# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 14:28:21 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 3-(3-carboxypropyl)benzene-1,2-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCc1cccc(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
 3JL  3JL  '3-(3-carboxypropyl)benzene-1,2-dicarboxylic acid'  ligand  30  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3JL
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
 3JL  C8   C  C     0   0.431  -0.9348  -1.3845   0.7538
 3JL  C4   C  CR6   0   0.155  -0.2595   0.9968   0.5936
 3JL  C5   C  CR6   0  -0.042  -1.2395   0.0318   0.3610
 3JL  C2   C  CR16  0  -0.221  -1.7702   2.6888  -0.2586
 3JL  C6   C  CR6   0  -0.065  -2.4797   0.3943  -0.1775
 3JL  O12  O  O     0  -0.444   4.3638   0.1411  -1.7192
 3JL  O15  O  OH1   0  -0.597   5.7682  -0.1485  -0.0125
 3JL  C11  C  C     0   0.549   4.5630   0.0652  -0.5324
 3JL  C10  C  CH2   0  -0.583   3.5100   0.1879   0.5335
 3JL  C9   C  CH2   0  -0.415   2.1331   0.5296  -0.0098
 3JL  C3   C  CR16  0  -0.297  -0.5467   2.3228   0.2735
 3JL  C7   C  CR16  0  -0.285  -2.7389   1.7260  -0.4855
 3JL  O10  O  OH1   0  -0.577  -0.3590  -2.0521  -0.2314
 3JL  O9   O  O     0  -0.426  -1.1056  -1.8153   1.8644
 3JL  C12  C  C     0   0.544  -3.4988  -0.6579  -0.4147
 3JL  O14  O  O     0  -0.436  -3.3114  -1.8281  -0.1811
 3JL  O13  O  OH1   0  -0.589  -4.6313  -0.1869  -0.9087
 3JL  H1   H  HCR6  0   0.272  -1.9726   3.7245  -0.4950
 3JL  H2   H  HOH1  0   0.479   6.4233  -0.2361  -0.7209
 3JL  H3   H  HCH2  0   0.283   3.4816  -0.7572   1.0864
 3JL  H4   H  HCH2  0   0.279   3.8370   0.9390   1.2588
 3JL  H5   H  HCH2  0   0.242   2.1736   1.4672  -0.5693
 3JL  H6   H  HCH2  0   0.242   1.8054  -0.2391  -0.7116
 3JL  H7   H  HCH2  0   0.262   1.4265   1.4560   1.8011
 3JL  H8   H  HCH2  0   0.253   1.0991  -0.2505   1.7193
 3JL  H9   H  HCR6  0   0.265   0.2079   3.0801   0.4504
 3JL  H10  H  HCR6  0   0.275  -3.6922   2.0204  -0.8999
 3JL  H11  H  HOH1  0   0.488  -0.1348  -2.9509   0.0577
 3JL  H12  H  HOH1  0   0.492  -5.2593  -0.9111  -1.0506
 3JL  C1   C  CH2   0  -0.535   1.1104   0.6621   1.1201

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
 3JL  O12  C11  double    1.206  0.020  1.206
 3JL  C11  O15  single    1.330  0.020  1.330
 3JL  C11  C10  single    1.503  0.020  1.503
 3JL  C2   C3   aromatic  1.383  0.020  1.383
 3JL  C2   C7   aromatic  1.385  0.020  1.385
 3JL  C3   C4   aromatic  1.394  0.020  1.394
 3JL  C9   C10  single    1.519  0.020  1.519
 3JL  C9   C1   single    1.530  0.020  1.530
 3JL  C7   C6   aromatic  1.391  0.020  1.391
 3JL  C4   C1   single    1.505  0.020  1.505
 3JL  C4   C5   aromatic  1.395  0.020  1.395
 3JL  O14  C12  double    1.208  0.020  1.208
 3JL  C6   C5   aromatic  1.400  0.020  1.400
 3JL  C6   C12  single    1.484  0.020  1.484
 3JL  C5   C8   single    1.501  0.020  1.501
 3JL  C12  O13  single    1.322  0.020  1.322
 3JL  O9   C8   double    1.203  0.020  1.203
 3JL  C8   O10  single    1.322  0.020  1.322
 3JL  C2   H1   single    0.930  0.020  1.080
 3JL  O15  H2   single    0.850  0.020  0.980
 3JL  C10  H3   single    0.970  0.020  1.090
 3JL  C10  H4   single    0.970  0.020  1.090
 3JL  C9   H5   single    0.970  0.020  1.090
 3JL  C9   H6   single    0.970  0.020  1.090
 3JL  C1   H7   single    0.970  0.020  1.090
 3JL  C1   H8   single    0.970  0.020  1.090
 3JL  C3   H9   single    0.930  0.020  1.080
 3JL  C7   H10  single    0.930  0.020  1.080
 3JL  O10  H11  single    0.850  0.020  0.980
 3JL  O13  H12  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
 3JL  O9   C8   O10  124.66  3.000
 3JL  O10  C8   C5   111.71  3.000
