# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 13:07:14 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  22  12  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.799   0.6335  -0.3669   4.9312
 SGR  CA    C  CH1    0  -0.236   0.0760   0.5477   3.9432
 SGR  C     C  C      0   0.415  -1.3281   0.9835   4.4197
 SGR  O     O  O      0  -0.616  -2.1685   0.0644   4.5055
 SGR  CB    C  CH2    0  -0.171  -0.0023  -0.1036   2.5713
 SGR  OG    O  O2     0  -0.606  -0.5975   0.8313   1.6587
 SGR  N4    N  NH2    0  -0.965  -1.7404   1.6300  -0.4000
 SGR  P1    P  P      0   1.447  -0.5722   0.5573   0.0836
 SGR  O5    O  O      0  -0.717  -0.6381  -0.8712  -0.3055
 SGR  O2    O  O2     0  -0.588   0.7933   1.1767  -0.4840
 SGR  C3    C  CH3    0  -0.417   1.2127   2.5020  -0.1624
 SGR  OXT   O  OC    -1  -0.607  -1.5030   2.1853   4.6903
 SGR  H     H  HNH2   0   0.342   1.5249  -0.7293   4.6136
 SGR  HBC1  H  HCH2   0   0.221  -0.6140  -1.0073   2.6239
 SGR  HBC2  H  HCH2   0   0.226   0.9994  -0.3868   2.2319
 SGR  H4N1  H  HNH2   0   0.407  -2.6508   1.5025   0.0220
 SGR  H4N2  H  HNH2   0   0.406  -1.8352   1.7337  -1.4016
 SGR  H3C1  H  HCH3   0   0.233   1.5202   2.5758   0.8813
 SGR  H3C2  H  HCH3   0   0.232   0.4258   3.2318  -0.3537
 SGR  H3C3  H  HCH3   0   0.246   2.0656   2.7299  -0.7972
 SGR  H1    H  HCH1   0   0.212   0.7310   1.4220   3.8824
 SGR  H2    H  HNH2   0   0.334   0.0152  -1.1635   5.0270

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  1.457  0.020  1.457
 SGR  CA  C     single  1.545  0.020  1.545
 SGR  C   O     deloc   1.248  0.020  1.248
 SGR  CA  CB    single  1.521  0.020  1.521
 SGR  CB  OG    single  1.436  0.020  1.436
 SGR  OG  P1    single  1.599  0.020  1.599
 SGR  N4  P1    single  1.658  0.020  1.658
 SGR  P1  O5    double  1.482  0.020  1.482
 SGR  P1  O2    single  1.603  0.020  1.603
 SGR  O2  C3    single  1.427  0.020  1.427
 SGR  C   OXT   deloc   1.244  0.020  1.244
 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  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     106.57  3.000
 SGR  H2    N   CA    108.91  3.000
 SGR  H     N   CA    110.40  3.000
 SGR  H1    CA  CB    108.84  3.000
 SGR  CB    CA  C     110.62  3.000
 SGR  H1    CA  C     109.61  3.000
 SGR  CB    CA  N     111.26  3.000
 SGR  C     CA  N     108.39  3.000
 SGR  H1    CA  N     108.07  3.000
 SGR  OXT   C   O     126.98  3.000
 SGR  OXT   C   CA    117.85  3.000
 SGR  O     C   CA    115.16  3.000
 SGR  HBC2  CB  HBC1  108.25  3.000
 SGR  HBC2  CB  OG    110.53  3.000
 SGR  HBC1  CB  OG    109.70  3.000
 SGR  HBC2  CB  CA    110.08  3.000
 SGR  HBC1  CB  CA    109.85  3.000
 SGR  OG    CB  CA    108.42  3.000
 SGR  P1    OG  CB    120.53  3.000
 SGR  H4N2  N4  H4N1  109.98  3.000
 SGR  H4N2  N4  P1    114.91  3.000
 SGR  H4N1  N4  P1    115.52  3.000
 SGR  O2    P1  O5    108.50  3.000
 SGR  O2    P1  N4    104.29  3.000
 SGR  O5    P1  N4    121.04  3.000
 SGR  O2    P1  OG    107.22  3.000
 SGR  O5    P1  OG    115.03  3.000
 SGR  N4    P1  OG     99.51  3.000
 SGR  C3    O2  P1    121.96  3.000
 SGR  H3C3  C3  H3C2  108.87  3.000
 SGR  H3C3  C3  H3C1  108.87  3.000
 SGR  H3C2  C3  H3C1  109.04  3.000
 SGR  H3C3  C3  O2    107.07  3.000
 SGR  H3C2  C3  O2    111.72  3.000
 SGR  H3C1  C3  O2    111.19  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  Var_01  N4    P1  OG  CB  163.57  30.0  3
 SGR  Var_02  H4N1  N4  P1  OG  -57.76  30.0  3
 SGR  Var_03  HBC1  CB  OG  P1  -71.54  30.0  1
 SGR  Var_04  H3C1  C3  O2  P1   70.51  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

