# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 16:29:00 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: [(2R)-3-amino-2-(4-chlorophenyl)propyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@H](C[P](O)(O)=O)c1ccc(Cl)cc1
#
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
 2BY  2BY  '[(2R)-3-amino-2-(4-chlorophenyl)propyl]phosphonic acid'  ligand  28  15  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2BY
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
 2BY  CL   CL  CL    0  -0.136  -5.0930   0.8222   0.0980
 2BY  C3   C   CR6   0  -0.061  -3.4087   0.4104   0.0190
 2BY  C2   C   CR16  0  -0.198  -2.6834   0.2757   1.1933
 2BY  C4   C   CR16  0  -0.196  -2.8077   0.2230  -1.2139
 2BY  C5   C   CR16  0  -0.338  -1.4597  -0.1065  -1.2622
 2BY  C6   C   CR6   0   0.229  -0.7053  -0.2487  -0.1035
 2BY  C1   C   CR16  0  -0.313  -1.3384  -0.0520   1.1216
 2BY  C7   C   CH1   0  -0.380   0.7636  -0.5907  -0.1759
 2BY  C8   C   CH2   0  -0.256   1.0476  -1.9691   0.4257
 2BY  N    N   NH2   0  -0.792   0.2558  -2.9909  -0.2350
 2BY  C9   C   CH2   0  -0.756   1.5927   0.5114   0.5058
 2BY  P    P   P     0   1.376   3.3452   0.5316   0.0696
 2BY  O1   O   OH1   0  -0.744   3.7965   1.9053   0.7737
 2BY  O3   O   O     0  -0.712   4.1652  -0.6578   0.4062
 2BY  O2   O   OH1   0  -0.750   3.4182   0.7744  -1.5214
 2BY  H1   H   HCR6  0   0.277  -3.1580   0.4259   2.1536
 2BY  H2   H   HCR6  0   0.277  -3.3765   0.3324  -2.1273
 2BY  H3   H   HCR6  0   0.258  -0.9924  -0.2544  -2.2284
 2BY  H4   H   HCR6  0   0.257  -0.7843  -0.1536   2.0475
 2BY  H5   H   HCH1  0   0.260   1.0362  -0.6260  -1.2362
 2BY  H6   H   HCH2  0   0.220   2.1271  -2.1529   0.3835
 2BY  H7   H   HCH2  0   0.216   0.7811  -1.9534   1.4866
 2BY  H8   H   HNH2  0   0.338   0.5512  -3.0716  -1.2005
 2BY  H9   H   HNH2  0   0.349   0.4568  -3.8893   0.1852
 2BY  H11  H   HCH2  0   0.302   1.1919   1.4932   0.2395
 2BY  H12  H   HCH2  0   0.289   1.5182   0.4315   1.5940
 2BY  H13  H   HOH1  0   0.493   4.7510   2.0611   0.7569
 2BY  H14  H   HOH1  0   0.490   2.9580   1.5606  -1.8436

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
 2BY  N   C8   single    1.452  0.020  1.452
 2BY  C8  C7   single    1.531  0.020  1.531
 2BY  C7  C9   single    1.538  0.020  1.538
 2BY  C7  C6   single    1.510  0.020  1.510
 2BY  C9  P    single    1.806  0.020  1.806
 2BY  O3  P    double    1.483  0.020  1.483
 2BY  O1  P    single    1.608  0.020  1.608
 2BY  C6  C5   aromatic  1.390  0.020  1.390
 2BY  C6  C1   aromatic  1.393  0.020  1.393
 2BY  C5  C4   aromatic  1.389  0.020  1.389
 2BY  P   O2   single    1.611  0.020  1.611
 2BY  C1  C2   aromatic  1.386  0.020  1.386
 2BY  C4  C3   aromatic  1.384  0.020  1.384
 2BY  C2  C3   aromatic  1.387  0.020  1.387
 2BY  C3  CL   single    1.736  0.020  1.736
 2BY  C2  H1   single    0.930  0.020  1.080
 2BY  C4  H2   single    0.930  0.020  1.080
 2BY  C5  H3   single    0.930  0.020  1.080
 2BY  C1  H4   single    0.930  0.020  1.080
 2BY  C7  H5   single    0.970  0.020  1.090
 2BY  C8  H6   single    0.970  0.020  1.090
 2BY  C8  H7   single    0.970  0.020  1.090
