# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 16:32:24 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: (3~{R})-4-cyclopropyl-~{N},1,3-trimethyl-~{N}-(4-methylphenyl)-2-oxidanylidene-3~{H}-quinoxaline-6-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1N(C2CC2)c3cc(ccc3N(C)C1=O)C(=O)N(C)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
 8XX  8XX  (3~{R})-4-cyclopropyl-~{N},1,3-trimethyl-~{N}-(4-methylphenyl)-2-oxidanylidene-3~{H}-quinoxaline-6-carboxamide  ligand  52  27  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8XX
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
 8XX  C10   C  CR16  0  -0.304   6.0290  -0.1313   1.1858
 8XX  C13   C  CR16  0  -0.260  -0.0455  -1.4803   1.0043
 8XX  C15   C  CR66  0   0.361  -2.3839  -1.0324   0.6488
 8XX  C20   C  CH2   0  -0.493  -2.6487   3.1713   0.5090
 8XX  C21   C  CR16  0  -0.255  -4.1373   0.0793  -1.1085
 8XX  C22   C  CH3   0  -0.672  -5.2411   0.8402  -1.8170
 8XX  C02   C  C     0   0.499   1.7095   0.1452   0.2072
 8XX  C04   C  CH3   0  -0.544   2.3713  -2.0433  -0.8009
 8XX  C05   C  CR6   0   0.299   4.0131  -0.3696  -0.1019
 8XX  C06   C  CR16  0  -0.257   4.6933   0.0740  -1.2280
 8XX  C07   C  CR16  0  -0.302   6.0367   0.4076  -1.1422
 8XX  C08   C  CR6   0   0.099   6.7263   0.3146   0.0654
 8XX  C09   C  CH3   0  -0.721   8.1724   0.7038   0.1623
 8XX  C11   C  CR16  0  -0.255   4.6868  -0.4734   1.1068
 8XX  C12   C  CR6   0  -0.074   0.2971  -0.3206   0.3181
 8XX  C14   C  CR16  0  -0.331  -1.3735  -1.8360   1.1718
 8XX  C16   C  CR66  0   0.282  -2.0448   0.1367  -0.0453
 8XX  C18   C  CH1   0  -0.113  -3.5177   1.9676   0.3302
 8XX  C19   C  CH2   0  -0.483  -3.9508   3.2903  -0.2174
 8XX  C23   C  CR6   0   0.547  -4.6843  -0.8461  -0.0281
 8XX  C27   C  CR16  0  -0.347  -0.7148   0.4855  -0.1937
 8XX  N03   N  NT    0  -0.559   2.6444  -0.7514  -0.1902
 8XX  N17   N  NR6   0  -0.487  -3.0816   0.9386  -0.5805
 8XX  N24   N  NR6   0  -0.569  -3.7359  -1.3430   0.8242
 8XX  O01   O  O     0  -0.474   1.9985   1.2997   0.4875
 8XX  O26   O  O     0  -0.458  -5.8604  -1.1387   0.0659
 8XX  H101  H  HCR6  0   0.251   6.5428  -0.2206   2.1357
 8XX  H131  H  HCR6  0   0.270   0.7204  -2.1178   1.4274
 8XX  H202  H  HCH2  0   0.256  -2.5635   3.5837   1.5056
 8XX  H201  H  HCH2  0   0.251  -1.7444   3.2350  -0.0812
 8XX  H211  H  HCR6  0   0.296  -3.6542  -0.5706  -1.8503
 8XX  H222  H  HCH3  0   0.240  -5.8421   1.4399  -1.1368
 8XX  H223  H  HCH3  0   0.242  -4.8071   1.4987  -2.5674
 8XX  H221  H  HCH3  0   0.249  -5.9028   0.1443  -2.3284
 8XX  H043  H  HCH3  0   0.250   2.5058  -2.8635  -0.0942
