# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 22:23:44 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: (3~{R})-4-cyclopropyl-1,3-dimethyl-6-[[(1~{S})-1-(4-methylphenyl)ethyl]amino]-3~{H}-quinoxalin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](Nc1ccc2N(C)C(=O)[C@@H](C)N(C3CC3)c2c1)c4ccc(C)cc4
#
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
 8F9  8F9  (3~{R})-4-cyclopropyl-1,3-dimethyl-6-[[(1~{S})-1-(4-methylphenyl)ethyl]amino]-3~{H}-quinoxalin-2-one  ligand  53  26  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_8F9
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
 8F9  C13  C  CH3   0  -0.672   5.1141   1.7111   1.2066
 8F9  C17  C  CH2   0  -0.493   1.9786   2.8822  -1.3110
 8F9  C20  C  CH3   0  -0.653  -2.9280  -2.3004   1.5808
 8F9  C21  C  CR16  0  -0.310  -4.7569  -0.6671  -1.0348
 8F9  C22  C  CR16  0  -0.280  -5.9268   0.0465  -1.2568
 8F9  C24  C  CR16  0  -0.285  -5.7567   1.0002   0.9238
 8F9  C01  C  CR16  0  -0.366   0.0699  -1.9399  -0.0368
 8F9  C02  C  CR6   0   0.406  -0.3897  -0.6700   0.3336
 8F9  C03  C  CR16  0  -0.440   0.5629   0.3537   0.4604
 8F9  C04  C  CR6   0   0.292   1.8995   0.1300   0.1989
 8F9  C05  C  CR6   0   0.309   2.3477  -1.1423  -0.1732
 8F9  C06  C  CR16  0  -0.324   1.4187  -2.1679  -0.2743
 8F9  C08  C  CH1   0  -0.251   4.0766   0.6442   0.9134
 8F9  C09  C  C     0   0.534   4.6522  -0.4955   0.0763
 8F9  C14  C  CH1   0  -0.111   3.0349   1.9035  -0.9102
 8F9  C16  C  CH1   0  -0.154  -2.7942  -1.3322   0.4043
 8F9  C18  C  CH2   0  -0.484   3.3136   3.3719  -0.8463
 8F9  C19  C  CR6   0   0.117  -4.0712  -0.5598   0.1699
 8F9  C23  C  CR6   0   0.084  -6.4446   0.8972  -0.2837
 8F9  C25  C  CR16  0  -0.288  -4.5915   0.2824   1.1502
 8F9  N07  N  NT    0  -0.489   2.8524   1.1739   0.3186
 8F9  N10  N  NT    0  -0.558   3.7163  -1.3245  -0.4570
 8F9  N15  N  NH1   0  -0.715  -1.7038  -0.3958   0.5940
 8F9  O12  O  O     0  -0.478   5.8493  -0.6543  -0.0975
 8F9  H1   H  HCH3  0   0.239   4.6660   2.5068   1.8000
 8F9  H2   H  HCH3  0   0.246   5.9322   1.2870   1.7855
 8F9  H3   H  HCH3  0   0.238   5.5322   2.1506   0.3029
 8F9  H4   H  HCH2  0   0.254   1.7318   2.9519  -2.3621
 8F9  H5   H  HCH2  0   0.250   1.1381   3.0131  -0.6430
 8F9  H6   H  HCH3  0   0.236  -2.0068  -2.8645   1.7312
 8F9  H7   H  HCH3  0   0.228  -3.1466  -1.7656   2.5056
 8F9  H8   H  HCH3  0   0.231  -3.7322  -3.0143   1.3997
 8F9  H9   H  HCR6  0   0.249  -4.3737  -1.3180  -1.8122
 8F9  H10  H  HCR6  0   0.247  -6.4404  -0.0589  -2.2053
 8F9  H11  H  HCR6  0   0.247  -6.1399   1.6488   1.7030
