# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 21 19:34:45 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: 4-(carboxymethyl)-1-methylpyridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[n+]1ccc(CC(O)=O)cc1
#
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
 PAA  PAA  4-(carboxymethyl)-1-methylpyridinium  ligand  21  11  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PAA
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
 PAA  CM    C  CH3   0  -0.534   3.8948   0.0705  -0.4366
 PAA  N1    N  NR6   1  -0.416   2.4677   0.0111  -0.1031
 PAA  C2    C  CR16  0   0.101   1.7761   1.1563  -0.0032
 PAA  C3    C  CR16  0  -0.370   0.4467   1.1476   0.3330
 PAA  C4    C  CR6   0   0.277  -0.1994  -0.0616   0.5797
 PAA  C5    C  CR16  0  -0.384   0.5450  -1.2281   0.4705
 PAA  C6    C  CR16  0   0.095   1.8760  -1.1650   0.1279
 PAA  C2'   C  CH2   0  -0.682  -1.6459  -0.0980   0.9478
 PAA  C1'   C  C     0   0.567  -2.5310   0.2034  -0.2407
 PAA  O1'   O  O     0  -0.425  -2.1302   0.5550  -1.3191
 PAA  O2'   O  OH1   0  -0.583  -3.8071   0.0391   0.0649
 PAA  HM1   H  HCH3  0   0.299   4.4465   0.4431   0.4223
 PAA  HM2   H  HCH3  0   0.287   4.2456  -0.9229  -0.6928
 PAA  HM3   H  HCH3  0   0.294   4.0364   0.7338  -1.2840
 PAA  H2    H  HCR6  0   0.350   2.3179   2.0694  -0.1993
 PAA  H3    H  HCR6  0   0.314  -0.0738   2.0912   0.4112
 PAA  H5    H  HCR6  0   0.315   0.1032  -2.1972   0.6523
 PAA  H6    H  HCR6  0   0.352   2.4882  -2.0489   0.0341
 PAA  H2'1  H  HCH2  0   0.324  -1.9187  -1.0695   1.3633
 PAA  H2'2  H  HCH2  0   0.333  -1.8554   0.6432   1.7249
 PAA  HO2   H  HOH1  0   0.488  -4.3659   0.2504  -0.6987

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
 PAA  CM   N1    single    1.467  0.020  1.467
 PAA  CM   HM1   single    0.970  0.020  1.090
 PAA  CM   HM2   single    0.970  0.020  1.090
 PAA  CM   HM3   single    0.970  0.020  1.090
 PAA  N1   C2    aromatic  1.342  0.020  1.342
 PAA  N1   C6    aromatic  1.337  0.020  1.337
 PAA  C2   C3    aromatic  1.371  0.020  1.371
 PAA  C2   H2    single    0.930  0.020  1.080
 PAA  C3   C4    aromatic  1.393  0.020  1.393
 PAA  C3   H3    single    0.930  0.020  1.080
 PAA  C4   C5    aromatic  1.388  0.020  1.388
 PAA  C4   C2'   single    1.493  0.020  1.493
 PAA  C5   C6    aromatic  1.376  0.020  1.376
 PAA  C5   H5    single    0.930  0.020  1.080
 PAA  C6   H6    single    0.930  0.020  1.080
 PAA  C2'  C1'   single    1.512  0.020  1.512
 PAA  C2'  H2'1  single    0.970  0.020  1.090
 PAA  C2'  H2'2  single    0.970  0.020  1.090
 PAA  C1'  O1'   double    1.203  0.020  1.203
 PAA  C1'  O2'   single    1.322  0.020  1.322
 PAA  O2'  HO2   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
