# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 11:12:31 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 3-(2-carboxyethyl)benzene-1,2-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCc1cccc(C(O)=O)c1C(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
 3JM  3JM  '3-(2-carboxyethyl)benzene-1,2-dicarboxylic acid'  ligand  24  17  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3JM
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
 3JM  C7   C  CR16   0  -0.308   2.3416   1.8458   0.2462
 3JM  O19  O  OC    -1  -0.635  -4.6103  -0.1902   1.3538
 3JM  C15  C  C      0   0.408  -3.9471   0.0250   0.3160
 3JM  O16  O  O      0  -0.610  -4.3803  -0.0113  -0.8529
 3JM  C14  C  CH2    0  -0.577  -2.4638   0.3680   0.5301
 3JM  C13  C  CH2    0  -0.500  -1.6414   0.5921  -0.7361
 3JM  C4   C  CR6    0   0.111  -0.2218   0.9920  -0.4205
 3JM  C3   C  CR6    0  -0.101   0.8013   0.0468  -0.2327
 3JM  C10  C  C      0   0.366   0.4457  -1.4193  -0.4389
 3JM  O12  O  OC    -1  -0.614  -0.0185  -2.0254   0.5449
 3JM  O11  O  O      0  -0.623   0.5529  -1.8472  -1.6046
 3JM  C5   C  CR16   0  -0.322   0.0617   2.3456  -0.2643
 3JM  C6   C  CR16   0  -0.249   1.3363   2.7797   0.0686
 3JM  C2   C  CR6    0  -0.141   2.0927   0.4813   0.0977
 3JM  C1   C  C      0   0.395   3.2503  -0.4875   0.3098
 3JM  O8   O  OC    -1  -0.603   4.3681   0.0147   0.5518
 3JM  O9   O  O      0  -0.584   2.9970  -1.7033   0.2275
 3JM  H1   H  HCR6   0   0.232   3.3412   2.1689   0.5036
 3JM  H3   H  HCH2   0   0.218  -2.4084   1.2613   1.1633
 3JM  H4   H  HCH2   0   0.232  -1.9993  -0.4303   1.1149
 3JM  H5   H  HCH2   0   0.222  -1.6591  -0.3058  -1.3550
 3JM  H6   H  HCH2   0   0.219  -2.1063   1.3792  -1.3343
 3JM  H8   H  HCR6   0   0.230  -0.7326   3.0706  -0.4091
 3JM  H9   H  HCR6   0   0.234   1.5414   3.8370   0.1837

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
 3JM  O16  C15  deloc     1.247  0.020  1.247
 3JM  C13  C4   single    1.508  0.020  1.508
 3JM  C13  C14  single    1.526  0.020  1.526
 3JM  C5   C4   aromatic  1.392  0.020  1.392
 3JM  C5   C6   aromatic  1.387  0.020  1.387
 3JM  C15  C14  single    1.537  0.020  1.537
 3JM  C15  O19  deloc     1.250  0.020  1.250
 3JM  C4   C3   aromatic  1.405  0.020  1.405
 3JM  C6   C7   aromatic  1.384  0.020  1.384
 3JM  O11  C10  deloc     1.246  0.020  1.246
 3JM  C3   C2   aromatic  1.402  0.020  1.402
 3JM  C3   C10  single    1.523  0.020  1.523
 3JM  C7   C2   aromatic  1.395  0.020  1.395
 3JM  C2   C1   single    1.524  0.020  1.524
 3JM  C10  O12  deloc     1.245  0.020  1.245
 3JM  O9   C1   deloc     1.245  0.020  1.245
 3JM  C1   O8   deloc     1.249  0.020  1.249
 3JM  C7   H1   single    0.930  0.020  1.080
 3JM  C14  H3   single    0.970  0.020  1.090
 3JM  C14  H4   single    0.970  0.020  1.090
 3JM  C13  H5   single    0.970  0.020  1.090
 3JM  C13  H6   single    0.970  0.020  1.090
 3JM  C5   H8   single    0.930  0.020  1.080
 3JM  C6   H9   single    0.930  0.020  1.080

