# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 15 14:08:23 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: [(1S)-4-[hydroxy(methyl)amino]-1-(4-methoxyphenyl)-4-oxobutyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)[C@H](CCC(=O)N(C)O)[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
 LSX  LSX  '[(1S)-4-[hydroxy(methyl)amino]-1-(4-methoxyphenyl)-4-oxobutyl]phosphonic acid'  ligand  38  20  .  2022-07-25  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LSX
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
 LSX  C2   C  CR16  0  -0.273  -2.3288  -0.0227   1.2635
 LSX  C3   C  CR6   0   0.088  -1.3975   0.0969   0.2401
 LSX  C4   C  CR16  0  -0.297  -1.8238   0.6594  -0.9642
 LSX  C6   C  CR6   0   0.371  -4.0477   0.9769  -0.0908
 LSX  C7   C  CH1   0  -0.604   0.0167  -0.4058   0.4252
 LSX  C14  C  C     0   0.559   3.4511   1.3070  -0.2253
 LSX  C17  C  CH3   0  -0.517   5.7818   2.1372  -0.1079
 LSX  O15  O  O     0  -0.494   3.1812   2.0275  -1.1750
 LSX  N16  N  NT    0  -0.207   4.7068   1.2555   0.2752
 LSX  O18  O  OH1   0  -0.546   4.9135   0.5798   1.4499
 LSX  C12  C  CH2   0  -0.430   1.0779   0.4704  -0.2606
 LSX  P8   P  P     0   1.379   0.0098  -2.1505  -0.1097
 LSX  O11  O  OH1   0  -0.740   1.5323  -2.6543  -0.2267
 LSX  O10  O  O     0  -0.703  -0.8881  -3.0015   0.7083
 LSX  C5   C  CR16  0  -0.326  -3.1250   1.0964  -1.1313
 LSX  C1   C  CR16  0  -0.371  -3.6391   0.4135   1.1156
 LSX  O19  O  O2    0  -0.471  -5.2911   1.4311  -0.3374
 LSX  C20  C  CH3   0  -0.438  -6.2508   1.3659   0.6985
 LSX  H1   H  HCR6  0   0.254  -2.0292  -0.4556   2.2101
 LSX  H2   H  HCR6  0   0.263  -1.1301   0.7769  -1.7875
 LSX  H3   H  HCH1  0   0.300   0.2197  -0.4366   1.5015
 LSX  H4   H  HOH1  0   0.495  -1.2199  -2.0422  -1.9105
 LSX  H5   H  HCH2  0   0.267   2.8089  -0.6134   0.4673
 LSX  H6   H  HCH2  0   0.274   2.3148   0.7111   1.4833
 LSX  H7   H  HCH3  0   0.245   5.9227   2.9336   0.6254
 LSX  H8   H  HCH3  0   0.248   6.7089   1.5721  -0.1996
 LSX  H9   H  HCH3  0   0.256   5.5550   2.5836  -1.0705
 LSX  H10  H  HOH1  0   0.478   5.3157  -0.2660   1.2082
 LSX  H11  H  HCH2  0   0.245   1.1817   0.2072  -1.3147
 LSX  H12  H  HCH2  0   0.257   0.7180   1.5005  -0.2415
 LSX  H13  H  HOH1  0   0.498   1.9069  -2.9378   0.6172
 LSX  H14  H  HCR6  0   0.263  -3.4357   1.5352  -2.0713
 LSX  H15  H  HCR6  0   0.279  -4.3202   0.3063   1.9487
 LSX  H16  H  HCH3  0   0.229  -6.4482   0.3369   1.0102
 LSX  H17  H  HCH3  0   0.229  -5.9460   1.9452   1.5739
 LSX  H18  H  HCH3  0   0.260  -7.1673   1.7929   0.2995
 LSX  O9   O  OH1   0  -0.749  -0.2830  -2.1233  -1.6913
 LSX  C13  C  CH2   0  -0.573   2.4287   0.4087   0.4382

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
 LSX  O10  P8   double    1.483  0.020  1.483
 LSX  O9   P8   single    1.609  0.020  1.609
