# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 03:55:29 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  37  19  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.518   5.2134  -1.1042   0.2543
 48S  C13  C  CR6   0   0.142  -1.0375  -0.6588   0.2409
 48S  C14  C  CR16  0  -0.298  -1.8208  -0.7775   1.3834
 48S  C15  C  CR16  0  -0.308  -1.5421  -1.1713  -0.9518
 48S  C16  C  CR16  0  -0.284  -2.7894  -1.7768  -0.9972
 48S  O5   O  OH1   0  -0.747  -0.2596   3.6253  -1.3545
 48S  O7   O  O     0  -0.717  -0.6678   3.0163   1.1562
 48S  O6   O  OH1   0  -0.743  -2.1986   2.0944  -0.6186
 48S  C1   C  CH2   0  -0.759   0.4284   1.1910  -0.6562
 48S  C2   C  CH1   0  -0.332   0.3214  -0.0002   0.3051
 48S  C3   C  CH2   0  -0.549   1.4105  -1.0367   0.0120
 48S  C8   C  C     0   0.561   2.8041  -0.5575   0.3658
 48S  N9   N  NT    0  -0.209   3.8310  -1.2977  -0.1101
 48S  O10  O  OH1   0  -0.545   3.5499  -2.5280  -0.6464
 48S  O12  O  O     0  -0.489   3.0091   0.4424   1.0388
 48S  C18  C  CR6   0   0.083  -3.5743  -1.8987   0.1474
 48S  C19  C  CH3   0  -0.722  -4.9088  -2.5845   0.1052
 48S  C17  C  CR16  0  -0.281  -3.0666  -1.3872   1.3386
 48S  H1   H  HCH3  0   0.246   5.5146  -1.7784   1.0586
 48S  H2   H  HCH3  0   0.250   5.8477  -1.2827  -0.6130
 48S  H3   H  HCH3  0   0.256   5.3611  -0.0800   0.5808
 48S  H4   H  HCR6  0   0.248  -1.4534  -0.3875   2.3256
 48S  H5   H  HCR6  0   0.249  -0.9641  -1.1020  -1.8672
 48S  H6   H  HCR6  0   0.246  -3.1579  -2.1601  -1.9417
 48S  H7   H  HOH1  0   0.491  -0.7014   4.4806  -1.2618
 48S  H8   H  HOH1  0   0.486  -2.2884   1.5674  -1.4226
 48S  H9   H  HCH2  0   0.283   0.2646   0.8779  -1.6909
 48S  H10  H  HCH2  0   0.303   1.4344   1.6129  -0.6126
 48S  H11  H  HCH1  0   0.266   0.4673   0.3693   1.3224
 48S  H12  H  HCH2  0   0.294   1.2085  -1.9395   0.5968
 48S  H13  H  HCH2  0   0.266   1.3614  -1.3481  -1.0335
 48S  H14  H  HOH1  0   0.478   3.6370  -2.4312  -1.6048
 48S  H15  H  HCH3  0   0.247  -4.8253  -3.6224   0.4342
 48S  H16  H  HCH3  0   0.243  -5.6317  -2.0977   0.7597
 48S  H17  H  HCH3  0   0.242  -5.3207  -2.5972  -0.9034
 48S  H18  H  HCR6  0   0.245  -3.6535  -1.4627   2.2471
 48S  P4   P  P     0   1.375  -0.6982   2.5398  -0.2484

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    1.352  0.020  1.352
 48S  C8   O12  double    1.223  0.020  1.223
 48S  C8   C3   single    1.516  0.020  1.516
 48S  O7   P4   double    1.484  0.020  1.484
 48S  C1   P4   single    1.804  0.020  1.804
 48S  C1   C2   single    1.534  0.020  1.534
 48S  C3   C2   single    1.532  0.020  1.532
 48S  P4   O5   single    1.611  0.020  1.611
 48S  P4   O6   single    1.608  0.020  1.608
 48S  C2   C13  single    1.511  0.020  1.511
 48S  C15  C13  aromatic  1.393  0.020  1.393
 48S  C15  C16  aromatic  1.387  0.020  1.387
 48S  C13  C14  aromatic  1.390  0.020  1.390
