# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 12:36:04 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: (2R)-2-methyl-1,4-dihydropyrido[2,3-b]pyrazin-3(2H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1Nc2cccnc2NC1=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
 1JX  1JX  (2R)-2-methyl-1,4-dihydropyrido[2,3-b]pyrazin-3(2H)-one  ligand  21  12  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_1JX
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
 1JX  O    O  O     0  -0.457  -2.9237  -1.2311  -0.2682
 1JX  C    C  C     0   0.533  -1.8587  -0.6488  -0.2035
 1JX  NAG  N  NH1   0  -0.692  -0.6755  -1.3032  -0.0925
 1JX  CAK  C  CR6   0   0.438   0.5654  -0.6796  -0.0225
 1JX  NAF  N  N     0  -0.425   1.5988  -1.4075   0.3322
 1JX  CAD  C  CR16  0  -0.102   2.7991  -0.8272   0.3581
 1JX  CAC  C  CR16  0  -0.327   2.9890   0.5019   0.0310
 1JX  CAE  C  CR16  0  -0.245   1.8876   1.2694  -0.3344
 1JX  CAJ  C  CR6   0   0.234   0.6351   0.6782  -0.3747
 1JX  N    N  NH1   0  -0.667  -0.5245   1.2931  -0.7859
 1JX  CA   C  CH1   0  -0.255  -1.7614   0.8662  -0.1593
 1JX  CB   C  CH3   0  -0.660  -1.9219   1.3443   1.2860
 1JX  H1   H  HNH1  0   0.408  -0.6929  -2.3113  -0.0081
 1JX  H2   H  HCR6  0   0.259   3.6334  -1.4552   0.6461
 1JX  H3   H  HCR6  0   0.267   3.9775   0.9386   0.0646
 1JX  H4   H  HCR6  0   0.276   2.0044   2.3134  -0.5981
 1JX  H5   H  HNH1  0   0.391  -0.4572   2.2924  -0.9115
 1JX  H6   H  HCH1  0   0.289  -2.5859   1.2545  -0.7575
 1JX  H7   H  HCH3  0   0.236  -1.1287   0.9568   1.9273
 1JX  H8   H  HCH3  0   0.252  -1.8846   2.4333   1.3206
 1JX  H9   H  HCH3  0   0.247  -2.8805   1.0294   1.6980

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
 1JX  CAD  CAC  aromatic  1.382  0.020  1.382
 1JX  CAD  NAF  aromatic  1.333  0.020  1.333
 1JX  CAC  CAE  aromatic  1.391  0.020  1.391
 1JX  NAF  CAK  aromatic  1.313  0.020  1.313
 1JX  CAK  CAJ  aromatic  1.404  0.020  1.404
 1JX  CAK  NAG  single    1.391  0.020  1.391
 1JX  CAE  CAJ  aromatic  1.386  0.020  1.386
 1JX  CAJ  N    single    1.375  0.020  1.375
 1JX  NAG  C    single    1.357  0.020  1.357
 1JX  N    CA   single    1.451  0.020  1.451
 1JX  C    O    double    1.215  0.020  1.215
 1JX  C    CA   single    1.519  0.020  1.519
 1JX  CA   CB   single    1.531  0.020  1.531
 1JX  NAG  H1   single    0.860  0.020  1.020
 1JX  CAD  H2   single    0.930  0.020  1.080
 1JX  CAC  H3   single    0.930  0.020  1.080
 1JX  CAE  H4   single    0.930  0.020  1.080
 1JX  N    H5   single    0.890  0.020  1.040
 1JX  CA   H6   single    0.970  0.020  1.090
 1JX  CB   H7   single    0.970  0.020  1.090
 1JX  CB   H8   single    0.970  0.020  1.090
 1JX  CB   H9   single    0.970  0.020  1.090