 LSX  P8   O11  single    1.608  0.020  1.608
 LSX  P8   C7   single    1.825  0.020  1.825
 LSX  C12  C7   single    1.538  0.020  1.538
 LSX  C12  C13  single    1.522  0.020  1.522
 LSX  O15  C14  double    1.222  0.020  1.222
 LSX  C7   C3   single    1.512  0.020  1.512
 LSX  C13  C14  single    1.514  0.020  1.514
 LSX  C14  N16  single    1.353  0.020  1.353
 LSX  C3   C2   aromatic  1.389  0.020  1.389
 LSX  C3   C4   aromatic  1.396  0.020  1.396
 LSX  C2   C1   aromatic  1.389  0.020  1.389
 LSX  N16  O18  single    1.371  0.020  1.371
 LSX  N16  C17  single    1.442  0.020  1.442
 LSX  C4   C5   aromatic  1.383  0.020  1.383
 LSX  C1   C6   aromatic  1.393  0.020  1.393
 LSX  C5   C6   aromatic  1.396  0.020  1.396
 LSX  C6   O19  single    1.346  0.020  1.346
 LSX  O19  C20  single    1.414  0.020  1.414
 LSX  C2   H1   single    0.930  0.020  1.080
 LSX  C4   H2   single    0.930  0.020  1.080
 LSX  C7   H3   single    0.970  0.020  1.090
 LSX  O9   H4   single    0.850  0.020  0.980
 LSX  C13  H5   single    0.970  0.020  1.090
 LSX  C13  H6   single    0.970  0.020  1.090
 LSX  C17  H7   single    0.970  0.020  1.090
 LSX  C17  H8   single    0.970  0.020  1.090
 LSX  C17  H9   single    0.970  0.020  1.090
 LSX  O18  H10  single    0.850  0.020  0.980
 LSX  C12  H11  single    0.970  0.020  1.090
 LSX  C12  H12  single    0.970  0.020  1.090
 LSX  O11  H13  single    0.850  0.020  0.980
 LSX  C5   H14  single    0.930  0.020  1.080
 LSX  C1   H15  single    0.930  0.020  1.080
 LSX  C20  H16  single    0.970  0.020  1.090
 LSX  C20  H17  single    0.970  0.020  1.090
 LSX  C20  H18  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
 LSX  H1   C2   C1   118.66  3.000
 LSX  H1   C2   C3   119.53  3.000
 LSX  C1   C2   C3   121.81  3.000
 LSX  C7   C3   C4   121.68  3.000
 LSX  C4   C3   C2   117.75  3.000
 LSX  C7   C3   C2   120.54  3.000
 LSX  H2   C4   C5   118.46  3.000
 LSX  H2   C4   C3   120.26  3.000
 LSX  C5   C4   C3   121.27  3.000
 LSX  O19  C6   C1   124.47  3.000
 LSX  O19  C6   C5   116.42  3.000
 LSX  C1   C6   C5   119.11  3.000
 LSX  H3   C7   P8   105.17  3.000
 LSX  H3   C7   C12  109.04  3.000
 LSX  P8   C7   C12  114.62  3.000
 LSX  H3   C7   C3   107.63  3.000
 LSX  C12  C7   C3   113.66  3.000
 LSX  P8   C7   C3   106.16  3.000
 LSX  N16  C14  O15  120.99  3.000
 LSX  N16  C14  C13  116.24  3.000
 LSX  O15  C14  C13  122.76  3.000
 LSX  H9   C17  H8   108.46  3.000
 LSX  H9   C17  H7   108.83  3.000
 LSX  H8   C17  H7   108.97  3.000
 LSX  H9   C17  N16  109.36  3.000
 LSX  H8   C17  N16  109.85  3.000
 LSX  H7   C17  N16  111.33  3.000
 LSX  O18  N16  C17  114.63  3.000
 LSX  C17  N16  C14  124.77  3.000
 LSX  O18  N16  C14  118.41  3.000
 LSX  H10  O18  N16  106.23  3.000
 LSX  H12  C12  H11  106.02  3.000
 LSX  H12  C12  C13  108.84  3.000
 LSX  H11  C12  C13  110.44  3.000