 2BY  N   H8   single    0.890  0.020  1.040
 2BY  N   H9   single    0.890  0.020  1.040
 2BY  C9  H11  single    0.970  0.020  1.090
 2BY  C9  H12  single    0.970  0.020  1.090
 2BY  O1  H13  single    0.850  0.020  0.980
 2BY  O2  H14  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
 2BY  C4   C3  C2   120.92  3.000
 2BY  C2   C3  CL   119.48  3.000
 2BY  C4   C3  CL   119.60  3.000
 2BY  H1   C2  C1   120.29  3.000
 2BY  H1   C2  C3   120.59  3.000
 2BY  C1   C2  C3   119.12  3.000
 2BY  H2   C4  C5   120.34  3.000
 2BY  H2   C4  C3   120.67  3.000
 2BY  C5   C4  C3   118.98  3.000
 2BY  H3   C5  C6   119.69  3.000
 2BY  H3   C5  C4   118.83  3.000
 2BY  C6   C5  C4   121.48  3.000
 2BY  C7   C6  C1   121.08  3.000
 2BY  C1   C6  C5   118.17  3.000
 2BY  C7   C6  C5   120.75  3.000
 2BY  H4   C1  C6   120.38  3.000
 2BY  H4   C1  C2   118.30  3.000
 2BY  C6   C1  C2   121.32  3.000
 2BY  H5   C7  C9   108.54  3.000
 2BY  H5   C7  C8   107.77  3.000
 2BY  C9   C7  C8   111.77  3.000
 2BY  H5   C7  C6   107.21  3.000
 2BY  C9   C7  C6   109.92  3.000
 2BY  C8   C7  C6   111.45  3.000
 2BY  H7   C8  H6   106.24  3.000
 2BY  H7   C8  N    108.57  3.000
 2BY  H6   C8  N    113.69  3.000
 2BY  H7   C8  C7   108.85  3.000
 2BY  H6   C8  C7   108.59  3.000
 2BY  N    C8  C7   110.72  3.000
 2BY  H9   N   H8   105.49  3.000
 2BY  H9   N   C8   109.12  3.000
 2BY  H8   N   C8   109.31  3.000
 2BY  H12  C9  H11  106.44  3.000
 2BY  H12  C9  P    107.89  3.000
 2BY  H11  C9  P    106.67  3.000
 2BY  H12  C9  C7   110.60  3.000
 2BY  H11  C9  C7   109.74  3.000
 2BY  P    C9  C7   115.08  3.000
 2BY  O2   P   O3   108.65  3.000
 2BY  O2   P   O1   106.91  3.000
 2BY  O3   P   O1   115.49  3.000
 2BY  O2   P   C9   106.51  3.000
 2BY  O1   P   C9   100.14  3.000
 2BY  O3   P   C9   118.21  3.000
 2BY  H13  O1  P    114.01  3.000
 2BY  H14  O2  P    115.49  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
 2BY  CONST_01  C6  C5  C4  C3    0.00   0.0  0
 2BY  CONST_02  C6  C1  C2  C3    0.00   0.0  0
 2BY  CONST_03  C5  C6  C1  C2    0.00   0.0  0
 2BY  CONST_04  C5  C4  C3  C2    0.00   0.0  0
 2BY  CONST_05  C1  C6  C5  C4    0.00   0.0  0
 2BY  CONST_06  C1  C2  C3  C4    0.00   0.0  0
 2BY  CONST_07  C5  C4  C3  CL  180.00   0.0  0
 2BY  CONST_08  C1  C2  C3  CL  180.00   0.0  0
 2BY  CONST_09  C7  C6  C1  C2  180.00   0.0  0
 2BY  CONST_10  C7  C6  C5  C4  180.00   0.0  0
 2BY  CONST_11  H3  C5  C4  C3  180.00   0.0  0
 2BY  CONST_12  H4  C1  C2  C3  180.00   0.0  0
 2BY  CONST_13  H2  C4  C3  C2  180.00   0.0  0
 2BY  CONST_14  H1  C2  C3  C4  180.00   0.0  0
 2BY  Var_01    O3  P   C9  C7  -61.87  30.0  3
 2BY  Var_02    H8  N   C8  C7   65.52  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
 2BY  chir_01  C7  C8  C9  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
 2BY  plan-1  CL  0.020
 2BY  plan-1  C3  0.020
 2BY  plan-1  C2  0.020
 2BY  plan-1  C4  0.020
 2BY  plan-1  C5  0.020
 2BY  plan-1  C6  0.020
 2BY  plan-1  C1  0.020
 2BY  plan-1  C7  0.020
 2BY  plan-1  H1  0.020
 2BY  plan-1  H2  0.020
 2BY  plan-1  H3  0.020
 2BY  plan-1  H4  0.020

