# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 22:18:14 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: (3~{R})-4-cyclopropyl-1,3-dimethyl-6-[[(1~{R})-1-phenylethyl]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)c4ccccc4
#
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
 8F6  8F6  (3~{R})-4-cyclopropyl-1,3-dimethyl-6-[[(1~{R})-1-phenylethyl]amino]-3~{H}-quinoxalin-2-one  ligand  50  25  .  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_8F6
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
 8F6  C13  C  CH3   0  -0.669   4.8016   1.4105   1.5747
 8F6  C17  C  CH2   0  -0.495   2.2231   2.7104  -1.4750
 8F6  C20  C  CH3   0  -0.654  -3.1070  -0.6852  -2.0910
 8F6  C21  C  CR16  0  -0.328  -5.2756  -0.9834   0.7772
 8F6  C22  C  CR16  0  -0.237  -6.4783  -0.4999   1.2777
 8F6  C24  C  CR16  0  -0.238  -6.0828   1.5977   0.1819
 8F6  C01  C  CR16  0  -0.347  -0.3965  -1.7421  -0.2737
 8F6  C02  C  CR6   0   0.377  -0.7536  -0.4125  -0.0295
 8F6  C03  C  CR16  0  -0.435   0.2803   0.5050   0.1998
 8F6  C04  C  CR6   0   0.289   1.6066   0.1198   0.1704
 8F6  C05  C  CR6   0   0.317   1.9524  -1.2141  -0.0692
 8F6  C06  C  CR16  0  -0.329   0.9349  -2.1345  -0.2790
 8F6  C08  C  CH1   0  -0.252   3.7028   0.4422   1.1823
 8F6  C09  C  C     0   0.533   4.2564  -0.8023   0.4930
 8F6  C14  C  CH1   0  -0.111   3.0926   1.6768  -0.8364
 8F6  C16  C  CH1   0  -0.210  -3.1556  -0.7209  -0.5624
 8F6  C18  C  CH2   0  -0.483   3.5085   3.1132  -0.8234
 8F6  C19  C  CR6   0   0.178  -4.4662  -0.1884  -0.0274
 8F6  C23  C  CR16  0  -0.269  -6.8847   0.7937   0.9826
 8F6  C25  C  CR16  0  -0.314  -4.8860   1.1079  -0.3217
 8F6  N07  N  NT    0  -0.488   2.6447   1.0615   0.3875
 8F6  N10  N  NT    0  -0.559   3.3153  -1.5642  -0.1270
 8F6  N15  N  NH1   0  -0.690  -2.0647   0.0120   0.0603
 8F6  O12  O  O     0  -0.475   5.4400  -1.0962   0.5034
 8F6  H1   H  HCH3  0   0.238   5.3683   1.7710   0.7180
 8F6  H2   H  HCH3  0   0.239   4.3710   2.2691   2.0883
 8F6  H3   H  HCH3  0   0.245   5.4962   0.9282   2.2597
 8F6  H4   H  HCH2  0   0.254   2.1600   2.7129  -2.5553
 8F6  H5   H  HCH2  0   0.251   1.3022   2.9788  -0.9747
 8F6  H7   H  HCH3  0   0.239  -2.1660  -1.0935  -2.4616
 8F6  H8   H  HCH3  0   0.236  -3.9196  -1.2739  -2.5174
 8F6  H9   H  HCR6  0   0.252  -4.9641  -1.9935   1.0159
 8F6  H10  H  HCR6  0   0.257  -7.0949  -1.1346   1.9009
 8F6  H11  H  HCR6  0   0.256  -6.3901   2.6083  -0.0543
 8F6  H12  H  HCR6  0   0.266  -1.1507  -2.4967  -0.4494
 8F6  H13  H  HCR6  0   0.253   0.0460   1.5402   0.4185
 8F6  H14  H  HCR6  0   0.274   1.1594  -3.1768  -0.4638
 8F6  H15  H  HCH1  0   0.289   3.2246   0.0931   2.1073
 8F6  H19  H  HCH1  0   0.250   3.6346   1.0320  -1.5299
 8F6  H20  H  HCH1  0   0.260  -3.0779  -1.7625  -0.2409
 8F6  H21  H  HCH2  0   0.252   4.3452   3.4033  -1.4458
 8F6  H22  H  HCH2  0   0.251   3.4417   3.6447   0.1166
 8F6  H23  H  HCR6  0   0.256  -7.8198   1.1735   1.3732
 8F6  H24  H  HCR6  0   0.251  -4.2819   1.7499  -0.9528
