# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 04:26:24 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: {(2R)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}-5-[4-(trifluoromethyl)phenyl]pentyl}phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(O)C(=O)C[C@@H](CCCc1ccc(cc1)C(F)(F)F)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
 L54  L54  '{(2R)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}-5-[4-(trifluoromethyl)phenyl]pentyl}phosphonic acid'  ligand  44  25  .  2021-08-12  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L54
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
 L54  O12  O  O      0  -0.503  -3.3563   1.9691  -1.5046
 L54  C4   C  C      0   0.544  -4.0793   1.6937  -0.5552
 L54  N9   N  NT     0  -0.206  -5.1882   2.4352  -0.3094
 L54  O10  O  OH1    0  -0.549  -5.9402   2.1745   0.8055
 L54  C11  C  CH3    0  -0.515  -5.5708   3.6269  -1.0229
 L54  C3   C  CH2    0  -0.594  -3.8430   0.5124   0.3536
 L54  C2   C  CH1    0  -0.204  -2.4580  -0.1156   0.2145
 L54  C1   C  CH2    0  -0.714  -2.4524  -1.5085   0.8506
 L54  P5   P  P      0   1.167  -3.3862  -2.8398  -0.0616
 L54  O7   O  OP    -1  -0.913  -3.0910  -4.1201   0.7351
 L54  O6   O  OP    -1  -0.895  -4.8748  -2.4438  -0.0277
 L54  O8   O  O      0  -0.911  -2.7936  -2.8445  -1.4786
 L54  C13  C  CH2    0  -0.403  -1.4012   0.8037   0.8377
 L54  C14  C  CH2    0  -0.417   0.0346   0.4658   0.4563
 L54  C15  C  CH2    0  -0.506   1.0468   1.3372   1.2043
 L54  C16  C  CR6    0   0.148   2.4627   1.0308   0.8128
 L54  C17  C  CR16   0  -0.301   3.0841   1.7240  -0.2229
 L54  C19  C  CR16   0  -0.259   4.3822   1.4287  -0.6074
 L54  C18  C  CR16   0  -0.300   3.1791   0.0207   1.4514
 L54  C20  C  CR16   0  -0.258   4.4774  -0.2844   1.0767
 L54  C21  C  CR6    0  -0.218   5.0866   0.4246   0.0470
 L54  C22  C  CT     0   1.048   6.4732   0.0750  -0.3853
 L54  F25  F  F      0  -0.309   7.1234   1.1219  -0.9086
 L54  F23  F  F      0  -0.309   7.2211  -0.3846   0.6260
 L54  F24  F  F      0  -0.317   6.4764  -0.8842  -1.3267
 L54  H1   H  HOH1   0   0.474  -6.6667   1.6035   0.5198
 L54  H2   H  HCH3   0   0.241  -6.5828   3.5287  -1.4193
 L54  H3   H  HCH3   0   0.243  -5.5326   4.4997  -0.3688
 L54  H4   H  HCH3   0   0.254  -4.8889   3.7822  -1.8521
 L54  H5   H  HCH2   0   0.238  -4.0107   0.7939   1.3968
 L54  H6   H  HCH2   0   0.291  -4.5963  -0.2530   0.1305
 L54  H7   H  HCH1   0   0.197  -2.2295  -0.2355  -0.8486
 L54  H8   H  HCH2   0   0.194  -1.4172  -1.8553   0.9441
 L54  H9   H  HCH2   0   0.178  -2.8241  -1.4291   1.8811
 L54  H12  H  HCH2   0   0.215  -1.5891   1.8428   0.5501
 L54  H13  H  HCH2   0   0.197  -1.5050   0.7671   1.9293
 L54  H14  H  HCH2   0   0.222   0.2481  -0.5860   0.6654
 L54  H15  H  HCH2   0   0.220   0.1656   0.6001  -0.6222
 L54  H16  H  HCH2   0   0.240   0.8330   2.3913   1.0078
 L54  H17  H  HCH2   0   0.241   0.9215   1.1862   2.2800
 L54  H18  H  HCR6   0   0.256   2.5483   2.5151  -0.7335
 L54  H19  H  HCR6   0   0.269   4.8343   1.9941  -1.4118
 L54  H20  H  HCR6   0   0.257   2.7194  -0.5331   2.2615
 L54  H21  H  HCR6   0   0.269   5.0063  -1.0705   1.5996

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
 L54  F23  C22  single    1.339  0.020  1.339
 L54  F25  C22  single    1.339  0.020  1.339