 8F9  H12  H  HCH3  0   0.248  -7.4522   2.6232  -1.0710
 8F9  H13  H  HCH3  0   0.243  -8.4021   1.1486  -1.1508
 8F9  H14  H  HCH3  0   0.243  -8.1824   1.9771   0.3913
 8F9  H15  H  HCR6  0   0.264  -0.6137  -2.7716  -0.1356
 8F9  H16  H  HCR6  0   0.252   0.2518   1.3418   0.7779
 8F9  H17  H  HCR6  0   0.272   1.7283  -3.1682  -0.5469
 8F9  H18  H  HCH1  0   0.288   3.7786   0.2022   1.8735
 8F9  H22  H  HCH1  0   0.249   3.5066   1.3616  -1.7312
 8F9  H23  H  HCH1  0   0.246  -2.6029  -1.9245  -0.4986
 8F9  H24  H  HCH2  0   0.252   4.0008   3.7890  -1.5710
 8F9  H25  H  HCH2  0   0.251   3.3642   3.8254   0.1347
 8F9  H26  H  HCR6  0   0.255  -4.0897   0.3839   2.1058
 8F9  H27  H  HNH1  0   0.387  -1.9482   0.5750   0.6933
 8F9  C11  C  CH3   0  -0.552   4.1271  -2.4653  -1.2518
 8F9  C26  C  CH3   0  -0.721  -7.6878   1.6990  -0.5389
 8F9  H19  H  HCH3  0   0.252   3.4319  -2.6059  -2.0771
 8F9  H20  H  HCH3  0   0.269   5.1168  -2.2878  -1.6591
 8F9  H21  H  HCH3  0   0.247   4.1559  -3.3816  -0.6596

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
 8F9  C11  N10  single    1.450  0.020  1.450
 8F9  C06  C01  aromatic  1.388  0.020  1.388
 8F9  C06  C05  aromatic  1.387  0.020  1.387
 8F9  C01  C02  aromatic  1.400  0.020  1.400
 8F9  N10  C05  single    1.410  0.020  1.410
 8F9  N10  C09  single    1.359  0.020  1.359
 8F9  C13  C08  single    1.517  0.020  1.517
 8F9  O12  C09  double    1.220  0.020  1.220
 8F9  C05  C04  aromatic  1.399  0.020  1.399
 8F9  C09  C08  single    1.527  0.020  1.527
 8F9  C02  N15  single    1.367  0.020  1.367
 8F9  C02  C03  aromatic  1.404  0.020  1.404
 8F9  C08  N07  single    1.460  0.020  1.460
 8F9  C04  C03  aromatic  1.380  0.020  1.380
 8F9  C04  N07  single    1.418  0.020  1.418
 8F9  N15  C16  single    1.450  0.020  1.450
 8F9  N07  C14  single    1.441  0.020  1.441
 8F9  C16  C20  single    1.530  0.020  1.530
 8F9  C16  C19  single    1.511  0.020  1.511
 8F9  C14  C17  single    1.495  0.020  1.495
 8F9  C14  C18  single    1.496  0.020  1.496
 8F9  C17  C18  single    1.496  0.020  1.496
 8F9  C25  C19  aromatic  1.393  0.020  1.393
 8F9  C25  C24  aromatic  1.387  0.020  1.387
 8F9  C19  C21  aromatic  1.390  0.020  1.390
 8F9  C24  C23  aromatic  1.394  0.020  1.394
 8F9  C21  C22  aromatic  1.388  0.020  1.388
 8F9  C23  C22  aromatic  1.392  0.020  1.392
 8F9  C23  C26  single    1.501  0.020  1.501
 8F9  C13  H1   single    0.970  0.020  1.090
 8F9  C13  H2   single    0.970  0.020  1.090
 8F9  C13  H3   single    0.970  0.020  1.090
