# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 21:33:38 2022
#   Inital geometry file: a 83 line input string
#   Ligand name: O-{(S)-ethoxy[(1-methylethyl)amino]phosphoryl}-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCO[P@@](=O)(NC(C)C)OC[C@H](N)C(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
 SXE  SXE  O-{(S)-ethoxy[(1-methylethyl)amino]phosphoryl}-L-serine  L-peptide  34  16  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_SXE
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
 SXE  N     N  NH2    0  -0.796  25.8211  12.3477  13.7934
 SXE  CA    C  CH1    0  -0.222  26.9482  13.0033  13.1448
 SXE  C     C  C      0   0.405  28.2697  12.4593  13.7386
 SXE  O     O  O      0  -0.598  29.1169  12.0146  12.9442
 SXE  CB    C  CH2    0  -0.192  26.8794  14.5136  13.3306
 SXE  OG    O  O2     0  -0.600  27.9563  15.1489  12.6265
 SXE  O1    O  O      0  -0.705  29.7798  15.8600  14.3850
 SXE  P1    P  P      0   1.442  28.8340  16.2912  13.3316
 SXE  N1    N  NH1    0  -0.790  27.7408  17.4191  13.8228
 SXE  C1    C  CH1    0  -0.086  27.7968  18.1644  15.0783
 SXE  C3    C  CH3    0  -0.658  27.3898  19.6116  14.8387
 SXE  C2    C  CH3    0  -0.642  26.9230  17.5118  16.1428
 SXE  O2    O  O2     0  -0.577  29.6591  16.8173  12.0632
 SXE  C4    C  CH2    0  -0.186  29.0473  17.5452  10.9915
 SXE  C5    C  CH3    0  -0.679  29.4046  19.0116  11.0734
 SXE  OXT   O  OC    -1  -0.610  28.3614  12.5312  14.9820
 SXE  HN1   H  HNH2   0   0.331  25.9039  12.4792  14.7944
 SXE  HN2   H  HNH2   0   0.337  24.9500  12.7844  13.5146
 SXE  HA    H  HCH1   0   0.210  26.9091  12.7784  12.0748
 SXE  HBC1  H  HCH2   0   0.220  26.9098  14.7450  14.4001
 SXE  HBC2  H  HCH2   0   0.231  25.9386  14.9054  12.9324
 SXE  H1    H  HNH1   0   0.398  26.8762  17.5107  13.3067
 SXE  HB    H  HCH1   0   0.237  28.8332  18.1486  15.4194
 SXE  H3C1  H  HCH3   0   0.221  26.3600  19.6723  14.4789
 SXE  H3C2  H  HCH3   0   0.240  28.0357  20.0878  14.1008
 SXE  H3C3  H  HCH3   0   0.231  27.4501  20.1862  15.7633
 SXE  H2C1  H  HCH3   0   0.232  27.2351  16.4835  16.3278
 SXE  H2C2  H  HCH3   0   0.217  25.8777  17.4977  15.8265
 SXE  H2C3  H  HCH3   0   0.225  26.9802  18.0586  17.0849
 SXE  H4C1  H  HCH2   0   0.222  27.9618  17.4173  10.9895
 SXE  H4C2  H  HCH2   0   0.240  29.4205  17.1072  10.0652
 SXE  H5C1  H  HCH3   0   0.233  30.4847  19.1577  11.0592
 SXE  H5C2  H  HCH3   0   0.237  29.0056  19.4671  11.9796
 SXE  H5C3  H  HCH3   0   0.232  28.9840  19.5406  10.2178

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
 SXE  N   CA    single  1.458  0.019  1.458
 SXE  CA  C     single  1.525  0.021  1.525
 SXE  C   O     deloc   1.231  0.020  1.231
 SXE  CA  CB    single  1.530  0.020  1.530
 SXE  CB  OG    single  1.435  0.020  1.435
 SXE  OG  P1    single  1.604  0.020  1.604
 SXE  O1  P1    double  1.480  0.020  1.480
 SXE  P1  N1    single  1.646  0.020  1.646
 SXE  N1  C1    single  1.461  0.020  1.461
 SXE  C1  C3    single  1.522  0.020  1.522
 SXE  C1  C2    single  1.524  0.020  1.524
 SXE  P1  O2    single  1.602  0.020  1.602
 SXE  O2  C4    single  1.433  0.020  1.433
 SXE  C4  C5    single  1.511  0.020  1.511
 SXE  C   OXT   deloc   1.249  0.020  1.249
 SXE  N   HN1   single  0.890  0.020  1.040
 SXE  N   HN2   single  0.890  0.020  1.040
 SXE  CA  HA    single  0.970  0.020  0.970
 SXE  CB  HBC1  single  0.970  0.020  1.090
 SXE  CB  HBC2  single  0.970  0.020  1.090