 L54  C22  F24  single    1.344  0.020  1.344
 L54  C22  C21  single    1.494  0.020  1.494
 L54  C20  C21  aromatic  1.391  0.020  1.391
 L54  C20  C18  aromatic  1.385  0.020  1.385
 L54  C21  C19  aromatic  1.390  0.020  1.390
 L54  C18  C16  aromatic  1.393  0.020  1.393
 L54  C19  C17  aromatic  1.386  0.020  1.386
 L54  C16  C17  aromatic  1.393  0.020  1.393
 L54  C16  C15  single    1.501  0.020  1.501
 L54  C11  N9   single    1.441  0.020  1.441
 L54  O10  N9   single    1.370  0.020  1.370
 L54  C15  C14  single    1.531  0.020  1.531
 L54  N9   C4   single    1.356  0.020  1.356
 L54  C13  C14  single    1.524  0.020  1.524
 L54  C13  C2   single    1.533  0.020  1.533
 L54  O8   P5   deloc     1.536  0.020  1.536
 L54  C4   O12  double    1.225  0.020  1.225
 L54  C4   C3   single    1.509  0.020  1.509
 L54  C2   C3   single    1.527  0.020  1.527
 L54  C2   C1   single    1.531  0.020  1.531
 L54  P5   C1   single    1.865  0.020  1.865
 L54  P5   O6   deloc     1.541  0.020  1.541
 L54  P5   O7   deloc     1.537  0.020  1.537
 L54  O10  H1   single    0.850  0.020  0.980
 L54  C11  H2   single    0.970  0.020  1.090
 L54  C11  H3   single    0.970  0.020  1.090
 L54  C11  H4   single    0.970  0.020  1.090
 L54  C3   H5   single    0.970  0.020  1.090
 L54  C3   H6   single    0.970  0.020  1.090
 L54  C2   H7   single    0.970  0.020  1.090
 L54  C1   H8   single    0.970  0.020  1.090
 L54  C1   H9   single    0.970  0.020  1.090
 L54  C13  H12  single    0.970  0.020  1.090
 L54  C13  H13  single    0.970  0.020  1.090
 L54  C14  H14  single    0.970  0.020  1.090
 L54  C14  H15  single    0.970  0.020  1.090
 L54  C15  H16  single    0.970  0.020  1.090
 L54  C15  H17  single    0.970  0.020  1.090
 L54  C17  H18  single    0.930  0.020  1.080
 L54  C19  H19  single    0.930  0.020  1.080
 L54  C18  H20  single    0.930  0.020  1.080
 L54  C20  H21  single    0.930  0.020  1.080

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
 L54  C3   C4   N9   116.54  3.000
 L54  C3   C4   O12  123.39  3.000
 L54  N9   C4   O12  120.01  3.000
 L54  C11  N9   O10  114.51  3.000
 L54  O10  N9   C4   119.48  3.000
 L54  C11  N9   C4   125.42  3.000
 L54  H1   O10  N9   106.52  3.000
 L54  H4   C11  H3   108.76  3.000
 L54  H4   C11  H2   108.55  3.000
 L54  H3   C11  H2   108.79  3.000
 L54  H4   C11  N9   109.28  3.000
 L54  H3   C11  N9   110.81  3.000
 L54  H2   C11  N9   110.60  3.000
 L54  H6   C3   H5   105.56  3.000
 L54  H6   C3   C2   108.50  3.000
 L54  H5   C3   C2   109.39  3.000
 L54  H6   C3   C4   108.43  3.000
 L54  H5   C3   C4   110.43  3.000
 L54  C2   C3   C4   114.15  3.000
 L54  H7   C2   C13  108.47  3.000
 L54  H7   C2   C1   107.65  3.000
 L54  C13  C2   C1   111.97  3.000
 L54  H7   C2   C3   108.85  3.000
 L54  C1   C2   C3   109.85  3.000
 L54  C13  C2   C3   109.97  3.000
 L54  H9   C1   H8   105.22  3.000
 L54  H9   C1   P5   109.95  3.000
 L54  H8   C1   P5   106.79  3.000
 L54  H9   C1   C2   108.83  3.000
 L54  H8   C1   C2   109.07  3.000
 L54  P5   C1   C2   116.39  3.000
 L54  O8   P5   O6   113.20  3.000
 L54  O6   P5   O7   112.85  3.000
 L54  O8   P5   O7   113.68  3.000
 L54  O7   P5   C1   104.19  3.000
 L54  O6   P5   C1   106.83  3.000
 L54  O8   P5   C1   105.09  3.000
 L54  H13  C13  H12  106.08  3.000
 L54  H13  C13  C14  109.32  3.000
