# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 11:05:40 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: [(2R)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}-5-(4-methylphenyl)pentyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(O)C(=O)C[C@@H](CCCc1ccc(C)cc1)C[P](O)(O)=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
 L50  L50  '[(2R)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}-5-(4-methylphenyl)pentyl]phosphonic acid'  ligand  44  22  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L50
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
 L50  O8   O  O      0  -0.908   0.2487   2.2210  -0.3905
 L50  P5   P  P      0   1.207  -0.2987   1.6215  -1.6952
 L50  O7   O  OP    -1  -0.918  -0.9960   2.6632  -2.5899
 L50  O6   O  OP    -1  -0.881   0.7146   0.7667  -2.4749
 L50  C1   C  CH2    0  -0.717  -1.7069   0.4991  -1.1897
 L50  C2   C  CH1    0  -0.195  -1.4872  -0.5685  -0.1126
 L50  C3   C  CH2    0  -0.558  -2.7812  -1.3483   0.1395
 L50  C4   C  C      0   0.546  -3.8872  -0.5171   0.7499
 L50  N9   N  NT     0  -0.211  -5.1665  -0.8722   0.4634
 L50  C11  C  CH3    0  -0.516  -6.3225  -0.2970   1.1082
 L50  O10  O  OH1    0  -0.549  -5.3951  -2.1070  -0.0927
 L50  O12  O  O      0  -0.496  -3.6660   0.4407   1.4772
 L50  C13  C  CH2    0  -0.408  -0.3627  -1.5501  -0.4844
 L50  C14  C  CH2    0  -0.441   0.9959  -1.1310   0.0686
 L50  C15  C  CH2    0  -0.490   2.1659  -1.7230  -0.7124
 L50  C16  C  CR6    0   0.102   3.4808  -1.1415  -0.2784
 L50  C18  C  CR16   0  -0.302   3.7535   0.2043  -0.5306
 L50  C20  C  CR16   0  -0.293   4.9471   0.7776  -0.1188
 L50  C21  C  CR6    0   0.080   5.9097   0.0332   0.5639
 L50  C19  C  CR16   0  -0.286   5.6359  -1.3087   0.8123
 L50  C17  C  CR16   0  -0.320   4.4405  -1.8856   0.3992
 L50  C22  C  CH3    0  -0.723   7.1876   0.6623   1.0408
 L50  H3   H  HCH2   0   0.193  -2.5190   1.1572  -0.8639
 L50  H4   H  HCH2   0   0.171  -2.0766  -0.0060  -2.0927
 L50  H5   H  HCH1   0   0.201  -1.2033  -0.0672   0.8182
 L50  H6   H  HCH2   0   0.240  -3.1037  -1.8222  -0.7889
 L50  H7   H  HCH2   0   0.263  -2.5917  -2.1706   0.8415
 L50  H8   H  HCH3   0   0.253  -6.0973   0.7185   1.4172
 L50  H9   H  HCH3   0   0.246  -7.1520  -0.2641   0.4027
 L50  H10  H  HCH3   0   0.240  -6.6265  -0.8729   1.9852
 L50  H11  H  HOH1   0   0.475  -5.6402  -1.9461  -1.0140
 L50  H12  H  HCH2   0   0.194  -0.5994  -2.5597  -0.1305
 L50  H13  H  HCH2   0   0.207  -0.2995  -1.6162  -1.5742
 L50  H14  H  HCH2   0   0.263   1.0719  -0.0454   0.0323
 L50  H15  H  HCH2   0   0.191   1.0722  -1.4161   1.1245
 L50  H16  H  HCH2   0   0.212   2.1827  -2.8132  -0.6214
 L50  H17  H  HCH2   0   0.232   1.9988  -1.4830  -1.7648
 L50  H18  H  HCR6   0   0.265   3.0079   0.7931  -1.0572
 L50  H19  H  HCR6   0   0.235   5.1374   1.8235  -0.3340
 L50  H20  H  HCR6   0   0.237   6.3659  -1.9148   1.3372
 L50  H21  H  HCR6   0   0.235   4.2558  -2.9335   0.6088
 L50  H22  H  HCH3   0   0.243   7.1024   0.9915   2.0789
 L50  H23  H  HCH3   0   0.239   8.0219  -0.0378   0.9941
 L50  H24  H  HCH3   0   0.239   7.4513   1.5375   0.4473

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
 L50  C22  C21  single    1.502  0.020  1.502
 L50  C20  C21  aromatic  1.395  0.020  1.395
 L50  C20  C18  aromatic  1.387  0.020  1.387
