# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 20:00:37 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: ethyl (2~{R})-2-methyl-3-oxidanylidene-2,4-dihydro-1~{H}-quinoxaline-6-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)c1ccc2N[C@H](C)C(=O)Nc2c1
#
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
 5SJ  5SJ  'ethyl (2~{R})-2-methyl-3-oxidanylidene-2,4-dihydro-1~{H}-quinoxaline-6-carboxylate'  ligand  31  17  .  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_5SJ
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
 5SJ  CAA  C  CH3   0  -0.687   5.8543   0.8181   0.0830
 5SJ  CAH  C  CH2   0  -0.178   4.9189  -0.3600   0.2044
 5SJ  OAK  O  O2    0  -0.463   3.5783   0.1239   0.0374
 5SJ  CAL  C  C     0   0.599   2.5880  -0.7541   0.0932
 5SJ  OAC  O  O     0  -0.462   2.7602  -1.9386   0.2772
 5SJ  CAN  C  CR6   0  -0.111   1.2613  -0.1350  -0.0915
 5SJ  CAG  C  CR16  0  -0.353   0.1386  -0.9651  -0.0555
 5SJ  CAP  C  CR6   0   0.372  -1.1248  -0.4425  -0.2252
 5SJ  NAI  N  NH1   0  -0.724  -2.2553  -1.2596  -0.2575
 5SJ  C    C  C     0   0.520  -3.5290  -0.8107  -0.1865
 5SJ  O    O  O     0  -0.464  -4.4913  -1.5539  -0.2363
 5SJ  CA   C  CH1   0  -0.250  -3.6704   0.6840   0.0374
 5SJ  CB   C  CH3   0  -0.659  -3.7591   0.9718   1.5379
 5SJ  N    N  NH1   0  -0.664  -2.5831   1.3826  -0.6214
 5SJ  CAO  C  CR6   0   0.326  -1.3074   0.9362  -0.4236
 5SJ  CAF  C  CR16  0  -0.342  -0.1833   1.7609  -0.4556
 5SJ  CAE  C  CR16  0  -0.279   1.0853   1.2326  -0.2994
 5SJ  H1   H  HCH3  0   0.236   5.7776   1.2945  -0.8943
 5SJ  H2   H  HCH3  0   0.236   5.6613   1.5657   0.8522
 5SJ  H3   H  HCH3  0   0.239   6.8800   0.4709   0.2048
 5SJ  H4   H  HCH2  0   0.235   5.1371  -1.1112  -0.5572
 5SJ  H5   H  HCH2  0   0.234   5.0183  -0.8352   1.1826
 5SJ  H6   H  HCR6  0   0.273   0.2563  -2.0312   0.0940
 5SJ  H7   H  HNH1  0   0.412  -2.1195  -2.2596  -0.3223
 5SJ  H8   H  HCH1  0   0.290  -4.5998   0.9923  -0.4418
 5SJ  H9   H  HCH3  0   0.236  -2.8462   0.6753   2.0563
 5SJ  H10  H  HCH3  0   0.253  -3.9130   2.0386   1.7003
 5SJ  H11  H  HCH3  0   0.248  -4.5977   0.4392   1.9863
 5SJ  H12  H  HNH1  0   0.395  -2.6977   2.3842  -0.6677
 5SJ  H13  H  HCR6  0   0.270  -0.3113   2.8253  -0.6084
 5SJ  H14  H  HCR6  0   0.260   1.9331   1.9022  -0.3296

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
 5SJ  O    C    double    1.217  0.020  1.217
 5SJ  CB   CA   single    1.530  0.020  1.530
 5SJ  C    CA   single    1.518  0.020  1.518
