# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 22:46:51 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (4,6-dihydroxy-3,5-dimethylpyridin-2-yl)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(O)nc(CC(O)=O)c(C)c1O
#
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
 57O  57O  '(4,6-dihydroxy-3,5-dimethylpyridin-2-yl)acetic acid'  ligand  24  14  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_57O
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
 57O  CAA  C  CH3    0  -0.775   3.6681   0.0028  -0.3539
 57O  CAB  C  CH3    0  -0.723  -0.7182  -2.3509   0.3911
 57O  CAM  C  CR6    0   0.260  -0.4798   0.1718   0.6211
 57O  OAD  O  OC    -1  -0.622  -4.1005   0.0427   0.0746
 57O  OAC  O  O      0  -0.594  -2.3947   0.0830  -1.3607
 57O  CAI  C  C      0   0.423  -2.8926   0.1254  -0.2221
 57O  CAG  C  CH2    0  -0.708  -1.9248   0.3370   0.9685
 57O  NAH  N  N      0  -0.506   0.2409   1.2955   0.5657
 57O  CAL  C  CR6    0   0.404   1.5196   1.2304   0.2594
 57O  CAJ  C  CR6    0  -0.171   2.2073   0.0500  -0.0110
 57O  CAN  C  CR6    0   0.406   1.4369  -1.1101   0.0489
 57O  OAF  O  OH1    0  -0.613   1.9688  -2.3165  -0.2068
 57O  CAK  C  CR6    0  -0.094   0.0745  -1.0777   0.3718
 57O  H1   H  HCH3   0   0.249   4.2243  -0.6547   0.3195
 57O  H2   H  HCH3   0   0.253   3.8377  -0.3532  -1.3735
 57O  H3   H  HCH3   0   0.272   4.1312   0.9829  -0.2813
 57O  H4   H  HCH3   0   0.239  -0.8760  -2.7369  -0.6185
 57O  H5   H  HCH3   0   0.238  -0.2155  -3.1343   0.9592
 57O  H6   H  HCH3   0   0.242  -1.7019  -2.2123   0.8339
 57O  H8   H  HCH2   0   0.242  -2.2125  -0.3255   1.7891
 57O  H9   H  HCH2   0   0.256  -2.0722   1.3548   1.3401
 57O  H10  H  HOH1   0   0.483   2.9084  -2.2488  -0.4106
 57O  H12  H  HOH1   0   0.465   1.5726   3.1025   0.4084
 57O  OAE  O  OH1    0  -0.627   2.1946   2.3913   0.2072

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
 57O  OAC  CAI  deloc     1.243  0.020  1.243
 57O  CAI  OAD  deloc     1.247  0.020  1.247
 57O  CAI  CAG  single    1.549  0.020  1.549
 57O  CAG  CAM  single    1.495  0.020  1.495
 57O  CAM  NAH  aromatic  1.336  0.020  1.336
 57O  CAM  CAK  aromatic  1.389  0.020  1.389
 57O  NAH  CAL  aromatic  1.316  0.020  1.316
 57O  CAB  CAK  single    1.500  0.020  1.500
 57O  CAK  CAN  aromatic  1.401  0.020  1.401
 57O  CAL  OAE  single    1.344  0.020  1.344
 57O  CAL  CAJ  aromatic  1.393  0.020  1.393
 57O  CAN  CAJ  aromatic  1.394  0.020  1.394
 57O  CAN  OAF  single    1.343  0.020  1.343
 57O  CAJ  CAA  single    1.501  0.020  1.501
 57O  CAA  H1   single    0.970  0.020  1.090
 57O  CAA  H2   single    0.970  0.020  1.090
 57O  CAA  H3   single    0.970  0.020  1.090
 57O  CAB  H4   single    0.970  0.020  1.090
 57O  CAB  H5   single    0.970  0.020  1.090
 57O  CAB  H6   single    0.970  0.020  1.090
 57O  CAG  H8   single    0.970  0.020  1.090
 57O  CAG  H9   single    0.970  0.020  1.090
 57O  OAF  H10  single    0.850  0.020  0.980
