# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 22:46:06 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  21  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   0.475  -0.7447   1.7364   0.2553
 KAY  C13  C  CR16  0  -0.302   1.5529   0.8412   0.0451
 KAY  C01  C  CH3   0  -0.722   3.9538   0.0837   0.0311
 KAY  C02  C  CR6   0   0.116   2.4818  -0.1964   0.0203
 KAY  C03  C  CR16  0  -0.279   2.0061  -1.5037   0.0057
 KAY  C04  C  CR16  0  -0.239   0.6464  -1.7685   0.0127
 KAY  C05  C  CR6   0  -0.068  -0.2770  -0.7286   0.0363
 KAY  C06  C  C     0   0.494  -1.7276  -1.0141  -0.1100
 KAY  C09  C  CR6   0  -0.002   0.1877   0.5884   0.0598
 KAY  O07  O  O     0  -0.433  -2.4839  -0.3124  -0.7347
 KAY  O08  O  OH1   0  -0.586  -2.0868  -2.1392   0.4877
 KAY  O11  O  OH1   0  -0.582  -0.4907   2.7339  -0.5758
 KAY  O12  O  O     0  -0.428  -1.5892   1.7659   1.1134
 KAY  H1   H  HCR6  0   0.271   1.9087   1.8636   0.0762
 KAY  H2   H  HCH3  0   0.258   4.3778  -0.1246   1.0150
 KAY  H3   H  HCH3  0   0.254   4.4792  -0.5472  -0.6855
 KAY  H4   H  HCH3  0   0.251   4.1678   1.1234  -0.2095
 KAY  H5   H  HCR6  0   0.266   2.7065  -2.3291  -0.0202
 KAY  H6   H  HCR6  0   0.276   0.3094  -2.7955  -0.0274
 KAY  H7   H  HOH1  0   0.490  -3.0241  -2.3215   0.3203
 KAY  H8   H  HOH1  0   0.490  -1.0627   3.4909  -0.3745

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  double    1.204  0.020  1.204
 KAY  O07  C06  double    1.206  0.020  1.206
 KAY  C06  O08  single    1.324  0.020  1.324
 KAY  C06  C05  single    1.486  0.020  1.486
 KAY  C10  C09  single    1.492  0.020  1.492
 KAY  C10  O11  single    1.323  0.020  1.323
 KAY  C05  C09  aromatic  1.397  0.020  1.397
 KAY  C05  C04  aromatic  1.391  0.020  1.391
 KAY  C09  C13  aromatic  1.389  0.020  1.389
 KAY  C04  C03  aromatic  1.385  0.020  1.385
 KAY  C13  C02  aromatic  1.393  0.020  1.393
 KAY  C03  C02  aromatic  1.391  0.020  1.391
 KAY  C02  C01  single    1.498  0.020  1.498
 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
 KAY  O08  H7   single    0.850  0.020  0.980
 KAY  O11  H8   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
 KAY  O12  C10  O11  124.32  3.000
 KAY  O11  C10  C09  112.20  3.000
 KAY  O12  C10  C09  123.40  3.000
 KAY  H1   C13  C09  119.64  3.000
 KAY  H1   C13  C02  118.99  3.000
 KAY  C09  C13  C02  121.35  3.000
 KAY  H4   C01  H3   108.23  3.000
 KAY  H4   C01  H2   107.77  3.000
 KAY  H3   C01  H2   107.15  3.000
 KAY  H4   C01  C02  111.73  3.000
 KAY  H3   C01  C02  111.14  3.000
 KAY  H2   C01  C02  110.63  3.000
 KAY  C03  C02  C01  120.78  3.000
 KAY  C01  C02  C13  121.04  3.000
 KAY  C03  C02  C13  118.17  3.000
 KAY  H5   C03  C04  119.29  3.000
 KAY  H5   C03  C02  119.69  3.000
 KAY  C04  C03  C02  121.02  3.000
 KAY  H6   C04  C05  120.25  3.000
 KAY  H6   C04  C03  119.15  3.000
 KAY  C05  C04  C03  120.58  3.000
 KAY  C09  C05  C06  120.50  3.000
 KAY  C09  C05  C04  118.98  3.000
 KAY  C06  C05  C04  120.19  3.000
 KAY  O08  C06  O07  123.93  3.000
 KAY  O08  C06  C05  112.57  3.000
 KAY  O07  C06  C05  123.47  3.000
 KAY  C05  C09  C13  119.90  3.000
 KAY  C13  C09  C10  118.41  3.000
 KAY  C05  C09  C10  121.33  3.000
 KAY  H7   O08  C06  110.13  3.000
 KAY  H8   O11  C10  110.17  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  CONST_16  H7   O08  C06  C05   180.00   0.0  0
 KAY  CONST_17  H8   O11  C10  C09   180.00   0.0  0
 KAY  Var_01    O12  C10  C09  C13  -125.91  30.0  3
 KAY  Var_02    O07  C06  C05  C04  -141.61  30.0  2
 KAY  Var_03    H2   C01  C02  C13   104.70  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-2  H8   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
 KAY  plan-3  H7   0.020