 5SJ  C    NAI  single    1.352  0.020  1.352
 5SJ  CA   N    single    1.451  0.020  1.451
 5SJ  NAI  CAP  single    1.395  0.020  1.395
 5SJ  N    CAO  single    1.366  0.020  1.366
 5SJ  CAP  CAO  aromatic  1.405  0.020  1.405
 5SJ  CAP  CAG  aromatic  1.378  0.020  1.378
 5SJ  CAO  CAF  aromatic  1.395  0.020  1.395
 5SJ  CAG  CAN  aromatic  1.397  0.020  1.397
 5SJ  CAF  CAE  aromatic  1.383  0.020  1.383
 5SJ  CAN  CAE  aromatic  1.394  0.020  1.394
 5SJ  CAN  CAL  single    1.476  0.020  1.476
 5SJ  OAC  CAL  double    1.211  0.020  1.211
 5SJ  CAL  OAK  single    1.325  0.020  1.325
 5SJ  OAK  CAH  single    1.435  0.020  1.435
 5SJ  CAH  CAA  single    1.509  0.020  1.509
 5SJ  CAA  H1   single    0.970  0.020  1.090
 5SJ  CAA  H2   single    0.970  0.020  1.090
 5SJ  CAA  H3   single    0.970  0.020  1.090
 5SJ  CAH  H4   single    0.970  0.020  1.090
 5SJ  CAH  H5   single    0.970  0.020  1.090
 5SJ  CAG  H6   single    0.930  0.020  1.080
 5SJ  NAI  H7   single    0.860  0.020  1.020
 5SJ  CA   H8   single    0.970  0.020  1.090
 5SJ  CB   H9   single    0.970  0.020  1.090
 5SJ  CB   H10  single    0.970  0.020  1.090
 5SJ  CB   H11  single    0.970  0.020  1.090
 5SJ  N    H12  single    0.890  0.020  1.040
 5SJ  CAF  H13  single    0.930  0.020  1.080
 5SJ  CAE  H14  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
 5SJ  H3   CAA  H2   107.84  3.000
 5SJ  H3   CAA  H1   107.81  3.000
 5SJ  H2   CAA  H1   108.70  3.000
 5SJ  H3   CAA  CAH  109.00  3.000
 5SJ  H2   CAA  CAH  111.65  3.000
 5SJ  H1   CAA  CAH  111.70  3.000
 5SJ  H5   CAH  H4   107.89  3.000
 5SJ  H5   CAH  OAK  109.63  3.000
 5SJ  H4   CAH  OAK  109.72  3.000
 5SJ  H5   CAH  CAA  110.82  3.000
 5SJ  H4   CAH  CAA  110.93  3.000
 5SJ  OAK  CAH  CAA  107.84  3.000
 5SJ  CAL  OAK  CAH  118.04  3.000
 5SJ  CAN  CAL  OAC  123.87  3.000
 5SJ  OAC  CAL  OAK  123.26  3.000
 5SJ  CAN  CAL  OAK  112.88  3.000
 5SJ  CAE  CAN  CAG  119.03  3.000
 5SJ  CAE  CAN  CAL  122.93  3.000
 5SJ  CAG  CAN  CAL  118.04  3.000
 5SJ  H6   CAG  CAP  119.35  3.000
 5SJ  H6   CAG  CAN  120.08  3.000
 5SJ  CAP  CAG  CAN  120.56  3.000
 5SJ  CAO  CAP  NAI  117.79  3.000
 5SJ  CAO  CAP  CAG  120.59  3.000
 5SJ  NAI  CAP  CAG  121.58  3.000
 5SJ  H7   NAI  C    117.27  3.000
 5SJ  H7   NAI  CAP  118.15  3.000
 5SJ  C    NAI  CAP  124.57  3.000
 5SJ  CA   C    O    122.26  3.000
 5SJ  CA   C    NAI  114.98  3.000
 5SJ  O    C    NAI  122.67  3.000
 5SJ  H8   CA   N    107.65  3.000
 5SJ  H8   CA   CB   109.17  3.000
 5SJ  N    CA   CB   113.47  3.000
