# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 17:22:23 2022
#   Inital geometry file: a 63 line input string
#   Ligand name: 2,3-bis(bromomethyl)quinoxaline 1,4-dioxide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][n+]1c(CBr)c(CBr)[n+]([O-])c2ccccc12
#
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
 QDO  QDO  '2,3-bis(bromomethyl)quinoxaline 1,4-dioxide'  ligand  24  16  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QDO
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
 QDO  O3   O   O     -1  -0.497   1.1200  -2.2688   1.4048
 QDO  N3   N   NR6    1  -0.092   1.1144  -1.1953   0.7494
 QDO  C2   C   CR6    0   0.282  -0.0283  -0.5897   0.4019
 QDO  C1   C   CH2    0  -0.627  -1.2779  -1.2181   0.8803
 QDO  C11  C   CR6    0   0.282  -0.0240   0.5712  -0.3922
 QDO  C12  C   CH2    0  -0.627  -1.2693   1.2114  -0.8664
 QDO  C4   C   CR66   0   0.315   2.3172  -0.6144   0.3704
 QDO  C5   C   CR16   0  -0.308   3.5268  -1.2188   0.7346
 QDO  C6   C   CR16   0  -0.237   4.7083  -0.6298   0.3632
 QDO  C7   C   CR16   0  -0.237   4.7127   0.5651  -0.3727
 QDO  C8   C   CR16   0  -0.308   3.5355   1.1659  -0.7387
 QDO  C9   C   CR66   0   0.315   2.3216   0.5736  -0.3690
 QDO  N10  N   NR6    1  -0.092   1.1231   1.1662  -0.7433
 QDO  O10  O   O     -1  -0.497   1.1366   2.2398  -1.3983
 QDO  H2   H   HCH2   0   0.344  -1.1446  -1.6575   1.8659
 QDO  H3   H   HCH2   0   0.319  -2.1095  -0.5213   0.9181
 QDO  H5   H   HCH2   0   0.344  -1.1351   1.6503  -1.8521
 QDO  H6   H   HCH2   0   0.319  -2.1074   0.5225  -0.9018
 QDO  H8   H   HCR6   0   0.302   3.5184  -2.1370   1.3019
 QDO  H9   H   HCR6   0   0.287   5.6452  -1.0923   0.6404
 QDO  H10  H   HCR6   0   0.287   5.6529   1.0183  -0.6543
 QDO  H11  H   HCR6   0   0.302   3.5333   2.0835  -1.3069
 QDO  BR1  BR  BR     0  -0.087  -1.7746   2.6815   0.3462
 QDO  BR2  BR  BR     0  -0.087  -1.8011  -2.6837  -0.3301

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
 QDO  C1   C2   single    1.478  0.020  1.478
 QDO  O3   N3   single    1.258  0.020  1.258
 QDO  C2   N3   aromatic  1.339  0.020  1.339
 QDO  C2   C11  aromatic  1.407  0.020  1.407
 QDO  N3   C4   aromatic  1.388  0.020  1.388
 QDO  C12  C11  single    1.478  0.020  1.478
 QDO  C11  N10  aromatic  1.339  0.020  1.339
 QDO  C4   C5   aromatic  1.400  0.020  1.400
 QDO  C4   C9   aromatic  1.399  0.020  1.399
 QDO  C5   C6   aromatic  1.371  0.020  1.371
 QDO  N10  C9   aromatic  1.388  0.020  1.388
 QDO  N10  O10  single    1.258  0.020  1.258
 QDO  C9   C8   aromatic  1.400  0.020  1.400
 QDO  C6   C7   aromatic  1.403  0.020  1.403
 QDO  C8   C7   aromatic  1.371  0.020  1.371
 QDO  C1   H2   single    0.970  0.020  1.090
 QDO  C1   H3   single    0.970  0.020  1.090
 QDO  C12  H5   single    0.970  0.020  1.090
 QDO  C12  H6   single    0.970  0.020  1.090
 QDO  C5   H8   single    0.930  0.020  1.080
 QDO  C6   H9   single    0.930  0.020  1.080
 QDO  C7   H10  single    0.930  0.020  1.080
 QDO  C8   H11  single    0.930  0.020  1.080
 QDO  C12  BR1  single    1.972  0.020  1.972
 QDO  C1   BR2  single    1.971  0.020  1.971

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
 QDO  C4   N3   C2   118.63  3.000
 QDO  C4   N3   O3   119.70  3.000
 QDO  C2   N3   O3   121.67  3.000
 QDO  C11  C2   C1   122.42  3.000
 QDO  C11  C2   N3   121.15  3.000
 QDO  C1   C2   N3   116.43  3.000
 QDO  BR2  C1   H3   107.18  3.000
 QDO  BR2  C1   H2   106.78  3.000
 QDO  H3   C1   H2   108.77  3.000
