# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 19:34:07 2022
#   Inital geometry file: a 63 line input string
#   Ligand name: O-[(S)-ethoxy(hydroxy)phosphoryl]-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCO[P@@](O)(=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
 MIR  MIR  O-[(S)-ethoxy(hydroxy)phosphoryl]-L-serine  L-peptide  23  13  .  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_MIR
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
 MIR  N    N  NH2    0  -0.792  52.1705  48.5080  -2.0391
 MIR  CA   C  CH1    0  -0.246  53.1210  48.4000  -3.1339
 MIR  CB   C  CH2    0  -0.170  54.1702  49.5132  -3.1934
 MIR  OG   O  O2     0  -0.625  55.2016  49.3313  -2.2366
 MIR  P    P  P      0   1.346  55.3039  50.2520  -0.8775
 MIR  O1P  O  OP    -1  -0.799  54.0465  50.1305  -0.0663
 MIR  O2P  O  O      0  -0.785  55.8571  51.5999  -1.2197
 MIR  O3P  O  O2     0  -0.614  56.5172  49.4082  -0.1733
 MIR  C1   C  CH2    0  -0.158  56.2461  48.1181   0.3589
 MIR  C2   C  CH3    0  -0.681  57.5368  47.3330   0.4439
 MIR  C    C  C      0   0.413  53.8406  47.0282  -3.1497
 MIR  O    O  O      0  -0.617  54.4761  46.7705  -4.1923
 MIR  OXT  O  OC    -1  -0.600  53.7476  46.3129  -2.1336
 MIR  HN   H  HNH2   0   0.329  52.6794  48.4806  -1.1642
 MIR  HNA  H  HNH2   0   0.321  51.7531  49.4315  -2.0660
 MIR  HA   H  HCH1   0   0.207  52.5528  48.4821  -4.0691
 MIR  HB   H  HCH2   0   0.204  54.6409  49.5141  -4.1799
 MIR  HBA  H  HCH2   0   0.200  53.6772  50.4872  -3.0793
 MIR  H1   H  HCH2   0   0.200  55.7984  48.2089   1.3539
 MIR  H1A  H  HCH2   0   0.199  55.5305  47.5715  -0.2632
 MIR  H2   H  HCH3   0   0.224  57.9775  47.1857  -0.5427
 MIR  H2A  H  HCH3   0   0.224  58.2706  47.8336   1.0767
 MIR  H2B  H  HCH3   0   0.223  57.3438  46.3493   0.8733

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
 MIR  CA   N    single  1.458  0.019  1.458
 MIR  N    HN   single  0.890  0.020  1.040
 MIR  N    HNA  single  0.890  0.020  1.040
 MIR  C    CA   single  1.525  0.021  1.525
 MIR  CB   CA   single  1.530  0.020  1.530
 MIR  CA   HA   single  0.970  0.020  0.970
 MIR  CB   OG   single  1.419  0.020  1.419
 MIR  CB   HB   single  0.970  0.020  1.090
 MIR  CB   HBA  single  0.970  0.020  1.090
 MIR  OG   P    single  1.645  0.020  1.645
 MIR  O2P  P    deloc   1.497  0.020  1.497
 MIR  P    O1P  deloc   1.501  0.020  1.501
 MIR  P    O3P  single  1.637  0.020  1.637
 MIR  O3P  C1   single  1.422  0.020  1.422
 MIR  C1   C2   single  1.513  0.020  1.513
 MIR  C1   H1   single  0.970  0.020  1.090
 MIR  C1   H1A  single  0.970  0.020  1.090
 MIR  C2   H2   single  0.970  0.020  1.090
 MIR  C2   H2A  single  0.970  0.020  1.090
 MIR  C2   H2B  single  0.970  0.020  1.090
 MIR  O    C    deloc   1.231  0.020  1.231
 MIR  C    OXT  deloc   1.246  0.020  1.246

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
 MIR  HNA  N    HN   104.74  3.000
 MIR  HNA  N    CA   108.47  3.000
 MIR  HN   N    CA   108.67  3.000
 MIR  HA   CA   C    109.00  3.000
 MIR  HA   CA   CB   109.00  3.000
 MIR  C    CA   CB   110.10  1.900
 MIR  HA   CA   N    110.00  3.000
 MIR  CB   CA   N    110.50  1.700
 MIR  C    CA   N    111.00  2.800
 MIR  HBA  CB   HB   106.65  3.000
 MIR  HBA  CB   OG   111.73  3.000
 MIR  HB   CB   OG   107.20  3.000
 MIR  HBA  CB   CA   109.48  3.000
 MIR  HB   CB   CA   109.32  3.000
 MIR  OG   CB   CA   112.26  3.000
 MIR  P    OG   CB   122.06  3.000
 MIR  O3P  P    O2P  106.78  3.000
 MIR  O3P  P    O1P  110.28  3.000
 MIR  O2P  P    O1P  120.39  3.000
 MIR  O3P  P    OG    96.49  3.000
 MIR  O1P  P    OG   110.43  3.000
 MIR  O2P  P    OG   109.77  3.000
 MIR  C1   O3P  P    119.17  3.000
 MIR  H1A  C1   H1   106.89  3.000
 MIR  H1A  C1   C2   109.31  3.000
 MIR  H1   C1   C2   109.92  3.000
 MIR  H1A  C1   O3P  111.42  3.000
 MIR  H1   C1   O3P  110.05  3.000
 MIR  C2   C1   O3P  109.22  3.000
 MIR  H2B  C2   H2A  107.74  3.000
 MIR  H2B  C2   H2   107.81  3.000
 MIR  H2A  C2   H2   108.36  3.000
 MIR  H2B  C2   C1   109.83  3.000
 MIR  H2A  C2   C1   111.62  3.000
 MIR  H2   C2   C1   111.34  3.000
 MIR  OXT  C    O    126.93  3.000
 MIR  OXT  C    CA   117.73  3.000
 MIR  O    C    CA   120.80  1.700

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
 MIR  Var_01  O2P  P   OG   CB   -76.92  30.0  3
 MIR  Var_02  C2   C1  O3P  P    157.80  30.0  3
 MIR  Var_03  HB   CB  OG   P    133.91  30.0  1
 MIR  Var_04  H2   C2  C1   O3P  -62.00  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
 MIR  chir_01  CA  N  C  CB  positiv

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

