# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 03:51:23 2022
#   Inital geometry file: a 64 line input string
#   Ligand name: (2R)-2-hydroxybutane-1,2,4-tricarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC[C@@](O)(CC(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
 HCA  HCA  '(2R)-2-hydroxybutane-1,2,4-tricarboxylic acid'  ligand  21  14  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HCA
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
 HCA  C1   C  C      0   0.390  96.0541  -20.4598  38.3079
 HCA  C2   C  CH2    0  -0.523  94.8680  -20.2463  39.2662
 HCA  C3   C  CT     0   0.095  93.7455  -21.2984  39.1309
 HCA  C4   C  CH2    0  -0.397  92.9836  -21.1591  37.8077
 HCA  C5   C  CH2    0  -0.588  91.7994  -22.1024  37.6572
 HCA  C6   C  C      0   0.403  91.1345  -22.1183  36.2650
 HCA  C7   C  C      0   0.408  92.7711  -21.1166  40.3283
 HCA  O1   O  O      0  -0.619  95.9004  -20.0902  37.1222
 HCA  O2   O  OC    -1  -0.617  97.0847  -20.9792  38.7849
 HCA  O3   O  O      0  -0.609  91.8097  -21.7294  35.2895
 HCA  O4   O  OC    -1  -0.626  89.9642  -22.5550  36.2230
 HCA  O5   O  O      0  -0.611  92.7093  -22.0986  41.1095
 HCA  O6   O  OC    -1  -0.592  92.1534  -20.0448  40.4305
 HCA  O7   O  OH1    0  -0.712  94.2971  -22.5967  39.2279
 HCA  H21  H  HCH2   0   0.186  95.2336  -20.2673  40.2985
 HCA  H22  H  HCH2   0   0.195  94.4332  -19.2572  39.1003
 HCA  H41  H  HCH2   0   0.184  92.6395  -20.1255  37.7096
 HCA  H42  H  HCH2   0   0.206  93.6808  -21.3177  36.9857
 HCA  H51  H  HCH2   0   0.211  92.1220  -23.1279  37.8744
 HCA  H52  H  HCH2   0   0.200  91.0307  -21.8771  38.4021
 HCA  HO7  H  HOH1   0   0.416  93.8740  -22.9252  40.0457

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
 HCA  C1  C2   single  1.540  0.020  1.540
 HCA  C1  O1   deloc   1.251  0.020  1.251
 HCA  C1  O2   deloc   1.249  0.020  1.249
 HCA  C2  C3   single  1.544  0.020  1.544
 HCA  C2  H21  single  0.970  0.020  1.090
 HCA  C2  H22  single  0.970  0.020  1.090
 HCA  C3  C4   single  1.533  0.020  1.533
 HCA  C3  C7   single  1.554  0.020  1.554
 HCA  C3  O7   single  1.414  0.020  1.414
 HCA  C4  C5   single  1.521  0.020  1.521
 HCA  C4  H41  single  0.970  0.020  1.090
 HCA  C4  H42  single  0.970  0.020  1.090
 HCA  C5  C6   single  1.543  0.020  1.543
 HCA  C5  H51  single  0.970  0.020  1.090
 HCA  C5  H52  single  0.970  0.020  1.090
 HCA  C6  O3   deloc   1.249  0.020  1.249
 HCA  C6  O4   deloc   1.250  0.020  1.250
 HCA  C7  O5   deloc   1.256  0.020  1.256
 HCA  C7  O6   deloc   1.241  0.020  1.241
 HCA  O7  HO7  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
 HCA  O2   C1  O1   125.89  3.000
 HCA  O2   C1  C2   117.11  3.000
 HCA  O1   C1  C2   117.00  3.000
 HCA  H22  C2  H21  107.05  3.000
 HCA  H22  C2  C3   108.30  3.000
 HCA  H21  C2  C3   108.18  3.000
 HCA  H22  C2  C1   109.72  3.000
 HCA  H21  C2  C1   109.07  3.000
 HCA  C3   C2  C1   114.26  3.000
 HCA  O7   C3  C7   107.41  3.000
 HCA  O7   C3  C4   109.67  3.000
 HCA  C7   C3  C4   110.04  3.000
 HCA  O7   C3  C2   109.63  3.000
 HCA  C7   C3  C2   107.96  3.000
 HCA  C4   C3  C2   112.01  3.000
 HCA  H42  C4  H41  105.74  3.000
 HCA  H42  C4  C5   109.46  3.000
 HCA  H41  C4  C5   109.40  3.000
 HCA  H42  C4  C3   108.66  3.000
 HCA  H41  C4  C3   108.64  3.000
 HCA  C5   C4  C3   114.57  3.000
 HCA  H52  C5  H51  105.33  3.000
 HCA  H52  C5  C6   108.28  3.000
 HCA  H51  C5  C6   107.21  3.000
 HCA  H52  C5  C4   110.60  3.000
 HCA  H51  C5  C4   109.34  3.000
 HCA  C6   C5  C4   115.53  3.000
 HCA  O4   C6  O3   126.09  3.000
 HCA  O4   C6  C5   115.94  3.000
 HCA  O3   C6  C5   117.95  3.000
 HCA  O6   C7  O5   126.81  3.000
 HCA  O6   C7  C3   118.45  3.000
 HCA  O5   C7  C3   114.73  3.000
 HCA  HO7  O7  C3   101.36  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
 HCA  Var_01  O1  C1  C2  C3    78.81  30.0  2
 HCA  Var_02  C6  C5  C4  C3  -172.03  30.0  3
 HCA  Var_03  O3  C6  C5  C4    22.04  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 HCA  chir_01  C3  C4  C7  O7  negativ

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
 HCA  plan-1  C1  0.020
 HCA  plan-1  C2  0.020
 HCA  plan-1  O1  0.020
 HCA  plan-1  O2  0.020
 HCA  plan-2  C5  0.020
 HCA  plan-2  C6  0.020
 HCA  plan-2  O3  0.020
 HCA  plan-2  O4  0.020
 HCA  plan-3  C3  0.020
 HCA  plan-3  C7  0.020
 HCA  plan-3  O5  0.020
 HCA  plan-3  O6  0.020

