# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 01:14:22 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  23  12  .  2022-07-22  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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  -0.789  -2.7388  -1.8509  3.3934
 SGX  CA    C  CH1   0  -0.249  -2.4844  -0.5020  2.9239
 SGX  C     C  C     0   0.564  -2.1206   0.3339  4.1396
 SGX  O     O  O     0  -0.446  -2.9156   0.6288  4.9975
 SGX  CB    C  CH2   0  -0.172  -3.6708   0.1229  2.2051
 SGX  OG    O  O2    0  -0.608  -3.3040   1.4587  1.8526
 SGX  O1    O  O     0  -0.713  -5.2740   1.7649  0.1932
 SGX  P2    P  P     0   1.454  -4.3820   2.4348  1.1679
 SGX  N3    N  NH2   0  -0.965  -3.3713   3.6642  0.7153
 SGX  O2    O  O2    0  -0.586  -5.2783   3.0525  2.3401
 SGX  C1    C  CH3   0  -0.423  -4.7080   3.6705  3.4945
 SGX  OXT   O  OH1   0  -0.581  -0.8422   0.6701  4.1750
 SGX  H     H  HNH2  0   0.369  -2.7964  -2.4849  2.6076
 SGX  HA1   H  HCH2  0   0.235  -4.5481   0.1191  2.8590
 SGX  HB2   H  HCH2  0   0.258  -3.9053  -0.4603  1.3120
 SGX  H3N1  H  HNH2  0   0.410  -3.8326   4.4833  0.3421
 SGX  H3N2  H  HNH2  0   0.409  -2.5904   3.4037  0.1278
 SGX  H1C1  H  HCH3  0   0.233  -3.9823   4.4371  3.2239
 SGX  H1C2  H  HCH3  0   0.235  -4.2268   2.9330  4.1366
 SGX  H1C3  H  HCH3  0   0.247  -5.5249   4.1335  4.0421
 SGX  HA    H  HOH1  0   0.482  -0.6521   1.1746  4.9814
 SGX  H1    H  HCH1  0   0.280  -1.6343  -0.5366  2.2405
 SGX  H2    H  HNH2  0   0.355  -3.6263  -1.8986  3.8789

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  1.451  0.020  1.451
 SGX  CA   C     single  1.520  0.020  1.520
 SGX  C    O     double  1.206  0.020  1.206
 SGX  CA   CB    single  1.521  0.020  1.521
 SGX  CB   OG    single  1.429  0.020  1.429
 SGX  OG   P2    single  1.607  0.020  1.607
 SGX  O1   P2    double  1.481  0.020  1.481
 SGX  P2   N3    single  1.655  0.020  1.655
 SGX  P2   O2    single  1.600  0.020  1.600
 SGX  O2   C1    single  1.428  0.020  1.428
 SGX  C    OXT   single  1.322  0.020  1.322
 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
 SGX  OXT  HA    single  0.850  0.020  0.980

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     107.05  3.000
 SGX  H     N    CA    109.96  3.000
 SGX  H2    N    CA    110.65  3.000
 SGX  H1    CA   CB    108.94  3.000
 SGX  CB    CA   C     109.80  3.000
 SGX  H1    CA   C     109.38  3.000
 SGX  CB    CA   N     113.46  3.000
 SGX  C     CA   N     107.14  3.000
 SGX  H1    CA   N     108.05  3.000
 SGX  OXT   C    O     123.78  3.000
 SGX  OXT   C    CA    113.13  3.000
 SGX  O     C    CA    123.07  3.000
 SGX  HB2   CB   HA1   108.34  3.000
 SGX  HB2   CB   OG    110.64  3.000
 SGX  HA1   CB   OG    110.88  3.000
 SGX  HB2   CB   CA    109.54  3.000
 SGX  HA1   CB   CA    109.97  3.000
 SGX  OG    CB   CA    107.47  3.000
 SGX  P2    OG   CB    120.03  3.000
 SGX  O2    P2   N3    104.82  3.000
 SGX  O2    P2   O1    108.62  3.000
 SGX  N3    P2   O1    121.59  3.000
 SGX  O2    P2   OG    107.34  3.000
 SGX  N3    P2   OG     99.09  3.000
 SGX  O1    P2   OG    114.18  3.000
 SGX  H3N2  N3   H3N1  110.27  3.000
 SGX  H3N2  N3   P2    116.05  3.000
 SGX  H3N1  N3   P2    115.09  3.000
 SGX  C1    O2   P2    122.39  3.000
 SGX  H1C3  C1   H1C2  108.86  3.000
 SGX  H1C3  C1   H1C1  109.02  3.000
 SGX  H1C2  C1   H1C1  109.17  3.000
 SGX  H1C3  C1   O2    106.94  3.000
 SGX  H1C2  C1   O2    111.08  3.000
 SGX  H1C1  C1   O2    111.69  3.000
 SGX  HA    OXT  C     110.12  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  CONST_01  HA    OXT  C   CA   180.00   0.0  0
 SGX  Var_01    O1    P2   OG  CB   -38.30  30.0  3
 SGX  Var_02    H3N1  N3   P2  OG  -173.11  30.0  3
 SGX  Var_03    HA1   CB   OG  P2   -55.40  30.0  1
 SGX  Var_04    H1C1  C1   O2  P2    52.16  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
 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
 SGX  plan-1  HA   0.020

