# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  2 04:49:59 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: (2E)-3-(2-aminopyrimidin-5-yl)prop-2-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncc(/C=C/C(O)=O)cn1
#
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
 XJ0  XJ0  '(2E)-3-(2-aminopyrimidin-5-yl)prop-2-enoic acid'  ligand  19  12  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XJ0
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
 XJ0  OB    O  O     0  -0.457   3.7666  -1.1923   0.0200
 XJ0  C     C  C     0   0.534   3.3874  -0.0419   0.0052
 XJ0  OA    O  OH1   0  -0.606   4.2241   0.9939  -0.0109
 XJ0  CA    C  C1    0  -0.432   1.9876   0.3955   0.0012
 XJ0  CB    C  C1    0  -0.210   0.9952  -0.5062   0.0132
 XJ0  CG    C  CR6   0  -0.035  -0.4240  -0.2364   0.0091
 XJ0  CD    C  CR16  0  -0.022  -1.3477  -1.2836   0.0095
 XJ0  NE    N  N     0  -0.449  -2.6512  -1.1090   0.0033
 XJ0  CZ    C  CR6   0   0.572  -3.0842   0.1601  -0.0041
 XJ0  NH2   N  NH2   0  -0.807  -4.4020   0.3636  -0.0126
 XJ0  NH1   N  N     0  -0.443  -2.2941   1.2492  -0.0023
 XJ0  C10   C  CR16  0  -0.031  -0.9988   1.0398   0.0041
 XJ0  HA    H  HOH1  0   0.479   5.1394   0.6777  -0.0102
 XJ0  HB    H  H     0   0.274   1.7995   1.4620  -0.0130
 XJ0  HC    H  H     0   0.271   1.2654  -1.5586   0.0259
 XJ0  HD    H  HCR6  0   0.276  -0.9986  -2.3123   0.0142
 XJ0  H10   H  HCR6  0   0.269  -0.3745   1.9282   0.0057
 XJ0  HH21  H  HNH2  0   0.408  -5.0385  -0.4135  -0.0252
 XJ0  HH22  H  HNH2  0   0.408  -4.7744   1.2966  -0.0286

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
 XJ0  OB   C     double    1.211  0.020  1.211
 XJ0  C    OA    single    1.332  0.020  1.332
 XJ0  C    CA    single    1.467  0.020  1.467
 XJ0  CA   CB    double    1.341  0.020  1.341
 XJ0  CB   CG    single    1.445  0.020  1.445
 XJ0  CG   CD    aromatic  1.396  0.020  1.396
 XJ0  CG   C10   aromatic  1.400  0.020  1.400
 XJ0  CD   NE    aromatic  1.315  0.020  1.315
 XJ0  NE   CZ    aromatic  1.341  0.020  1.341
 XJ0  CZ   NH2   single    1.333  0.020  1.333
 XJ0  CZ   NH1   aromatic  1.345  0.020  1.345
 XJ0  NH1  C10   aromatic  1.312  0.020  1.312
 XJ0  OA   HA    single    0.850  0.020  0.980
 XJ0  CA   HB    single    0.930  0.020  1.080
 XJ0  CB   HC    single    0.930  0.020  1.080
 XJ0  CD   HD    single    0.930  0.020  1.080
 XJ0  C10  H10   single    0.930  0.020  1.080
 XJ0  NH2  HH21  single    0.860  0.020  1.020
 XJ0  NH2  HH22  single    0.860  0.020  1.020

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
 XJ0  CA    C    OA    111.58  3.000
 XJ0  CA    C    OB    125.60  3.000