 8F6  H25  H  HNH1  0   0.376  -2.1671   1.0149   0.0018
 8F6  C11  C  CH3   0  -0.553   3.6971  -2.8021  -0.7781
 8F6  H6   H  HCH3  0   0.226  -3.1968   0.3364  -2.4631
 8F6  H16  H  HCH3  0   0.252   3.1500  -2.9122  -1.7131
 8F6  H17  H  HCH3  0   0.270   4.7591  -2.7847  -0.9979
 8F6  H18  H  HCH3  0   0.248   3.4885  -3.6684  -0.1479

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
 8F6  C24  C23  aromatic  1.389  0.020  1.389
 8F6  C24  C25  aromatic  1.388  0.020  1.388
 8F6  C23  C22  aromatic  1.388  0.020  1.388
 8F6  C25  C19  aromatic  1.394  0.020  1.394
 8F6  C22  C21  aromatic  1.389  0.020  1.389
 8F6  C17  C18  single    1.496  0.020  1.496
 8F6  C17  C14  single    1.494  0.020  1.494
 8F6  C19  C21  aromatic  1.391  0.020  1.391
 8F6  C19  C16  single    1.512  0.020  1.512
 8F6  C18  C14  single    1.495  0.020  1.495
 8F6  C20  C16  single    1.530  0.020  1.530
 8F6  C16  N15  single    1.454  0.020  1.454
 8F6  C14  N07  single    1.441  0.020  1.441
 8F6  N07  C04  single    1.418  0.020  1.418
 8F6  N07  C08  single    1.461  0.020  1.461
 8F6  C03  C04  aromatic  1.381  0.020  1.381
 8F6  C03  C02  aromatic  1.401  0.020  1.401
 8F6  N15  C02  single    1.381  0.020  1.381
 8F6  C04  C05  aromatic  1.399  0.020  1.399
 8F6  C02  C01  aromatic  1.398  0.020  1.398
 8F6  C08  C09  single    1.527  0.020  1.527
 8F6  C08  C13  single    1.516  0.020  1.516
 8F6  C09  O12  double    1.220  0.020  1.220
 8F6  C09  N10  single    1.360  0.020  1.360
 8F6  C05  N10  single    1.408  0.020  1.408
 8F6  C05  C06  aromatic  1.388  0.020  1.388
 8F6  C01  C06  aromatic  1.388  0.020  1.388
 8F6  N10  C11  single    1.450  0.020  1.450
 8F6  C13  H1   single    0.970  0.020  1.090
 8F6  C13  H2   single    0.970  0.020  1.090
 8F6  C13  H3   single    0.970  0.020  1.090
 8F6  C17  H4   single    0.970  0.020  1.090
 8F6  C17  H5   single    0.970  0.020  1.090
 8F6  C20  H6   single    0.970  0.020  1.090
 8F6  C20  H7   single    0.970  0.020  1.090
 8F6  C20  H8   single    0.970  0.020  1.090
 8F6  C21  H9   single    0.930  0.020  1.080
 8F6  C22  H10  single    0.930  0.020  1.080
 8F6  C24  H11  single    0.930  0.020  1.080
 8F6  C01  H12  single    0.930  0.020  1.080
 8F6  C03  H13  single    0.930  0.020  1.080
 8F6  C06  H14  single    0.930  0.020  1.080
 8F6  C08  H15  single    0.970  0.020  1.090
 8F6  C11  H16  single    0.970  0.020  1.090
 8F6  C11  H17  single    0.970  0.020  1.090
 8F6  C11  H18  single    0.970  0.020  1.090
 8F6  C14  H19  single    0.970  0.020  1.090
 8F6  C16  H20  single    0.970  0.020  1.090
 8F6  C18  H21  single    0.970  0.020  1.090
 8F6  C18  H22  single    0.970  0.020  1.090
 8F6  C23  H23  single    0.930  0.020  1.080
 8F6  C25  H24  single    0.930  0.020  1.080
 8F6  N15  H25  single    0.890  0.020  1.040

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
 8F6  H3   C13  H2   107.75  3.000
 8F6  H3   C13  H1   108.06  3.000
 8F6  H2   C13  H1   108.41  3.000
 8F6  H3   C13  C08  110.03  3.000
 8F6  H2   C13  C08  109.81  3.000
