# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 06:35:56 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: 3-C-carboxy-2-deoxy-D-erythro-pentaric acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H](C(O)=O)[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
 7A3  7A3  '3-C-carboxy-2-deoxy-D-erythro-pentaric acid'  ligand  19  14  .  2021-08-05  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_7A3
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
 7A3  O2  O  OH1    0  -0.680  -0.2466   1.2406  -1.0708
 7A3  O3  O  OC    -1  -0.774   0.2163  -0.8142   1.8295
 7A3  C1  C  CH2    0  -0.558  -1.3656  -0.8041  -0.6833
 7A3  O1  O  O      0  -0.454  -2.8416   0.3222   0.7927
 7A3  C2  C  CT     0   0.143  -0.1292   0.0348  -0.3610
 7A3  C5  C  C      0   0.333   2.4164   0.1431  -0.5977
 7A3  C3  C  C      0   0.443   0.0336   0.2483   1.1638
 7A3  C4  C  CH1    0  -0.116   1.1541  -0.7194  -0.8399
 7A3  C   C  C      0   0.380  -2.6841  -0.0827  -0.3772
 7A3  O   O  OC    -1  -0.760  -3.5160   0.0170  -1.3053
 7A3  O4  O  O      0  -0.587   0.0637   1.3938   1.6256
 7A3  O5  O  OH1    0  -0.708   1.2461  -1.9949  -0.2731
 7A3  O6  O  O      0  -0.353   3.3882  -0.3633  -0.0252
 7A3  O7  O  OC    -1  -0.820   2.3549   1.3284  -1.0331
 7A3  H3  H  HOH1   0   0.413   0.6779   1.5725  -1.1313
 7A3  H1  H  HCH2   0   0.244  -1.3277  -1.0887  -1.7399
 7A3  H2  H  HCH2   0   0.265  -1.3379  -1.7309  -0.1063
 7A3  H5  H  HCH1   0   0.197   1.0552  -0.8425  -1.9293
 7A3  H6  H  HOH1   0   0.395   0.9469  -1.8478   0.6534

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
 7A3  O1  C   deloc   1.248  0.020  1.248
 7A3  O6  C5  deloc   1.236  0.020  1.236
 7A3  O   C   deloc   1.250  0.020  1.250
 7A3  C   C1  single  1.534  0.020  1.534
 7A3  C1  C2  single  1.529  0.020  1.529
 7A3  C5  O7  deloc   1.264  0.020  1.264
 7A3  C5  C4  single  1.548  0.020  1.548
 7A3  O2  C2  single  1.404  0.020  1.404
 7A3  C2  C4  single  1.564  0.020  1.564
 7A3  C2  C3  single  1.548  0.020  1.548
 7A3  C4  O5  single  1.399  0.020  1.399
 7A3  C3  O4  deloc   1.235  0.020  1.235
 7A3  C3  O3  deloc   1.267  0.020  1.267
 7A3  O2  H3  single  0.850  0.020  0.980
 7A3  C1  H1  single  0.970  0.020  1.090
 7A3  C1  H2  single  0.970  0.020  1.090
 7A3  C4  H5  single  0.970  0.020  1.090
 7A3  O5  H6  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
 7A3  H3  O2  C2  104.01  3.000
 7A3  H2  C1  H1  106.77  3.000
 7A3  H2  C1  C   108.40  3.000
 7A3  H1  C1  C   110.16  3.000
 7A3  H2  C1  C2  109.50  3.000
 7A3  H1  C1  C2  108.55  3.000
 7A3  C   C1  C2  113.27  3.000
 7A3  C4  C2  C3  106.37  3.000
 7A3  C3  C2  C1  111.62  3.000
 7A3  C4  C2  C1  109.55  3.000
 7A3  C3  C2  O2  112.84  3.000
 7A3  C4  C2  O2  109.15  3.000
 7A3  C1  C2  O2  107.29  3.000
 7A3  O7  C5  O6  125.58  3.000
 7A3  O7  C5  C4  115.40  3.000
 7A3  O6  C5  C4  119.02  3.000
 7A3  O4  C3  C2  119.90  3.000
 7A3  O4  C3  O3  125.28  3.000
 7A3  C2  C3  O3  114.64  3.000
 7A3  H5  C4  O5  107.76  3.000
 7A3  H5  C4  C5  106.89  3.000
 7A3  O5  C4  C5  113.02  3.000
 7A3  H5  C4  C2  106.45  3.000
 7A3  O5  C4  C2  111.70  3.000
 7A3  C5  C4  C2  110.64  3.000
 7A3  O   C   O1  125.87  3.000
 7A3  O   C   C1  117.47  3.000
 7A3  O1  C   C1  116.63  3.000
 7A3  H6  O5  C4  103.01  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
 7A3  Var_01  C2  C1  C  O1  -56.72  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
 7A3  chir_01  C2  O2  C4  C3  negativ
 7A3  chir_02  C4  O5  C2  C5  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
 7A3  plan-1  C5  0.020
 7A3  plan-1  C4  0.020
 7A3  plan-1  O6  0.020
 7A3  plan-1  O7  0.020
 7A3  plan-2  O3  0.020
 7A3  plan-2  C2  0.020
 7A3  plan-2  C3  0.020
 7A3  plan-2  O4  0.020
 7A3  plan-3  C1  0.020
 7A3  plan-3  O1  0.020
 7A3  plan-3  C   0.020
 7A3  plan-3  O   0.020

