# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 05:43:52 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: 3-C-carboxy-2-deoxy-L-threo-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
 7A2  7A2  '3-C-carboxy-2-deoxy-L-threo-pentaric acid'  ligand  19  14  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7A2
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
 7A2  C   C  C      0   0.393   2.6607  -0.4260   0.0650
 7A2  O   O  O      0  -0.618   3.0895   0.7427  -0.0326
 7A2  C1  C  CH2    0  -0.550   1.3714  -0.7659  -0.6941
 7A2  C2  C  CT     0   0.078   0.1266  -0.1630  -0.0200
 7A2  C3  C  C      0   0.440   0.1454   1.3751  -0.1746
 7A2  C4  C  CH1    0  -0.087  -1.1509  -0.7485  -0.6619
 7A2  C5  C  C      0   0.402  -2.4215  -0.2736   0.0814
 7A2  O1  O  OC    -1  -0.631   3.1918  -1.3441   0.7278
 7A2  O2  O  OH1    0  -0.686   0.1273  -0.4881   1.3579
 7A2  O3  O  OC    -1  -0.640   0.1080   1.7926  -1.3525
 7A2  O4  O  O      0  -0.620   0.2085   2.0681   0.8529
 7A2  O5  O  OH1    0  -0.708  -1.1362  -2.1592  -0.6187
 7A2  O6  O  OC    -1  -0.581  -2.7129   0.9292   0.0592
 7A2  O7  O  O      0  -0.622  -3.0664  -1.1940   0.6446
 7A2  H2  H  HCH2   0   0.201   1.4269  -0.3929  -1.7192
 7A2  H3  H  HCH2   0   0.197   1.2596  -1.8512  -0.7504
 7A2  H   H  HCH1   0   0.189  -1.2012  -0.4069  -1.7025
 7A2  H4  H  HOH1   0   0.420   0.1451  -1.4498   1.4139
 7A2  H6  H  HOH1   0   0.424  -1.9113  -2.3378  -0.0471

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
 7A2  O   C   deloc   1.249  0.020  1.249
 7A2  O1  C   deloc   1.251  0.020  1.251
 7A2  O7  C5  deloc   1.257  0.020  1.257
 7A2  C   C1  single  1.534  0.020  1.534
 7A2  C1  C2  single  1.539  0.020  1.539
 7A2  C5  O6  deloc   1.238  0.020  1.238
 7A2  C5  C4  single  1.547  0.020  1.547
 7A2  O2  C2  single  1.416  0.020  1.416
 7A2  C2  C4  single  1.545  0.020  1.545
 7A2  C2  C3  single  1.546  0.020  1.546
 7A2  C4  O5  single  1.412  0.020  1.412
 7A2  C3  O4  deloc   1.241  0.020  1.241
 7A2  C3  O3  deloc   1.250  0.020  1.250
 7A2  C1  H2  single  0.970  0.020  1.090
 7A2  C1  H3  single  0.970  0.020  1.090
 7A2  C4  H   single  0.970  0.020  1.090
 7A2  O2  H4  single  0.850  0.020  0.980
 7A2  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
 7A2  O1  C   C1  117.16  3.000
 7A2  C1  C   O   117.21  3.000
 7A2  O1  C   O   125.63  3.000
 7A2  H3  C1  H2  107.22  3.000
 7A2  H3  C1  C2  109.21  3.000
 7A2  H2  C1  C2  108.57  3.000
 7A2  H3  C1  C   109.36  3.000
 7A2  H2  C1  C   110.24  3.000
 7A2  C2  C1  C   112.11  3.000
 7A2  O2  C2  C4  108.53  3.000
 7A2  C4  C2  C3  110.21  3.000
 7A2  O2  C2  C3  109.01  3.000
 7A2  C3  C2  C1  109.64  3.000
 7A2  C4  C2  C1  109.79  3.000
 7A2  O2  C2  C1  109.63  3.000
 7A2  O4  C3  O3  126.52  3.000
 7A2  O3  C3  C2  115.22  3.000
 7A2  O4  C3  C2  118.26  3.000
 7A2  H   C4  O5  109.93  3.000
 7A2  H   C4  C5  108.83  3.000
 7A2  O5  C4  C5  107.50  3.000
 7A2  H   C4  C2  108.31  3.000
 7A2  O5  C4  C2  110.94  3.000
 7A2  C5  C4  C2  111.30  3.000
 7A2  O7  C5  O6  126.78  3.000
 7A2  O6  C5  C4  118.89  3.000
 7A2  O7  C5  C4  114.33  3.000
 7A2  H4  O2  C2  106.61  3.000
 7A2  H6  O5  C4  101.06  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
 7A2  Var_01  C2  C1  C  O  -74.03  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
 7A2  chir_01  C2  O2  C4  C3  negativ
 7A2  chir_02  C4  O5  C2  C5  positiv

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
 7A2  plan-1  C   0.020
 7A2  plan-1  O   0.020
 7A2  plan-1  C1  0.020
 7A2  plan-1  O1  0.020
 7A2  plan-2  C2  0.020
 7A2  plan-2  C3  0.020
 7A2  plan-2  O3  0.020
 7A2  plan-2  O4  0.020
 7A2  plan-3  C4  0.020
 7A2  plan-3  C5  0.020
 7A2  plan-3  O6  0.020
 7A2  plan-3  O7  0.020