 8F6  H1   C13  C08  112.65  3.000
 8F6  H5   C17  H4   114.29  3.000
 8F6  H5   C17  C18  117.59  3.000
 8F6  H4   C17  C18  118.96  3.000
 8F6  H5   C17  C14  117.99  3.000
 8F6  H4   C17  C14  117.53  3.000
 8F6  C18  C17  C14   60.01  3.000
 8F6  H8   C20  H7   107.94  3.000
 8F6  H8   C20  H6   108.11  3.000
 8F6  H7   C20  H6   107.80  3.000
 8F6  H8   C20  C16  110.76  3.000
 8F6  H7   C20  C16  110.99  3.000
 8F6  H6   C20  C16  111.11  3.000
 8F6  H9   C21  C19  119.54  3.000
 8F6  H9   C21  C22  119.59  3.000
 8F6  C19  C21  C22  120.88  3.000
 8F6  H10  C22  C23  120.15  3.000
 8F6  H10  C22  C21  119.77  3.000
 8F6  C23  C22  C21  120.08  3.000
 8F6  H11  C24  C25  119.68  3.000
 8F6  H11  C24  C23  120.15  3.000
 8F6  C25  C24  C23  120.17  3.000
 8F6  H12  C01  C06  118.11  3.000
 8F6  H12  C01  C02  120.92  3.000
 8F6  C06  C01  C02  120.96  3.000
 8F6  N15  C02  C03  119.25  3.000
 8F6  N15  C02  C01  123.10  3.000
 8F6  C03  C02  C01  117.57  3.000
 8F6  H13  C03  C04  118.57  3.000
 8F6  H13  C03  C02  119.94  3.000
 8F6  C04  C03  C02  121.49  3.000
 8F6  N07  C04  C05  118.58  3.000
 8F6  C05  C04  C03  120.46  3.000
 8F6  N07  C04  C03  120.95  3.000
 8F6  N10  C05  C06  122.57  3.000
 8F6  C06  C05  C04  118.49  3.000
 8F6  N10  C05  C04  118.91  3.000
 8F6  H14  C06  C05  120.83  3.000
 8F6  H14  C06  C01  118.16  3.000
 8F6  C05  C06  C01  121.00  3.000
 8F6  H15  C08  N07  106.11  3.000
 8F6  H15  C08  C09  106.20  3.000
 8F6  N07  C08  C09  111.26  3.000
 8F6  H15  C08  C13  107.49  3.000
 8F6  C09  C08  C13  112.00  3.000
 8F6  N07  C08  C13  113.26  3.000
 8F6  O12  C09  N10  122.71  3.000
 8F6  N10  C09  C08  114.30  3.000
 8F6  O12  C09  C08  122.99  3.000
 8F6  H19  C14  N07  116.22  3.000
 8F6  H19  C14  C18  115.79  3.000
 8F6  N07  C14  C18  119.28  3.000
 8F6  H19  C14  C17  115.23  3.000
 8F6  N07  C14  C17  118.52  3.000
 8F6  C18  C14  C17   60.07  3.000
 8F6  H20  C16  N15  107.52  3.000
 8F6  H20  C16  C19  107.05  3.000
 8F6  N15  C16  C19  108.73  3.000
 8F6  H20  C16  C20  108.29  3.000
 8F6  N15  C16  C20  113.09  3.000
 8F6  C19  C16  C20  111.88  3.000
 8F6  H22  C18  H21  114.56  3.000
 8F6  H22  C18  C14  117.54  3.000
 8F6  H21  C18  C14  117.87  3.000
 8F6  H22  C18  C17  117.23  3.000
 8F6  H21  C18  C17  119.06  3.000
 8F6  C14  C18  C17   59.92  3.000
 8F6  C25  C19  C16  120.91  3.000
 8F6  C16  C19  C21  120.51  3.000
 8F6  C25  C19  C21  118.58  3.000
 8F6  H23  C23  C24  120.23  3.000
 8F6  H23  C23  C22  120.23  3.000
 8F6  C24  C23  C22  119.54  3.000
 8F6  H24  C25  C19  120.38  3.000
 8F6  H24  C25  C24  118.87  3.000
 8F6  C19  C25  C24  120.75  3.000
 8F6  C14  N07  C08  114.69  3.000
 8F6  C08  N07  C04  109.39  3.000
 8F6  C14  N07  C04  112.39  3.000
 8F6  C11  N10  C09  120.05  3.000
 8F6  C11  N10  C05  119.05  3.000
 8F6  C09  N10  C05  120.77  3.000
 8F6  H25  N15  C16  113.55  3.000
 8F6  H25  N15  C02  113.44  3.000
 8F6  C16  N15  C02  121.97  3.000
 8F6  H18  C11  H17  108.47  3.000
 8F6  H18  C11  H16  108.63  3.000
