# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 13:19:04 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  22  14  .  2021-08-06  2021-08-06  
;
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  -0.643  -0.1353   1.4051  -0.7753
 7A3  O3  O  OH1   0  -0.592  -0.2624  -0.9230   1.8371
 7A3  C1  C  CH2   0  -0.598  -1.3610  -0.6830  -0.7388
 7A3  O1  O  O     0  -0.432  -2.7215   0.6208   0.7520
 7A3  C2  C  CT    0   0.061  -0.1283   0.0988  -0.2876
 7A3  C5  C  C     0   0.517   2.3988   0.1038  -0.3709
 7A3  C3  C  C     0   0.552  -0.0494   0.2373   1.2332
 7A3  C4  C  CH1   0  -0.068   1.1471  -0.6455  -0.8115
 7A3  C   C  C     0   0.567  -2.6418  -0.0937  -0.2156
 7A3  O   O  OH1   0  -0.589  -3.6871  -0.4792  -0.9314
 7A3  O4  O  O     0  -0.421   0.2388   1.2535   1.8014
 7A3  O5  O  OH1   0  -0.639   1.2204  -1.9841  -0.4455
 7A3  O6  O  O     0  -0.435   2.9575  -0.1398   0.6690
 7A3  O7  O  OH1   0  -0.571   2.7906   1.0154  -1.2373
 7A3  H3  H  HOH1  0   0.461  -0.1772   1.3835  -1.7380
 7A3  H4  H  HOH1  0   0.490  -0.1622  -0.8232   2.7965
 7A3  H1  H  HCH2  0   0.301  -1.3885  -0.7108  -1.8316
 7A3  H2  H  HCH2  0   0.317  -1.3121  -1.7274  -0.4221
 7A3  H5  H  HCH1  0   0.295   1.0826  -0.6262  -1.9036
 7A3  H7  H  HOH1  0   0.484  -4.5043  -0.1204  -0.5525
 7A3  H6  H  HOH1  0   0.456   1.4031  -2.0611   0.4985
 7A3  H8  H  HOH1  0   0.488   3.5772   1.4785  -0.9087

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   double  1.205  0.020  1.205
 7A3  O6  C5  double  1.205  0.020  1.205
 7A3  O   C   single  1.324  0.020  1.324
 7A3  C   C1  single  1.504  0.020  1.504
 7A3  C1  C2  single  1.528  0.020  1.528
 7A3  C5  O7  single  1.317  0.020  1.317
 7A3  C5  C4  single  1.524  0.020  1.524
 7A3  O2  C2  single  1.394  0.020  1.394
 7A3  C2  C4  single  1.567  0.020  1.567
 7A3  C2  C3  single  1.529  0.020  1.529
 7A3  C4  O5  single  1.390  0.020  1.390
 7A3  C3  O4  double  1.199  0.020  1.199
 7A3  C3  O3  single  1.325  0.020  1.325
 7A3  O2  H3  single  0.850  0.020  0.980
 7A3  O3  H4  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  O   H7  single  0.850  0.020  0.980
 7A3  O5  H6  single  0.850  0.020  0.980
 7A3  O7  H8  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  109.18  3.000
 7A3  H4  O3  C3  110.13  3.000
 7A3  H2  C1  H1  105.46  3.000
 7A3  H2  C1  C   108.18  3.000
 7A3  H1  C1  C   109.65  3.000
 7A3  H2  C1  C2  111.55  3.000
 7A3  H1  C1  C2  109.17  3.000
 7A3  C   C1  C2  112.58  3.000
 7A3  C4  C2  C3  109.49  3.000
 7A3  C3  C2  C1  112.44  3.000
 7A3  C4  C2  C1  108.36  3.000
 7A3  C3  C2  O2  105.26  3.000
 7A3  C4  C2  O2  109.40  3.000
 7A3  C1  C2  O2  111.84  3.000
 7A3  O7  C5  O6  124.71  3.000
 7A3  O7  C5  C4  113.23  3.000
 7A3  O6  C5  C4  122.05  3.000
 7A3  O4  C3  C2  124.08  3.000
 7A3  O4  C3  O3  124.37  3.000
 7A3  C2  C3  O3  111.44  3.000
 7A3  H5  C4  O5  106.44  3.000
 7A3  H5  C4  C5  109.16  3.000
 7A3  O5  C4  C5  110.74  3.000
 7A3  H5  C4  C2  106.10  3.000
 7A3  O5  C4  C2  114.36  3.000
 7A3  C5  C4  C2  109.78  3.000
 7A3  O   C   O1  123.66  3.000
 7A3  O   C   C1  111.73  3.000
 7A3  O1  C   C1  124.60  3.000
 7A3  H7  O   C   110.26  3.000
 7A3  H6  O5  C4  110.17  3.000
 7A3  H8  O7  C5  110.41  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  CONST_01  H7  O   C   C1  180.00   0.0  0
 7A3  CONST_02  H4  O3  C3  C2  180.00   0.0  0
 7A3  CONST_03  H8  O7  C5  C4  180.00   0.0  0
 7A3  Var_01    C2  C1  C   O1  -21.95  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-1  H8  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-2  H4  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
 7A3  plan-3  H7  0.020

