# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 11:50:28 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 4-(2-chloropyrido[2,3-d]pyrimidin-4-yl)-7-methoxy-3,4-dihydroquinoxalin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2N(CC(=O)Nc2c1)c3nc(Cl)nc4ncccc34
#
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
 J7S  J7S  4-(2-chloropyrido[2,3-d]pyrimidin-4-yl)-7-methoxy-3,4-dihydroquinoxalin-2(1H)-one  ligand  36  24  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J7S
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
 J7S  O1   O   O     0  -0.447  -1.4794   2.9830  -3.2621
 J7S  N    N   NR6   0  -0.585  -0.0823   0.5257  -1.1708
 J7S  C    C   CH3   0  -0.439  -4.8143  -2.2649   2.1245
 J7S  C1   C   CR6   0   0.395  -3.5691  -0.7950   0.7400
 J7S  C10  C   CR16  0  -0.323   1.0646   0.7957   3.0551
 J7S  C11  C   CR16  0  -0.049   2.4110   0.4719   3.2809
 J7S  C12  C   C     0  -0.453  -0.3468   1.0081  -2.5140
 J7S  C13  C   CR66  0   0.382  -2.4041   0.7509  -0.6870
 J7S  C14  C   CR6   0   0.518  -1.4374   2.0626  -2.4728
 J7S  C15  C   CR16  0  -0.425  -3.5704   0.3450  -0.0638
 J7S  C2   C   CR16  0  -0.387  -2.4014  -1.5464   0.8770
 J7S  C3   C   CR16  0  -0.269  -1.2440  -1.1380   0.2315
 J7S  C4   C   CR66  0   0.227  -1.2219   0.0298  -0.5103
 J7S  C5   C   CR6   0   0.530   1.1807   0.4703  -0.6842
 J7S  C6   C   CR6   0   0.290   3.3919   0.2934  -1.1129
 J7S  C7   C   CR66  0   0.371   2.8483   0.2923   1.0549
 J7S  C8   C   CR66  0  -0.125   1.4906   0.4997   0.7208
 J7S  C9   C   CR16  0  -0.146   0.6015   0.8059   1.7670
 J7S  N1   N   N     0  -0.445   2.1559   0.4201  -1.5719
 J7S  N2   N   N     0  -0.402   3.8070   0.1722   0.1034
 J7S  N3   N   N     0  -0.412   3.2782   0.2445   2.3251
 J7S  N4   N   NR16  0  -0.727  -2.3714   1.8742  -1.5057
 J7S  CL   CL  CL    0  -0.094   4.6088   0.2515  -2.3461
 J7S  H1   H   HCH3  0   0.263  -5.8364  -2.3213   2.4895
 J7S  H2   H   HCH3  0   0.232  -4.5937  -3.1695   1.5525
 J7S  H3   H   HCH3  0   0.232  -4.1372  -2.2127   2.9806
 J7S  H4   H   HCR6  0   0.286   0.4156   1.0284   3.8868
 J7S  H5   H   HCR6  0   0.283   2.7851   0.4177   4.2974
 J7S  H6   H   H     0   0.312   0.5500   1.4473  -2.9392
 J7S  H7   H   H     0   0.301  -0.6652   0.1907  -3.1705
 J7S  H8   H   HCR6  0   0.285  -4.4866   0.9066  -0.2012
 J7S  H9   H   HCR6  0   0.288  -2.3724  -2.4503   1.4684
 J7S  H10  H   HCR6  0   0.287  -0.3456  -1.7329   0.3331
 J7S  H11  H   HCR6  0   0.298  -0.4291   1.0620   1.5731
 J7S  H12  H   HNR6  0   0.418  -3.1623   2.5041  -1.4923
 J7S  O    O   O2    0  -0.469  -4.7395  -1.1019   1.3217

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
 J7S  CL   C6   single    1.733  0.020  1.733
 J7S  C6   N2   aromatic  1.291  0.020  1.291
 J7S  C6   N1   aromatic  1.325  0.020  1.325
 J7S  N2   C7   aromatic  1.356  0.020  1.356
 J7S  N1   C5   aromatic  1.320  0.020  1.320
 J7S  C7   N3   aromatic  1.342  0.020  1.342
 J7S  C7   C8   aromatic  1.414  0.020  1.414
 J7S  N3   C11  aromatic  1.310  0.020  1.310
 J7S  C5   C8   aromatic  1.439  0.020  1.439
 J7S  C5   N    single    1.355  0.020  1.355
 J7S  C11  C10  aromatic  1.403  0.020  1.403
 J7S  C8   C9   aromatic  1.407  0.020  1.407
 J7S  C12  N    single    1.452  0.020  1.452
 J7S  C12  C14  single    1.518  0.020  1.518
 J7S  N    C4   single    1.407  0.020  1.407
