# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 15:01:49 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  27  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 OK
;

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   0.366  -0.8601  -1.3565   0.6684
 3JL  C4   C  CR6    0   0.118  -0.2997   1.0926   0.6780
 3JL  C5   C  CR6    0  -0.104  -1.2372   0.0899   0.3806
 3JL  C2   C  CR16   0  -0.250  -1.8292   2.7741  -0.1527
 3JL  C6   C  CR6    0  -0.115  -2.4588   0.4391  -0.2098
 3JL  O12  O  O      0  -0.610   4.2258   0.1738  -1.6978
 3JL  O15  O  OC    -1  -0.635   5.6589  -0.4114  -0.0988
 3JL  C11  C  C      0   0.408   4.5384  -0.0395  -0.5097
 3JL  C10  C  CH2    0  -0.583   3.4642   0.1817   0.5703
 3JL  C9   C  CH2    0  -0.396   2.0703   0.5116   0.0648
 3JL  C3   C  CR16   0  -0.325  -0.6128   2.4232   0.4138
 3JL  C7   C  CR16   0  -0.310  -2.7370   1.7797  -0.4746
 3JL  O10  O  OC    -1  -0.613  -0.4278  -2.0111  -0.2990
 3JL  O9   O  O      0  -0.618  -0.9333  -1.7267   1.8555
 3JL  C12  C  C      0   0.380  -3.5168  -0.5967  -0.5655
 3JL  O14  O  O      0  -0.586  -3.4837  -1.6778   0.0495
 3JL  O13  O  OC    -1  -0.607  -4.3467  -0.2672  -1.4390
 3JL  H1   H  HCR6   0   0.235  -2.0634   3.8138  -0.3455
 3JL  H3   H  HCH2   0   0.215   3.4272  -0.7095   1.2077
 3JL  H4   H  HCH2   0   0.216   3.8146   0.9840   1.2317
 3JL  H5   H  HCH2   0   0.202   2.1063   1.3931  -0.5812
 3JL  H6   H  HCH2   0   0.212   1.6881  -0.3053  -0.5504
 3JL  H7   H  HCH2   0   0.221   1.4376   1.6087   1.8047
 3JL  H8   H  HCH2   0   0.228   1.0415  -0.0952   1.8657
 3JL  H9   H  HCR6   0   0.230   0.1123   3.1941   0.6537
 3JL  H10  H  HCR6   0   0.232  -3.6816   2.0410  -0.9334
 3JL  C1   C  CH2    0  -0.511   1.0762   0.7702   1.2017

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  deloc     1.247  0.020  1.247
 3JL  C11  O15  deloc     1.250  0.020  1.250
 3JL  C11  C10  single    1.539  0.020  1.539
 3JL  C2   C3   aromatic  1.387  0.020  1.387
 3JL  C2   C7   aromatic  1.384  0.020  1.384
 3JL  C3   C4   aromatic  1.392  0.020  1.392
 3JL  C9   C10  single    1.519  0.020  1.519
 3JL  C9   C1   single    1.532  0.020  1.532
 3JL  C7   C6   aromatic  1.395  0.020  1.395
 3JL  C4   C1   single    1.507  0.020  1.507
 3JL  C4   C5   aromatic  1.405  0.020  1.405
 3JL  O14  C12  deloc     1.244  0.020  1.244
 3JL  C6   C5   aromatic  1.401  0.020  1.401
 3JL  C6   C12  single    1.523  0.020  1.523
 3JL  C5   C8   single    1.522  0.020  1.522
 3JL  C12  O13  deloc     1.249  0.020  1.249
 3JL  O9   C8   deloc     1.246  0.020  1.246
 3JL  C8   O10  deloc     1.245  0.020  1.245
 3JL  C2   H1   single    0.930  0.020  1.080
 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

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  127.19  3.000
 3JL  O10  C8   C5   116.01  3.000
 3JL  O9   C8   C5   116.62  3.000
 3JL  C3   C4   C1   118.41  3.000
 3JL  C1   C4   C5   122.02  3.000
 3JL  C3   C4   C5   119.47  3.000
 3JL  C6   C5   C4   119.56  3.000
 3JL  C6   C5   C8   122.18  3.000
 3JL  C4   C5   C8   118.23  3.000
 3JL  H1   C2   C7   120.43  3.000
 3JL  H1   C2   C3   120.35  3.000
 3JL  C7   C2   C3   119.23  3.000
 3JL  C12  C6   C7   118.09  3.000
 3JL  C12  C6   C5   122.33  3.000
 3JL  C7   C6   C5   119.58  3.000
 3JL  C10  C11  O15  115.95  3.000
 3JL  C10  C11  O12  117.97  3.000
 3JL  O15  C11  O12  126.07  3.000
 3JL  H4   C10  H3   104.76  3.000
 3JL  H4   C10  C9   109.56  3.000
 3JL  H3   C10  C9   109.82  3.000
 3JL  H4   C10  C11  107.77  3.000
 3JL  H3   C10  C11  108.34  3.000
 3JL  C9   C10  C11  115.98  3.000
 3JL  H6   C9   H5   106.37  3.000
 3JL  H6   C9   C1   108.50  3.000
 3JL  H5   C9   C1   108.89  3.000
 3JL  H6   C9   C10  110.26  3.000
 3JL  H5   C9   C10  109.97  3.000
 3JL  C1   C9   C10  112.65  3.000
 3JL  H9   C3   C2   119.77  3.000
 3JL  H9   C3   C4   119.12  3.000
 3JL  C2   C3   C4   121.11  3.000
 3JL  H10  C7   C6   119.13  3.000
 3JL  H10  C7   C2   119.84  3.000
 3JL  C6   C7   C2   121.04  3.000
 3JL  O13  C12  O14  126.34  3.000
 3JL  O13  C12  C6   116.46  3.000
 3JL  O14  C12  C6   117.20  3.000
 3JL  H8   C1   H7   106.43  3.000
 3JL  H8   C1   C9   109.78  3.000
 3JL  H7   C1   C9   108.90  3.000
 3JL  H8   C1   C4   110.61  3.000
 3JL  H7   C1   C4   109.21  3.000
 3JL  C9   C1   C4   111.75  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  Var_01    O9   C8   C5   C4     78.11  30.0  2
 3JL  Var_02    C9   C1   C4   C5     87.01  30.0  2
 3JL  Var_03    O14  C12  C6   C5     22.87  30.0  2
 3JL  Var_04    C10  C9   C1   C4   -179.89  30.0  1
 3JL  Var_05    C9   C10  C11  O12     5.85  30.0  3
 3JL  Var_06    C1   C9   C10  C11  -177.75  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-3  O12  0.020
 3JL  plan-3  O15  0.020
 3JL  plan-3  C11  0.020
 3JL  plan-3  C10  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

