.6195
 GUA  O2   O  OH1   0  -0.597  -0.7494  -0.0060   3.6047
 GUA  O3   O  O     0  -0.444   1.2781  -0.0111  -2.5810
 GUA  O4   O  OH1   0  -0.597  -0.7116   0.0090  -3.5859
 GUA  H21  H  HCH2  0   0.280  -1.4196  -0.8476   1.2623
 GUA  H22  H  HCH2  0   0.280  -1.3812   0.8941   1.2682
 GUA  H31  H  HCH2  0   0.242   0.8044   0.8565   0.0204
 GUA  H32  H  HCH2  0   0.242   0.7682  -0.8956   0.0151
 GUA  H41  H  HCH2  0   0.280  -1.4062  -0.8400  -1.2564
 GUA  H42  H  HCH2  0   0.280  -1.3670   0.9016  -1.2516
 GUA  HO2  H  HOH1  0   0.479  -0.2190  -0.0182   4.4154
 GUA  HO4  H  HOH1  0   0.479  -0.1729   0.0023  -4.3909

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
 GUA  C1  C2   single  1.504  0.020  1.504
 GUA  C1  O1   double  1.206  0.020  1.206
 GUA  C1  O2   single  1.330  0.020  1.330
 GUA  C2  C3   single  1.520  0.020  1.520
 GUA  C2  H21  single  0.970  0.020  1.090
 GUA  C2  H22  single  0.970  0.020  1.090
 GUA  C3  C4   single  1.520  0.020  1.520
 GUA  C3  H31  single  0.970  0.020  1.090
 GUA  C3  H32  single  0.970  0.020  1.090
 GUA  C4  C5   single  1.503  0.020  1.503
 GUA  C4  H41  single  0.970  0.020  1.090
 GUA  C4  H42  single  0.970  0.020  1.090
 GUA  C5  O3   double  1.206  0.020  1.206
 GUA  C5  O4   single  1.330  0.020  1.330
 GUA  O2  HO2  single  0.850  0.020  0.980
 GUA  O4  HO4  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
 GUA  O2   C1  O1   123.02  3.000
 GUA  O2   C1  C2   111.72  3.000
 GUA  O1   C1  C2   125.25  3.000
 GUA  H22  C2  H21  105.43  3.000
 GUA  H22  C2  C3   110.71  3.000
 GUA  H21  C2  C3   110.74  3.000
 GUA  H22  C2  C1   108.05  3.000
 GUA  H21  C2  C1   108.11  3.000
 GUA  C3   C2  C1   113.44  3.000
 GUA  H32  C3  H31  106.84  3.000
 GUA  H32  C3  C4   109.88  3.000
 GUA  H31  C3  C4   109.88  3.000
 GUA  H32  C3  C2   109.87  3.000
 GUA  H31  C3  C2   109.86  3.000
 GUA  C4   C3  C2   110.45  3.000
 GUA  H42  C4  H41  105.42  3.000
 GUA  H42  C4  C5   108.01  3.000
 GUA  H41  C4  C5   108.10  3.000
 GUA  H42  C4  C3   110.70  3.000
 GUA  H41  C4  C3   110.77  3.000
 GUA  C5   C4  C3   113.47  3.000
 GUA  O4   C5  O3   123.01  3.000
 GUA  O4   C5  C4   111.70  3.000
 GUA  O3   C5  C4   125.29  3.000
 GUA  HO2  O2  C1   110.00  3.000
 GUA  HO4  O4  C5   109.98  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
 GUA  CONST_01  HO2  O2  C1  C2   180.00   0.0  0
 GUA  CONST_02  HO4  O4  C5  C4   180.00   0.0  0
 GUA  Var_01    C4   C3  C2  C1   179.98  30.0  3
 GUA  Var_02    C5   C4  C3  C2  -179.99  30.0  3
 GUA  Var_03    O1   C1  C2  C3     0.40  30.0  2
 GUA  Var_04    O3   C5  C4  C3    -0.67  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
 GUA  plan-1  C1   0.020
 GUA  plan-1  C2   0.020
 GUA  plan-1  O1   0.020
 GUA  plan-1  O2   0.020
 GUA  plan-1  HO2  0.020
 GUA  plan-2  C4   0.020
 GUA  plan-2  C5   0.020
 GUA  plan-2  O3   0.020
 GUA  plan-2  O4   0.020
 GUA  plan-2  HO4  0.020

