# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 03:55:23 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 4-[(5-phenylpyridin-3-yl)carbonyl]-3,4-dihydroquinoxalin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1CN(C(=O)c2cncc(c2)c3ccccc3)c4ccccc4N1
#
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
 Y81  Y81  4-[(5-phenylpyridin-3-yl)carbonyl]-3,4-dihydroquinoxalin-2(1H)-one  ligand  40  25  .  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_Y81
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
 Y81  O1   O  O     0  -0.435   0.8189  -1.9411   0.3795
 Y81  C2   C  C     0   0.531   0.7805  -0.7405   0.5597
 Y81  N    N  NT    0  -0.578   1.8954   0.0509   0.4925
 Y81  C1   C  CH2   0  -0.463   1.8613   1.4737   0.2000
 Y81  C14  C  CR6   0   0.321   3.1652  -0.5413   0.3134
 Y81  C19  C  CR6   0   0.352   3.9390  -0.0675  -0.7439
 Y81  C18  C  CR16  0  -0.326   5.2040  -0.5974  -0.9722
 Y81  C17  C  CR16  0  -0.255   5.6867  -1.6004  -0.1485
 Y81  C16  C  CR16  0  -0.272   4.9226  -2.0622   0.9171
 Y81  C15  C  CR16  0  -0.292   3.6662  -1.5268   1.1523
 Y81  N2   N  NH1   0  -0.723   3.4183   0.9331  -1.5610
 Y81  C    C  C     0   0.520   2.4188   1.7639  -1.1821
 Y81  O    O  O     0  -0.451   2.0186   2.6822  -1.8681
 Y81  C3   C  CR6   0  -0.173  -0.5047  -0.0805   0.9265
 Y81  C13  C  CR16  0  -0.201  -1.6610  -0.4010   0.2294
 Y81  C6   C  CR6   0   0.005  -2.8740   0.1503   0.6244
 Y81  C5   C  CR16  0  -0.087  -2.8560   0.9807   1.7467
 Y81  N1   N  N     0  -0.389  -1.7627   1.2722   2.4348
 Y81  C4   C  CR16  0  -0.059  -0.6099   0.7602   2.0293
 Y81  C7   C  CR6   0   0.084  -4.1291  -0.1314  -0.0947
 Y81  C12  C  CR16  0  -0.305  -5.0807   0.8719  -0.2815
 Y81  C11  C  CR16  0  -0.240  -6.2618   0.6071  -0.9593
 Y81  C10  C  CR16  0  -0.261  -6.5098  -0.6639  -1.4607
 Y81  C9   C  CR16  0  -0.239  -5.5688  -1.6692  -1.2798
 Y81  C8   C  CR16  0  -0.308  -4.3877  -1.4055  -0.6024
 Y81  H1   H  HCH2  0   0.307   0.8464   1.8561   0.2381
 Y81  H2   H  HCH2  0   0.309   2.4515   2.0271   0.9373
 Y81  H3   H  HCR6  0   0.277   5.8040  -0.2220  -1.7918
 Y81  H4   H  HCR6  0   0.266   6.6697  -2.0126  -0.3325
 Y81  H5   H  HCR6  0   0.263   5.3079  -2.8333   1.5701
 Y81  H6   H  HCR6  0   0.272   3.0764  -1.8755   1.9890
 Y81  H7   H  HNH1  0   0.417   3.8789   1.1257  -2.4402
 Y81  H8   H  HCR6  0   0.280  -1.6103  -1.0521  -0.6347
 Y81  H9   H  HCR6  0   0.272  -3.7808   1.4130   2.1143
 Y81  H10  H  HCR6  0   0.281   0.2663   1.0142   2.6172
 Y81  H11  H  HCR6  0   0.258  -4.8914   1.8735   0.0845
 Y81  H12  H  HCR6  0   0.261  -6.9851   1.3990  -1.1033
 Y81  H13  H  HCR6  0   0.261  -7.4307  -0.8702  -1.9906
 Y81  H14  H  HCR6  0   0.261  -5.7562  -2.6639  -1.6627