 8F6  H17  C11  H16  108.64  3.000
 8F6  H18  C11  N10  111.60  3.000
 8F6  H17  C11  N10  109.58  3.000
 8F6  H16  C11  N10  109.86  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
 8F6  CONST_01  C24  C23  C22  C21     0.00   0.0  0
 8F6  CONST_02  C24  C25  C19  C21     0.00   0.0  0
 8F6  CONST_03  C25  C24  C23  C22     0.00   0.0  0
 8F6  CONST_04  C25  C19  C21  C22     0.00   0.0  0
 8F6  CONST_05  C04  C03  C02  C01     0.00   0.0  0
 8F6  CONST_06  C04  C05  C06  C01     0.00   0.0  0
 8F6  CONST_07  C05  C04  C03  C02     0.00   0.0  0
 8F6  CONST_08  C05  C06  C01  C02     0.00   0.0  0
 8F6  CONST_09  C06  C05  C04  C03     0.00   0.0  0
 8F6  CONST_10  C06  C01  C02  C03     0.00   0.0  0
 8F6  CONST_11  C23  C24  C25  C19     0.00   0.0  0
 8F6  CONST_12  C23  C22  C21  C19     0.00   0.0  0
 8F6  CONST_13  C08  C09  N10  C05     0.00   0.0  0
 8F6  CONST_14  C16  C19  C21  C22   180.00   0.0  0
 8F6  CONST_15  C16  C19  C25  C24   180.00   0.0  0
 8F6  CONST_16  N15  C02  C03  C04   180.00   0.0  0
 8F6  CONST_17  N15  C02  C01  C06   180.00   0.0  0
 8F6  CONST_18  O12  C09  N10  C05   180.00   0.0  0
 8F6  CONST_19  C11  N10  C09  C08   180.00   0.0  0
 8F6  CONST_20  H23  C23  C22  C21   180.00   0.0  0
 8F6  CONST_21  H24  C25  C19  C21   180.00   0.0  0
 8F6  CONST_22  H11  C24  C23  C22   180.00   0.0  0
 8F6  CONST_23  H10  C22  C23  C24   180.00   0.0  0
 8F6  CONST_24  H13  C03  C02  C01   180.00   0.0  0
 8F6  CONST_25  H14  C06  C01  C02   180.00   0.0  0
 8F6  CONST_26  H12  C01  C02  C03   180.00   0.0  0
 8F6  CONST_27  H9   C21  C22  C23   180.00   0.0  0
 8F6  CONST_30  O12  C09  N10  C11     0.00   0.0  0
 8F6  CONST_31  H25  N15  C02  C01   180.00   0.0  0
 8F6  Var_01    N07  C14  C18  C17  -107.99  30.0  1
 8F6  Var_02    C04  N07  C14  C17    74.73  30.0  3
 8F6  Var_03    C14  N07  C04  C03   -90.11  30.0  1
 8F6  Var_04    C09  N10  C05  C04    23.76  30.0  1
 8F6  Var_05    H16  C11  N10  C05    44.07  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
 8F6  chir_01  C08  N07  C09  C13  negativ
 8F6  chir_03  C16  C19  C20  N15  negativ
 8F6  chir_04  C14  C17  C18  N07  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
 8F6  plan-1  C21  0.020
 8F6  plan-1  C22  0.020
 8F6  plan-1  C24  0.020
 8F6  plan-1  C16  0.020
 8F6  plan-1  C19  0.020
 8F6  plan-1  C23  0.020
 8F6  plan-1  C25  0.020
 8F6  plan-1  H9   0.020
 8F6  plan-1  H10  0.020
 8F6  plan-1  H11  0.020
 8F6  plan-1  H23  0.020
 8F6  plan-1  H24  0.020
 8F6  plan-2  C01  0.020
 8F6  plan-2  C02  0.020
 8F6  plan-2  C03  0.020
 8F6  plan-2  C04  0.020
 8F6  plan-2  C05  0.020
 8F6  plan-2  C06  0.020
 8F6  plan-2  N07  0.020
 8F6  plan-2  N10  0.020
 8F6  plan-2  N15  0.020
 8F6  plan-2  H12  0.020
 8F6  plan-2  H13  0.020
 8F6  plan-2  H14  0.020
 8F6  plan-3  C02  0.020
 8F6  plan-3  C16  0.020
 8F6  plan-3  N15  0.020
 8F6  plan-3  H25  0.020
 8F6  plan-4  C05  0.020
 8F6  plan-4  C08  0.020
 8F6  plan-4  C09  0.020
 8F6  plan-4  N10  0.020
 8F6  plan-4  O12  0.020
 8F6  plan-4  C11  0.020