 XJ0  OA    C    OB    122.83  3.000
 XJ0  HA    OA   C     109.87  3.000
 XJ0  HB    CA   CB    122.26  3.000
 XJ0  HB    CA   C     117.36  3.000
 XJ0  CB    CA   C     120.38  3.000
 XJ0  HC    CB   CG    115.16  3.000
 XJ0  HC    CB   CA    117.87  3.000
 XJ0  CG    CB   CA    126.97  3.000
 XJ0  C10   CG   CD    114.34  3.000
 XJ0  C10   CG   CB    125.02  3.000
 XJ0  CD    CG   CB    120.65  3.000
 XJ0  HD    CD   NE    116.37  3.000
 XJ0  HD    CD   CG    119.84  3.000
 XJ0  NE    CD   CG    123.79  3.000
 XJ0  CZ    NE   CD    116.46  3.000
 XJ0  NH1   CZ   NH2   117.18  3.000
 XJ0  NH1   CZ   NE    125.21  3.000
 XJ0  NH2   CZ   NE    117.62  3.000
 XJ0  HH22  NH2  HH21  118.90  3.000
 XJ0  HH22  NH2  CZ    120.54  3.000
 XJ0  HH21  NH2  CZ    120.54  3.000
 XJ0  C10   NH1  CZ    116.77  3.000
 XJ0  H10   C10  NH1   115.91  3.000
 XJ0  H10   C10  CG    120.65  3.000
 XJ0  NH1   C10  CG    123.43  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
 XJ0  CONST_01  CZ    NE   CD   CG      0.00   0.0  0
 XJ0  CONST_02  CZ    NH1  C10  CG      0.00   0.0  0
 XJ0  CONST_03  NH1   C10  CG   CD      0.00   0.0  0
 XJ0  CONST_04  NH1   CZ   NE   CD      0.00   0.0  0
 XJ0  CONST_05  C10   CG   CD   NE      0.00   0.0  0
 XJ0  CONST_06  C10   NH1  CZ   NE      0.00   0.0  0
 XJ0  CONST_07  NE    CD   CG   CB    180.00   0.0  0
 XJ0  CONST_08  NH1   C10  CG   CB    180.00   0.0  0
 XJ0  CONST_09  NH2   CZ   NE   CD    180.00   0.0  0
 XJ0  CONST_10  C10   NH1  CZ   NH2   180.00   0.0  0
 XJ0  CONST_11  H10   C10  CG   CD    180.00   0.0  0
 XJ0  CONST_12  HD    CD   NE   CZ    180.00   0.0  0
 XJ0  CONST_13  HH21  NH2  CZ   NE      0.00   0.0  0
 XJ0  CONST_14  HH22  NH2  CZ   NE    180.00   0.0  0
 XJ0  CONST_15  HA    OA   C    OB      0.00   0.0  0
 XJ0  Var_01    CD    CG   CB   CA    179.35  30.0  2
 XJ0  Var_02    CG    CB   CA   C    -179.89   0.0  2
 XJ0  Var_03    CB    CA   C    OB     -0.07  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
 XJ0  plan-1  CB    0.020
 XJ0  plan-1  CG    0.020
 XJ0  plan-1  CD    0.020
 XJ0  plan-1  NE    0.020
 XJ0  plan-1  CZ    0.020
 XJ0  plan-1  NH2   0.020
 XJ0  plan-1  NH1   0.020
 XJ0  plan-1  C10   0.020
 XJ0  plan-1  HD    0.020
 XJ0  plan-1  H10   0.020
 XJ0  plan-2  CZ    0.020
 XJ0  plan-2  NH2   0.020
 XJ0  plan-2  HH21  0.020
 XJ0  plan-2  HH22  0.020
 XJ0  plan-3  OB    0.020
 XJ0  plan-3  C     0.020
 XJ0  plan-3  OA    0.020
 XJ0  plan-3  CA    0.020
 XJ0  plan-3  HA    0.020
 XJ0  plan-4  C     0.020
 XJ0  plan-4  CA    0.020
 XJ0  plan-4  CB    0.020
 XJ0  plan-4  CG    0.020
 XJ0  plan-4  HB    0.020
 XJ0  plan-4  HC    0.020