 J7S  C10  C9   aromatic  1.369  0.020  1.369
 J7S  C3   C4   aromatic  1.384  0.020  1.384
 J7S  C3   C2   aromatic  1.387  0.020  1.387
 J7S  C4   C13  aromatic  1.396  0.020  1.396
 J7S  O1   C14  double    1.213  0.020  1.213
 J7S  C14  N4   single    1.358  0.020  1.358
 J7S  C2   C1   aromatic  1.395  0.020  1.395
 J7S  C13  N4   single    1.390  0.020  1.390
 J7S  C13  C15  aromatic  1.383  0.020  1.383
 J7S  C1   C15  aromatic  1.395  0.020  1.395
 J7S  C1   O    single    1.343  0.020  1.343
 J7S  O    C    single    1.415  0.020  1.415
 J7S  C    H1   single    0.970  0.020  1.090
 J7S  C    H2   single    0.970  0.020  1.090
 J7S  C    H3   single    0.970  0.020  1.090
 J7S  C10  H4   single    0.930  0.020  1.080
 J7S  C11  H5   single    0.930  0.020  1.080
 J7S  C12  H6   single    0.970  0.020  1.090
 J7S  C12  H7   single    0.970  0.020  1.090
 J7S  C15  H8   single    0.930  0.020  1.080
 J7S  C2   H9   single    0.930  0.020  1.080
 J7S  C3   H10  single    0.930  0.020  1.080
 J7S  C9   H11  single    0.930  0.020  1.080
 J7S  N4   H12  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
 J7S  C5   N    C4   124.89  3.000
 J7S  C4   N    C12  113.81  3.000
 J7S  C5   N    C12  121.06  3.000
 J7S  H3   C    H2   108.94  3.000
 J7S  H3   C    H1   108.79  3.000
 J7S  H2   C    H1   108.83  3.000
 J7S  H3   C    O    111.87  3.000
 J7S  H2   C    O    111.88  3.000
 J7S  H1   C    O    106.43  3.000
 J7S  C2   C1   C15  119.84  3.000
 J7S  C15  C1   O    115.83  3.000
 J7S  C2   C1   O    124.33  3.000
 J7S  H4   C10  C9   121.31  3.000
 J7S  H4   C10  C11  120.15  3.000
 J7S  C9   C10  C11  118.54  3.000
 J7S  H5   C11  N3   116.53  3.000
 J7S  H5   C11  C10  119.56  3.000
 J7S  N3   C11  C10  123.90  3.000
 J7S  H7   C12  H6   107.89  3.000
 J7S  H7   C12  C14  109.01  3.000
 J7S  H6   C12  C14  108.86  3.000
 J7S  H7   C12  N    111.07  3.000
 J7S  H6   C12  N    110.27  3.000
 J7S  C14  C12  N    109.68  3.000
 J7S  N4   C13  C4   118.16  3.000
 J7S  N4   C13  C15  121.48  3.000
 J7S  C4   C13  C15  120.36  3.000
 J7S  N4   C14  C12  114.67  3.000
 J7S  N4   C14  O1   123.02  3.000
 J7S  C12  C14  O1   122.30  3.000
 J7S  H8   C15  C13  120.25  3.000
 J7S  H8   C15  C1   119.84  3.000
 J7S  C13  C15  C1   119.91  3.000
 J7S  H9   C2   C3   118.60  3.000
 J7S  H9   C2   C1   121.78  3.000
 J7S  C3   C2   C1   119.61  3.000
 J7S  H10  C3   C4   120.06  3.000
 J7S  H10  C3   C2   119.16  3.000
 J7S  C4   C3   C2   120.76  3.000
 J7S  C3   C4   C13  119.36  3.000
 J7S  C13  C4   N    116.38  3.000
 J7S  C3   C4   N    124.19  3.000
 J7S  N1   C5   C8   119.90  3.000
 J7S  C8   C5   N    123.41  3.000
 J7S  N1   C5   N    116.67  3.000
 J7S  CL   C6   N2   116.25  3.000
 J7S  N2   C6   N1   129.46  3.000
 J7S  CL   C6   N1   114.27  3.000
 J7S  N3   C7   N2   115.76  3.000
 J7S  N3   C7   C8   122.45  3.000
 J7S  N2   C7   C8   121.76  3.000
 J7S  C9   C8   C7   117.60  3.000
 J7S  C9   C8   C5   126.47  3.000
 J7S  C7   C8   C5   115.76  3.000
 J7S  H11  C9   C8   121.43  3.000
 J7S  H11  C9   C10  119.59  3.000
 J7S  C8   C9   C10  118.97  3.000
 J7S  C6   N1   C5   117.39  3.000
 J7S  C7   N2   C6   115.18  3.000
 J7S  C7   N3   C11  118.18  3.000
 J7S  H12  N4   C14  117.46  3.000
 J7S  H12  N4   C13  118.49  3.000
 J7S  C14  N4   C13  123.21  3.000
