# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 22:55:56 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: 2-[3-methyl-4,6-bis(oxidanyl)pyridin-2-yl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(O)cc(O)nc1CC(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
 9KH  9KH  '2-[3-methyl-4,6-bis(oxidanyl)pyridin-2-yl]ethanoic acid'  ligand  21  13  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9KH
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
 9KH  C2   C  C      0   0.421  -1.7195   0.8981   0.2495
 9KH  C3   C  C      0  -0.123  -0.3891   0.9876  -0.1772
 9KH  C4   C  C      0   0.252   0.2444  -0.2143  -0.5016
 9KH  C6   C  C      0   0.456  -1.6070  -1.4576  -0.0257
 9KH  O1   O  OH1    0  -0.618  -2.4629   1.9580   0.6002
 9KH  N5   N  N      0  -0.476  -0.3544  -1.4033  -0.4318
 9KH  C7   C  C1     0  -0.543  -2.3461  -0.3407   0.3292
 9KH  O8   O  OH1    0  -0.617  -2.1223  -2.6985   0.0133
 9KH  C9   C  CH3    0  -0.738   0.3541   2.2901  -0.2693
 9KH  C10  C  CH2    0  -0.692   1.6672  -0.2286  -0.9586
 9KH  C12  C  C      0   0.425   2.7042  -0.0957   0.1875
 9KH  O13  O  O      0  -0.595   2.2720  -0.0869   1.3534
 9KH  O14  O  OC    -1  -0.618   3.8936  -0.0277  -0.1762
 9KH  H2   H  HOH1   0   0.472  -1.9609   2.7774   0.5341
 9KH  H3   H  H      0   0.275  -3.3768  -0.4128   0.6545
 9KH  H4   H  HCH3   0   0.257   1.1456   2.3449   0.4790
 9KH  H5   H  HCH3   0   0.254   0.8210   2.4129  -1.2472
 9KH  H6   H  HCH3   0   0.231  -0.2712   3.1726  -0.1302
 9KH  H7   H  HCH2   0   0.256   1.8553  -1.1748  -1.4722
 9KH  H8   H  HCH2   0   0.245   1.8535   0.5599  -1.6927
 9KH  H1   H  HOH1   0   0.476  -3.0362  -2.6730   0.3178

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
 9KH  O1   C2   single    1.341  0.020  1.341
 9KH  C2   C7   aromatic  1.390  0.020  1.390
 9KH  C2   C3   aromatic  1.400  0.020  1.400
 9KH  C7   C6   aromatic  1.385  0.020  1.385
 9KH  C9   C3   single    1.502  0.020  1.502
 9KH  C3   C4   aromatic  1.397  0.020  1.397
 9KH  C6   O8   single    1.344  0.020  1.344
 9KH  C6   N5   aromatic  1.318  0.020  1.318
 9KH  C4   N5   aromatic  1.333  0.020  1.333
 9KH  C4   C10  single    1.495  0.020  1.495
 9KH  C10  C12  single    1.551  0.020  1.551
 9KH  C12  O13  deloc     1.243  0.020  1.243
 9KH  C12  O14  deloc     1.246  0.020  1.246
 9KH  O1   H2   single    0.850  0.020  0.980
 9KH  C7   H3   single    0.930  0.020  1.080
 9KH  C9   H4   single    0.970  0.020  1.090
 9KH  C9   H5   single    0.970  0.020  1.090
 9KH  C9   H6   single    0.970  0.020  1.090
 9KH  C10  H7   single    0.970  0.020  1.090
 9KH  C10  H8   single    0.970  0.020  1.090
 9KH  O8   H1   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
 9KH  C7   C2   O1   116.06  3.000
 9KH  C7   C2   C3   120.18  3.000
 9KH  O1   C2   C3   123.76  3.000
 9KH  C9   C3   C4   120.49  3.000
 9KH  C4   C3   C2   116.53  3.000
 9KH  C9   C3   C2   122.97  3.000
 9KH  C10  C4   N5   115.79  3.000
 9KH  C10  C4   C3   120.73  3.000
 9KH  N5   C4   C3   123.48  3.000
 9KH  O8   C6   C7   122.16  3.000
 9KH  O8   C6   N5   114.28  3.000
 9KH  C7   C6   N5   123.56  3.000
 9KH  H2   O1   C2   111.43  3.000
 9KH  C6   N5   C4   118.67  3.000
 9KH  H3   C7   C6   122.06  3.000
 9KH  H3   C7   C2   120.35  3.000
 9KH  C6   C7   C2   117.59  3.000
 9KH  H1   O8   C6   110.39  3.000
 9KH  H6   C9   H5   105.59  3.000
 9KH  H6   C9   H4   106.74  3.000
 9KH  H5   C9   H4   107.39  3.000
 9KH  H6   C9   C3   114.21  3.000
 9KH  H5   C9   C3   111.37  3.000
 9KH  H4   C9   C3   111.13  3.000
 9KH  H8   C10  H7   106.24  3.000
 9KH  H8   C10  C12  108.69  3.000
 9KH  H7   C10  C12  107.84  3.000
 9KH  H8   C10  C4   111.14  3.000
 9KH  H7   C10  C4   108.40  3.000
 9KH  C12  C10  C4   114.18  3.000
 9KH  O14  C12  O13  127.25  3.000
 9KH  O14  C12  C10  115.29  3.000
 9KH  O13  C12  C10  117.46  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
 9KH  CONST_01  N5   C6   C7   C2    0.00   0.0  0
 9KH  CONST_02  N5   C4   C3   C2    0.00   0.0  0
 9KH  CONST_03  C6   C7   C2   C3    0.00   0.0  0
 9KH  CONST_04  C6   N5   C4   C3    0.00   0.0  0
 9KH  CONST_05  C7   C2   C3   C4    0.00   0.0  0
 9KH  CONST_06  C7   C6   N5   C4    0.00   0.0  0
 9KH  CONST_07  O8   C6   C7   C2  180.00   0.0  0
 9KH  CONST_08  C10  C4   C3   C2  180.00   0.0  0
 9KH  CONST_09  O1   C2   C3   C4  180.00   0.0  0
 9KH  CONST_10  O8   C6   N5   C4  180.00   0.0  0
 9KH  CONST_11  O1   C2   C7   C6  180.00   0.0  0
 9KH  CONST_12  C10  C4   N5   C6  180.00   0.0  0
 9KH  CONST_13  C9   C3   C4   N5  180.00   0.0  0
 9KH  CONST_14  C9   C3   C2   C7  180.00   0.0  0
 9KH  CONST_15  H3   C7   C2   C3  180.00   0.0  0
 9KH  Var_01    C12  C10  C4   C3   78.86  30.0  2
 9KH  Var_02    H4   C9   C3   C2  111.56  30.0  2
 9KH  Var_03    O13  C12  C10  C4    4.91  30.0  3

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
 9KH  plan-1  C2   0.020
 9KH  plan-1  C3   0.020
 9KH  plan-1  C4   0.020
 9KH  plan-1  C6   0.020
 9KH  plan-1  O1   0.020
 9KH  plan-1  N5   0.020
 9KH  plan-1  C7   0.020
 9KH  plan-1  O8   0.020
 9KH  plan-1  C9   0.020
 9KH  plan-1  C10  0.020
 9KH  plan-1  H3   0.020
 9KH  plan-2  C10  0.020
 9KH  plan-2  C12  0.020
 9KH  plan-2  O13  0.020
 9KH  plan-2  O14  0.020

