# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 20:58:09 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: [(2R)-4-[hydroxy(methyl)amino]-2-(4-methylphenyl)-4-oxobutyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(O)C(=O)C[C@@H](C[P](O)(O)=O)c1ccc(C)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
 48S  48S  '[(2R)-4-[hydroxy(methyl)amino]-2-(4-methylphenyl)-4-oxobutyl]phosphonic acid'  ligand  35  19  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_48S
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
 48S  C11  C  CH3    0  -0.515   5.0574  -0.6138   0.0268
 48S  C13  C  CR6    0   0.218  -1.0629  -0.7213   0.2803
 48S  C14  C  CR16   0  -0.324  -1.9288  -0.7285   1.3684
 48S  C15  C  CR16   0  -0.290  -1.5087  -1.3076  -0.8991
 48S  C16  C  CR16   0  -0.298  -2.7737  -1.8694  -0.9902
 48S  O5   O  OP    -1  -0.922   0.3840   3.3281  -1.6549
 48S  O7   O  O      0  -0.915  -0.2527   2.9113   0.7981
 48S  O6   O  OP    -1  -0.893  -1.7411   2.0083  -1.0970
 48S  C1   C  CH2    0  -0.698   0.6979   0.8520  -0.6652
 48S  C2   C  CH1    0  -0.326   0.3339  -0.1670   0.4121
 48S  C3   C  CH2    0  -0.516   1.3213  -1.3501   0.4525
 48S  C8   C  C      0   0.520   2.7200  -0.8875   0.7852
 48S  N9   N  NT     0  -0.197   3.7042  -1.0922  -0.1211
 48S  O10  O  OH1    0  -0.545   3.3809  -1.4575  -1.4024
 48S  O12  O  O      0  -0.505   2.9691  -0.3645   1.8648
 48S  C18  C  CR6    0   0.074  -3.6462  -1.8640   0.0959
 48S  C19  C  CH3    0  -0.724  -5.0240  -2.4551  -0.0010
 48S  C17  C  CR16   0  -0.285  -3.1972  -1.2853   1.2805
 48S  H1   H  HCH3   0   0.245   5.7554  -1.3736  -0.3243
 48S  H2   H  HCH3   0   0.244   5.2199   0.3038  -0.5426
 48S  H3   H  HCH3   0   0.254   5.2607  -0.4181   1.0741
 48S  H4   H  HCR6   0   0.231  -1.6061  -0.2901   2.3063
 48S  H5   H  HCR6   0   0.228  -0.8615  -1.3294  -1.7684
 48S  H6   H  HCR6   0   0.233  -3.0919  -2.3160  -1.9260
 48S  H9   H  HCH2   0   0.185   0.6693   0.3800  -1.6543
 48S  H10  H  HCH2   0   0.195   1.7410   1.1561  -0.5172
 48S  H11  H  HCH1   0   0.224   0.3894   0.3476   1.3746
 48S  H12  H  HCH2   0   0.259   1.0310  -2.0392   1.2518
 48S  H13  H  HCH2   0   0.247   1.2705  -1.9069  -0.4812
 48S  H14  H  HOH1   0   0.475   3.5728  -2.4028  -1.4701
 48S  H15  H  HCH3   0   0.239  -5.1823  -3.2309   0.7501
 48S  H16  H  HCH3   0   0.240  -5.7938  -1.6975   0.1575
 48S  H17  H  HCH3   0   0.238  -5.1986  -2.9008  -0.9798
 48S  H18  H  HCR6   0   0.234  -3.8486  -1.2694   2.1478
 48S  P4   P  P      0   1.170  -0.3313   2.4061  -0.6513

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
 48S  O10  N9   single    1.371  0.020  1.371
 48S  C11  N9   single    1.443  0.020  1.443
 48S  N9   C8   single    1.353  0.020  1.353
 48S  C8   O12  double    1.225  0.020  1.225
 48S  C8   C3   single    1.510  0.020  1.510
 48S  O7   P4   deloc     1.537  0.020  1.537
 48S  C1   P4   single    1.864  0.020  1.864
 48S  C1   C2   single    1.527  0.020  1.527
 48S  C3   C2   single    1.542  0.020  1.542
 48S  P4   O5   deloc     1.539  0.020  1.539
 48S  P4   O6   deloc     1.531  0.020  1.531
 48S  C2   C13  single    1.509  0.020  1.509
 48S  C15  C13  aromatic  1.391  0.020  1.391
 48S  C15  C16  aromatic  1.387  0.020  1.387
 48S  C13  C14  aromatic  1.391  0.020  1.391
 48S  C16  C18  aromatic  1.393  0.020  1.393
 48S  C14  C17  aromatic  1.388  0.020  1.388
 48S  C18  C17  aromatic  1.393  0.020  1.393
 48S  C18  C19  single    1.502  0.020  1.502
 48S  C11  H1   single    0.970  0.020  1.090
 48S  C11  H2   single    0.970  0.020  1.090
 48S  C11  H3   single    0.970  0.020  1.090
 48S  C14  H4   single    0.930  0.020  1.080
 48S  C15  H5   single    0.930  0.020  1.080
 48S  C16  H6   single    0.930  0.020  1.080
 48S  C1   H9   single    0.970  0.020  1.090
 48S  C1   H10  single    0.970  0.020  1.090
 48S  C2   H11  single    0.970  0.020  1.090
 48S  C3   H12  single    0.970  0.020  1.090
 48S  C3   H13  single    0.970  0.020  1.090
 48S  O10  H14  single    0.850  0.020  0.980
 48S  C19  H15  single    0.970  0.020  1.090
