# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:30:24 2022
#   Inital geometry file: a 82 line input string
#   Ligand name: 3-[(1E)-3-carboxyprop-1-en-1-yl]benzene-1,2-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C\C=C\c1cccc(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
 3JN  3JN  '3-[(1E)-3-carboxyprop-1-en-1-yl]benzene-1,2-dicarboxylic acid'  ligand  25  18  .  2022-03-10  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3JN
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
 3JN  O15  O  O      0  -0.604  -4.4285   0.2444   1.4627
 3JN  C11  C  C      0   0.418  -4.6683  -0.4610   0.4649
 3JN  O12  O  OC    -1  -0.625  -5.6190  -1.2555   0.3238
 3JN  C10  C  CH2    0  -0.654  -3.7146  -0.3314  -0.7454
 3JN  C9   C  C1     0  -0.180  -2.4481   0.4016  -0.4658
 3JN  C1   C  C1     0  -0.298  -1.2261  -0.0873  -0.6881
 3JN  C4   C  CR6    0   0.091   0.0375   0.6333  -0.4581
 3JN  C3   C  CR16   0  -0.335   0.0819   2.0225  -0.5806
 3JN  C2   C  CR16   0  -0.247   1.2573   2.7184  -0.3523
 3JN  C7   C  CR16   0  -0.303   2.4065   2.0225  -0.0161
 3JN  C5   C  CR6    0  -0.091   1.2107  -0.0705  -0.1221
 3JN  C8   C  C      0   0.362   1.0869  -1.5809   0.0264
 3JN  O10  O  OC    -1  -0.612   0.7454  -1.9850   1.1525
 3JN  O9   O  O      0  -0.624   1.2200  -2.2551  -1.0121
 3JN  C6   C  CR6    0  -0.143   2.4011   0.6326   0.0991
 3JN  C12  C  C      0   0.396   3.7068  -0.0672   0.4607
 3JN  O14  O  O      0  -0.578   3.6852  -1.3087   0.5349
 3JN  O13  O  OC    -1  -0.604   4.7010   0.6645   0.6522
 3JN  H2   H  HCH2   0   0.232  -3.5039  -1.3234  -1.1557
 3JN  H3   H  HCH2   0   0.239  -4.2724   0.1980  -1.5293
 3JN  H4   H  H      0   0.223  -2.5557   1.4020  -0.0573
 3JN  H5   H  H      0   0.229  -1.1401  -1.1004  -1.0696
 3JN  H6   H  HCR6   0   0.236  -0.8122   2.5609  -0.8717
 3JN  H7   H  HCR6   0   0.238   1.2783   3.7967  -0.4498
 3JN  H8   H  HCR6   0   0.234   3.3298   2.5582   0.1588

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
 3JN  O15  C11  deloc     1.245  0.020  1.245
 3JN  O12  C11  deloc     1.247  0.020  1.247
 3JN  C11  C10  single    1.546  0.020  1.546
 3JN  C2   C3   aromatic  1.385  0.020  1.385
 3JN  C2   C7   aromatic  1.385  0.020  1.385
 3JN  C3   C4   aromatic  1.395  0.020  1.395
 3JN  C7   C6   aromatic  1.395  0.020  1.395
 3JN  C9   C10  single    1.490  0.020  1.490
 3JN  C9   C1   double    1.335  0.020  1.335
 3JN  C4   C1   single    1.473  0.020  1.473
 3JN  C4   C5   aromatic  1.409  0.020  1.409
 3JN  O14  C12  deloc     1.244  0.020  1.244
 3JN  C6   C5   aromatic  1.400  0.020  1.400
 3JN  C6   C12  single    1.525  0.020  1.525
 3JN  C5   C8   single    1.523  0.020  1.523
 3JN  C12  O13  deloc     1.249  0.020  1.249
 3JN  O9   C8   deloc     1.245  0.020  1.245
 3JN  C8   O10  deloc     1.244  0.020  1.244
 3JN  C10  H2   single    0.970  0.020  1.090
 3JN  C10  H3   single    0.970  0.020  1.090
 3JN  C9   H4   single    0.930  0.020  1.080
 3JN  C1   H5   single    0.930  0.020  1.080
 3JN  C3   H6   single    0.930  0.020  1.080
 3JN  C2   H7   single    0.930  0.020  1.080
 3JN  C7   H8   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
 3JN  C10  C11  O12  115.79  3.000
 3JN  C10  C11  O15  117.45  3.000