 SXE  N1  H1    single  0.860  0.020  1.020
 SXE  C1  HB    single  0.970  0.020  1.090
 SXE  C3  H3C1  single  0.970  0.020  1.090
 SXE  C3  H3C2  single  0.970  0.020  1.090
 SXE  C3  H3C3  single  0.970  0.020  1.090
 SXE  C2  H2C1  single  0.970  0.020  1.090
 SXE  C2  H2C2  single  0.970  0.020  1.090
 SXE  C2  H2C3  single  0.970  0.020  1.090
 SXE  C4  H4C1  single  0.970  0.020  1.090
 SXE  C4  H4C2  single  0.970  0.020  1.090
 SXE  C5  H5C1  single  0.970  0.020  1.090
 SXE  C5  H5C2  single  0.970  0.020  1.090
 SXE  C5  H5C3  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
 SXE  HN2   N   HN1   106.63  3.000
 SXE  HN2   N   CA    110.40  3.000
 SXE  HN1   N   CA    108.56  3.000
 SXE  HA    CA  CB    109.00  3.000
 SXE  HA    CA  C     109.00  3.000
 SXE  CB    CA  C     110.10  1.900
 SXE  HA    CA  N     110.00  3.000
 SXE  CB    CA  N     110.50  1.700
 SXE  C     CA  N     111.00  2.800
 SXE  OXT   C   O     127.35  3.000
 SXE  OXT   C   CA    115.11  3.000
 SXE  O     C   CA    120.80  1.700
 SXE  HBC2  CB  HBC1  107.68  3.000
 SXE  HBC2  CB  OG    107.95  3.000
 SXE  HBC1  CB  OG    111.41  3.000
 SXE  HBC2  CB  CA    110.46  3.000
 SXE  HBC1  CB  CA    109.11  3.000
 SXE  OG    CB  CA    110.19  3.000
 SXE  P1    OG  CB    120.68  3.000
 SXE  O2    P1  N1    110.69  3.000
 SXE  O2    P1  O1    109.28  3.000
 SXE  N1    P1  O1    114.31  3.000
 SXE  O2    P1  OG     99.65  3.000
 SXE  N1    P1  OG    104.82  3.000
 SXE  O1    P1  OG    117.08  3.000
 SXE  H1    N1  C1    115.16  3.000
 SXE  H1    N1  P1    118.54  3.000
 SXE  C1    N1  P1    125.49  3.000
 SXE  HB    C1  C2    108.67  3.000
 SXE  HB    C1  C3    108.47  3.000
 SXE  C2    C1  C3    111.33  3.000
 SXE  HB    C1  N1    107.31  3.000
 SXE  C2    C1  N1    111.09  3.000
 SXE  C3    C1  N1    109.84  3.000
 SXE  H3C3  C3  H3C2  108.12  3.000
 SXE  H3C3  C3  H3C1  107.59  3.000
 SXE  H3C2  C3  H3C1  108.13  3.000
 SXE  H3C3  C3  C1    110.66  3.000
 SXE  H3C2  C3  C1    111.31  3.000
 SXE  H3C1  C3  C1    110.89  3.000
 SXE  H2C3  C2  H2C2  107.87  3.000
 SXE  H2C3  C2  H2C1  108.13  3.000
 SXE  H2C2  C2  H2C1  108.11  3.000
 SXE  H2C3  C2  C1    111.01  3.000
 SXE  H2C2  C2  C1    110.61  3.000
 SXE  H2C1  C2  C1    110.99  3.000
 SXE  C4    O2  P1    122.63  3.000
 SXE  H4C2  C4  H4C1  106.94  3.000
 SXE  H4C2  C4  C5    110.78  3.000
 SXE  H4C1  C4  C5    110.39  3.000
 SXE  H4C2  C4  O2    106.57  3.000
 SXE  H4C1  C4  O2    111.47  3.000
 SXE  C5    C4  O2    110.57  3.000
 SXE  H5C3  C5  H5C2  107.97  3.000
 SXE  H5C3  C5  H5C1  107.88  3.000
 SXE  H5C2  C5  H5C1  108.52  3.000
 SXE  H5C3  C5  C4    109.69  3.000
 SXE  H5C2  C5  C4    111.34  3.000
 SXE  H5C1  C5  C4    111.32  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
 SXE  Var_01  O1    P1  OG  CB   72.45  30.0  3
 SXE  Var_02  C1    N1  P1  OG  141.21  30.0  3
 SXE  Var_03  C3    C1  N1  P1  139.81  30.0  3
 SXE  Var_04  C5    C4  O2  P1  105.30  30.0  3
 SXE  Var_05  HBC1  CB  OG  P1  -12.56  30.0  1
 SXE  Var_06  H3C1  C3  C1  N1   62.06  30.0  3
 SXE  Var_07  H2C1  C2  C1  N1   58.66  30.0  3
 SXE  Var_08  H5C1  C5  C4  O2   57.16  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
 SXE  chir_01  CA  N   C   CB  positiv
 SXE  chir_02  P1  O1  N1  O2  both

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
 SXE  plan-1  CA   0.020
 SXE  plan-1  C    0.020
 SXE  plan-1  O    0.020
 SXE  plan-1  OXT  0.020