 L54  H12  C13  C14  107.85  3.000
 L54  H13  C13  C2   108.62  3.000
 L54  H12  C13  C2   110.13  3.000
 L54  C14  C13  C2   114.51  3.000
 L54  H15  C14  H14  106.44  3.000
 L54  H15  C14  C15  109.42  3.000
 L54  H14  C14  C15  108.97  3.000
 L54  H15  C14  C13  109.40  3.000
 L54  H14  C14  C13  110.45  3.000
 L54  C15  C14  C13  112.00  3.000
 L54  H17  C15  H16  106.71  3.000
 L54  H17  C15  C16  109.67  3.000
 L54  H16  C15  C16  109.54  3.000
 L54  H17  C15  C14  109.05  3.000
 L54  H16  C15  C14  109.37  3.000
 L54  C16  C15  C14  112.34  3.000
 L54  C18  C16  C17  118.18  3.000
 L54  C17  C16  C15  120.89  3.000
 L54  C18  C16  C15  120.90  3.000
 L54  H18  C17  C19  119.22  3.000
 L54  H18  C17  C16  119.55  3.000
 L54  C19  C17  C16  121.22  3.000
 L54  H19  C19  C21  121.04  3.000
 L54  H19  C19  C17  119.10  3.000
 L54  C21  C19  C17  119.86  3.000
 L54  H20  C18  C20  119.16  3.000
 L54  H20  C18  C16  119.67  3.000
 L54  C20  C18  C16  121.17  3.000
 L54  H21  C20  C21  120.93  3.000
 L54  H21  C20  C18  119.16  3.000
 L54  C21  C20  C18  119.90  3.000
 L54  C22  C21  C20  120.10  3.000
 L54  C20  C21  C19  119.66  3.000
 L54  C22  C21  C19  120.21  3.000
 L54  F24  C22  F23  106.42  3.000
 L54  F24  C22  F25  106.44  3.000
 L54  F23  C22  F25  106.99  3.000
 L54  F24  C22  C21  111.83  3.000
 L54  F25  C22  C21  112.39  3.000
 L54  F23  C22  C21  112.35  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
 L54  CONST_01  C21  C20  C18  C16     0.00   0.0  0
 L54  CONST_02  C21  C19  C17  C16     0.00   0.0  0
 L54  CONST_03  C20  C21  C19  C17     0.00   0.0  0
 L54  CONST_04  C20  C18  C16  C17     0.00   0.0  0
 L54  CONST_05  C18  C20  C21  C19     0.00   0.0  0
 L54  CONST_06  C18  C16  C17  C19     0.00   0.0  0
 L54  CONST_07  C20  C18  C16  C15   180.00   0.0  0
 L54  CONST_08  C19  C17  C16  C15   180.00   0.0  0
 L54  CONST_09  C22  C21  C19  C17   180.00   0.0  0
 L54  CONST_10  C22  C21  C20  C18   180.00   0.0  0
 L54  CONST_11  H21  C20  C18  C16   180.00   0.0  0
 L54  CONST_12  H19  C19  C17  C16   180.00   0.0  0
 L54  CONST_13  H20  C18  C16  C17   180.00   0.0  0
 L54  CONST_14  H18  C17  C16  C18   180.00   0.0  0
 L54  CONST_15  C11  N9   C4   O12     0.00   0.0  0
 L54  CONST_16  O10  N9   C4   O12   180.00   0.0  0
 L54  CONST_17  C3   C4   N9   O10     0.00   0.0  0
 L54  CONST_18  C3   C4   N9   C11   180.00   0.0  0
 L54  Var_01    C18  C16  C15  C14   -86.82  30.0  2
 L54  Var_02    F23  C22  C21  C19   150.40  30.0  3
 L54  Var_03    C16  C15  C14  C13  -178.79  30.0  2
 L54  Var_04    C2   C3   C4   O12    14.13  30.0  3
 L54  Var_05    C15  C14  C13  C2   -174.96  30.0  3
 L54  Var_06    O8   P5   C1   C2     55.11  30.0  3
 L54  Var_07    H2   C11  N9   C4    125.16  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
 L54  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
 L54  plan-1  C15  0.020
 L54  plan-1  C16  0.020
 L54  plan-1  C17  0.020
 L54  plan-1  C19  0.020
 L54  plan-1  C18  0.020
 L54  plan-1  C20  0.020
 L54  plan-1  C21  0.020
 L54  plan-1  C22  0.020
 L54  plan-1  H18  0.020
 L54  plan-1  H19  0.020
 L54  plan-1  H20  0.020
 L54  plan-1  H21  0.020
 L54  plan-2  O12  0.020
 L54  plan-2  C4   0.020
 L54  plan-2  N9   0.020
 L54  plan-2  O10  0.020
 L54  plan-2  C11  0.020
 L54  plan-2  C3   0.020