 3JN  O12  C11  O15  126.76  3.000
 3JN  H3   C10  H2   105.50  3.000
 3JN  H3   C10  C9   109.18  3.000
 3JN  H2   C10  C9   110.66  3.000
 3JN  H3   C10  C11  106.61  3.000
 3JN  H2   C10  C11  109.65  3.000
 3JN  C9   C10  C11  114.75  3.000
 3JN  H4   C9   C1   119.39  3.000
 3JN  H4   C9   C10  116.08  3.000
 3JN  C1   C9   C10  124.53  3.000
 3JN  H5   C1   C4   116.32  3.000
 3JN  H5   C1   C9   118.21  3.000
 3JN  C4   C1   C9   125.47  3.000
 3JN  C5   C4   C3   119.46  3.000
 3JN  C5   C4   C1   120.48  3.000
 3JN  C3   C4   C1   120.05  3.000
 3JN  H6   C3   C2   119.66  3.000
 3JN  H6   C3   C4   119.48  3.000
 3JN  C2   C3   C4   120.85  3.000
 3JN  H7   C2   C7   120.40  3.000
 3JN  H7   C2   C3   120.13  3.000
 3JN  C7   C2   C3   119.46  3.000
 3JN  H8   C7   C6   118.92  3.000
 3JN  H8   C7   C2   119.91  3.000
 3JN  C6   C7   C2   121.17  3.000
 3JN  C6   C5   C8   123.49  3.000
 3JN  C8   C5   C4   116.81  3.000
 3JN  C6   C5   C4   119.66  3.000
 3JN  O9   C8   O10  127.46  3.000
 3JN  O10  C8   C5   115.65  3.000
 3JN  O9   C8   C5   116.55  3.000
 3JN  C12  C6   C5   122.34  3.000
 3JN  C12  C6   C7   118.27  3.000
 3JN  C5   C6   C7   119.39  3.000
 3JN  O13  C12  O14  126.11  3.000
 3JN  O13  C12  C6   116.68  3.000
 3JN  O14  C12  C6   117.21  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
 3JN  CONST_01  C7   C2   C3   C4      0.00   0.0  0
 3JN  CONST_02  C7   C6   C5   C4      0.00   0.0  0
 3JN  CONST_03  C6   C7   C2   C3      0.00   0.0  0
 3JN  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 3JN  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 3JN  CONST_06  C5   C6   C7   C2      0.00   0.0  0
 3JN  CONST_07  C2   C3   C4   C1    180.00   0.0  0
 3JN  CONST_08  C6   C5   C4   C1    180.00   0.0  0
 3JN  CONST_09  C12  C6   C5   C4    180.00   0.0  0
 3JN  CONST_10  C8   C5   C4   C3    180.00   0.0  0
 3JN  CONST_11  C12  C6   C7   C2    180.00   0.0  0
 3JN  CONST_12  C8   C5   C6   C7    180.00   0.0  0
 3JN  CONST_13  H7   C2   C3   C4    180.00   0.0  0
 3JN  CONST_14  H8   C7   C2   C3    180.00   0.0  0
 3JN  CONST_15  H6   C3   C2   C7    180.00   0.0  0
 3JN  Var_01    C3   C4   C1   C9    -29.84  30.0  2
 3JN  Var_02    O9   C8   C5   C4     87.05  30.0  2
 3JN  Var_03    O14  C12  C6   C7   -178.75  30.0  2
 3JN  Var_04    C4   C1   C9   C10   178.03   0.0  2
 3JN  Var_05    C9   C10  C11  O15    12.85  30.0  3
 3JN  Var_06    C1   C9   C10  C11   124.80  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
 3JN  plan-1  C1   0.020
 3JN  plan-1  C4   0.020
 3JN  plan-1  C3   0.020
 3JN  plan-1  C2   0.020
 3JN  plan-1  C7   0.020
 3JN  plan-1  C5   0.020
 3JN  plan-1  C8   0.020
 3JN  plan-1  C6   0.020
 3JN  plan-1  C12  0.020
 3JN  plan-1  H6   0.020
 3JN  plan-1  H7   0.020
 3JN  plan-1  H8   0.020
 3JN  plan-2  O15  0.020
 3JN  plan-2  C11  0.020
 3JN  plan-2  O12  0.020
 3JN  plan-2  C10  0.020
 3JN  plan-3  C5   0.020
 3JN  plan-3  C8   0.020
 3JN  plan-3  O10  0.020
 3JN  plan-3  O9   0.020
 3JN  plan-4  C6   0.020
 3JN  plan-4  C12  0.020
 3JN  plan-4  O14  0.020
 3JN  plan-4  O13  0.020
 3JN  plan-5  C10  0.020
 3JN  plan-5  C9   0.020
 3JN  plan-5  C1   0.020
 3JN  plan-5  C4   0.020
 3JN  plan-5  H4   0.020
 3JN  plan-5  H5   0.020

