# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 22:01:57 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: (2E)-3-pyridin-4-ylprop-2-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)\C=C\c1ccncc1
#
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
 XIZ  XIZ  '(2E)-3-pyridin-4-ylprop-2-enoic acid'  ligand  17  11  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XIZ
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
 XIZ  C1   C  C      0   0.404   2.9839  -0.0797  -0.0186
 XIZ  O1   O  O      0  -0.595   3.2420  -1.2988  -0.0171
 XIZ  O2   O  OC    -1  -0.610   3.8019   0.8624  -0.0237
 XIZ  C2   C  C1     0  -0.417   1.5265   0.3313  -0.0141
 XIZ  C3   C  C1     0  -0.250   0.5219  -0.5463  -0.0006
 XIZ  C1'  C  CR6    0   0.234  -0.9061  -0.2268  -0.0007
 XIZ  C2'  C  CR16   0  -0.382  -1.8440  -1.2593  -0.0204
 XIZ  C3'  C  CR16   0  -0.060  -3.1965  -0.9560  -0.0270
 XIZ  C5'  C  CR16   0  -0.063  -2.7809   1.2712   0.0066
 XIZ  C6'  C  CR16   0  -0.388  -1.4119   1.0755   0.0148
 XIZ  N4   N  N      0  -0.411  -3.6723   0.2828  -0.0137
 XIZ  HA   H  H      0   0.238   1.3276   1.3989  -0.0243
 XIZ  H3   H  H      0   0.243   0.7653  -1.6044   0.0076
 XIZ  H2'  H  HCR6   0   0.266  -1.5263  -2.2942  -0.0328
 XIZ  H6'  H  HCR6   0   0.265  -0.7552   1.9352   0.0330
 XIZ  H3'  H  HCR6   0   0.263  -3.9276  -1.7568  -0.0445
 XIZ  H5'  H  HCR6   0   0.264  -3.1787   2.2801   0.0177

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
 XIZ  C1   O1   deloc     1.246  0.020  1.246
 XIZ  C1   O2   deloc     1.248  0.020  1.248
 XIZ  C1   C2   single    1.514  0.020  1.514
 XIZ  C2   C3   double    1.334  0.020  1.334
 XIZ  C3   C1'  single    1.463  0.020  1.463
 XIZ  C1'  C2'  aromatic  1.395  0.020  1.395
 XIZ  C1'  C6'  aromatic  1.397  0.020  1.397
 XIZ  C2'  C3'  aromatic  1.386  0.020  1.386
 XIZ  C3'  N4   aromatic  1.327  0.020  1.327
 XIZ  C5'  C6'  aromatic  1.383  0.020  1.383
 XIZ  C5'  N4   aromatic  1.331  0.020  1.331
 XIZ  C2   HA   single    0.930  0.020  1.080
 XIZ  C3   H3   single    0.930  0.020  1.080
 XIZ  C2'  H2'  single    0.930  0.020  1.080
 XIZ  C6'  H6'  single    0.930  0.020  1.080
 XIZ  C3'  H3'  single    0.930  0.020  1.080
 XIZ  C5'  H5'  single    0.930  0.020  1.080

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
 XIZ  C2   C1   O2   115.22  3.000
 XIZ  C2   C1   O1   117.70  3.000
 XIZ  O2   C1   O1   127.08  3.000
 XIZ  HA   C2   C3   120.58  3.000
 XIZ  HA   C2   C1   116.30  3.000
 XIZ  C3   C2   C1   123.11  3.000
 XIZ  H3   C3   C1'  115.57  3.000
 XIZ  H3   C3   C2   118.18  3.000
 XIZ  C1'  C3   C2   126.25  3.000
 XIZ  C6'  C1'  C2'  116.53  3.000
 XIZ  C6'  C1'  C3   123.83  3.000
 XIZ  C2'  C1'  C3   119.64  3.000
 XIZ  H2'  C2'  C3'  119.70  3.000
 XIZ  H2'  C2'  C1'  120.69  3.000
 XIZ  C3'  C2'  C1'  119.62  3.000
 XIZ  H3'  C3'  N4   116.60  3.000
 XIZ  H3'  C3'  C2'  119.76  3.000
 XIZ  N4   C3'  C2'  123.64  3.000
 XIZ  H5'  C5'  N4   116.44  3.000
 XIZ  H5'  C5'  C6'  119.65  3.000
 XIZ  N4   C5'  C6'  123.92  3.000
 XIZ  H6'  C6'  C5'  119.25  3.000
 XIZ  H6'  C6'  C1'  121.41  3.000
 XIZ  C5'  C6'  C1'  119.35  3.000
 XIZ  C5'  N4   C3'  116.95  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
 XIZ  CONST_01  N4   C3'  C2'  C1'     0.00   0.0  0
 XIZ  CONST_02  N4   C5'  C6'  C1'     0.00   0.0  0
 XIZ  CONST_03  C5'  C6'  C1'  C2'     0.00   0.0  0
 XIZ  CONST_04  C5'  N4   C3'  C2'     0.00   0.0  0
 XIZ  CONST_05  C6'  C1'  C2'  C3'     0.00   0.0  0
 XIZ  CONST_06  C6'  C5'  N4   C3'     0.00   0.0  0
 XIZ  CONST_07  C3'  C2'  C1'  C3    180.00   0.0  0
 XIZ  CONST_08  C5'  C6'  C1'  C3    180.00   0.0  0
 XIZ  CONST_09  H3'  C3'  C2'  C1'   180.00   0.0  0
 XIZ  CONST_10  H5'  C5'  C6'  C1'   180.00   0.0  0
 XIZ  CONST_11  H6'  C6'  C1'  C2'   180.00   0.0  0
 XIZ  CONST_12  H2'  C2'  C1'  C6'   180.00   0.0  0
 XIZ  Var_01    C2'  C1'  C3   C2    178.35  30.0  2
 XIZ  Var_02    C1'  C3   C2   C1   -179.74   0.0  2
 XIZ  Var_03    C3   C2   C1   O1      0.42  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
 XIZ  plan-1  C3   0.020
 XIZ  plan-1  C1'  0.020
 XIZ  plan-1  C2'  0.020
 XIZ  plan-1  C3'  0.020
 XIZ  plan-1  C5'  0.020
 XIZ  plan-1  C6'  0.020
 XIZ  plan-1  N4   0.020
 XIZ  plan-1  H2'  0.020
 XIZ  plan-1  H6'  0.020
 XIZ  plan-1  H3'  0.020
 XIZ  plan-1  H5'  0.020
 XIZ  plan-2  C1   0.020
 XIZ  plan-2  O1   0.020
 XIZ  plan-2  O2   0.020
 XIZ  plan-2  C2   0.020
 XIZ  plan-3  C1   0.020
 XIZ  plan-3  C2   0.020
 XIZ  plan-3  C3   0.020
 XIZ  plan-3  C1'  0.020
 XIZ  plan-3  HA   0.020
 XIZ  plan-3  H3   0.020