 QDO  BR2  C1   C2   109.98  3.000
 QDO  H3   C1   C2   112.70  3.000
 QDO  H2   C1   C2   111.19  3.000
 QDO  N10  C11  C12  116.43  3.000
 QDO  N10  C11  C2   121.15  3.000
 QDO  C12  C11  C2   122.41  3.000
 QDO  BR1  C12  H6   107.18  3.000
 QDO  BR1  C12  H5   106.75  3.000
 QDO  H6   C12  H5   108.78  3.000
 QDO  BR1  C12  C11  109.97  3.000
 QDO  H6   C12  C11  112.71  3.000
 QDO  H5   C12  C11  111.20  3.000
 QDO  C9   C4   C5   120.08  3.000
 QDO  C9   C4   N3   120.14  3.000
 QDO  C5   C4   N3   119.78  3.000
 QDO  H8   C5   C6   120.96  3.000
 QDO  H8   C5   C4   119.81  3.000
 QDO  C6   C5   C4   119.23  3.000
 QDO  H9   C6   C7   119.74  3.000
 QDO  H9   C6   C5   119.57  3.000
 QDO  C7   C6   C5   120.69  3.000
 QDO  H10  C7   C8   119.56  3.000
 QDO  H10  C7   C6   119.76  3.000
 QDO  C8   C7   C6   120.68  3.000
 QDO  H11  C8   C9   119.79  3.000
 QDO  H11  C8   C7   120.98  3.000
 QDO  C9   C8   C7   119.23  3.000
 QDO  N10  C9   C8   119.78  3.000
 QDO  C8   C9   C4   120.08  3.000
 QDO  N10  C9   C4   120.14  3.000
 QDO  O10  N10  C9   119.70  3.000
 QDO  O10  N10  C11  121.67  3.000
 QDO  C9   N10  C11  118.63  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
 QDO  CONST_01  N10  C11  C2   N3     0.00   0.0  0
 QDO  CONST_02  C6   C5   C4   N3   180.00   0.0  0
 QDO  CONST_03  N10  C9   C4   N3     0.00   0.0  0
 QDO  CONST_04  C8   C9   C4   N3   180.00   0.0  0
 QDO  CONST_05  C5   C4   N3   C2   180.00   0.0  0
 QDO  CONST_06  C9   C4   N3   C2     0.00   0.0  0
 QDO  CONST_07  C9   N10  C11  C2     0.00   0.0  0
 QDO  CONST_08  C4   N3   C2   C11    0.00   0.0  0
 QDO  CONST_09  C4   C9   N10  C11    0.00   0.0  0
 QDO  CONST_10  C8   C9   N10  C11  180.00   0.0  0
 QDO  CONST_11  C7   C6   C5   C4     0.00   0.0  0
 QDO  CONST_12  C7   C8   C9   C4     0.00   0.0  0
 QDO  CONST_13  N10  C9   C4   C5   180.00   0.0  0
 QDO  CONST_14  C8   C9   C4   C5     0.00   0.0  0
 QDO  CONST_15  C8   C7   C6   C5     0.00   0.0  0
 QDO  CONST_16  C9   C4   C5   C6     0.00   0.0  0
 QDO  CONST_17  C9   C8   C7   C6     0.00   0.0  0
 QDO  CONST_18  N10  C9   C8   C7   180.00   0.0  0
 QDO  CONST_19  C11  C2   N3   O3   180.00   0.0  0
 QDO  CONST_20  C5   C4   N3   O3     0.00   0.0  0
 QDO  CONST_21  C9   C4   N3   O3   180.00   0.0  0
 QDO  CONST_22  C12  C11  C2   N3   180.00   0.0  0
 QDO  CONST_23  O10  N10  C11  C2   180.00   0.0  0
 QDO  CONST_24  C4   N3   C2   C1   180.00   0.0  0
 QDO  CONST_25  N10  C11  C2   C1   180.00   0.0  0
 QDO  CONST_26  C9   N10  C11  C12  180.00   0.0  0
 QDO  CONST_27  O10  N10  C9   C4   180.00   0.0  0
 QDO  CONST_28  O10  N10  C9   C8     0.00   0.0  0
 QDO  CONST_29  H8   C5   C4   N3     0.00   0.0  0
 QDO  CONST_30  H9   C6   C5   C4   180.00   0.0  0
 QDO  CONST_31  H11  C8   C9   C4   180.00   0.0  0
 QDO  CONST_32  H10  C7   C6   C5   180.00   0.0  0
 QDO  Var_01    BR2  C1   C2   N3   -83.01  30.0  2
 QDO  Var_02    BR1  C12  C11  C2    96.10  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
 QDO  plan-1  O3   0.020
 QDO  plan-1  N3   0.020
 QDO  plan-1  C2   0.020
 QDO  plan-1  C1   0.020
 QDO  plan-1  C11  0.020
 QDO  plan-1  C12  0.020
 QDO  plan-1  C4   0.020
 QDO  plan-1  C5   0.020
 QDO  plan-1  C6   0.020
 QDO  plan-1  C7   0.020
 QDO  plan-1  C8   0.020
 QDO  plan-1  C9   0.020
 QDO  plan-1  N10  0.020
 QDO  plan-1  O10  0.020
 QDO  plan-1  H8   0.020
 QDO  plan-1  H9   0.020
 QDO  plan-1  H10  0.020
 QDO  plan-1  H11  0.020

