# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 21:03:56 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: 4-methylbenzene-1,2-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(C(O)=O)c(c1)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
 KAY  KAY  '4-methylbenzene-1,2-dicarboxylic acid'  ligand  19  13  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_KAY
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
 KAY  C10  C  C      0   0.359  -0.7971   1.6873   0.1825
 KAY  C13  C  CR16   0  -0.347   1.5300   0.7878   0.0478
 KAY  C01  C  CH3    0  -0.724   3.9536   0.0890   0.0737
 KAY  C02  C  CR6    0   0.100   2.4855  -0.2241   0.0180
 KAY  C03  C  CR16   0  -0.309   2.0377  -1.5412  -0.0444
 KAY  C04  C  CR16   0  -0.278   0.6795  -1.8210  -0.0671
 KAY  C05  C  CR6    0  -0.102  -0.2735  -0.8052  -0.0414
 KAY  C06  C  C      0   0.361  -1.7400  -1.1683  -0.1829
 KAY  C09  C  CR6    0  -0.036   0.1623   0.5203   0.0317
 KAY  O07  O  O      0  -0.601  -2.4195  -0.4470  -0.9373
 KAY  O08  O  OC    -1  -0.611  -2.1273  -2.1847   0.4293
 KAY  O11  O  OC    -1  -0.616  -0.6794   2.6191  -0.6375
 KAY  O12  O  O      0  -0.610  -1.5692   1.6361   1.1576
 KAY  H1   H  HCR6   0   0.229   1.8635   1.8194   0.0969
 KAY  H2   H  HCH3   0   0.242   4.3520  -0.0652   1.0790
 KAY  H3   H  HCH3   0   0.239   4.5253  -0.5528  -0.5975
 KAY  H4   H  HCH3   0   0.239   4.1548   1.1242  -0.2002
 KAY  H5   H  HCR6   0   0.233   2.7557  -2.3532  -0.0773
 KAY  H6   H  HCR6   0   0.234   0.3515  -2.8521  -0.1216

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
 KAY  O12  C10  deloc     1.245  0.020  1.245
 KAY  O07  C06  deloc     1.245  0.020  1.245
 KAY  C06  O08  deloc     1.248  0.020  1.248
 KAY  C06  C05  single    1.517  0.020  1.517
 KAY  C10  C09  single    1.518  0.020  1.518
 KAY  C10  O11  deloc     1.247  0.020  1.247
 KAY  C05  C09  aromatic  1.397  0.020  1.397
 KAY  C05  C04  aromatic  1.393  0.020  1.393
 KAY  C09  C13  aromatic  1.394  0.020  1.394
 KAY  C04  C03  aromatic  1.387  0.020  1.387
 KAY  C13  C02  aromatic  1.392  0.020  1.392
 KAY  C03  C02  aromatic  1.393  0.020  1.393
 KAY  C02  C01  single    1.502  0.020  1.502
 KAY  C13  H1   single    0.930  0.020  1.080
 KAY  C01  H2   single    0.970  0.020  1.090
 KAY  C01  H3   single    0.970  0.020  1.090
 KAY  C01  H4   single    0.970  0.020  1.090
 KAY  C03  H5   single    0.930  0.020  1.080
 KAY  C04  H6   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
 KAY  O12  C10  O11  127.19  3.000
 KAY  O11  C10  C09  116.71  3.000
 KAY  O12  C10  C09  115.99  3.000
 KAY  H1   C13  C09  118.98  3.000
 KAY  H1   C13  C02  118.75  3.000
 KAY  C09  C13  C02  122.26  3.000
 KAY  H4   C01  H3   107.92  3.000
 KAY  H4   C01  H2   107.34  3.000
 KAY  H3   C01  H2   106.99  3.000
 KAY  H4   C01  C02  111.67  3.000
 KAY  H3   C01  C02  111.52  3.000
 KAY  H2   C01  C02  111.17  3.000
 KAY  C03  C02  C01  120.87  3.000
 KAY  C01  C02  C13  121.23  3.000
 KAY  C03  C02  C13  117.89  3.000
 KAY  H5   C03  C04  119.79  3.000
 KAY  H5   C03  C02  119.78  3.000
 KAY  C04  C03  C02  120.43  3.000
 KAY  H6   C04  C05  119.20  3.000
 KAY  H6   C04  C03  119.29  3.000
 KAY  C05  C04  C03  121.50  3.000
 KAY  C09  C05  C06  122.23  3.000
 KAY  C09  C05  C04  118.64  3.000
 KAY  C06  C05  C04  119.01  3.000
 KAY  O08  C06  O07  126.83  3.000
 KAY  O08  C06  C05  116.68  3.000
 KAY  O07  C06  C05  116.43  3.000
 KAY  C05  C09  C13  119.26  3.000
 KAY  C13  C09  C10  118.13  3.000
 KAY  C05  C09  C10  122.50  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
 KAY  CONST_01  C04  C05  C09  C13     0.00   0.0  0
 KAY  CONST_02  C04  C03  C02  C13     0.00   0.0  0
 KAY  CONST_03  C05  C09  C13  C02     0.00   0.0  0
 KAY  CONST_04  C05  C04  C03  C02     0.00   0.0  0
 KAY  CONST_05  C09  C05  C04  C03     0.00   0.0  0
 KAY  CONST_06  C09  C13  C02  C03     0.00   0.0  0
 KAY  CONST_07  C04  C05  C09  C10   180.00   0.0  0
 KAY  CONST_08  C02  C13  C09  C10   180.00   0.0  0
 KAY  CONST_09  C06  C05  C09  C13   180.00   0.0  0
 KAY  CONST_10  C09  C13  C02  C01   180.00   0.0  0
 KAY  CONST_11  C04  C03  C02  C01   180.00   0.0  0
 KAY  CONST_12  C06  C05  C04  C03   180.00   0.0  0
 KAY  CONST_13  H5   C03  C02  C13   180.00   0.0  0
 KAY  CONST_14  H6   C04  C03  C02   180.00   0.0  0
 KAY  CONST_15  H1   C13  C02  C03   180.00   0.0  0
 KAY  Var_01    O12  C10  C09  C13  -120.39  30.0  2
 KAY  Var_02    O07  C06  C05  C04  -136.55  30.0  2
 KAY  Var_03    H2   C01  C02  C13   100.55  30.0  2

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
 KAY  plan-1  C10  0.020
 KAY  plan-1  C13  0.020
 KAY  plan-1  C01  0.020
 KAY  plan-1  C02  0.020
 KAY  plan-1  C03  0.020
 KAY  plan-1  C04  0.020
 KAY  plan-1  C05  0.020
 KAY  plan-1  C06  0.020
 KAY  plan-1  C09  0.020
 KAY  plan-1  H1   0.020
 KAY  plan-1  H5   0.020
 KAY  plan-1  H6   0.020
 KAY  plan-2  C10  0.020
 KAY  plan-2  C09  0.020
 KAY  plan-2  O11  0.020
 KAY  plan-2  O12  0.020
 KAY  plan-3  C05  0.020
 KAY  plan-3  C06  0.020
 KAY  plan-3  O07  0.020
 KAY  plan-3  O08  0.020