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
 3JM  H1   C7   C2   118.85  3.000
 3JM  H1   C7   C6   120.03  3.000
 3JM  C2   C7   C6   121.13  3.000
 3JM  C14  C15  O16  118.17  3.000
 3JM  C14  C15  O19  115.76  3.000
 3JM  O16  C15  O19  126.07  3.000
 3JM  H4   C14  H3   105.34  3.000
 3JM  H4   C14  C13  108.79  3.000
 3JM  H3   C14  C13  109.40  3.000
 3JM  H4   C14  C15  108.75  3.000
 3JM  H3   C14  C15  108.12  3.000
 3JM  C13  C14  C15  115.92  3.000
 3JM  H6   C13  H5   105.99  3.000
 3JM  H6   C13  C4   108.91  3.000
 3JM  H5   C13  C4   110.62  3.000
 3JM  H6   C13  C14  109.32  3.000
 3JM  H5   C13  C14  109.95  3.000
 3JM  C4   C13  C14  111.87  3.000
 3JM  C5   C4   C3   119.39  3.000
 3JM  C3   C4   C13  122.33  3.000
 3JM  C5   C4   C13  118.23  3.000
 3JM  C2   C3   C10  123.06  3.000
 3JM  C10  C3   C4   117.35  3.000
 3JM  C2   C3   C4   119.57  3.000
 3JM  O11  C10  O12  127.14  3.000
 3JM  O12  C10  C3   116.66  3.000
 3JM  O11  C10  C3   115.92  3.000
 3JM  H8   C5   C6   119.71  3.000
 3JM  H8   C5   C4   119.06  3.000
 3JM  C6   C5   C4   121.23  3.000
 3JM  H9   C6   C5   120.33  3.000
 3JM  H9   C6   C7   120.51  3.000
 3JM  C5   C6   C7   119.16  3.000
 3JM  C1   C2   C3   122.36  3.000
 3JM  C1   C2   C7   118.13  3.000
 3JM  C3   C2   C7   119.51  3.000
 3JM  O9   C1   O8   126.00  3.000
 3JM  O8   C1   C2   116.80  3.000
 3JM  O9   C1   C2   117.20  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
 3JM  CONST_01  C4   C5   C6   C7     0.00   0.0  0
 3JM  CONST_02  C4   C3   C2   C7     0.00   0.0  0
 3JM  CONST_03  C6   C5   C4   C3     0.00   0.0  0
 3JM  CONST_04  C6   C7   C2   C3     0.00   0.0  0
 3JM  CONST_05  C2   C3   C4   C5     0.00   0.0  0
 3JM  CONST_06  C2   C7   C6   C5     0.00   0.0  0
 3JM  CONST_07  C10  C3   C2   C7   180.00   0.0  0
 3JM  CONST_08  C6   C5   C4   C13  180.00   0.0  0
 3JM  CONST_09  C2   C3   C4   C13  180.00   0.0  0
 3JM  CONST_10  C1   C2   C3   C4   180.00   0.0  0
 3JM  CONST_11  C5   C4   C3   C10  180.00   0.0  0
 3JM  CONST_12  C1   C2   C7   C6   180.00   0.0  0
 3JM  CONST_13  H8   C5   C6   C7   180.00   0.0  0
 3JM  CONST_14  H9   C6   C5   C4   180.00   0.0  0
 3JM  CONST_15  H1   C7   C2   C3   180.00   0.0  0
 3JM  Var_01    O9   C1   C2   C7   177.10  30.0  2
 3JM  Var_02    C5   C4   C13  C14  -88.83  30.0  2
 3JM  Var_03    O11  C10  C3   C4    87.68  30.0  2
 3JM  Var_04    C4   C13  C14  C15  177.04  30.0  2
 3JM  Var_05    C13  C14  C15  O19  178.31  30.0  3

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
 3JM  plan-1  C7   0.020
 3JM  plan-1  C13  0.020
 3JM  plan-1  C4   0.020
 3JM  plan-1  C3   0.020
 3JM  plan-1  C10  0.020
 3JM  plan-1  C5   0.020
 3JM  plan-1  C6   0.020
 3JM  plan-1  C2   0.020
 3JM  plan-1  C1   0.020
 3JM  plan-1  H1   0.020
 3JM  plan-1  H8   0.020
 3JM  plan-1  H9   0.020
 3JM  plan-2  O19  0.020
 3JM  plan-2  C15  0.020
 3JM  plan-2  O16  0.020
 3JM  plan-2  C14  0.020
 3JM  plan-3  C3   0.020
 3JM  plan-3  C10  0.020
 3JM  plan-3  O12  0.020
 3JM  plan-3  O11  0.020
 3JM  plan-4  C2   0.020
 3JM  plan-4  C1   0.020
 3JM  plan-4  O8   0.020
 3JM  plan-4  O9   0.020

