# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 11:05:10 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: (2~{R})-2-(4-bromanylphenoxy)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](Oc1ccc(Br)cc1)C(N)=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
 YCS  YCS  "(2~{R})-2-(4-bromanylphenoxy)propanamide"
  ligand  23  13  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YCS
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
 YCS  C10   C   CR6   0  -0.136  -1.3673  -3.3258  -11.0121
 YCS  C01   C   CH3   0  -0.669  -7.4001  -5.4054  -10.7529
 YCS  C02   C   CH1   0  -0.102  -6.2754  -4.4316  -11.0641
 YCS  C03   C   C     0   0.482  -6.4465  -3.8710  -12.4816
 YCS  C07   C   CR6   0   0.398  -3.8924  -4.4886  -10.9980
 YCS  C08   C   CR16  0  -0.367  -3.7582  -3.1045  -11.0698
 YCS  C09   C   CR16  0  -0.212  -2.4945  -2.5264  -11.0775
 YCS  C11   C   CR16  0  -0.210  -1.4887  -4.7077  -10.9394
 YCS  C12   C   CR16  0  -0.346  -2.7463  -5.2821  -10.9325
 YCS  N05   N   NH2   0  -0.799  -7.2767  -2.8234  -12.5629
 YCS  O04   O   O     0  -0.462  -5.8905  -4.3807  -13.4375
 YCS  O06   O   O2    0  -0.467  -5.0665  -5.1481  -10.9651
 YCS  BR13  BR  BR    0  -0.057   0.3492  -2.5343  -11.0223
 YCS  H011  H   HCH3  0   0.246  -8.3620  -4.8974  -10.8010
 YCS  H012  H   HCH3  0   0.245  -7.4138  -6.2330  -11.4624
 YCS  H021  H   HCH1  0   0.263  -6.3021  -3.6156  -10.3305
 YCS  H081  H   HCR6  0   0.286  -4.6141  -2.4449  -11.1197
 YCS  H091  H   HCR6  0   0.282  -2.4111  -1.4493  -11.1345
 YCS  H111  H   HCR6  0   0.280  -0.6147  -5.3434  -10.8879
 YCS  H121  H   HCR6  0   0.273  -2.8455  -6.3586  -10.8750
 YCS  H052  H   HNH2  0   0.404  -7.5183  -2.4331  -13.4599
 YCS  H051  H   HNH2  0   0.412  -7.7169  -2.4214  -11.7522
 YCS  H013  H   HCH3  0   0.256  -7.2839  -5.8077   -9.7473

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
 YCS  O04  C03   double    1.218  0.020  1.218
 YCS  N05  C03   single    1.339  0.020  1.339
 YCS  C03  C02   single    1.534  0.020  1.534
 YCS  O06  C07   single    1.347  0.020  1.347
 YCS  O06  C02   single    1.409  0.020  1.409
 YCS  C08  C07   aromatic  1.392  0.020  1.392
 YCS  C08  C09   aromatic  1.390  0.020  1.390
 YCS  C07  C12   aromatic  1.395  0.020  1.395
 YCS  C02  C01   single    1.520  0.020  1.520
 YCS  C09  C10   aromatic  1.383  0.020  1.383
 YCS  C12  C11   aromatic  1.383  0.020  1.383
 YCS  C10  C11   aromatic  1.389  0.020  1.389
 YCS  C10  BR13  single    1.890  0.020  1.890
 YCS  C01  H013  single    0.970  0.020  1.090
 YCS  C01  H011  single    0.970  0.020  1.090
 YCS  C01  H012  single    0.970  0.020  1.090
 YCS  C02  H021  single    0.970  0.020  1.090
 YCS  C08  H081  single    0.930  0.020  1.080
 YCS  C09  H091  single    0.930  0.020  1.080
 YCS  C11  H111  single    0.930  0.020  1.080
 YCS  C12  H121  single    0.930  0.020  1.080
 YCS  N05  H052  single    0.860  0.020  1.020
 YCS  N05  H051  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
 YCS  BR13  C10  C11   119.75  3.000
 YCS  BR13  C10  C09   119.85  3.000
 YCS  C11   C10  C09   120.40  3.000
 YCS  H012  C01  H011  108.32  3.000