 J7S  C1   O    C    118.67  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
 J7S  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 J7S  CONST_02  C4   C13  C15  C1      0.00   0.0  0
 J7S  CONST_03  C7   N3   C11  C10     0.00   0.0  0
 J7S  CONST_04  C7   C8   C9   C10     0.00   0.0  0
 J7S  CONST_05  C5   C8   C9   C10   180.00   0.0  0
 J7S  CONST_06  N2   C7   N3   C11   180.00   0.0  0
 J7S  CONST_07  C8   C7   N3   C11     0.00   0.0  0
 J7S  CONST_08  C8   C9   C10  C11     0.00   0.0  0
 J7S  CONST_09  C2   C3   C4   C13     0.00   0.0  0
 J7S  CONST_10  C2   C1   C15  C13     0.00   0.0  0
 J7S  CONST_11  C3   C4   C13  C15     0.00   0.0  0
 J7S  CONST_12  C3   C2   C1   C15     0.00   0.0  0
 J7S  CONST_13  N2   C6   N1   C5      0.00   0.0  0
 J7S  CONST_14  N2   C7   C8   C5      0.00   0.0  0
 J7S  CONST_15  N3   C7   C8   C5    180.00   0.0  0
 J7S  CONST_16  N3   C7   N2   C6    180.00   0.0  0
 J7S  CONST_17  C8   C7   N2   C6      0.00   0.0  0
 J7S  CONST_18  C8   C5   N1   C6      0.00   0.0  0
 J7S  CONST_19  N1   C6   N2   C7      0.00   0.0  0
 J7S  CONST_20  N1   C5   C8   C7      0.00   0.0  0
 J7S  CONST_21  N2   C7   C8   C9    180.00   0.0  0
 J7S  CONST_22  N3   C7   C8   C9      0.00   0.0  0
 J7S  CONST_23  N1   C5   C8   C9    180.00   0.0  0
 J7S  CONST_24  N3   C11  C10  C9      0.00   0.0  0
 J7S  CONST_25  C6   N1   C5   N     180.00   0.0  0
 J7S  CONST_26  C7   C8   C5   N     180.00   0.0  0
 J7S  CONST_27  C9   C8   C5   N       0.00   0.0  0
 J7S  CONST_28  C13  N4   C14  C12     0.00   0.0  0
 J7S  CONST_29  C3   C2   C1   O     180.00   0.0  0
 J7S  CONST_30  C13  C15  C1   O     180.00   0.0  0
 J7S  CONST_31  CL   C6   N1   C5    180.00   0.0  0
 J7S  CONST_32  CL   C6   N2   C7    180.00   0.0  0
 J7S  CONST_33  C13  N4   C14  O1    180.00   0.0  0
 J7S  CONST_34  H10  C3   C4   N       0.00   0.0  0
 J7S  CONST_35  H11  C9   C10  C11   180.00   0.0  0
 J7S  CONST_36  H9   C2   C1   C15   180.00   0.0  0
 J7S  CONST_37  H8   C15  C1   C2    180.00   0.0  0
 J7S  CONST_38  H5   C11  N3   C7    180.00   0.0  0
 J7S  CONST_39  H4   C10  C9   C8    180.00   0.0  0
 J7S  CONST_40  H12  N4   C14  C12   180.00   0.0  0
 J7S  Var_01    N4   C14  C12  N     -32.64  30.0  1
 J7S  Var_02    N1   C5   N    C12   -22.59  30.0  2
 J7S  Var_03    C3   C4   N    C12   136.27  30.0  1
 J7S  Var_04    C4   C13  N4   C14    22.95  30.0  1
 J7S  Var_05    C2   C1   O    C      -0.36  30.0  2
 J7S  Var_06    H1   C    O    C1   -179.95  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
 J7S  plan-1  N    0.020
 J7S  plan-1  C10  0.020
 J7S  plan-1  C11  0.020
 J7S  plan-1  C5   0.020
 J7S  plan-1  C6   0.020
 J7S  plan-1  C7   0.020
 J7S  plan-1  C8   0.020
 J7S  plan-1  C9   0.020
 J7S  plan-1  N1   0.020
 J7S  plan-1  N2   0.020
 J7S  plan-1  N3   0.020
 J7S  plan-1  CL   0.020
 J7S  plan-1  H4   0.020
 J7S  plan-1  H5   0.020
 J7S  plan-1  H11  0.020
 J7S  plan-2  N    0.020
 J7S  plan-2  C1   0.020
 J7S  plan-2  C13  0.020
 J7S  plan-2  C15  0.020
 J7S  plan-2  C2   0.020
 J7S  plan-2  C3   0.020
 J7S  plan-2  C4   0.020
 J7S  plan-2  N4   0.020
 J7S  plan-2  H8   0.020
 J7S  plan-2  H9   0.020
 J7S  plan-2  H10  0.020
 J7S  plan-2  O    0.020
 J7S  plan-3  O1   0.020
 J7S  plan-3  C12  0.020
 J7S  plan-3  C13  0.020
 J7S  plan-3  C14  0.020
 J7S  plan-3  N4   0.020
 J7S  plan-3  H12  0.020