 48S  C16  C18  aromatic  1.393  0.020  1.393
 48S  C14  C17  aromatic  1.388  0.020  1.388
 48S  C18  C17  aromatic  1.392  0.020  1.392
 48S  C18  C19  single    1.501  0.020  1.501
 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  O5   H7   single    0.850  0.020  0.980
 48S  O6   H8   single    0.850  0.020  0.980
 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   108.36  3.000
 48S  H3   C11  H1   108.88  3.000
 48S  H2   C11  H1   108.95  3.000
 48S  H3   C11  N9   109.46  3.000
 48S  H2   C11  N9   109.56  3.000
 48S  H1   C11  N9   111.57  3.000
 48S  C2   C13  C15  121.49  3.000
 48S  C15  C13  C14  117.92  3.000
 48S  C2   C13  C14  120.59  3.000
 48S  H4   C14  C17  119.37  3.000
 48S  H4   C14  C13  119.51  3.000
 48S  C17  C14  C13  121.12  3.000
 48S  H5   C15  C16  118.64  3.000
 48S  H5   C15  C13  120.41  3.000
 48S  C16  C15  C13  120.96  3.000
 48S  H6   C16  C18  119.56  3.000
 48S  H6   C16  C15  119.25  3.000
 48S  C18  C16  C15  121.19  3.000
 48S  H7   O5   P4   113.94  3.000
 48S  H8   O6   P4   115.44  3.000
 48S  H10  C1   H9   106.65  3.000
 48S  H10  C1   C2   109.83  3.000
 48S  H9   C1   C2   111.11  3.000
 48S  H10  C1   P4   106.11  3.000
 48S  H9   C1   P4   109.54  3.000
 48S  C2   C1   P4   113.28  3.000
 48S  H11  C2   C3   108.19  3.000
 48S  H11  C2   C1   108.16  3.000
 48S  C3   C2   C1   110.84  3.000
 48S  H11  C2   C13  107.88  3.000
 48S  C3   C2   C13  109.65  3.000
 48S  C1   C2   C13  111.98  3.000
 48S  H13  C3   H12  105.55  3.000
 48S  H13  C3   C8   110.79  3.000
 48S  H12  C3   C8   107.81  3.000
 48S  H13  C3   C2   110.14  3.000
 48S  H12  C3   C2   108.94  3.000
 48S  C8   C3   C2   113.28  3.000
 48S  O12  C8   N9   120.94  3.000
 48S  O12  C8   C3   122.77  3.000
 48S  N9   C8   C3   116.30  3.000
 48S  O10  N9   C8   118.23  3.000
 48S  C8   N9   C11  124.42  3.000
 48S  O10  N9   C11  114.56  3.000
 48S  H14  O10  N9   106.21  3.000
 48S  C17  C18  C19  121.08  3.000
 48S  C19  C18  C16  121.18  3.000
 48S  C17  C18  C16  117.73  3.000
 48S  H17  C19  H16  108.08  3.000
 48S  H17  C19  H15  107.27  3.000
 48S  H16  C19  H15  107.12  3.000
 48S  H17  C19  C18  111.56  3.000
 48S  H16  C19  C18  111.64  3.000
 48S  H15  C19  C18  110.96  3.000
 48S  H18  C17  C18  119.60  3.000
 48S  H18  C17  C14  119.31  3.000
 48S  C18  C17  C14  121.09  3.000
 48S  C1   P4   O6   108.87  3.000
 48S  O6   P4   O7   109.03  3.000
 48S  C1   P4   O7   116.19  3.000
 48S  O6   P4   O5   106.42  3.000
 48S  C1   P4   O5   100.29  3.000
 48S  O7   P4   O5   115.35  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
 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    97.37  30.0  2
 48S  Var_02    C2   C1   P4   O5    176.21  30.0  2
 48S  Var_03    N9   C8   C3   C2   -167.03  30.0  2
 48S  Var_04    H1   C11  N9   C8     96.02  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