 LSX  H12  C12  C7   107.60  3.000
 LSX  H11  C12  C7   111.04  3.000
 LSX  C13  C12  C7   112.62  3.000
 LSX  O10  P8   O11  115.70  3.000
 LSX  O11  P8   O9    96.09  3.000
 LSX  O10  P8   O9   116.22  3.000
 LSX  O11  P8   C7   108.50  3.000
 LSX  O9   P8   C7   105.83  3.000
 LSX  O10  P8   C7   112.91  3.000
 LSX  H13  O11  P8   113.30  3.000
 LSX  H14  C5   C6   119.48  3.000
 LSX  H14  C5   C4   120.20  3.000
 LSX  C6   C5   C4   120.32  3.000
 LSX  H15  C1   C6   121.51  3.000
 LSX  H15  C1   C2   118.75  3.000
 LSX  C6   C1   C2   119.74  3.000
 LSX  C20  O19  C6   118.50  3.000
 LSX  H18  C20  H17  108.72  3.000
 LSX  H18  C20  H16  108.79  3.000
 LSX  H17  C20  H16  108.72  3.000
 LSX  H18  C20  O19  106.58  3.000
 LSX  H17  C20  O19  111.91  3.000
 LSX  H16  C20  O19  112.02  3.000
 LSX  H4   O9   P8   113.65  3.000
 LSX  H6   C13  H5   105.65  3.000
 LSX  H6   C13  C12  109.57  3.000
 LSX  H5   C13  C12  111.07  3.000
 LSX  H6   C13  C14  108.96  3.000
 LSX  H5   C13  C14  109.40  3.000
 LSX  C12  C13  C14  111.96  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
 LSX  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 LSX  CONST_02  C5   C6   C1   C2      0.00   0.0  0
 LSX  CONST_03  C6   C1   C2   C3      0.00   0.0  0
 LSX  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 LSX  CONST_05  C1   C2   C3   C4      0.00   0.0  0
 LSX  CONST_06  C1   C6   C5   C4      0.00   0.0  0
 LSX  CONST_07  O19  C6   C1   C2    180.00   0.0  0
 LSX  CONST_08  O19  C6   C5   C4    180.00   0.0  0
 LSX  CONST_09  C1   C2   C3   C7    180.00   0.0  0
 LSX  CONST_10  C5   C4   C3   C7    180.00   0.0  0
 LSX  CONST_11  H2   C4   C3   C2    180.00   0.0  0
 LSX  CONST_12  H15  C1   C2   C3    180.00   0.0  0
 LSX  CONST_13  H14  C5   C4   C3    180.00   0.0  0
 LSX  CONST_14  H1   C2   C3   C4    180.00   0.0  0
 LSX  CONST_15  O18  N16  C14  C13     0.00   0.0  0
 LSX  CONST_16  C17  N16  C14  C13   180.00   0.0  0
 LSX  CONST_17  O15  C14  N16  C17     0.00   0.0  0
 LSX  CONST_18  O18  N16  C14  O15   180.00   0.0  0
 LSX  Var_01    H16  C20  O19  C6    -62.05  30.0  3
 LSX  Var_02    C14  C13  C12  C7   -178.36  30.0  3
 LSX  Var_03    C12  C13  C14  O15     2.78  30.0  1
 LSX  Var_04    H7   C17  N16  C14   100.02  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
 LSX  chir_01  C7  P8  C12  C3  negativ

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
 LSX  plan-1  C2   0.020
 LSX  plan-1  C3   0.020
 LSX  plan-1  C4   0.020
 LSX  plan-1  C6   0.020
 LSX  plan-1  C7   0.020
 LSX  plan-1  C5   0.020
 LSX  plan-1  C1   0.020
 LSX  plan-1  O19  0.020
 LSX  plan-1  H1   0.020
 LSX  plan-1  H2   0.020
 LSX  plan-1  H14  0.020
 LSX  plan-1  H15  0.020
 LSX  plan-2  C14  0.020
 LSX  plan-2  C17  0.020
 LSX  plan-2  O15  0.020
 LSX  plan-2  N16  0.020
 LSX  plan-2  O18  0.020
 LSX  plan-2  C13  0.020