 Y81  H15  H  HCR6  0   0.259  -3.6720  -2.2044  -0.4509

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
 Y81  C10  C9   aromatic  1.389  0.020  1.389
 Y81  C10  C11  aromatic  1.389  0.020  1.389
 Y81  C9   C8   aromatic  1.387  0.020  1.387
 Y81  C11  C12  aromatic  1.387  0.020  1.387
 Y81  C8   C7   aromatic  1.396  0.020  1.396
 Y81  C12  C7   aromatic  1.395  0.020  1.395
 Y81  C17  C18  aromatic  1.385  0.020  1.385
 Y81  C17  C16  aromatic  1.390  0.020  1.390
 Y81  C7   C6   single    1.474  0.020  1.474
 Y81  C18  C19  aromatic  1.390  0.020  1.390
 Y81  C16  C15  aromatic  1.386  0.020  1.386
 Y81  C6   C13  aromatic  1.390  0.020  1.390
 Y81  C6   C5   aromatic  1.396  0.020  1.396
 Y81  C19  N2   single    1.393  0.020  1.393
 Y81  C19  C14  aromatic  1.393  0.020  1.393
 Y81  C15  C14  aromatic  1.388  0.020  1.388
 Y81  N2   C    single    1.354  0.020  1.354
 Y81  C13  C3   aromatic  1.388  0.020  1.388
 Y81  C5   N1   aromatic  1.324  0.020  1.324
 Y81  C14  N    single    1.412  0.020  1.412
 Y81  C    O    double    1.214  0.020  1.214
 Y81  C    C1   single    1.518  0.020  1.518
 Y81  C3   C4   aromatic  1.391  0.020  1.391
 Y81  C3   C2   single    1.491  0.020  1.491
 Y81  N1   C4   aromatic  1.325  0.020  1.325
 Y81  N    C2   single    1.369  0.020  1.369
 Y81  N    C1   single    1.453  0.020  1.453
 Y81  C2   O1   double    1.215  0.020  1.215
 Y81  C1   H1   single    0.970  0.020  1.090
 Y81  C1   H2   single    0.970  0.020  1.090
 Y81  C18  H3   single    0.930  0.020  1.080
 Y81  C17  H4   single    0.930  0.020  1.080
 Y81  C16  H5   single    0.930  0.020  1.080
 Y81  C15  H6   single    0.930  0.020  1.080
 Y81  N2   H7   single    0.860  0.020  1.020
 Y81  C13  H8   single    0.930  0.020  1.080
 Y81  C5   H9   single    0.930  0.020  1.080
 Y81  C4   H10  single    0.930  0.020  1.080
 Y81  C12  H11  single    0.930  0.020  1.080
 Y81  C11  H12  single    0.930  0.020  1.080
 Y81  C10  H13  single    0.930  0.020  1.080
 Y81  C9   H14  single    0.930  0.020  1.080
 Y81  C8   H15  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
 Y81  C3   C2   N    117.28  3.000
 Y81  N    C2   O1   122.57  3.000
 Y81  C3   C2   O1   120.09  3.000
 Y81  C14  N    C1   113.96  3.000
 Y81  C1   N    C2   123.84  3.000
 Y81  C14  N    C2   119.74  3.000
 Y81  H2   C1   H1   107.60  3.000
 Y81  H2   C1   C    108.57  3.000
 Y81  H1   C1   C    107.94  3.000
 Y81  H2   C1   N    110.29  3.000
 Y81  H1   C1   N    111.09  3.000
 Y81  C    C1   N    111.21  3.000
 Y81  C15  C14  C19  119.98  3.000
 Y81  C15  C14  N    123.06  3.000
 Y81  C19  C14  N    116.93  3.000
 Y81  N2   C19  C18  121.17  3.000
 Y81  N2   C19  C14  118.81  3.000
 Y81  C18  C19  C14  120.02  3.000