 8F9  C17  H4   single    0.970  0.020  1.090
 8F9  C17  H5   single    0.970  0.020  1.090
 8F9  C20  H6   single    0.970  0.020  1.090
 8F9  C20  H7   single    0.970  0.020  1.090
 8F9  C20  H8   single    0.970  0.020  1.090
 8F9  C21  H9   single    0.930  0.020  1.080
 8F9  C22  H10  single    0.930  0.020  1.080
 8F9  C24  H11  single    0.930  0.020  1.080
 8F9  C26  H12  single    0.970  0.020  1.090
 8F9  C26  H13  single    0.970  0.020  1.090
 8F9  C26  H14  single    0.970  0.020  1.090
 8F9  C01  H15  single    0.930  0.020  1.080
 8F9  C03  H16  single    0.930  0.020  1.080
 8F9  C06  H17  single    0.930  0.020  1.080
 8F9  C08  H18  single    0.970  0.020  1.090
 8F9  C11  H19  single    0.970  0.020  1.090
 8F9  C11  H20  single    0.970  0.020  1.090
 8F9  C11  H21  single    0.970  0.020  1.090
 8F9  C14  H22  single    0.970  0.020  1.090
 8F9  C16  H23  single    0.970  0.020  1.090
 8F9  C18  H24  single    0.970  0.020  1.090
 8F9  C18  H25  single    0.970  0.020  1.090
 8F9  C25  H26  single    0.930  0.020  1.080
 8F9  N15  H27  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
 8F9  H3   C13  H2   108.07  3.000
 8F9  H3   C13  H1   108.39  3.000
 8F9  H2   C13  H1   107.71  3.000
 8F9  H3   C13  C08  112.72  3.000
 8F9  H2   C13  C08  110.06  3.000
 8F9  H1   C13  C08  109.74  3.000
 8F9  H5   C17  H4   114.51  3.000
 8F9  H5   C17  C18  117.52  3.000
 8F9  H4   C17  C18  118.96  3.000
 8F9  H5   C17  C14  117.57  3.000
 8F9  H4   C17  C14  117.64  3.000
 8F9  C18  C17  C14   60.03  3.000
 8F9  H8   C20  H7   108.31  3.000
 8F9  H8   C20  H6   107.89  3.000
 8F9  H7   C20  H6   107.82  3.000
 8F9  H8   C20  C16  110.56  3.000
 8F9  H7   C20  C16  111.06  3.000
 8F9  H6   C20  C16  111.07  3.000
 8F9  H9   C21  C19  119.57  3.000
 8F9  H9   C21  C22  119.47  3.000
 8F9  C19  C21  C22  120.96  3.000
 8F9  H10  C22  C23  119.66  3.000
 8F9  H10  C22  C21  119.30  3.000
 8F9  C23  C22  C21  121.05  3.000
 8F9  H11  C24  C25  119.30  3.000
 8F9  H11  C24  C23  119.51  3.000
 8F9  C25  C24  C23  121.19  3.000
 8F9  H15  C01  C06  118.19  3.000
 8F9  H15  C01  C02  120.95  3.000
 8F9  C06  C01  C02  120.86  3.000
 8F9  N15  C02  C03  119.25  3.000
 8F9  C03  C02  C01  117.54  3.000
 8F9  N15  C02  C01  123.21  3.000
 8F9  H16  C03  C04  118.78  3.000
 8F9  H16  C03  C02  119.77  3.000
 8F9  C04  C03  C02  121.45  3.000
 8F9  N07  C04  C05  118.45  3.000
 8F9  N07  C04  C03  121.02  3.000
 8F9  C05  C04  C03  120.53  3.000
 8F9  N10  C05  C06  122.68  3.000
 8F9  N10  C05  C04  118.82  3.000
 8F9  C06  C05  C04  118.49  3.000
