# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 18:03:42 2022
#   Inital geometry file: a 90 line input string
#   Ligand name: [(1~{S})-1-[[7-bromanyl-2,3-bis(oxidanylidene)-1,4-dihydroquinoxalin-5-yl]methylamino]ethyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NCc1cc(Br)cc2NC(=O)C(=O)Nc12)[P](O)(O)=O
#
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
 J86  J86  '[(1~{S})-1-[[7-bromanyl-2,3-bis(oxidanylidene)-1,4-dihydroquinoxalin-5-yl]methylamino]ethyl]phosphonic acid'  ligand  32  21  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J86
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
 J86  P1   P   P      0   1.170  135.1484  113.4438  133.9734
 J86  C1   C   CH1    0  -0.326  136.6291  114.4724  133.4167
 J86  N1   N   NH1    0  -0.644  137.7691  113.5642  133.2921
 J86  O1   O   OP    -1  -0.894  135.4109  113.1184  135.4495
 J86  C2   C   CH2    0  -0.306  138.9124  114.0749  132.5575
 J86  N2   N   NR16   0  -0.734  139.6465  112.4810  134.8541
 J86  O2   O   OP    -1  -0.894  133.9251  114.3363  133.7336
 J86  C3   C   CR6    0   0.034  140.0640  113.0990  132.5534
 J86  N3   N   NR16   0  -0.729  141.8501  110.8957  134.8824
 J86  O3   O   O      0  -0.893  135.2263  112.2204  133.0402
 J86  C4   C   CR66   0   0.308  140.4083  112.3803  133.7042
 J86  C5   C   CR66   0   0.380  141.5316  111.5572  133.7089
 J86  C6   C   CH3    0  -0.664  136.9367  115.6209  134.3634
 J86  C7   C   CR16   0  -0.310  140.8365  112.9392  131.4120
 J86  C8   C   CR16   0  -0.320  142.3099  111.4098  132.5671
 J86  C9   C   CR6    0  -0.113  141.9430  112.1002  131.4279
 J86  C10  C   CR6    0   0.402  139.9051  111.8491  136.0136
 J86  C11  C   CR6    0   0.412  141.1614  110.9855  136.0452
 J86  BR1  BR  BR     0  -0.042  142.9707  111.8920  129.8579
 J86  H1   H   HCH1   0   0.161  136.3840  114.8980  132.4277
 J86  H12  H   HNH1   0   0.346  137.4210  112.7216  132.8434
 J86  H3   H   HCH2   0   0.252  139.2543  114.9941  133.0433
 J86  H2   H   HCH2   0   0.232  138.6681  114.3496  131.5221
 J86  H9   H   HNR6   0   0.425  138.7296  112.9555  134.6866
 J86  H11  H   HNR6   0   0.424  142.6729  110.3047  134.8872
 J86  H6   H   HCH3   0   0.204  137.7551  116.2597  134.0210
 J86  H7   H   HCH3   0   0.210  136.0586  116.2590  134.4716
 J86  H5   H   HCH3   0   0.206  137.1978  115.2423  135.3532
 J86  H8   H   HCR6   0   0.277  140.5671  113.4819  130.5149
 J86  H10  H   HCR6   0   0.298  143.1771  110.7621  132.5857
 J86  O4   O   O      0  -0.441  139.2026  111.9230  137.0010
 J86  O5   O   O      0  -0.431  141.4847  110.4060  137.0588

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
 J86  BR1  C9   single    1.888  0.020  1.888
 J86  C9   C7   aromatic  1.389  0.020  1.389
 J86  C9   C8   aromatic  1.382  0.020  1.382
 J86  C7   C3   aromatic  1.388  0.020  1.388
 J86  O3   P1   deloc     1.541  0.020  1.541
 J86  C8   C5   aromatic  1.390  0.020  1.390
 J86  C3   C2   single    1.509  0.020  1.509
 J86  C3   C4   aromatic  1.400  0.020  1.400
 J86  P1   O2   deloc     1.533  0.020  1.533
 J86  P1   C1   single    1.887  0.020  1.887
 J86  P1   O1   deloc     1.534  0.020  1.534
 J86  N1   C2   single    1.452  0.020  1.452
 J86  N1   C1   single    1.463  0.020  1.463
 J86  C1   C6   single    1.520  0.020  1.520
 J86  C5   C4   aromatic  1.393  0.020  1.393
 J86  C5   N3   single    1.384  0.020  1.384
 J86  C4   N2   single    1.383  0.020  1.383
 J86  N3   C11  single    1.354  0.020  1.354
 J86  N2   C10  single    1.346  0.020  1.346
 J86  C11  C10  single    1.525  0.020  1.525
 J86  C11  O5   double    1.212  0.020  1.212
 J86  C10  O4   double    1.214  0.020  1.214
 J86  C1   H1   single    0.970  0.020  1.090
 J86  N1   H12  single    0.890  0.020  1.040
 J86  C2   H3   single    0.970  0.020  1.090
 J86  C2   H2   single    0.970  0.020  1.090
 J86  N2   H9   single    0.860  0.020  1.020
 J86  N3   H11  single    0.860  0.020  1.020
