# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 00:31:23 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: O-[(R)-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
 SGR  SGR  O-[(R)-amino(methoxy)phosphoryl]-L-serine  ligand  23  12  .  2021-08-23  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SGR
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
 SGR  N     N  NH2   0  -0.788   0.4318  -0.3597   5.0132
 SGR  CA    C  CH1   0  -0.245  -0.1008   0.5438   4.0115
 SGR  C     C  C     0   0.556  -1.6004   0.6465   4.2350
 SGR  O     O  O     0  -0.443  -2.3507  -0.2855   4.0891
 SGR  CB    C  CH2   0  -0.173   0.1666   0.0846   2.5849
 SGR  OG    O  O2    0  -0.609  -0.4603   1.0167   1.7024
 SGR  N4    N  NH2   0  -0.964  -1.7485   1.8689  -0.2393
 SGR  P1    P  P     0   1.455  -0.6867   0.6608   0.1514
 SGR  O5    O  O     0  -0.711  -1.0036  -0.7610  -0.1142
 SGR  O2    O  O2    0  -0.586   0.6614   1.0399  -0.6221
 SGR  C3    C  CH3   0  -0.419   1.2983   2.3077  -0.4629
 SGR  OXT   O  OH1   0  -0.582  -1.9865   1.8499   4.6252
 SGR  H     H  HNH2  0   0.368   1.4428  -0.3451   4.9825
 SGR  HBC1  H  HCH2  0   0.238  -0.2298  -0.9226   2.4343
 SGR  HBC2  H  HCH2  0   0.255   1.2453   0.0593   2.4092
 SGR  H4N1  H  HNH2  0   0.408  -2.5860   1.9246   0.3248
 SGR  H4N2  H  HNH2  0   0.410  -1.9830   1.9309  -1.2213
 SGR  H3C1  H  HCH3  0   0.235   1.7655   2.3916   0.5189
 SGR  H3C2  H  HCH3  0   0.234   0.5960   3.1307  -0.5949
 SGR  H3C3  H  HCH3  0   0.248   2.0694   2.3747  -1.2261
 SGR  HXT   H  HOH1  0   0.481  -2.9449   1.8618   4.7734
 SGR  H1    H  HCH1  0   0.278   0.3554   1.5232   4.1653
 SGR  H2    H  HNH2  0   0.354   0.1452  -1.3123   4.8225

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
 SGR  CA   H1    single  0.970  0.020  1.090
 SGR  N    CA    single  1.450  0.020  1.450
 SGR  CA   C     single  1.520  0.020  1.520
 SGR  C    O     double  1.205  0.020  1.205
 SGR  CA   CB    single  1.522  0.020  1.522
 SGR  CB   OG    single  1.429  0.020  1.429
 SGR  OG   P1    single  1.607  0.020  1.607
 SGR  N4   P1    single  1.655  0.020  1.655
 SGR  P1   O5    double  1.481  0.020  1.481
 SGR  P1   O2    single  1.600  0.020  1.600
 SGR  O2   C3    single  1.428  0.020  1.428
 SGR  C    OXT   single  1.323  0.020  1.323
 SGR  N    H     single  0.860  0.020  1.020
 SGR  CB   HBC1  single  0.970  0.020  1.090
 SGR  CB   HBC2  single  0.970  0.020  1.090
 SGR  N4   H4N1  single  0.890  0.020  1.040
 SGR  N4   H4N2  single  0.890  0.020  1.040
 SGR  C3   H3C1  single  0.970  0.020  1.090
 SGR  C3   H3C2  single  0.970  0.020  1.090
 SGR  C3   H3C3  single  0.970  0.020  1.090
 SGR  OXT  HXT   single  0.850  0.020  0.980
 SGR  N    H2    single  0.890  0.020  1.040

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
 SGR  H2    N    H     106.90  3.000
 SGR  H2    N    CA    110.61  3.000
 SGR  H     N    CA    109.69  3.000
 SGR  H1    CA   CB    109.23  3.000
 SGR  CB    CA   C     109.36  3.000
 SGR  H1    CA   C     109.34  3.000
 SGR  CB    CA   N     113.26  3.000
 SGR  C     CA   N     107.63  3.000
 SGR  H1    CA   N     107.96  3.000
 SGR  OXT   C    O     123.88  3.000
 SGR  OXT   C    CA    113.14  3.000
 SGR  O     C    CA    122.97  3.000
 SGR  HBC2  CB   HBC1  108.33  3.000
 SGR  HBC2  CB   OG    110.42  3.000
 SGR  HBC1  CB   OG    110.91  3.000
 SGR  HBC2  CB   CA    109.32  3.000
 SGR  HBC1  CB   CA    110.09  3.000
 SGR  OG    CB   CA    107.76  3.000
 SGR  P1    OG   CB    120.89  3.000
 SGR  H4N2  N4   H4N1  110.25  3.000
 SGR  H4N2  N4   P1    115.00  3.000
 SGR  H4N1  N4   P1    116.09  3.000
 SGR  O2    P1   O5    108.73  3.000
 SGR  O2    P1   N4    104.68  3.000
 SGR  O5    P1   N4    121.42  3.000
 SGR  O2    P1   OG    107.18  3.000
 SGR  O5    P1   OG    114.57  3.000
 SGR  N4    P1   OG     99.00  3.000
 SGR  C3    O2   P1    122.17  3.000
 SGR  H3C3  C3   H3C2  109.00  3.000
 SGR  H3C3  C3   H3C1  108.87  3.000
 SGR  H3C2  C3   H3C1  109.09  3.000
 SGR  H3C3  C3   O2    107.03  3.000
 SGR  H3C2  C3   O2    111.69  3.000
 SGR  H3C1  C3   O2    111.09  3.000
 SGR  HXT   OXT  C     110.17  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
 SGR  CONST_01  HXT   OXT  C   CA  180.00   0.0  0
 SGR  Var_01    N4    P1   OG  CB  166.25  30.0  3
 SGR  Var_02    H4N1  N4   P1  OG  -55.48  30.0  3
 SGR  Var_03    HBC1  CB   OG  P1  -44.52  30.0  1
 SGR  Var_04    H3C1  C3   O2  P1   71.73  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
 SGR  chir_01  CA  N   C   CB  positiv
 SGR  chir_02  P1  N4  O5  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
 SGR  plan-1  CA   0.020
 SGR  plan-1  C    0.020
 SGR  plan-1  O    0.020
 SGR  plan-1  OXT  0.020
 SGR  plan-1  HXT  0.020

