# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 13:44:35 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: O-[(S)-amino(methoxy)phosphoryl]-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[P@](N)(=O)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
 SGX  SGX  O-[(S)-amino(methoxy)phosphoryl]-L-serine  ligand  22  12  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SGX
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
 SGX  N     N  NH2    0  -0.798  -2.8113  -1.8746   3.4266
 SGX  CA    C  CH1    0  -0.233  -2.5975  -0.4729   3.0912
 SGX  C     C  C      0   0.436  -2.8118   0.3773   4.3638
 SGX  O     O  O      0  -0.612  -3.9487   0.2988   4.8706
 SGX  CB    C  CH2    0  -0.174  -3.5432  -0.0204   1.9881
 SGX  OG    O  O2     0  -0.604  -3.2614   1.3480   1.6566
 SGX  O1    O  O      0  -0.721  -5.5853   1.7430   0.5855
 SGX  P2    P  P      0   1.436  -4.4422   2.3657   1.2963
 SGX  N3    N  NH2    0  -0.965  -3.5508   3.5779   0.5993
 SGX  O2    O  O2     0  -0.587  -4.9784   3.0068   2.6597
 SGX  C1    C  CH3    0  -0.420  -4.1257   3.7068   3.5657
 SGX  OXT   O  OC    -1  -0.614  -1.8498   1.0502   4.7799
 SGX  H     H  HNH2   0   0.341  -2.7495  -2.4496   2.5947
 SGX  HA1   H  HCH2   0   0.216  -4.5745  -0.1476   2.3268
 SGX  HB2   H  HCH2   0   0.231  -3.4059  -0.6280   1.0890
 SGX  H3N1  H  HNH2   0   0.406  -4.0572   4.4365   0.4285
 SGX  H3N2  H  HNH2   0   0.407  -3.0226   3.3182  -0.2230
 SGX  H1C1  H  HCH3   0   0.230  -3.8722   4.6931   3.1769
 SGX  H1C2  H  HCH3   0   0.237  -3.2101   3.1555   3.7759
 SGX  H1C3  H  HCH3   0   0.240  -4.6792   3.8233   4.4944
 SGX  H1    H  HCH1   0   0.214  -1.5660  -0.3593   2.7447
 SGX  H2    H  HNH2   0   0.334  -3.7523  -1.9857   3.7854

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
 SGX  CA  H1    single  0.970  0.020  1.090
 SGX  N   H2    single  0.890  0.020  1.040
 SGX  N   CA    single  1.457  0.020  1.457
 SGX  CA  C     single  1.545  0.020  1.545
 SGX  C   O     deloc   1.247  0.020  1.247
 SGX  CA  CB    single  1.522  0.020  1.522
 SGX  CB  OG    single  1.436  0.020  1.436
 SGX  OG  P2    single  1.600  0.020  1.600
 SGX  O1  P2    double  1.483  0.020  1.483
 SGX  P2  N3    single  1.658  0.020  1.658
 SGX  P2  O2    single  1.599  0.020  1.599
 SGX  O2  C1    single  1.427  0.020  1.427
 SGX  C   OXT   deloc   1.246  0.020  1.246
 SGX  N   H     single  0.860  0.020  1.020
 SGX  CB  HA1   single  0.970  0.020  1.090
 SGX  CB  HB2   single  0.970  0.020  1.090
 SGX  N3  H3N1  single  0.890  0.020  1.040
 SGX  N3  H3N2  single  0.890  0.020  1.040
 SGX  C1  H1C1  single  0.970  0.020  1.090
 SGX  C1  H1C2  single  0.970  0.020  1.090
 SGX  C1  H1C3  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
 SGX  H2    N   H     106.57  3.000
 SGX  H     N   CA    110.36  3.000
 SGX  H2    N   CA    108.86  3.000
 SGX  H1    CA  CB    108.99  3.000
 SGX  CB    CA  C     110.31  3.000
 SGX  H1    CA  C     109.54  3.000
 SGX  CB    CA  N     111.21  3.000
 SGX  C     CA  N     108.62  3.000
 SGX  H1    CA  N     108.13  3.000
 SGX  OXT   C   O     127.03  3.000
 SGX  OXT   C   CA    117.72  3.000
 SGX  O     C   CA    115.24  3.000
 SGX  HB2   CB  HA1   107.97  3.000
 SGX  HB2   CB  OG    108.36  3.000
 SGX  HA1   CB  OG    111.57  3.000
 SGX  HB2   CB  CA    110.65  3.000
 SGX  HA1   CB  CA    109.10  3.000
 SGX  OG    CB  CA    109.19  3.000
 SGX  P2    OG  CB    120.89  3.000
 SGX  O2    P2  N3    104.21  3.000
 SGX  O2    P2  O1    108.57  3.000
 SGX  N3    P2  O1    121.32  3.000
 SGX  O2    P2  OG    108.08  3.000
 SGX  N3    P2  OG     99.38  3.000
 SGX  O1    P2  OG    114.19  3.000
 SGX  H3N2  N3  H3N1  110.02  3.000
 SGX  H3N2  N3  P2    115.77  3.000
 SGX  H3N1  N3  P2    114.99  3.000
 SGX  C1    O2  P2    122.51  3.000
 SGX  H1C3  C1  H1C2  108.50  3.000
 SGX  H1C3  C1  H1C1  109.03  3.000
 SGX  H1C2  C1  H1C1  109.35  3.000
 SGX  H1C3  C1  O2    106.89  3.000
 SGX  H1C2  C1  O2    112.11  3.000
 SGX  H1C1  C1  O2    110.87  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
 SGX  Var_01  O1    P2  OG  CB   -33.73  30.0  3
 SGX  Var_02  H3N1  N3  P2  OG  -169.31  30.0  3
 SGX  Var_03  HA1   CB  OG  P2   -21.74  30.0  1
 SGX  Var_04  H1C1  C1  O2  P2    74.49  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
 SGX  chir_01  CA  N   C   CB  positiv
 SGX  chir_02  P2  O1  N3  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
 SGX  plan-1  CA   0.020
 SGX  plan-1  C    0.020
 SGX  plan-1  O    0.020
 SGX  plan-1  OXT  0.020

