# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 00:33:15 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  22  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 PERFECT
;

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  CR6   0   0.444  -1.6222   0.9819   0.2863
 9KH  C3   C  CR6   0  -0.086  -0.2923   1.0020  -0.1628
 9KH  C4   C  CR6   0   0.240   0.2682  -0.2302  -0.4688
 9KH  C6   C  CR6   0   0.464  -1.6308  -1.3789   0.0482
 9KH  O1   O  OH1   0  -0.609  -2.1808   2.1550   0.6010
 9KH  N5   N  N     0  -0.471  -0.3834  -1.3909  -0.3691
 9KH  C7   C  CR16  0  -0.571  -2.3103  -0.2163   0.3951
 9KH  O8   O  OH1   0  -0.612  -2.2057  -2.5882   0.1151
 9KH  C9   C  CH3   0  -0.726   0.4432   2.3055  -0.2569
 9KH  C10  C  CH2   0  -0.703   1.6854  -0.3440  -0.9529
 9KH  C12  C  C     0   0.556   2.6960  -0.1371   0.1467
 9KH  O13  O  O     0  -0.432   2.4312  -0.0158   1.3151
 9KH  O14  O  OH1   0  -0.591   3.9347  -0.1242  -0.3305
 9KH  H2   H  HOH1  0   0.482  -3.0937   2.0350   0.8882
 9KH  H3   H  HCR6  0   0.290  -3.3386  -0.2421   0.7390
 9KH  H4   H  HCH3  0   0.249   0.6904   2.6958   0.7324
 9KH  H5   H  HCH3  0   0.242   1.3776   2.2161  -0.8074
 9KH  H6   H  HCH3  0   0.250  -0.1521   3.0656  -0.7631
 9KH  H7   H  HCH2  0   0.318   1.8401  -1.3463  -1.3600
 9KH  H8   H  HCH2  0   0.304   1.8954   0.3490  -1.7709
 9KH  H9   H  HOH1  0   0.482   4.5693  -0.0133   0.3934
 9KH  H1   H  HOH1  0   0.480  -3.1147  -2.5152   0.4269

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    1.337  0.020  1.337
 9KH  C2   C7   aromatic  1.386  0.020  1.386
 9KH  C2   C3   aromatic  1.404  0.020  1.404
 9KH  C7   C6   aromatic  1.391  0.020  1.391
 9KH  C9   C3   single    1.500  0.020  1.500
 9KH  C3   C4   aromatic  1.388  0.020  1.388
 9KH  C6   O8   single    1.341  0.020  1.341
 9KH  C6   N5   aromatic  1.315  0.020  1.315
 9KH  C4   N5   aromatic  1.335  0.020  1.335
 9KH  C4   C10  single    1.502  0.020  1.502
 9KH  C10  C12  single    1.508  0.020  1.508
 9KH  C12  O13  double    1.204  0.020  1.204
 9KH  C12  O14  single    1.327  0.020  1.327
 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  O14  H9   single    0.850  0.020  0.980
 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   122.19  3.000
 9KH  C7   C2   C3   120.51  3.000
 9KH  O1   C2   C3   117.29  3.000
 9KH  C9   C3   C4   124.04  3.000
 9KH  C4   C3   C2   116.13  3.000
 9KH  C9   C3   C2   119.81  3.000
 9KH  C10  C4   N5   114.76  3.000
 9KH  C10  C4   C3   121.30  3.000
 9KH  N5   C4   C3   123.95  3.000
 9KH  O8   C6   C7   122.15  3.000
 9KH  O8   C6   N5   114.47  3.000
 9KH  C7   C6   N5   123.38  3.000
 9KH  H2   O1   C2   110.87  3.000
 9KH  C6   N5   C4   118.59  3.000
 9KH  H3   C7   C6   121.50  3.000
 9KH  H3   C7   C2   121.07  3.000
 9KH  C6   C7   C2   117.43  3.000
 9KH  H1   O8   C6   110.63  3.000
 9KH  H6   C9   H5   106.94  3.000
 9KH  H6   C9   H4   107.17  3.000
 9KH  H5   C9   H4   107.06  3.000
 9KH  H6   C9   C3   111.55  3.000
 9KH  H5   C9   C3   112.43  3.000
 9KH  H4   C9   C3   111.39  3.000
 9KH  H8   C10  H7   106.00  3.000
 9KH  H8   C10  C12  109.28  3.000
 9KH  H7   C10  C12  107.62  3.000
 9KH  H8   C10  C4   112.00  3.000
 9KH  H7   C10  C4   108.86  3.000
 9KH  C12  C10  C4   112.77  3.000
 9KH  O14  C12  O13  123.57  3.000
 9KH  O14  C12  C10  111.38  3.000
 9KH  O13  C12  C10  125.04  3.000
 9KH  H9   O14  C12  110.11  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  CONST_16  H9   O14  C12  C10  180.00   0.0  0
 9KH  Var_01    C12  C10  C4   C3    74.32  30.0  2
 9KH  Var_02    H4   C9   C3   C2    71.85  30.0  2
 9KH  Var_03    O13  C12  C10  C4     6.57  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
 9KH  plan-2  H9   0.020