 J86  C6   H6   single    0.970  0.020  1.090
 J86  C6   H7   single    0.970  0.020  1.090
 J86  C6   H5   single    0.970  0.020  1.090
 J86  C7   H8   single    0.930  0.020  1.080
 J86  C8   H10  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
 J86  O3   P1   O2   114.07  3.000
 J86  O2   P1   O1   114.24  3.000
 J86  O3   P1   O1   113.94  3.000
 J86  O1   P1   C1   105.38  3.000
 J86  O2   P1   C1   105.23  3.000
 J86  O3   P1   C1   102.38  3.000
 J86  H1   C1   C6   108.16  3.000
 J86  H1   C1   N1   109.63  3.000
 J86  C6   C1   N1   111.38  3.000
 J86  H1   C1   P1   107.47  3.000
 J86  C6   C1   P1   112.77  3.000
 J86  N1   C1   P1   107.35  3.000
 J86  H12  N1   C2   109.76  3.000
 J86  H12  N1   C1   106.59  3.000
 J86  C2   N1   C1   116.00  3.000
 J86  H2   C2   H3   106.13  3.000
 J86  H2   C2   C3   109.19  3.000
 J86  H3   C2   C3   107.81  3.000
 J86  H2   C2   N1   112.93  3.000
 J86  H3   C2   N1   108.47  3.000
 J86  C3   C2   N1   112.01  3.000
 J86  H9   N2   C10  121.30  3.000
 J86  H9   N2   C4   112.51  3.000
 J86  C10  N2   C4   125.20  3.000
 J86  C7   C3   C4   118.70  3.000
 J86  C4   C3   C2   121.16  3.000
 J86  C7   C3   C2   120.09  3.000
 J86  H11  N3   C11  116.59  3.000
 J86  H11  N3   C5   118.01  3.000
 J86  C11  N3   C5   125.39  3.000
 J86  C5   C4   C3   120.31  3.000
 J86  C5   C4   N2   118.98  3.000
 J86  C3   C4   N2   120.71  3.000
 J86  C8   C5   C4   120.77  3.000
 J86  C4   C5   N3   118.09  3.000
 J86  C8   C5   N3   121.13  3.000
 J86  H5   C6   H7   107.80  3.000
 J86  H5   C6   H6   107.92  3.000
 J86  H7   C6   H6   106.97  3.000
 J86  H5   C6   C1   110.56  3.000
 J86  H7   C6   C1   109.93  3.000
 J86  H6   C6   C1   113.45  3.000
 J86  H8   C7   C9   120.71  3.000
 J86  H8   C7   C3   119.04  3.000
 J86  C9   C7   C3   120.25  3.000
 J86  H10  C8   C9   121.72  3.000
 J86  H10  C8   C5   119.87  3.000
 J86  C9   C8   C5   118.41  3.000
 J86  BR1  C9   C8   119.08  3.000
 J86  C8   C9   C7   121.53  3.000
 J86  BR1  C9   C7   119.39  3.000
 J86  C11  C10  O4   119.63  3.000
 J86  O4   C10  N2   124.12  3.000
 J86  C11  C10  N2   116.24  3.000
 J86  C10  C11  O5   120.54  3.000
 J86  O5   C11  N3   123.42  3.000
 J86  C10  C11  N3   116.03  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
 J86  CONST_01  C8   C9   C7   C3     0.00   0.0  0
 J86  CONST_02  C8   C5   C4   C3     0.00   0.0  0
 J86  CONST_03  C9   C7   C3   C4     0.00   0.0  0
 J86  CONST_04  C9   C8   C5   C4     0.00   0.0  0
 J86  CONST_05  C7   C9   C8   C5     0.00   0.0  0
 J86  CONST_06  C7   C3   C4   C5     0.00   0.0  0
 J86  CONST_07  C11  C10  N2   C4     0.00   0.0  0
 J86  CONST_08  C10  C11  N3   C5     0.00   0.0  0
 J86  CONST_09  C9   C7   C3   C2   180.00   0.0  0
 J86  CONST_10  C5   C4   C3   C2   180.00   0.0  0
 J86  CONST_11  N2   C4   C3   C2     0.00   0.0  0
 J86  CONST_12  BR1  C9   C7   C3   180.00   0.0  0
 J86  CONST_13  BR1  C9   C8   C5   180.00   0.0  0
 J86  CONST_14  O4   C10  N2   C4   180.00   0.0  0
 J86  CONST_15  O5   C11  N3   C5   180.00   0.0  0
 J86  CONST_16  H10  C8   C5   N3     0.00   0.0  0
 J86  CONST_17  H8   C7   C3   C4   180.00   0.0  0
 J86  CONST_18  H11  N3   C11  C10  180.00   0.0  0
 J86  CONST_19  H9   N2   C10  C11  180.00   0.0  0
 J86  Var_01    C7   C3   C2   N1   141.33  30.0  2
 J86  Var_02    C3   C2   N1   C1   176.64  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
 J86  chir_01  C1  P1  N1  C6  positiv

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
 J86  plan-1  C2   0.020
 J86  plan-1  N2   0.020
 J86  plan-1  C3   0.020
 J86  plan-1  N3   0.020
 J86  plan-1  C4   0.020
 J86  plan-1  C5   0.020
 J86  plan-1  C7   0.020
 J86  plan-1  C8   0.020
 J86  plan-1  C9   0.020
 J86  plan-1  C10  0.020
 J86  plan-1  C11  0.020
 J86  plan-1  BR1  0.020
 J86  plan-1  H9   0.020
 J86  plan-1  H11  0.020
 J86  plan-1  H8   0.020
 J86  plan-1  H10  0.020
 J86  plan-1  O4   0.020
 J86  plan-1  O5   0.020

