# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 06:20:51 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: ethyl (2R,3S)-3-(5-bromopyridin-2-yl)-2-fluoro-3-hydroxypropanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)[C@H](F)[C@@H](O)c1ccc(Br)cn1
#
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
 RK7  RK7  'ethyl (2R,3S)-3-(5-bromopyridin-2-yl)-2-fluoro-3-hydroxypropanoate'  ligand  27  16  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RK7
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
 RK7  C4   C   CH1   0  -0.069  -1.6065  -0.3909   0.4217
 RK7  C5   C   CR6   0   0.234  -0.0960  -0.2932   0.4529
 RK7  C6   C   CR16  0  -0.315   0.5603   0.8574   0.8667
 RK7  C7   C   CR16  0  -0.112   1.9435   0.8786   0.8467
 RK7  C8   C   CR6   0  -0.193   2.6097  -0.2591   0.4150
 RK7  N    N   N     0  -0.445   0.5530  -1.3726   0.0482
 RK7  C    C   CH3   0  -0.690  -6.2793   0.9421   1.3511
 RK7  C1   C   CH2   0  -0.183  -5.7387   0.3708   0.0646
 RK7  C3   C   CH1   0   0.092  -2.1444   0.4080  -0.7696
 RK7  C9   C   CR16  0  -0.032   1.8774  -1.3704   0.0256
 RK7  F    F   F     0  -0.355  -1.4823   0.0334  -1.9189
 RK7  O2   O   OH1   0  -0.664  -2.0295  -1.7192   0.3611
 RK7  BR   BR  BR    0  -0.013   4.4866  -0.3103   0.3645
 RK7  H1   H   HCH1  0   0.284  -2.0084   0.0712   1.3289
 RK7  H2   H   HCR6  0   0.287   0.0092   1.7236   1.2093
 RK7  H3   H   HCR6  0   0.301   2.4811   1.7601   1.1687
 RK7  H4   H   HCH3  0   0.239  -5.8487   0.4478   2.2217
 RK7  H5   H   HCH3  0   0.239  -6.0895   2.0128   1.4262
 RK7  H6   H   HCH3  0   0.243  -7.3580   0.7920   1.3805
 RK7  H7   H   HCH2  0   0.242  -5.9546  -0.6960  -0.0142
 RK7  H8   H   HCH2  0   0.242  -6.1742   0.8707  -0.8021
 RK7  H9   H   HCH1  0   0.272  -1.9868   1.4786  -0.6074
 RK7  H10  H   HCR6  0   0.291   2.3650  -2.2781  -0.3098
 RK7  H11  H   HOH1  0   0.454  -1.3012  -2.2305  -0.0249
 RK7  C2   C   C     0   0.534  -3.6234   0.1370  -0.9747
 RK7  O1   O   O     0  -0.431  -4.0855  -0.3918  -1.9487
 RK7  O    O   O2    0  -0.454  -4.3114   0.5689   0.0627

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
 RK7  BR  C8   single    1.878  0.020  1.878
 RK7  C8  C9   aromatic  1.387  0.020  1.387
 RK7  C8  C7   aromatic  1.387  0.020  1.387
 RK7  C9  N    aromatic  1.325  0.020  1.325
 RK7  C7  C6   aromatic  1.384  0.020  1.384
 RK7  N   C5   aromatic  1.323  0.020  1.323
 RK7  C6  C5   aromatic  1.388  0.020  1.388
 RK7  C5  C4   single    1.514  0.020  1.514
 RK7  C4  O2   single    1.395  0.020  1.395
 RK7  C4  C3   single    1.532  0.020  1.532
 RK7  C3  F    single    1.378  0.020  1.378
 RK7  C3  C2   single    1.518  0.020  1.518
 RK7  O   C2   single    1.318  0.020  1.318
 RK7  O   C1   single    1.441  0.020  1.441
 RK7  C2  O1   double    1.201  0.020  1.201
 RK7  C1  C    single    1.508  0.020  1.508
 RK7  C4  H1   single    0.970  0.020  1.090
 RK7  C6  H2   single    0.930  0.020  1.080
 RK7  C7  H3   single    0.930  0.020  1.080
 RK7  C   H4   single    0.970  0.020  1.090
 RK7  C   H5   single    0.970  0.020  1.090
 RK7  C   H6   single    0.970  0.020  1.090
