# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 10:51:50 2022
#   Inital geometry file: a 58 line input string
#   Ligand name: 3-carboxy-2,3-dideoxy-L-threo-pentaric acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]([C@H](CC(O)=O)C(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
 ICT  ICT  '3-carboxy-2,3-dideoxy-L-threo-pentaric acid'  ligand  18  13  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_ICT
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
 ICT  C1   C  C      0   0.391  35.2900  34.7261  69.5033
 ICT  O1   O  O      0  -0.630  35.3655  35.9730  69.4486
 ICT  O2   O  OC    -1  -0.610  34.6470  33.9851  68.7381
 ICT  C2   C  CH1    0  -0.077  36.1503  34.0763  70.6098
 ICT  O7   O  OH1    0  -0.678  36.1309  32.6675  70.4740
 ICT  C3   C  CH1    0  -0.388  35.7557  34.5175  72.0311
 ICT  C4   C  CH2    0  -0.554  36.8453  34.1733  73.0457
 ICT  C5   C  C      0   0.394  38.1796  34.9189  72.8594
 ICT  O3   O  O      0  -0.621  39.2252  34.2665  73.0675
 ICT  O4   O  OC    -1  -0.617  38.1188  36.1312  72.5593
 ICT  C6   C  C      0   0.419  34.3671  33.9475  72.4015
 ICT  O5   O  O      0  -0.618  33.3885  34.4518  71.8099
 ICT  O6   O  OC    -1  -0.608  34.3134  33.0359  73.2537
 ICT  H2   H  HCH1   0   0.178  37.1738  34.4498  70.4354
 ICT  HO7  H  HOH1   0   0.430  36.6335  32.2996  71.2067
 ICT  H3   H  HCH1   0   0.197  35.6740  35.6059  71.9968
 ICT  H41  H  HCH2   0   0.215  36.4768  34.4215  74.0481
 ICT  H42  H  HCH2   0   0.177  37.0321  33.0957  73.0812

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
 ICT  C1  O1   deloc   1.250  0.020  1.250
 ICT  C1  O2   deloc   1.244  0.020  1.244
 ICT  C1  C2   single  1.545  0.020  1.545
 ICT  C2  O7   single  1.416  0.020  1.416
 ICT  C2  C3   single  1.540  0.020  1.540
 ICT  C2  H2   single  0.970  0.020  1.090
 ICT  O7  HO7  single  0.850  0.020  0.980
 ICT  C3  C4   single  1.528  0.020  1.528
 ICT  C3  C6   single  1.546  0.020  1.546
 ICT  C3  H3   single  0.970  0.020  1.090
 ICT  C4  C5   single  1.540  0.020  1.540
 ICT  C4  H41  single  0.970  0.020  1.090
 ICT  C4  H42  single  0.970  0.020  1.090
 ICT  C5  O3   deloc   1.250  0.020  1.250
 ICT  C5  O4   deloc   1.250  0.020  1.250
 ICT  C6  O5   deloc   1.250  0.020  1.250
 ICT  C6  O6   deloc   1.249  0.020  1.249

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
 ICT  C2   C1  O2   118.54  3.000
 ICT  C2   C1  O1   114.65  3.000
 ICT  O2   C1  O1   126.75  3.000
 ICT  H2   C2  C3   106.66  3.000
 ICT  H2   C2  O7   109.54  3.000
 ICT  C3   C2  O7   111.73  3.000
 ICT  H2   C2  C1   105.13  3.000
 ICT  C3   C2  C1   113.45  3.000
 ICT  O7   C2  C1   110.02  3.000
 ICT  HO7  O7  C2   107.49  3.000
 ICT  H3   C3  C6   107.92  3.000
 ICT  H3   C3  C4   107.38  3.000
 ICT  C6   C3  C4   113.47  3.000
 ICT  H3   C3  C2   106.01  3.000
 ICT  C6   C3  C2   110.23  3.000
 ICT  C4   C3  C2   111.45  3.000
 ICT  H42  C4  H41  104.51  3.000
 ICT  H42  C4  C5   109.44  3.000
 ICT  H41  C4  C5   106.99  3.000
 ICT  H42  C4  C3   111.42  3.000
 ICT  H41  C4  C3   108.45  3.000
 ICT  C5   C4  C3   115.37  3.000
 ICT  O4   C5  O3   125.93  3.000
 ICT  O4   C5  C4   117.15  3.000
 ICT  O3   C5  C4   116.87  3.000
 ICT  O6   C6  O5   125.72  3.000
 ICT  O6   C6  C3   118.11  3.000
 ICT  O5   C6  C3   116.18  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
 ICT  Var_01  O3  C5  C4  C3  -141.52  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
 ICT  chir_01  C2  C1  O7  C3  positiv
 ICT  chir_02  C3  C2  C4  C6  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
 ICT  plan-1  C1  0.020
 ICT  plan-1  O1  0.020
 ICT  plan-1  O2  0.020
 ICT  plan-1  C2  0.020
 ICT  plan-2  C4  0.020
 ICT  plan-2  C5  0.020
 ICT  plan-2  O3  0.020
 ICT  plan-2  O4  0.020
 ICT  plan-3  C3  0.020
 ICT  plan-3  C6  0.020
 ICT  plan-3  O5  0.020
 ICT  plan-3  O6  0.020