 YCS  H012  C01  H013  108.77  3.000
 YCS  H011  C01  H013  107.90  3.000
 YCS  H012  C01  C02   111.25  3.000
 YCS  H011  C01  C02   110.23  3.000
 YCS  H013  C01  C02   110.28  3.000
 YCS  H021  C02  O06   110.61  3.000
 YCS  H021  C02  C03   110.08  3.000
 YCS  O06   C02  C03   110.28  3.000
 YCS  H021  C02  C01   108.75  3.000
 YCS  O06   C02  C01   107.14  3.000
 YCS  C03   C02  C01   109.93  3.000
 YCS  O04   C03  N05   124.25  3.000
 YCS  N05   C03  C02   114.28  3.000
 YCS  O04   C03  C02   121.44  3.000
 YCS  O06   C07  C12   115.87  3.000
 YCS  C12   C07  C08   119.24  3.000
 YCS  O06   C07  C08   124.88  3.000
 YCS  H081  C08  C09   117.75  3.000
 YCS  H081  C08  C07   122.16  3.000
 YCS  C09   C08  C07   120.10  3.000
 YCS  H091  C09  C08   118.98  3.000
 YCS  H091  C09  C10   121.00  3.000
 YCS  C08   C09  C10   120.02  3.000
 YCS  H111  C11  C12   119.37  3.000
 YCS  H111  C11  C10   121.09  3.000
 YCS  C12   C11  C10   119.54  3.000
 YCS  H121  C12  C11   119.78  3.000
 YCS  H121  C12  C07   119.52  3.000
 YCS  C11   C12  C07   120.70  3.000
 YCS  H051  N05  H052  117.23  3.000
 YCS  H051  N05  C03   122.33  3.000
 YCS  H052  N05  C03   120.38  3.000
 YCS  C07   O06  C02   119.82  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
 YCS  CONST_01  C07   C08  C09  C10     0.00   0.0  0
 YCS  CONST_02  C07   C12  C11  C10     0.00   0.0  0
 YCS  CONST_03  C11   C12  C07  C08     0.00   0.0  0
 YCS  CONST_04  C11   C10  C09  C08     0.00   0.0  0
 YCS  CONST_05  C12   C07  C08  C09     0.00   0.0  0
 YCS  CONST_06  C12   C11  C10  C09     0.00   0.0  0
 YCS  CONST_07  BR13  C10  C09  C08   180.00   0.0  0
 YCS  CONST_08  O06   C07  C08  C09   180.00   0.0  0
 YCS  CONST_09  O06   C07  C12  C11   180.00   0.0  0
 YCS  CONST_10  BR13  C10  C11  C12   180.00   0.0  0
 YCS  CONST_11  H081  C08  C09  C10   180.00   0.0  0
 YCS  CONST_12  H121  C12  C11  C10   180.00   0.0  0
 YCS  CONST_13  H091  C09  C08  C07   180.00   0.0  0
 YCS  CONST_14  H111  C11  C12  C07   180.00   0.0  0
 YCS  CONST_15  H121  C12  C07  C08   180.00   0.0  0
 YCS  CONST_16  H111  C11  C10  C09   180.00   0.0  0
 YCS  CONST_17  H091  C09  C10  C11   180.00   0.0  0
 YCS  CONST_18  H081  C08  C07  C12   180.00   0.0  0
 YCS  CONST_19  H052  N05  C03  C02   180.00   0.0  0
 YCS  CONST_20  H051  N05  C03  C02     0.00   0.0  0
 YCS  CONST_21  H052  N05  C03  O04     0.00   0.0  0
 YCS  CONST_22  H051  N05  C03  O04   180.00   0.0  0
 YCS  Var_01    C08   C07  O06  C02     2.83  30.0  2
 YCS  Var_02    C12   C07  O06  C02  -178.22  30.0  2

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
 YCS  chir_01  C02  C03  O06  C01  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
 YCS  plan-1  C10   0.020
 YCS  plan-1  C07   0.020
 YCS  plan-1  C08   0.020
 YCS  plan-1  C09   0.020
 YCS  plan-1  C11   0.020
 YCS  plan-1  C12   0.020
 YCS  plan-1  O06   0.020
 YCS  plan-1  BR13  0.020
 YCS  plan-1  H081  0.020
 YCS  plan-1  H091  0.020
 YCS  plan-1  H111  0.020
 YCS  plan-1  H121  0.020
 YCS  plan-2  C02   0.020
 YCS  plan-2  C03   0.020
 YCS  plan-2  N05   0.020
 YCS  plan-2  O04   0.020
 YCS  plan-2  H052  0.020
 YCS  plan-2  H051  0.020