 RK7  C1  H7   single    0.970  0.020  1.090
 RK7  C1  H8   single    0.970  0.020  1.090
 RK7  C3  H9   single    0.970  0.020  1.090
 RK7  C9  H10  single    0.930  0.020  1.080
 RK7  O2  H11  single    0.850  0.020  0.980

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
 RK7  H1   C4  O2  109.06  3.000
 RK7  H1   C4  C3  107.18  3.000
 RK7  O2   C4  C3  110.87  3.000
 RK7  H1   C4  C5  108.78  3.000
 RK7  C3   C4  C5  109.43  3.000
 RK7  O2   C4  C5  111.39  3.000
 RK7  N    C5  C6  122.39  3.000
 RK7  C6   C5  C4  122.11  3.000
 RK7  N    C5  C4  115.50  3.000
 RK7  H2   C6  C7  120.09  3.000
 RK7  H2   C6  C5  121.14  3.000
 RK7  C7   C6  C5  118.76  3.000
 RK7  H3   C7  C8  121.49  3.000
 RK7  H3   C7  C6  120.34  3.000
 RK7  C8   C7  C6  118.17  3.000
 RK7  BR   C8  C9  119.89  3.000
 RK7  C9   C8  C7  119.41  3.000
 RK7  BR   C8  C7  120.70  3.000
 RK7  C9   N   C5  119.63  3.000
 RK7  H6   C   H5  107.81  3.000
 RK7  H6   C   H4  107.89  3.000
 RK7  H5   C   H4  108.77  3.000
 RK7  H6   C   C1  109.01  3.000
 RK7  H5   C   C1  111.63  3.000
 RK7  H4   C   C1  111.60  3.000
 RK7  H8   C1  H7  108.15  3.000
 RK7  H8   C1  O   109.35  3.000
 RK7  H7   C1  O   109.29  3.000
 RK7  H8   C1  C   111.16  3.000
 RK7  H7   C1  C   111.16  3.000
 RK7  O    C1  C   107.70  3.000
 RK7  H9   C3  F   108.68  3.000
 RK7  H9   C3  C2  109.58  3.000
 RK7  F    C3  C2  107.87  3.000
 RK7  H9   C3  C4  110.15  3.000
 RK7  C2   C3  C4  110.74  3.000
 RK7  F    C3  C4  109.76  3.000
 RK7  H10  C9  N   116.98  3.000
 RK7  H10  C9  C8  121.38  3.000
 RK7  N    C9  C8  121.64  3.000
 RK7  H11  O2  C4  106.94  3.000
 RK7  O1   C2  C3  124.29  3.000
 RK7  O1   C2  O   125.60  3.000
 RK7  C3   C2  O   110.12  3.000
 RK7  C2   O   C1  118.24  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
 RK7  CONST_01  C8   C9  N   C5     0.00   0.0  0
 RK7  CONST_02  C8   C7  C6  C5     0.00   0.0  0
 RK7  CONST_03  C9   C8  C7  C6     0.00   0.0  0
 RK7  CONST_04  C9   N   C5  C6     0.00   0.0  0
 RK7  CONST_05  N    C9  C8  C7     0.00   0.0  0
 RK7  CONST_06  N    C5  C6  C7     0.00   0.0  0
 RK7  CONST_07  C9   N   C5  C4   180.00   0.0  0
 RK7  CONST_08  C7   C6  C5  C4   180.00   0.0  0
 RK7  CONST_09  BR   C8  C7  C6   180.00   0.0  0
 RK7  CONST_10  BR   C8  C9  N    180.00   0.0  0
 RK7  CONST_11  H10  C9  N   C5   180.00   0.0  0
 RK7  CONST_12  H3   C7  C6  C5   180.00   0.0  0
 RK7  CONST_13  H2   C6  C7  C8   180.00   0.0  0
 RK7  Var_01    C3   C2  O   C1  -178.59  30.0  3
 RK7  Var_02    H4   C   C1  O    -60.23  30.0  3
 RK7  Var_03    H7   C1  O   C2    58.84  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
 RK7  chir_01  C4  C5  O2  C3  positiv
 RK7  chir_02  C3  F   C4  C2  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
 RK7  plan-1  C4   0.020
 RK7  plan-1  C5   0.020
 RK7  plan-1  C6   0.020
 RK7  plan-1  C7   0.020
 RK7  plan-1  C8   0.020
 RK7  plan-1  N    0.020
 RK7  plan-1  C9   0.020
 RK7  plan-1  BR   0.020
 RK7  plan-1  H2   0.020
 RK7  plan-1  H3   0.020
 RK7  plan-1  H10  0.020
 RK7  plan-2  C3   0.020
 RK7  plan-2  C2   0.020
 RK7  plan-2  O1   0.020
 RK7  plan-2  O    0.020