 8F9  H17  C06  C05  120.67  3.000
 8F9  H17  C06  C01  118.22  3.000
 8F9  C05  C06  C01  121.11  3.000
 8F9  H18  C08  N07  105.94  3.000
 8F9  H18  C08  C09  106.34  3.000
 8F9  N07  C08  C09  111.32  3.000
 8F9  H18  C08  C13  107.44  3.000
 8F9  N07  C08  C13  113.39  3.000
 8F9  C09  C08  C13  111.91  3.000
 8F9  O12  C09  N10  122.71  3.000
 8F9  O12  C09  C08  123.04  3.000
 8F9  N10  C09  C08  114.25  3.000
 8F9  H22  C14  N07  116.43  3.000
 8F9  H22  C14  C18  116.05  3.000
 8F9  N07  C14  C18  118.96  3.000
 8F9  H22  C14  C17  115.40  3.000
 8F9  C18  C14  C17   60.03  3.000
 8F9  N07  C14  C17  118.09  3.000
 8F9  H23  C16  N15  108.99  3.000
 8F9  H23  C16  C19  107.21  3.000
 8F9  N15  C16  C19  109.02  3.000
 8F9  H23  C16  C20  107.86  3.000
 8F9  C19  C16  C20  111.66  3.000
 8F9  N15  C16  C20  111.96  3.000
 8F9  H25  C18  H24  114.58  3.000
 8F9  H25  C18  C14  117.31  3.000
 8F9  H24  C18  C14  117.90  3.000
 8F9  H25  C18  C17  117.43  3.000
 8F9  H24  C18  C17  118.99  3.000
 8F9  C14  C18  C17   59.94  3.000
 8F9  C25  C19  C16  121.03  3.000
 8F9  C25  C19  C21  118.17  3.000
 8F9  C16  C19  C21  120.79  3.000
 8F9  C26  C23  C24  121.11  3.000
 8F9  C26  C23  C22  121.03  3.000
 8F9  C24  C23  C22  117.85  3.000
 8F9  H26  C25  C19  120.26  3.000
 8F9  H26  C25  C24  118.96  3.000
 8F9  C19  C25  C24  120.78  3.000
 8F9  C14  N07  C08  115.14  3.000
 8F9  C14  N07  C04  112.70  3.000
 8F9  C08  N07  C04  109.30  3.000
 8F9  C11  N10  C09  119.99  3.000
 8F9  C09  N10  C05  120.71  3.000
 8F9  C11  N10  C05  119.16  3.000
 8F9  H27  N15  C16  116.97  3.000
 8F9  H27  N15  C02  116.48  3.000
 8F9  C16  N15  C02  124.63  3.000
 8F9  H21  C11  H20  108.48  3.000
 8F9  H21  C11  H19  108.66  3.000
 8F9  H20  C11  H19  108.61  3.000
 8F9  H21  C11  N10  111.75  3.000
 8F9  H20  C11  N10  109.61  3.000
 8F9  H19  C11  N10  109.66  3.000
 8F9  H14  C26  H13  108.10  3.000
 8F9  H14  C26  H12  107.33  3.000
 8F9  H13  C26  H12  107.17  3.000
 8F9  H14  C26  C23  111.54  3.000
 8F9  H13  C26  C23  111.63  3.000
 8F9  H12  C26  C23  110.87  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
 8F9  CONST_01  C24  C25  C19  C21     0.00   0.0  0
 8F9  CONST_02  C24  C23  C22  C21     0.00   0.0  0
 8F9  CONST_03  C25  C19  C21  C22     0.00   0.0  0
 8F9  CONST_04  C25  C24  C23  C22     0.00   0.0  0
 8F9  CONST_05  C04  C05  C06  C01     0.00   0.0  0
 8F9  CONST_06  C04  C03  C02  C01     0.00   0.0  0
 8F9  CONST_07  C05  C06  C01  C02     0.00   0.0  0
 8F9  CONST_08  C05  C04  C03  C02     0.00   0.0  0
