# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 19:47:20 2021
#   Inital geometry file: a 50 line input string
#   Ligand name: 5-bromanyl-1,3-dihydroindol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Brc1ccc2NC(=O)Cc2c1
#
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
 NYQ  NYQ  5-bromanyl-1,3-dihydroindol-2-one  ligand  17  11  .  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_NYQ
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
 NYQ  C1  C   CR16  0  -0.291  75.8553  15.0758  106.9919
 NYQ  C2  C   CR56  0   0.006  74.4998  15.1927  107.2071
 NYQ  C3  C   CR56  0   0.419  74.0032  16.1692  108.0711
 NYQ  C4  C   CR5   0   0.517  72.1394  15.0808  107.3188
 NYQ  C5  C   CH2   0  -0.619  73.3418  14.4244  106.6570
 NYQ  C6  C   CR16  0  -0.299  74.8384  17.0471  108.7339
 NYQ  C7  C   CR16  0  -0.239  76.2091  16.9328  108.5176
 NYQ  O   O   O     0  -0.452  70.9714  14.7896  107.1778
 NYQ  N   N   NR15  0  -0.739  72.6209  16.0781  108.1161
 NYQ  C   C   CR6   0  -0.121  76.7011  15.9606  107.6595
 NYQ  BR  BR  BR    0  -0.055  78.5672  15.8275  107.3846
 NYQ  H1  H   HCR6  0   0.279  76.2453  14.3188  106.3239
 NYQ  H2  H   HCH2  0   0.309  73.2547  14.4999  105.5703
 NYQ  H3  H   HCH2  0   0.309  73.3716  13.3603  106.9017
 NYQ  H4  H   HCR6  0   0.279  74.4527  17.8048  109.4028
 NYQ  H5  H   HCR6  0   0.282  76.8800  17.6113  109.0271
 NYQ  H6  H   HNR5  0   0.415  72.0289  16.6751  108.6740

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
 NYQ  C5  C2  single    1.495  0.020  1.495
 NYQ  C5  C4  single    1.521  0.020  1.521
 NYQ  C1  C2  aromatic  1.377  0.020  1.377
 NYQ  C1  C   aromatic  1.394  0.020  1.394
 NYQ  O   C4  double    1.212  0.020  1.212
 NYQ  BR  C   single    1.891  0.020  1.891
 NYQ  C2  C3  aromatic  1.395  0.020  1.395
 NYQ  C4  N   single    1.365  0.020  1.365
 NYQ  C   C7  aromatic  1.387  0.020  1.387
 NYQ  N   C3  single    1.386  0.020  1.386
 NYQ  C3  C6  aromatic  1.381  0.020  1.381
 NYQ  C7  C6  aromatic  1.392  0.020  1.392
 NYQ  C1  H1  single    0.930  0.020  1.080
 NYQ  C5  H2  single    0.970  0.020  1.090
 NYQ  C5  H3  single    0.970  0.020  1.090
 NYQ  C6  H4  single    0.930  0.020  1.080
 NYQ  C7  H5  single    0.930  0.020  1.080
 NYQ  N   H6  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
 NYQ  H1  C1  C   121.39  3.000
 NYQ  H1  C1  C2  120.69  3.000
 NYQ  C   C1  C2  117.92  3.000
 NYQ  C5  C2  C3  108.18  3.000
 NYQ  C3  C2  C1  120.42  3.000
 NYQ  C5  C2  C1  131.40  3.000
 NYQ  N   C3  C6  129.00  3.000
 NYQ  C6  C3  C2  121.79  3.000
 NYQ  N   C3  C2  109.21  3.000
 NYQ  N   C4  O   125.71  3.000
 NYQ  N   C4  C5  106.89  3.000
 NYQ  O   C4  C5  127.40  3.000
 NYQ  H3  C5  H2  107.00  3.000
 NYQ  H3  C5  C4  110.14  3.000
 NYQ  H2  C5  C4  109.86  3.000
 NYQ  H3  C5  C2  113.40  3.000
 NYQ  H2  C5  C2  113.10  3.000
 NYQ  C4  C5  C2  103.32  3.000
 NYQ  H4  C6  C7  120.30  3.000
 NYQ  H4  C6  C3  121.76  3.000
 NYQ  C7  C6  C3  117.94  3.000
 NYQ  H5  C7  C   120.74  3.000
 NYQ  H5  C7  C6  119.07  3.000
 NYQ  C   C7  C6  120.19  3.000
 NYQ  H6  N   C4  123.26  3.000
 NYQ  H6  N   C3  124.34  3.000
 NYQ  C4  N   C3  112.40  3.000
 NYQ  BR  C   C7  119.30  3.000
 NYQ  C7  C   C1  121.73  3.000
 NYQ  BR  C   C1  118.97  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
 NYQ  CONST_01  C6  C3  C2  C1    0.00   0.0  0
 NYQ  CONST_02  C6  C7  C   C1    0.00   0.0  0
 NYQ  CONST_03  C7  C   C1  C2    0.00   0.0  0
 NYQ  CONST_04  C7  C6  C3  C2    0.00   0.0  0
 NYQ  CONST_05  C   C1  C2  C3    0.00   0.0  0
 NYQ  CONST_06  C   C7  C6  C3    0.00   0.0  0
 NYQ  CONST_07  C5  C4  N   C3    0.00   0.0  0
 NYQ  CONST_08  BR  C   C1  C2  180.00   0.0  0
 NYQ  CONST_09  BR  C   C7  C6  180.00   0.0  0
 NYQ  CONST_10  O   C4  N   C3  180.00   0.0  0
 NYQ  CONST_11  H5  C7  C   C1  180.00   0.0  0
 NYQ  CONST_12  H4  C6  C3  C2  180.00   0.0  0
 NYQ  CONST_13  H1  C1  C2  C3  180.00   0.0  0
 NYQ  CONST_14  H6  N   C4  C5  180.00   0.0  0
 NYQ  Var_01    H2  C5  C2  C1  -61.39  30.0  1

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
 NYQ  plan-1  C1  0.020
 NYQ  plan-1  C2  0.020
 NYQ  plan-1  C3  0.020
 NYQ  plan-1  C4  0.020
 NYQ  plan-1  C5  0.020
 NYQ  plan-1  C6  0.020
 NYQ  plan-1  C7  0.020
 NYQ  plan-1  O   0.020
 NYQ  plan-1  N   0.020
 NYQ  plan-1  C   0.020
 NYQ  plan-1  BR  0.020
 NYQ  plan-1  H1  0.020
 NYQ  plan-1  H4  0.020
 NYQ  plan-1  H5  0.020
 NYQ  plan-1  H6  0.020