 8XX  H041  H  HCH3  0   0.263   1.3604  -2.0816  -1.1962
 8XX  H042  H  HCH3  0   0.264   3.0578  -2.1947  -1.6324
 8XX  H061  H  HCR6  0   0.260   4.1736   0.1556  -2.1748
 8XX  H071  H  HCR6  0   0.252   6.5547   0.7476  -2.0310
 8XX  H093  H  HCH3  0   0.250   8.2760   1.7657   0.3949
 8XX  H092  H  HCH3  0   0.245   8.6822   0.1498   0.9499
 8XX  H091  H  HCH3  0   0.245   8.7003   0.5248  -0.7738
 8XX  H111  H  HCR6  0   0.257   4.1638  -0.8286   1.9859
 8XX  H141  H  HCR6  0   0.284  -1.6082  -2.7412   1.7138
 8XX  H181  H  HCH1  0   0.253  -4.0353   1.6299   1.2294
 8XX  H191  H  HCH2  0   0.254  -4.7793   3.7904   0.2671
 8XX  H192  H  HCH2  0   0.253  -3.9072   3.4248  -1.2898
 8XX  H252  H  HCH3  0   0.257  -3.5953  -2.0726   2.7773
 8XX  H253  H  HCH3  0   0.276  -5.1854  -2.2241   2.0293
 8XX  H251  H  HCH3  0   0.253  -3.8862  -3.3205   1.5525
 8XX  H271  H  HCR6  0   0.260  -0.4696   1.3913  -0.7328
 8XX  C25   C  CH3   0  -0.557  -4.1187  -2.2971   1.8498

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
 8XX  C09  C08   single    1.501  0.020  1.501
 8XX  C08  C07   aromatic  1.394  0.020  1.394
 8XX  C08  C10   aromatic  1.393  0.020  1.393
 8XX  C07  C06   aromatic  1.387  0.020  1.387
 8XX  C10  C11   aromatic  1.387  0.020  1.387
 8XX  C06  C05   aromatic  1.388  0.020  1.388
 8XX  C20  C19   single    1.496  0.020  1.496
 8XX  C20  C18   single    1.495  0.020  1.495
 8XX  C19  C18   single    1.496  0.020  1.496
 8XX  C11  C05   aromatic  1.388  0.020  1.388
 8XX  C05  N03   single    1.424  0.020  1.424
 8XX  C18  N17   single    1.442  0.020  1.442
 8XX  C04  N03   single    1.455  0.020  1.455
 8XX  N03  C02   single    1.355  0.020  1.355
 8XX  N17  C16   single    1.416  0.020  1.416
 8XX  N17  C21   single    1.460  0.020  1.460
 8XX  C27  C16   aromatic  1.383  0.020  1.383
 8XX  C27  C12   aromatic  1.391  0.020  1.391
 8XX  C16  C15   aromatic  1.401  0.020  1.401
 8XX  C21  C23   single    1.524  0.020  1.524
 8XX  C21  C22   single    1.516  0.020  1.516
 8XX  C02  C12   single    1.491  0.020  1.491
 8XX  C02  O01   double    1.223  0.020  1.223
 8XX  C12  C13   aromatic  1.390  0.020  1.390
 8XX  C23  O26   double    1.216  0.020  1.216
 8XX  C23  N24   single    1.368  0.020  1.368
 8XX  C15  N24   single    1.398  0.020  1.398
 8XX  C15  C14   aromatic  1.393  0.020  1.393
 8XX  N24  C25   single    1.452  0.020  1.452
 8XX  C13  C14   aromatic  1.385  0.020  1.385
 8XX  C10  H101  single    0.930  0.020  1.080
 8XX  C13  H131  single    0.930  0.020  1.080
 8XX  C20  H202  single    0.970  0.020  1.090
 8XX  C20  H201  single    0.970  0.020  1.090
 8XX  C21  H211  single    0.970  0.020  1.090