 8F9  CONST_09  C06  C01  C02  C03     0.00   0.0  0
 8F9  CONST_10  C06  C05  C04  C03     0.00   0.0  0
 8F9  CONST_11  C23  C24  C25  C19     0.00   0.0  0
 8F9  CONST_12  C23  C22  C21  C19     0.00   0.0  0
 8F9  CONST_13  C08  C09  N10  C05     0.00   0.0  0
 8F9  CONST_14  C26  C23  C22  C21   180.00   0.0  0
 8F9  CONST_15  C16  C19  C21  C22   180.00   0.0  0
 8F9  CONST_16  C16  C19  C25  C24   180.00   0.0  0
 8F9  CONST_17  C25  C24  C23  C26   180.00   0.0  0
 8F9  CONST_18  N15  C02  C03  C04   180.00   0.0  0
 8F9  CONST_19  N15  C02  C01  C06   180.00   0.0  0
 8F9  CONST_20  O12  C09  N10  C05   180.00   0.0  0
 8F9  CONST_21  C11  N10  C09  C08   180.00   0.0  0
 8F9  CONST_22  H26  C25  C19  C21   180.00   0.0  0
 8F9  CONST_23  H11  C24  C23  C22   180.00   0.0  0
 8F9  CONST_24  H10  C22  C23  C24   180.00   0.0  0
 8F9  CONST_25  H16  C03  C02  C01   180.00   0.0  0
 8F9  CONST_26  H17  C06  C01  C02   180.00   0.0  0
 8F9  CONST_27  H15  C01  C02  C03   180.00   0.0  0
 8F9  CONST_28  H9   C21  C22  C23   180.00   0.0  0
 8F9  CONST_29  C16  N15  C02  C01     0.00   0.0  0
 8F9  CONST_30  C16  N15  C02  C03   180.00   0.0  0
 8F9  CONST_31  O12  C09  N10  C11     0.00   0.0  0
 8F9  CONST_32  H27  N15  C02  C01   180.00   0.0  0
 8F9  Var_01    C08  N07  C14  C17  -157.71  30.0  2
 8F9  Var_02    N07  C14  C18  C17  -107.58  30.0  1
 8F9  Var_03    C09  N10  C05  C04    24.66  30.0  1
 8F9  Var_04    H12  C26  C23  C22   -83.74  30.0  2
 8F9  Var_05    H19  C11  N10  C05    41.62  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
 8F9  chir_01  C08  C13  C09  N07  positiv
 8F9  chir_03  C16  N15  C20  C19  negativ
 8F9  chir_04  C14  N07  C17  C18  both

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
 8F9  plan-1  C21  0.020
 8F9  plan-1  C22  0.020
 8F9  plan-1  C24  0.020
 8F9  plan-1  C16  0.020
 8F9  plan-1  C19  0.020
 8F9  plan-1  C23  0.020
 8F9  plan-1  C25  0.020
 8F9  plan-1  H9   0.020
 8F9  plan-1  H10  0.020
 8F9  plan-1  H11  0.020
 8F9  plan-1  H26  0.020
 8F9  plan-1  C26  0.020
 8F9  plan-2  C01  0.020
 8F9  plan-2  C02  0.020
 8F9  plan-2  C03  0.020
 8F9  plan-2  C04  0.020
 8F9  plan-2  C05  0.020
 8F9  plan-2  C06  0.020
 8F9  plan-2  N07  0.020
 8F9  plan-2  N10  0.020
 8F9  plan-2  N15  0.020
 8F9  plan-2  H15  0.020
 8F9  plan-2  H16  0.020
 8F9  plan-2  H17  0.020
 8F9  plan-3  C02  0.020
 8F9  plan-3  C16  0.020
 8F9  plan-3  N15  0.020
 8F9  plan-3  H27  0.020
 8F9  plan-4  C05  0.020
 8F9  plan-4  C08  0.020
 8F9  plan-4  C09  0.020
 8F9  plan-4  N10  0.020
 8F9  plan-4  O12  0.020
 8F9  plan-4  C11  0.020