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
 1JX  CA   C    NAG  115.01  3.000
 1JX  CA   C    O    122.38  3.000
 1JX  NAG  C    O    122.51  3.000
 1JX  H1   NAG  CAK  117.25  3.000
 1JX  H1   NAG  C    118.19  3.000
 1JX  CAK  NAG  C    124.48  3.000
 1JX  CAJ  CAK  NAF  124.38  3.000
 1JX  CAJ  CAK  NAG  117.72  3.000
 1JX  NAF  CAK  NAG  117.87  3.000
 1JX  CAD  NAF  CAK  118.20  3.000
 1JX  H2   CAD  CAC  120.98  3.000
 1JX  H2   CAD  NAF  116.49  3.000
 1JX  CAC  CAD  NAF  122.52  3.000
 1JX  H3   CAC  CAE  120.61  3.000
 1JX  H3   CAC  CAD  120.44  3.000
 1JX  CAE  CAC  CAD  118.95  3.000
 1JX  H4   CAE  CAJ  120.11  3.000
 1JX  H4   CAE  CAC  120.69  3.000
 1JX  CAJ  CAE  CAC  119.20  3.000
 1JX  N    CAJ  CAE  125.45  3.000
 1JX  N    CAJ  CAK  117.73  3.000
 1JX  CAE  CAJ  CAK  116.75  3.000
 1JX  H5   N    CA   113.70  3.000
 1JX  H5   N    CAJ  115.06  3.000
 1JX  CA   N    CAJ  117.27  3.000
 1JX  H6   CA   CB   109.12  3.000
 1JX  H6   CA   N    107.64  3.000
 1JX  CB   CA   N    113.91  3.000
 1JX  H6   CA   C    106.91  3.000
 1JX  CB   CA   C    109.41  3.000
 1JX  N    CA   C    109.61  3.000
 1JX  H9   CB   H8   107.86  3.000
 1JX  H9   CB   H7   108.33  3.000
 1JX  H8   CB   H7   108.13  3.000
 1JX  H9   CB   CA   111.03  3.000
 1JX  H8   CB   CA   109.78  3.000
 1JX  H7   CB   CA   111.58  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
 1JX  CONST_01  CAC  CAD  NAF  CAK    0.00   0.0  0
 1JX  CONST_02  CAC  CAE  CAJ  CAK    0.00   0.0  0
 1JX  CONST_03  CAE  CAC  CAD  NAF    0.00   0.0  0
 1JX  CONST_04  CAE  CAJ  CAK  NAF    0.00   0.0  0
 1JX  CONST_05  CAJ  CAE  CAC  CAD    0.00   0.0  0
 1JX  CONST_06  CAJ  CAK  NAF  CAD    0.00   0.0  0
 1JX  CONST_07  CA   C    NAG  CAK    0.00   0.0  0
 1JX  CONST_08  CAK  NAG  C    O    180.00   0.0  0
 1JX  CONST_09  H2   CAD  NAF  CAK  180.00   0.0  0
 1JX  CONST_10  H4   CAE  CAJ  CAK  180.00   0.0  0
 1JX  CONST_11  H3   CAC  CAD  NAF  180.00   0.0  0
 1JX  CONST_12  H1   NAG  C    CA   180.00   0.0  0
 1JX  Var_01    NAF  CAK  NAG  C    167.49  30.0  1
 1JX  Var_02    CA   N    CAJ  CAK   34.52  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 1JX  chir_01  CA  N  C  CB  negativ

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
 1JX  plan-1  O    0.020
 1JX  plan-1  C    0.020
 1JX  plan-1  NAG  0.020
 1JX  plan-1  CAK  0.020
 1JX  plan-1  CA   0.020
 1JX  plan-1  H1   0.020
 1JX  plan-2  NAG  0.020
 1JX  plan-2  CAK  0.020
 1JX  plan-2  NAF  0.020
 1JX  plan-2  CAD  0.020
 1JX  plan-2  CAC  0.020
 1JX  plan-2  CAE  0.020
 1JX  plan-2  CAJ  0.020
 1JX  plan-2  N    0.020
 1JX  plan-2  H2   0.020
 1JX  plan-2  H3   0.020
 1JX  plan-2  H4   0.020