 Y81  H3   C18  C17  120.54  3.000
 Y81  H3   C18  C19  119.75  3.000
 Y81  C17  C18  C19  119.71  3.000
 Y81  H4   C17  C16  120.22  3.000
 Y81  H4   C17  C18  119.44  3.000
 Y81  C16  C17  C18  120.33  3.000
 Y81  H5   C16  C15  119.73  3.000
 Y81  H5   C16  C17  120.26  3.000
 Y81  C15  C16  C17  120.01  3.000
 Y81  H6   C15  C16  120.08  3.000
 Y81  H6   C15  C14  119.99  3.000
 Y81  C16  C15  C14  119.93  3.000
 Y81  H7   N2   C    117.57  3.000
 Y81  H7   N2   C19  118.46  3.000
 Y81  C    N2   C19  123.55  3.000
 Y81  O    C    N2   123.32  3.000
 Y81  O    C    C1   122.54  3.000
 Y81  N2   C    C1   114.12  3.000
 Y81  C4   C3   C13  118.35  3.000
 Y81  C4   C3   C2   121.87  3.000
 Y81  C13  C3   C2   119.51  3.000
 Y81  H8   C13  C6   120.40  3.000
 Y81  H8   C13  C3   120.04  3.000
 Y81  C6   C13  C3   119.53  3.000
 Y81  C7   C6   C5   121.12  3.000
 Y81  C5   C6   C13  116.95  3.000
 Y81  C7   C6   C13  121.93  3.000
 Y81  H9   C5   N1   116.10  3.000
 Y81  H9   C5   C6   119.89  3.000
 Y81  N1   C5   C6   124.00  3.000
 Y81  C4   N1   C5   118.31  3.000
 Y81  H10  C4   N1   116.50  3.000
 Y81  H10  C4   C3   120.66  3.000
 Y81  N1   C4   C3   122.83  3.000
 Y81  C8   C7   C12  118.77  3.000
 Y81  C12  C7   C6   120.58  3.000
 Y81  C8   C7   C6   120.65  3.000
 Y81  H11  C12  C11  119.37  3.000
 Y81  H11  C12  C7   120.03  3.000
 Y81  C11  C12  C7   120.58  3.000
 Y81  H12  C11  C10  120.16  3.000
 Y81  H12  C11  C12  119.63  3.000
 Y81  C10  C11  C12  120.21  3.000
 Y81  H13  C10  C9   120.16  3.000
 Y81  H13  C10  C11  120.21  3.000
 Y81  C9   C10  C11  119.63  3.000
 Y81  H14  C9   C8   119.67  3.000
 Y81  H14  C9   C10  120.12  3.000
 Y81  C8   C9   C10  120.20  3.000
 Y81  H15  C8   C9   119.39  3.000
 Y81  H15  C8   C7   120.00  3.000
 Y81  C9   C8   C7   120.60  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
 Y81  CONST_01  C17  C18  C19  C14    0.00   0.0  0
 Y81  CONST_02  C17  C16  C15  C14    0.00   0.0  0
 Y81  CONST_03  C16  C17  C18  C19    0.00   0.0  0
 Y81  CONST_04  C16  C15  C14  C19    0.00   0.0  0
 Y81  CONST_05  C15  C16  C17  C18    0.00   0.0  0
 Y81  CONST_06  C15  C14  C19  C18    0.00   0.0  0
 Y81  CONST_07  C7   C6   C13  C3   180.00   0.0  0
 Y81  CONST_08  C5   C6   C13  C3     0.00   0.0  0
 Y81  CONST_09  C5   N1   C4   C3     0.00   0.0  0
 Y81  CONST_12  N1   C5   C6   C13    0.00   0.0  0
 Y81  CONST_13  N1   C4   C3   C13    0.00   0.0  0
 Y81  CONST_14  C9   C8   C7   C6   180.00   0.0  0
 Y81  CONST_15  C11  C12  C7   C6   180.00   0.0  0
 Y81  CONST_16  C4   C3   C13  C6     0.00   0.0  0
 Y81  CONST_17  C4   N1   C5   C6     0.00   0.0  0
 Y81  CONST_20  C7   C6   C5   N1   180.00   0.0  0
 Y81  CONST_21  C10  C9   C8   C7     0.00   0.0  0