 5SJ  H8   CA   C    107.04  3.000
 5SJ  N    CA   C    109.72  3.000
 5SJ  CB   CA   C    109.58  3.000
 5SJ  H11  CB   H10  107.96  3.000
 5SJ  H11  CB   H9   108.40  3.000
 5SJ  H10  CB   H9   108.26  3.000
 5SJ  H11  CB   CA   110.86  3.000
 5SJ  H10  CB   CA   109.77  3.000
 5SJ  H9   CB   CA   111.48  3.000
 5SJ  H12  N    CAO  115.91  3.000
 5SJ  H12  N    CA   114.43  3.000
 5SJ  CAO  N    CA   118.48  3.000
 5SJ  CAF  CAO  N    123.80  3.000
 5SJ  CAF  CAO  CAP  118.61  3.000
 5SJ  N    CAO  CAP  117.55  3.000
 5SJ  H13  CAF  CAE  119.99  3.000
 5SJ  H13  CAF  CAO  119.29  3.000
 5SJ  CAE  CAF  CAO  120.72  3.000
 5SJ  H14  CAE  CAF  118.67  3.000
 5SJ  H14  CAE  CAN  120.85  3.000
 5SJ  CAF  CAE  CAN  120.48  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
 5SJ  CONST_01  CAO  CAP  CAG  CAN    0.00   0.0  0
 5SJ  CONST_02  CAO  CAF  CAE  CAN    0.00   0.0  0
 5SJ  CONST_03  CAF  CAO  CAP  CAG    0.00   0.0  0
 5SJ  CONST_04  CAF  CAE  CAN  CAG    0.00   0.0  0
 5SJ  CONST_05  CAE  CAF  CAO  CAP    0.00   0.0  0
 5SJ  CONST_06  CAE  CAN  CAG  CAP    0.00   0.0  0
 5SJ  CONST_07  CA   C    NAI  CAP    0.00   0.0  0
 5SJ  CONST_08  CAP  CAG  CAN  CAL  180.00   0.0  0
 5SJ  CONST_09  CAF  CAE  CAN  CAL  180.00   0.0  0
 5SJ  CONST_10  O    C    NAI  CAP  180.00   0.0  0
 5SJ  CONST_11  H13  CAF  CAE  CAN  180.00   0.0  0
 5SJ  CONST_12  H14  CAE  CAN  CAG  180.00   0.0  0
 5SJ  CONST_13  H6   CAG  CAP  NAI    0.00   0.0  0
 5SJ  CONST_14  H7   NAI  C    CA   180.00   0.0  0
 5SJ  Var_01    C    NAI  CAP  CAG  167.93  30.0  1
 5SJ  Var_02    CA   N    CAO  CAP   32.14  30.0  1
 5SJ  Var_03    CAG  CAN  CAL  OAK  179.85  30.0  3
 5SJ  Var_04    CAN  CAL  OAK  CAH  179.97  30.0  1
 5SJ  Var_05    H1   CAA  CAH  OAK  -60.85  30.0  3
 5SJ  Var_06    H4   CAH  OAK  CAL   58.35  30.0  3

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
 5SJ  chir_01  CA  CB  C  N  positiv

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
 5SJ  plan-1  CAP  0.020
 5SJ  plan-1  NAI  0.020
 5SJ  plan-1  C    0.020
 5SJ  plan-1  O    0.020
 5SJ  plan-1  CA   0.020
 5SJ  plan-1  H7   0.020
 5SJ  plan-2  CAL  0.020
 5SJ  plan-2  CAN  0.020
 5SJ  plan-2  CAG  0.020
 5SJ  plan-2  CAP  0.020
 5SJ  plan-2  NAI  0.020
 5SJ  plan-2  N    0.020
 5SJ  plan-2  CAO  0.020
 5SJ  plan-2  CAF  0.020
 5SJ  plan-2  CAE  0.020
 5SJ  plan-2  H6   0.020
 5SJ  plan-2  H13  0.020
 5SJ  plan-2  H14  0.020
 5SJ  plan-3  OAK  0.020
 5SJ  plan-3  CAL  0.020
 5SJ  plan-3  OAC  0.020
 5SJ  plan-3  CAN  0.020