 3JL  O9   C8   C5   123.40  3.000
 3JL  C3   C4   C1   118.64  3.000
 3JL  C1   C4   C5   122.95  3.000
 3JL  C3   C4   C5   118.36  3.000
 3JL  C6   C5   C4   120.50  3.000
 3JL  C6   C5   C8   121.66  3.000
 3JL  C4   C5   C8   117.81  3.000
 3JL  H1   C2   C7   119.95  3.000
 3JL  H1   C2   C3   120.20  3.000
 3JL  C7   C2   C3   119.85  3.000
 3JL  C12  C6   C7   121.02  3.000
 3JL  C12  C6   C5   119.10  3.000
 3JL  C7   C6   C5   119.87  3.000
 3JL  H2   O15  C11  109.97  3.000
 3JL  C10  C11  O15  111.76  3.000
 3JL  C10  C11  O12  125.24  3.000
 3JL  O15  C11  O12  123.00  3.000
 3JL  H4   C10  H3   105.39  3.000
 3JL  H4   C10  C9   110.70  3.000
 3JL  H3   C10  C9   110.56  3.000
 3JL  H4   C10  C11  108.46  3.000
 3JL  H3   C10  C11  107.80  3.000
 3JL  C9   C10  C11  113.56  3.000
 3JL  H6   C9   H5   106.63  3.000
 3JL  H6   C9   C1   109.59  3.000
 3JL  H5   C9   C1   109.19  3.000
 3JL  H6   C9   C10  110.10  3.000
 3JL  H5   C9   C10  110.04  3.000
 3JL  C1   C9   C10  111.18  3.000
 3JL  H9   C3   C2   119.58  3.000
 3JL  H9   C3   C4   118.94  3.000
 3JL  C2   C3   C4   121.48  3.000
 3JL  H10  C7   C6   120.67  3.000
 3JL  H10  C7   C2   119.39  3.000
 3JL  C6   C7   C2   119.94  3.000
 3JL  H11  O10  C8   110.27  3.000
 3JL  O13  C12  O14  123.38  3.000
 3JL  O13  C12  C6   113.29  3.000
 3JL  O14  C12  C6   123.33  3.000
 3JL  H12  O13  C12  110.10  3.000
 3JL  H8   C1   H7   105.56  3.000
 3JL  H8   C1   C9   109.87  3.000
 3JL  H7   C1   C9   109.26  3.000
 3JL  H8   C1   C4   111.62  3.000
 3JL  H7   C1   C4   108.64  3.000
 3JL  C9   C1   C4   111.68  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
 3JL  CONST_01  C7   C2   C3   C4      0.00   0.0  0
 3JL  CONST_02  C7   C6   C5   C4      0.00   0.0  0
 3JL  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 3JL  CONST_04  C2   C7   C6   C5      0.00   0.0  0
 3JL  CONST_05  C3   C2   C7   C6      0.00   0.0  0
 3JL  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 3JL  CONST_07  C3   C4   C5   C8    180.00   0.0  0
 3JL  CONST_08  C7   C6   C5   C8    180.00   0.0  0
 3JL  CONST_09  C12  C6   C5   C4    180.00   0.0  0
 3JL  CONST_10  C1   C4   C3   C2    180.00   0.0  0
 3JL  CONST_11  C12  C6   C7   C2    180.00   0.0  0
 3JL  CONST_12  C1   C4   C5   C6    180.00   0.0  0
 3JL  CONST_13  H1   C2   C3   C4    180.00   0.0  0
 3JL  CONST_14  H9   C3   C4   C5    180.00   0.0  0
 3JL  CONST_15  H10  C7   C6   C5    180.00   0.0  0
 3JL  CONST_16  H11  O10  C8   C5    180.00   0.0  0
 3JL  CONST_17  H12  O13  C12  C6    180.00   0.0  0
 3JL  CONST_18  H2   O15  C11  O12     0.00   0.0  0
 3JL  Var_01    O9   C8   C5   C4     85.08  30.0  2
 3JL  Var_02    C9   C1   C4   C5     96.32  30.0  2
 3JL  Var_03    O14  C12  C6   C5     -0.91  30.0  2
 3JL  Var_04    C10  C9   C1   C4   -179.83  30.0  1
 3JL  Var_05    C9   C10  C11  O12    -4.39  30.0  3
 3JL  Var_06    C1   C9   C10  C11  -179.13  30.0  1

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
 3JL  plan-1  C8   0.020
 3JL  plan-1  C4   0.020
 3JL  plan-1  C5   0.020
 3JL  plan-1  C2   0.020
 3JL  plan-1  C6   0.020
 3JL  plan-1  C3   0.020
 3JL  plan-1  C7   0.020
 3JL  plan-1  C12  0.020
 3JL  plan-1  H1   0.020
 3JL  plan-1  H9   0.020
 3JL  plan-1  H10  0.020
 3JL  plan-1  C1   0.020
 3JL  plan-2  C8   0.020
 3JL  plan-2  C5   0.020
 3JL  plan-2  O10  0.020
 3JL  plan-2  O9   0.020
 3JL  plan-2  H11  0.020
 3JL  plan-3  O12  0.020
 3JL  plan-3  O15  0.020
 3JL  plan-3  C11  0.020
 3JL  plan-3  C10  0.020
 3JL  plan-3  H2   0.020
 3JL  plan-4  C6   0.020
 3JL  plan-4  C12  0.020
 3JL  plan-4  O14  0.020
 3JL  plan-4  O13  0.020
 3JL  plan-4  H12  0.020