 8XX  C22  H222  single    0.970  0.020  1.090
 8XX  C22  H223  single    0.970  0.020  1.090
 8XX  C22  H221  single    0.970  0.020  1.090
 8XX  C04  H043  single    0.970  0.020  1.090
 8XX  C04  H041  single    0.970  0.020  1.090
 8XX  C04  H042  single    0.970  0.020  1.090
 8XX  C06  H061  single    0.930  0.020  1.080
 8XX  C07  H071  single    0.930  0.020  1.080
 8XX  C09  H093  single    0.970  0.020  1.090
 8XX  C09  H092  single    0.970  0.020  1.090
 8XX  C09  H091  single    0.970  0.020  1.090
 8XX  C11  H111  single    0.930  0.020  1.080
 8XX  C14  H141  single    0.930  0.020  1.080
 8XX  C18  H181  single    0.970  0.020  1.090
 8XX  C19  H191  single    0.970  0.020  1.090
 8XX  C19  H192  single    0.970  0.020  1.090
 8XX  C25  H252  single    0.970  0.020  1.090
 8XX  C25  H253  single    0.970  0.020  1.090
 8XX  C25  H251  single    0.970  0.020  1.090
 8XX  C27  H271  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
 8XX  H101  C10  C11   119.24  3.000
 8XX  H101  C10  C08   119.60  3.000
 8XX  C11   C10  C08   121.16  3.000
 8XX  H131  C13  C14   118.67  3.000
 8XX  H131  C13  C12   120.65  3.000
 8XX  C14   C13  C12   120.67  3.000
 8XX  N24   C15  C16   118.78  3.000
 8XX  N24   C15  C14   121.75  3.000
 8XX  C16   C15  C14   119.45  3.000
 8XX  H201  C20  H202  114.48  3.000
 8XX  H201  C20  C19   117.26  3.000
 8XX  H202  C20  C19   119.05  3.000
 8XX  H201  C20  C18   117.90  3.000
 8XX  H202  C20  C18   117.57  3.000
 8XX  C19   C20  C18    60.00  3.000
 8XX  H211  C21  N17   105.93  3.000
 8XX  H211  C21  C23   106.10  3.000
 8XX  N17   C21  C23   111.13  3.000
 8XX  H211  C21  C22   107.55  3.000
 8XX  C23   C21  C22   112.01  3.000
 8XX  N17   C21  C22   113.58  3.000
 8XX  H221  C22  H223  107.78  3.000
 8XX  H221  C22  H222  108.09  3.000
 8XX  H223  C22  H222  108.53  3.000
 8XX  H221  C22  C21   109.96  3.000
 8XX  H223  C22  C21   109.60  3.000
 8XX  H222  C22  C21   112.74  3.000
 8XX  O01   C02  N03   121.94  3.000
 8XX  O01   C02  C12   120.11  3.000
 8XX  N03   C02  C12   117.95  3.000
 8XX  H042  C04  H041  107.70  3.000
 8XX  H042  C04  H043  108.20  3.000
 8XX  H041  C04  H043  108.90  3.000
 8XX  H042  C04  N03   109.01  3.000
 8XX  H041  C04  N03   111.03  3.000
 8XX  H043  C04  N03   111.87  3.000
 8XX  N03   C05  C11   120.04  3.000
 8XX  N03   C05  C06   120.43  3.000
 8XX  C11   C05  C06   119.51  3.000
 8XX  H061  C06  C07   120.04  3.000
 8XX  H061  C06  C05   119.87  3.000
 8XX  C07   C06  C05   120.09  3.000
 8XX  H071  C07  C08   119.68  3.000
 8XX  H071  C07  C06   119.21  3.000
 8XX  C08   C07  C06   121.12  3.000
 8XX  C09   C08  C07   121.03  3.000