 L50  C21  C19  aromatic  1.392  0.020  1.392
 L50  C18  C16  aromatic  1.396  0.020  1.396
 L50  C19  C17  aromatic  1.390  0.020  1.390
 L50  C16  C17  aromatic  1.391  0.020  1.391
 L50  C16  C15  single    1.502  0.020  1.502
 L50  C15  C14  single    1.526  0.020  1.526
 L50  C11  N9   single    1.443  0.020  1.443
 L50  O10  N9   single    1.373  0.020  1.373
 L50  C13  C14  single    1.526  0.020  1.526
 L50  C13  C2   single    1.538  0.020  1.538
 L50  N9   C4   single    1.358  0.020  1.358
 L50  O8   P5   deloc     1.537  0.020  1.537
 L50  C4   O12  double    1.223  0.020  1.223
 L50  C4   C3   single    1.512  0.020  1.512
 L50  C2   C3   single    1.532  0.020  1.532
 L50  C2   C1   single    1.532  0.020  1.532
 L50  C1   P5   single    1.870  0.020  1.870
 L50  P5   O6   deloc     1.538  0.020  1.538
 L50  P5   O7   deloc     1.540  0.020  1.540
 L50  C1   H3   single    0.970  0.020  1.090
 L50  C1   H4   single    0.970  0.020  1.090
 L50  C2   H5   single    0.970  0.020  1.090
 L50  C3   H6   single    0.970  0.020  1.090
 L50  C3   H7   single    0.970  0.020  1.090
 L50  C11  H8   single    0.970  0.020  1.090
 L50  C11  H9   single    0.970  0.020  1.090
 L50  C11  H10  single    0.970  0.020  1.090
 L50  O10  H11  single    0.850  0.020  0.980
 L50  C13  H12  single    0.970  0.020  1.090
 L50  C13  H13  single    0.970  0.020  1.090
 L50  C14  H14  single    0.970  0.020  1.090
 L50  C14  H15  single    0.970  0.020  1.090
 L50  C15  H16  single    0.970  0.020  1.090
 L50  C15  H17  single    0.970  0.020  1.090
 L50  C18  H18  single    0.930  0.020  1.080
 L50  C20  H19  single    0.930  0.020  1.080
 L50  C19  H20  single    0.930  0.020  1.080
 L50  C17  H21  single    0.930  0.020  1.080
 L50  C22  H22  single    0.970  0.020  1.090
 L50  C22  H23  single    0.970  0.020  1.090
 L50  C22  H24  single    0.970  0.020  1.090

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
 L50  C1   P5   O6   107.43  3.000
 L50  O6   P5   O7   112.32  3.000
 L50  C1   P5   O7   102.83  3.000
 L50  O7   P5   O8   113.00  3.000
 L50  O6   P5   O8   114.37  3.000
 L50  C1   P5   O8   105.83  3.000
 L50  H4   C1   H3   105.74  3.000
 L50  H4   C1   C2   107.80  3.000
 L50  H3   C1   C2   108.41  3.000
 L50  H4   C1   P5   107.89  3.000
 L50  H3   C1   P5   106.15  3.000
 L50  C2   C1   P5   120.01  3.000
 L50  H5   C2   C13  107.95  3.000
 L50  H5   C2   C3   108.20  3.000
 L50  C13  C2   C3   109.42  3.000
 L50  H5   C2   C1   108.41  3.000
 L50  C3   C2   C1   110.44  3.000
 L50  C13  C2   C1   112.30  3.000
 L50  H7   C3   H6   105.66  3.000
 L50  H7   C3   C4   106.25  3.000
 L50  H6   C3   C4   111.47  3.000
 L50  H7   C3   C2   109.92  3.000
 L50  H6   C3   C2   109.32  3.000
 L50  C4   C3   C2   113.86  3.000
 L50  O12  C4   N9   120.04  3.000
 L50  O12  C4   C3   122.57  3.000
 L50  N9   C4   C3   117.39  3.000
 L50  O10  N9   C11  113.95  3.000
 L50  O10  N9   C4   118.50  3.000
 L50  C11  N9   C4   123.78  3.000
 L50  H10  C11  H9   108.90  3.000
 L50  H10  C11  H8   108.81  3.000
 L50  H9   C11  H8   108.31  3.000
 L50  H10  C11  N9   111.81  3.000
 L50  H9   C11  N9   109.43  3.000
 L50  H8   C11  N9   109.51  3.000
 L50  H11  O10  N9   106.17  3.000
 L50  H13  C13  H12  106.18  3.000
 L50  H13  C13  C14  109.05  3.000
 L50  H12  C13  C14  109.17  3.000