 Y81  CONST_22  C10  C11  C12  C7     0.00   0.0  0
 Y81  CONST_23  C9   C10  C11  C12    0.00   0.0  0
 Y81  CONST_24  C9   C8   C7   C12    0.00   0.0  0
 Y81  CONST_25  C8   C9   C10  C11    0.00   0.0  0
 Y81  CONST_26  C8   C7   C12  C11    0.00   0.0  0
 Y81  CONST_27  C19  N2   C    C1     0.00   0.0  0
 Y81  CONST_28  C6   C13  C3   C2   180.00   0.0  0
 Y81  CONST_29  N1   C4   C3   C2   180.00   0.0  0
 Y81  CONST_31  C3   C2   N    C14  180.00   0.0  0
 Y81  CONST_32  O    C    N2   C19  180.00   0.0  0
 Y81  CONST_33  H6   C15  C14  N      0.00   0.0  0
 Y81  CONST_34  H3   C18  C19  C14  180.00   0.0  0
 Y81  CONST_35  H5   C16  C15  C14  180.00   0.0  0
 Y81  CONST_36  H4   C17  C18  C19  180.00   0.0  0
 Y81  CONST_37  H9   C5   C6   C13  180.00   0.0  0
 Y81  CONST_38  H10  C4   C3   C13  180.00   0.0  0
 Y81  CONST_39  H15  C8   C7   C6     0.00   0.0  0
 Y81  CONST_40  H11  C12  C7   C6     0.00   0.0  0
 Y81  CONST_41  H8   C13  C6   C5   180.00   0.0  0
 Y81  CONST_42  H14  C9   C8   C7   180.00   0.0  0
 Y81  CONST_43  H12  C11  C12  C7   180.00   0.0  0
 Y81  CONST_44  H13  C10  C11  C12  180.00   0.0  0
 Y81  CONST_45  H7   N2   C    C1   180.00   0.0  0
 Y81  CONST_46  C14  N    C2   O1     0.00   0.0  0
 Y81  Var_01    N2   C    C1   N    -33.47  30.0  1
 Y81  Var_02    C19  C14  N    C1   -36.28  30.0  1
 Y81  Var_03    C    N2   C19  C14   21.37  30.0  1
 Y81  Var_04    C    C1   N    C14   53.03  30.0  1
 Y81  Var_05    C13  C3   C2   N    136.58  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
 Y81  plan-1  C2   0.020
 Y81  plan-1  C3   0.020
 Y81  plan-1  C13  0.020
 Y81  plan-1  C6   0.020
 Y81  plan-1  C5   0.020
 Y81  plan-1  N1   0.020
 Y81  plan-1  C4   0.020
 Y81  plan-1  C7   0.020
 Y81  plan-1  H8   0.020
 Y81  plan-1  H9   0.020
 Y81  plan-1  H10  0.020
 Y81  plan-2  C6   0.020
 Y81  plan-2  C7   0.020
 Y81  plan-2  C12  0.020
 Y81  plan-2  C11  0.020
 Y81  plan-2  C10  0.020
 Y81  plan-2  C9   0.020
 Y81  plan-2  C8   0.020
 Y81  plan-2  H11  0.020
 Y81  plan-2  H12  0.020
 Y81  plan-2  H13  0.020
 Y81  plan-2  H14  0.020
 Y81  plan-2  H15  0.020
 Y81  plan-3  N    0.020
 Y81  plan-3  C14  0.020
 Y81  plan-3  C19  0.020
 Y81  plan-3  C18  0.020
 Y81  plan-3  C17  0.020
 Y81  plan-3  C16  0.020
 Y81  plan-3  C15  0.020
 Y81  plan-3  N2   0.020
 Y81  plan-3  H3   0.020
 Y81  plan-3  H4   0.020
 Y81  plan-3  H5   0.020
 Y81  plan-3  H6   0.020
 Y81  plan-4  O1   0.020
 Y81  plan-4  C2   0.020
 Y81  plan-4  N    0.020
 Y81  plan-4  C1   0.020
 Y81  plan-4  C14  0.020
 Y81  plan-4  C3   0.020
 Y81  plan-5  C1   0.020
 Y81  plan-5  C19  0.020
 Y81  plan-5  N2   0.020
 Y81  plan-5  C    0.020
 Y81  plan-5  O    0.020
 Y81  plan-5  H7   0.020