 PAA  HM3   CM   HM2   109.47  3.000
 PAA  HM3   CM   HM1   109.96  3.000
 PAA  HM2   CM   HM1   109.67  3.000
 PAA  HM3   CM   N1    109.22  3.000
 PAA  HM2   CM   N1    109.36  3.000
 PAA  HM1   CM   N1    109.15  3.000
 PAA  C6    N1   C2    120.66  3.000
 PAA  C6    N1   CM    120.37  3.000
 PAA  C2    N1   CM    118.94  3.000
 PAA  H2    C2   C3    122.44  3.000
 PAA  H2    C2   N1    116.72  3.000
 PAA  C3    C2   N1    120.84  3.000
 PAA  H3    C3   C4    121.45  3.000
 PAA  H3    C3   C2    118.64  3.000
 PAA  C4    C3   C2    119.91  3.000
 PAA  C2'   C4   C5    121.23  3.000
 PAA  C2'   C4   C3    120.95  3.000
 PAA  C5    C4   C3    117.83  3.000
 PAA  H5    C5   C6    118.60  3.000
 PAA  H5    C5   C4    121.42  3.000
 PAA  C6    C5   C4    119.99  3.000
 PAA  H6    C6   C5    122.20  3.000
 PAA  H6    C6   N1    117.03  3.000
 PAA  C5    C6   N1    120.77  3.000
 PAA  H2'2  C2'  H2'1  106.55  3.000
 PAA  H2'2  C2'  C1'   108.12  3.000
 PAA  H2'1  C2'  C1'   109.29  3.000
 PAA  H2'2  C2'  C4    110.12  3.000
 PAA  H2'1  C2'  C4    110.97  3.000
 PAA  C1'   C2'  C4    111.62  3.000
 PAA  O2'   C1'  O1'   124.40  3.000
 PAA  O2'   C1'  C2'   111.00  3.000
 PAA  O1'   C1'  C2'   124.59  3.000
 PAA  HO2   O2'  C1'   110.31  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
 PAA  CONST_01  C4   C3   C2   N1     0.00   0.0  0
 PAA  CONST_02  C4   C5   C6   N1     0.00   0.0  0
 PAA  CONST_03  C5   C6   N1   C2     0.00   0.0  0
 PAA  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 PAA  CONST_05  C6   N1   C2   C3     0.00   0.0  0
 PAA  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 PAA  CONST_07  C3   C2   N1   CM   180.00   0.0  0
 PAA  CONST_08  C5   C6   N1   CM   180.00   0.0  0
 PAA  CONST_09  C2'  C4   C3   C2   180.00   0.0  0
 PAA  CONST_10  C2'  C4   C5   C6   180.00   0.0  0
 PAA  CONST_11  H3   C3   C2   N1   180.00   0.0  0
 PAA  CONST_12  H5   C5   C6   N1   180.00   0.0  0
 PAA  CONST_13  H6   C6   N1   C2   180.00   0.0  0
 PAA  CONST_14  H2   C2   C3   C4   180.00   0.0  0
 PAA  CONST_15  HO2  O2'  C1'  C2'  180.00   0.0  0
 PAA  Var_01    C1'  C2'  C4   C3    73.22  30.0  2
 PAA  Var_02    HM1  CM   N1   C2    72.50  30.0  2
 PAA  Var_03    O1'  C1'  C2'  C4    -6.66  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
 PAA  plan-1  CM   0.020
 PAA  plan-1  N1   0.020
 PAA  plan-1  C2   0.020
 PAA  plan-1  C3   0.020
 PAA  plan-1  C4   0.020
 PAA  plan-1  C5   0.020
 PAA  plan-1  C6   0.020
 PAA  plan-1  C2'  0.020
 PAA  plan-1  H2   0.020
 PAA  plan-1  H3   0.020
 PAA  plan-1  H5   0.020
 PAA  plan-1  H6   0.020
 PAA  plan-2  C2'  0.020
 PAA  plan-2  C1'  0.020
 PAA  plan-2  O1'  0.020
 PAA  plan-2  O2'  0.020
 PAA  plan-2  HO2  0.020