 48S  C19  H16  single    0.970  0.020  1.090
 48S  C19  H17  single    0.970  0.020  1.090
 48S  C17  H18  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
 48S  H3   C11  H2   108.90  3.000
 48S  H3   C11  H1   108.47  3.000
 48S  H2   C11  H1   108.81  3.000
 48S  H3   C11  N9   109.55  3.000
 48S  H2   C11  N9   111.39  3.000
 48S  H1   C11  N9   109.66  3.000
 48S  C2   C13  C15  121.73  3.000
 48S  C15  C13  C14  117.50  3.000
 48S  C2   C13  C14  120.67  3.000
 48S  H4   C14  C17  119.26  3.000
 48S  H4   C14  C13  119.30  3.000
 48S  C17  C14  C13  121.44  3.000
 48S  H5   C15  C16  118.93  3.000
 48S  H5   C15  C13  119.81  3.000
 48S  C16  C15  C13  121.26  3.000
 48S  H6   C16  C18  119.38  3.000
 48S  H6   C16  C15  119.41  3.000
 48S  C18  C16  C15  121.22  3.000
 48S  H10  C1   H9   105.42  3.000
 48S  H10  C1   C2   108.46  3.000
 48S  H9   C1   C2   110.06  3.000
 48S  H10  C1   P4   107.04  3.000
 48S  H9   C1   P4   110.56  3.000
 48S  C2   C1   P4   114.81  3.000
 48S  H11  C2   C3   107.81  3.000
 48S  H11  C2   C1   107.16  3.000
 48S  C3   C2   C1   112.21  3.000
 48S  H11  C2   C13  107.28  3.000
 48S  C3   C2   C13  108.26  3.000
 48S  C1   C2   C13  113.85  3.000
 48S  H13  C3   H12  106.98  3.000
 48S  H13  C3   C8   112.89  3.000
 48S  H12  C3   C8   106.12  3.000
 48S  H13  C3   C2   109.89  3.000
 48S  H12  C3   C2   109.42  3.000
 48S  C8   C3   C2   111.34  3.000
 48S  O12  C8   N9   120.45  3.000
 48S  O12  C8   C3   120.87  3.000
 48S  N9   C8   C3   118.66  3.000
 48S  O10  N9   C8   119.64  3.000
 48S  C8   N9   C11  124.28  3.000
 48S  O10  N9   C11  113.91  3.000
 48S  H14  O10  N9   106.20  3.000
 48S  C17  C18  C19  120.93  3.000
 48S  C19  C18  C16  121.50  3.000
 48S  C17  C18  C16  117.57  3.000
 48S  H17  C19  H16  107.53  3.000
 48S  H17  C19  H15  107.71  3.000
 48S  H16  C19  H15  106.93  3.000
 48S  H17  C19  C18  111.46  3.000
 48S  H16  C19  C18  111.36  3.000
 48S  H15  C19  C18  111.61  3.000
 48S  H18  C17  C18  119.51  3.000
 48S  H18  C17  C14  119.49  3.000
 48S  C18  C17  C14  121.00  3.000
 48S  C1   P4   O6   106.84  3.000
 48S  O6   P4   O7   114.01  3.000
 48S  C1   P4   O7   104.65  3.000
 48S  O6   P4   O5   113.18  3.000
 48S  C1   P4   O5   103.77  3.000
 48S  O7   P4   O5   113.22  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
 48S  CONST_01  C18  C16  C15  C13     0.00   0.0  0
 48S  CONST_02  C18  C17  C14  C13     0.00   0.0  0
 48S  CONST_03  C16  C15  C13  C14     0.00   0.0  0
 48S  CONST_04  C16  C18  C17  C14     0.00   0.0  0
 48S  CONST_05  C17  C14  C13  C15     0.00   0.0  0
 48S  CONST_06  C17  C18  C16  C15     0.00   0.0  0
 48S  CONST_07  C19  C18  C17  C14   180.00   0.0  0
 48S  CONST_08  C19  C18  C16  C15   180.00   0.0  0
 48S  CONST_09  C2   C13  C15  C16   180.00   0.0  0
 48S  CONST_10  C17  C14  C13  C2    180.00   0.0  0
 48S  CONST_11  H6   C16  C15  C13   180.00   0.0  0
 48S  CONST_12  H18  C17  C14  C13   180.00   0.0  0
 48S  CONST_13  H5   C15  C13  C14   180.00   0.0  0
 48S  CONST_14  H4   C14  C13  C15   180.00   0.0  0
 48S  CONST_15  O12  C8   N9   C11     0.00   0.0  0
 48S  CONST_16  C3   C8   N9   C11   180.00   0.0  0
 48S  CONST_17  O10  N9   C8   C3      0.00   0.0  0
 48S  CONST_18  O12  C8   N9   O10   180.00   0.0  0
 48S  Var_01    H15  C19  C18  C16   123.04  30.0  2
 48S  Var_02    C2   C1   P4   O5    170.99  30.0  2
 48S  Var_03    N9   C8   C3   C2   -118.48  30.0  2
 48S  Var_04    H1   C11  N9   C8    140.15  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
 48S  chir_01  C2  C1  C3  C13  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
 48S  plan-1  C13  0.020
 48S  plan-1  C14  0.020
 48S  plan-1  C15  0.020
 48S  plan-1  C16  0.020
 48S  plan-1  C2   0.020
 48S  plan-1  C18  0.020
 48S  plan-1  C19  0.020
 48S  plan-1  C17  0.020
 48S  plan-1  H4   0.020
 48S  plan-1  H5   0.020
 48S  plan-1  H6   0.020
 48S  plan-1  H18  0.020
 48S  plan-2  C11  0.020
 48S  plan-2  C3   0.020
 48S  plan-2  C8   0.020
 48S  plan-2  N9   0.020
 48S  plan-2  O10  0.020
 48S  plan-2  O12  0.020