 8XX  C07   C08  C10   118.07  3.000
 8XX  C09   C08  C10   120.89  3.000
 8XX  H091  C09  H092  108.11  3.000
 8XX  H091  C09  H093  107.26  3.000
 8XX  H092  C09  H093  107.22  3.000
 8XX  H091  C09  C08   111.64  3.000
 8XX  H092  C09  C08   111.45  3.000
 8XX  H093  C09  C08   110.94  3.000
 8XX  H111  C11  C05   119.82  3.000
 8XX  H111  C11  C10   120.12  3.000
 8XX  C05   C11  C10   120.05  3.000
 8XX  C27   C12  C02   118.72  3.000
 8XX  C02   C12  C13   122.04  3.000
 8XX  C27   C12  C13   119.06  3.000
 8XX  H141  C14  C15   120.92  3.000
 8XX  H141  C14  C13   118.94  3.000
 8XX  C15   C14  C13   120.13  3.000
 8XX  N17   C16  C27   121.38  3.000
 8XX  C27   C16  C15   119.76  3.000
 8XX  N17   C16  C15   118.86  3.000
 8XX  H181  C18  N17   116.30  3.000
 8XX  H181  C18  C19   115.98  3.000
 8XX  N17   C18  C19   119.18  3.000
 8XX  H181  C18  C20   115.23  3.000
 8XX  N17   C18  C20   118.32  3.000
 8XX  C19   C18  C20    60.01  3.000
 8XX  H192  C19  H191  114.66  3.000
 8XX  H192  C19  C18   117.46  3.000
 8XX  H191  C19  C18   117.81  3.000
 8XX  H192  C19  C20   117.14  3.000
 8XX  H191  C19  C20   119.07  3.000
 8XX  C18   C19  C20    59.98  3.000
 8XX  O26   C23  N24   122.34  3.000
 8XX  N24   C23  C21   114.41  3.000
 8XX  O26   C23  C21   123.24  3.000
 8XX  H271  C27  C16   118.85  3.000
 8XX  H271  C27  C12   120.23  3.000
 8XX  C16   C27  C12   120.92  3.000
 8XX  C05   N03  C04   116.40  3.000
 8XX  C04   N03  C02   125.53  3.000
 8XX  C05   N03  C02   117.89  3.000
 8XX  C18   N17  C16   112.77  3.000
 8XX  C16   N17  C21   109.44  3.000
 8XX  C18   N17  C21   115.46  3.000
 8XX  C25   N24  C23   119.72  3.000
 8XX  C25   N24  C15   119.30  3.000
 8XX  C23   N24  C15   120.75  3.000
 8XX  H251  C25  H253  108.54  3.000
 8XX  H251  C25  H252  108.87  3.000
 8XX  H253  C25  H252  108.55  3.000
 8XX  H251  C25  N24   111.58  3.000
 8XX  H253  C25  N24   109.39  3.000
 8XX  H252  C25  N24   109.85  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
 8XX  CONST_01  C06   C07  C08  C10     0.00   0.0  0
 8XX  CONST_02  C06   C05  C11  C10     0.00   0.0  0
 8XX  CONST_03  C16   C27  C12  C13     0.00   0.0  0
 8XX  CONST_04  C16   C15  C14  C13     0.00   0.0  0
 8XX  CONST_05  C12   C27  C16  C15     0.00   0.0  0
 8XX  CONST_06  C12   C13  C14  C15     0.00   0.0  0
 8XX  CONST_07  C08   C07  C06  C05     0.00   0.0  0
 8XX  CONST_08  C08   C10  C11  C05     0.00   0.0  0
 8XX  CONST_09  C11   C10  C08  C07     0.00   0.0  0
 8XX  CONST_10  C11   C05  C06  C07     0.00   0.0  0
 8XX  CONST_11  C27   C16  C15  C14     0.00   0.0  0
 8XX  CONST_12  C27   C12  C13  C14     0.00   0.0  0