 L50  H13  C13  C2   108.77  3.000
 L50  H12  C13  C2   110.61  3.000
 L50  C14  C13  C2   112.83  3.000
 L50  H15  C14  H14  106.65  3.000
 L50  H15  C14  C15  109.79  3.000
 L50  H14  C14  C15  108.43  3.000
 L50  H15  C14  C13  109.86  3.000
 L50  H14  C14  C13  108.90  3.000
 L50  C15  C14  C13  112.99  3.000
 L50  H17  C15  H16  107.54  3.000
 L50  H17  C15  C16  109.10  3.000
 L50  H16  C15  C16  110.38  3.000
 L50  H17  C15  C14  106.89  3.000
 L50  H16  C15  C14  110.84  3.000
 L50  C16  C15  C14  111.91  3.000
 L50  C17  C16  C18  117.97  3.000
 L50  C17  C16  C15  122.54  3.000
 L50  C18  C16  C15  119.48  3.000
 L50  H18  C18  C20  120.71  3.000
 L50  H18  C18  C16  118.43  3.000
 L50  C20  C18  C16  120.87  3.000
 L50  H19  C20  C21  119.37  3.000
 L50  H19  C20  C18  119.39  3.000
 L50  C21  C20  C18  121.24  3.000
 L50  C22  C21  C19  120.96  3.000
 L50  C19  C21  C20  117.77  3.000
 L50  C22  C21  C20  121.25  3.000
 L50  H20  C19  C17  119.39  3.000
 L50  H20  C19  C21  119.53  3.000
 L50  C17  C19  C21  121.08  3.000
 L50  H21  C17  C19  119.35  3.000
 L50  H21  C17  C16  119.58  3.000
 L50  C19  C17  C16  121.08  3.000
 L50  H24  C22  H23  107.89  3.000
 L50  H24  C22  H22  107.12  3.000
 L50  H23  C22  H22  107.09  3.000
 L50  H24  C22  C21  111.67  3.000
 L50  H23  C22  C21  111.63  3.000
 L50  H22  C22  C21  111.20  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
 L50  CONST_01  C21  C20  C18  C16     0.00   0.0  0
 L50  CONST_02  C21  C19  C17  C16     0.00   0.0  0
 L50  CONST_03  C19  C21  C20  C18     0.00   0.0  0
 L50  CONST_04  C19  C17  C16  C18     0.00   0.0  0
 L50  CONST_05  C17  C19  C21  C20     0.00   0.0  0
 L50  CONST_06  C17  C16  C18  C20     0.00   0.0  0
 L50  CONST_07  C20  C18  C16  C15   180.00   0.0  0
 L50  CONST_08  C19  C17  C16  C15   180.00   0.0  0
 L50  CONST_09  C22  C21  C20  C18   180.00   0.0  0
 L50  CONST_10  C22  C21  C19  C17   180.00   0.0  0
 L50  CONST_11  H19  C20  C18  C16   180.00   0.0  0
 L50  CONST_12  H20  C19  C17  C16   180.00   0.0  0
 L50  CONST_13  H21  C17  C16  C18   180.00   0.0  0
 L50  CONST_14  H18  C18  C20  C21   180.00   0.0  0
 L50  CONST_15  C11  N9   C4   C3    180.00   0.0  0
 L50  CONST_16  O10  N9   C4   C3      0.00   0.0  0
 L50  CONST_17  O12  C4   N9   C11     0.00   0.0  0
 L50  CONST_18  O12  C4   N9   O10   180.00   0.0  0
 L50  Var_01    C18  C16  C15  C14   -67.02  30.0  3
 L50  Var_02    H22  C22  C21  C20    94.52  30.0  2
 L50  Var_03    C16  C15  C14  C13   171.69  30.0  1
 L50  Var_04    C2   C1   P5   O8    -52.03  30.0  2
 L50  Var_05    C15  C14  C13  C2   -156.84  30.0  3
 L50  Var_06    N9   C4   C3   C2    150.69  30.0  2
 L50  Var_07    H8   C11  N9   C4     28.89  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
 L50  chir_01  C2  C13  C3  C1  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
 L50  plan-1  C15  0.020
 L50  plan-1  C16  0.020
 L50  plan-1  C18  0.020
 L50  plan-1  C20  0.020
 L50  plan-1  C21  0.020
 L50  plan-1  C19  0.020
 L50  plan-1  C17  0.020
 L50  plan-1  C22  0.020
 L50  plan-1  H18  0.020
 L50  plan-1  H19  0.020
 L50  plan-1  H20  0.020
 L50  plan-1  H21  0.020
 L50  plan-2  C3   0.020
 L50  plan-2  C4   0.020
 L50  plan-2  N9   0.020
 L50  plan-2  C11  0.020
 L50  plan-2  O10  0.020
 L50  plan-2  O12  0.020