 57O  OAE  H12  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
 57O  H3   CAA  H2   106.85  3.000
 57O  H3   CAA  H1   106.53  3.000
 57O  H2   CAA  H1   107.44  3.000
 57O  H3   CAA  CAJ  111.79  3.000
 57O  H2   CAA  CAJ  111.98  3.000
 57O  H1   CAA  CAJ  111.92  3.000
 57O  H6   CAB  H5   107.24  3.000
 57O  H6   CAB  H4   106.90  3.000
 57O  H5   CAB  H4   107.11  3.000
 57O  H6   CAB  CAK  112.03  3.000
 57O  H5   CAB  CAK  111.89  3.000
 57O  H4   CAB  CAK  111.37  3.000
 57O  CAK  CAM  NAH  122.25  3.000
 57O  CAK  CAM  CAG  121.77  3.000
 57O  NAH  CAM  CAG  115.97  3.000
 57O  CAG  CAI  OAC  117.28  3.000
 57O  CAG  CAI  OAD  115.57  3.000
 57O  OAC  CAI  OAD  127.13  3.000
 57O  H9   CAG  H8   105.87  3.000
 57O  H9   CAG  CAI  107.71  3.000
 57O  H8   CAG  CAI  109.26  3.000
 57O  H9   CAG  CAM  108.18  3.000
 57O  H8   CAG  CAM  111.21  3.000
 57O  CAI  CAG  CAM  114.21  3.000
 57O  CAL  NAH  CAM  119.47  3.000
 57O  CAJ  CAL  NAH  124.52  3.000
 57O  CAJ  CAL  OAE  118.46  3.000
 57O  NAH  CAL  OAE  117.01  3.000
 57O  CAN  CAJ  CAL  115.10  3.000
 57O  CAN  CAJ  CAA  121.43  3.000
 57O  CAL  CAJ  CAA  123.47  3.000
 57O  CAK  CAN  OAF  116.74  3.000
 57O  OAF  CAN  CAJ  121.37  3.000
 57O  CAK  CAN  CAJ  121.89  3.000
 57O  H10  OAF  CAN  111.30  3.000
 57O  CAN  CAK  CAM  116.76  3.000
 57O  CAN  CAK  CAB  119.83  3.000
 57O  CAM  CAK  CAB  123.38  3.000
 57O  H12  OAE  CAL  107.73  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
 57O  CONST_01  CAJ  CAL  NAH  CAM    0.00   0.0  0
 57O  CONST_02  CAJ  CAN  CAK  CAM    0.00   0.0  0
 57O  CONST_03  CAN  CAK  CAM  NAH    0.00   0.0  0
 57O  CONST_04  CAN  CAJ  CAL  NAH    0.00   0.0  0
 57O  CONST_05  CAK  CAM  NAH  CAL    0.00   0.0  0
 57O  CONST_06  CAK  CAN  CAJ  CAL    0.00   0.0  0
 57O  CONST_07  NAH  CAL  CAJ  CAA  180.00   0.0  0
 57O  CONST_08  CAK  CAN  CAJ  CAA  180.00   0.0  0
 57O  CONST_09  NAH  CAM  CAK  CAB  180.00   0.0  0
 57O  CONST_10  CAJ  CAN  CAK  CAB  180.00   0.0  0
 57O  CONST_11  CAM  NAH  CAL  OAE  180.00   0.0  0
 57O  CONST_12  CAN  CAJ  CAL  OAE  180.00   0.0  0
 57O  CONST_13  OAF  CAN  CAK  CAM  180.00   0.0  0
 57O  CONST_14  CAL  NAH  CAM  CAG  180.00   0.0  0
 57O  CONST_15  CAN  CAK  CAM  CAG  180.00   0.0  0
 57O  CONST_16  OAF  CAN  CAJ  CAL  180.00   0.0  0
 57O  Var_01    NAH  CAM  CAG  CAI  107.05  30.0  2
 57O  Var_02    H4   CAB  CAK  CAM  106.86  30.0  2
 57O  Var_03    H1   CAA  CAJ  CAL  124.25  30.0  2
 57O  Var_04    OAC  CAI  CAG  CAM  -12.48  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
 57O  plan-1  CAA  0.020
 57O  plan-1  CAB  0.020
 57O  plan-1  CAM  0.020
 57O  plan-1  CAG  0.020
 57O  plan-1  NAH  0.020
 57O  plan-1  CAL  0.020
 57O  plan-1  CAJ  0.020
 57O  plan-1  CAN  0.020
 57O  plan-1  OAF  0.020
 57O  plan-1  CAK  0.020
 57O  plan-1  OAE  0.020
 57O  plan-2  OAD  0.020
 57O  plan-2  OAC  0.020
 57O  plan-2  CAI  0.020
 57O  plan-2  CAG  0.020