 8XX  CONST_13  C21   C23  N24  C15     0.00   0.0  0
 8XX  CONST_14  N03   C05  C11  C10   180.00   0.0  0
 8XX  CONST_15  C16   C27  C12  C02   180.00   0.0  0
 8XX  CONST_16  C14   C13  C12  C02   180.00   0.0  0
 8XX  CONST_17  C09   C08  C07  C06   180.00   0.0  0
 8XX  CONST_18  N03   C05  C06  C07   180.00   0.0  0
 8XX  CONST_19  C11   C10  C08  C09   180.00   0.0  0
 8XX  CONST_20  O26   C23  N24  C15   180.00   0.0  0
 8XX  CONST_21  C25   N24  C23  C21   180.00   0.0  0
 8XX  CONST_22  H071  C07  C08  C10   180.00   0.0  0
 8XX  CONST_23  H271  C27  C12  C13   180.00   0.0  0
 8XX  CONST_24  H131  C13  C14  C15   180.00   0.0  0
 8XX  CONST_25  H101  C10  C11  C05   180.00   0.0  0
 8XX  CONST_26  H111  C11  C05  C06   180.00   0.0  0
 8XX  CONST_27  H061  C06  C07  C08   180.00   0.0  0
 8XX  CONST_28  H141  C14  C13  C12   180.00   0.0  0
 8XX  CONST_29  C12   C02  N03  C05   180.00   0.0  0
 8XX  CONST_34  O26   C23  N24  C25     0.00   0.0  0
 8XX  CONST_35  C12   C02  N03  C04     0.00   0.0  0
 8XX  CONST_36  O01   C02  N03  C05     0.00   0.0  0
 8XX  CONST_37  O01   C02  N03  C04   180.00   0.0  0
 8XX  Var_01    C18   N17  C16  C15    91.61  30.0  1
 8XX  Var_02    N17   C18  C19  C20  -107.76  30.0  1
 8XX  Var_03    C16   N17  C18  C20    75.85  30.0  3
 8XX  Var_04    C23   N24  C15  C14  -157.88  30.0  1
 8XX  Var_05    N03   C02  C12  C13    49.55  30.0  2
 8XX  Var_06    H093  C09  C08  C10   -90.29  30.0  2
 8XX  Var_07    H252  C25  N24  C15    45.97  30.0  3
 8XX  Var_08    H043  C04  N03  C05    81.51  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
 8XX  chir_01  C21  N17  C23  C22  negativ
 8XX  chir_02  C18  C20  C19  N17  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
 8XX  plan-1  C10   0.020
 8XX  plan-1  C05   0.020
 8XX  plan-1  C06   0.020
 8XX  plan-1  C07   0.020
 8XX  plan-1  C08   0.020
 8XX  plan-1  C09   0.020
 8XX  plan-1  C11   0.020
 8XX  plan-1  N03   0.020
 8XX  plan-1  H101  0.020
 8XX  plan-1  H061  0.020
 8XX  plan-1  H071  0.020
 8XX  plan-1  H111  0.020
 8XX  plan-2  C13   0.020
 8XX  plan-2  C15   0.020
 8XX  plan-2  C02   0.020
 8XX  plan-2  C12   0.020
 8XX  plan-2  C14   0.020
 8XX  plan-2  C16   0.020
 8XX  plan-2  C27   0.020
 8XX  plan-2  N17   0.020
 8XX  plan-2  N24   0.020
 8XX  plan-2  H131  0.020
 8XX  plan-2  H141  0.020
 8XX  plan-2  H271  0.020
 8XX  plan-3  C02   0.020
 8XX  plan-3  C04   0.020
 8XX  plan-3  C05   0.020
 8XX  plan-3  C12   0.020
 8XX  plan-3  N03   0.020
 8XX  plan-3  O01   0.020
 8XX  plan-4  C15   0.020
 8XX  plan-4  C21   0.020
 8XX  plan-4  C23   0.020
 8XX  plan-4  N24   0.020
 8XX  plan-4  O26   0.020
 8XX  plan-4  C25   0.020

