# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 21:52:49 2020
#   Inital geometry file: a 44 line input string
#   Ligand name: methoxy-[(1~{R})-1-oxidanylethyl]phosphinic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[P](O)(=O)[C@H](C)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
 ALK  ALK  'methoxy-[(1~{R})-1-oxidanylethyl]phosphinic acid'  ligand  16  8  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ALK
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
 ALK  O3  O  O2     0  -0.628   1.2492  -0.6911   0.5284
 ALK  C5  C  CH3    0  -0.400   2.6179  -0.6407   0.1833
 ALK  C3  C  CH3    0  -0.696  -1.6344  -1.6814  -0.0179
 ALK  C2  C  CH1    0  -0.206  -1.3343  -0.2806   0.4901
 ALK  O5  O  OH1    0  -0.685  -2.3380   0.6436   0.1004
 ALK  O1  O  OP    -1  -0.807   0.4959   1.7705   0.4208
 ALK  O2  O  O      0  -0.812   0.2889   0.2486  -1.6748
 ALK  P1  P  P      0   1.271   0.2375   0.4137  -0.1787
 ALK  H1  H  HCH3   0   0.207   2.7814  -0.8246  -0.8821
 ALK  H2  H  HCH3   0   0.204   3.0719   0.3226   0.4348
 ALK  H3  H  HCH3   0   0.226   3.1381  -1.4159   0.7459
 ALK  H4  H  HCH3   0   0.226  -2.5878  -2.0399   0.3786
 ALK  H5  H  HCH3   0   0.224  -1.6902  -1.6991  -1.1068
 ALK  H6  H  HCH3   0   0.226  -0.8659  -2.3883   0.2932
 ALK  H7  H  HCH1   0   0.206  -1.2492  -0.3143   1.5862
 ALK  H8  H  HOH1   0   0.446  -3.1783   0.3327   0.4527

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
 ALK  C5  O3  single  1.412  0.020  1.412
 ALK  O3  P1  single  1.657  0.020  1.657
 ALK  O2  P1  deloc   1.506  0.020  1.506
 ALK  P1  O1  deloc   1.506  0.020  1.506
 ALK  P1  C2  single  1.844  0.020  1.844
 ALK  C3  C2  single  1.520  0.020  1.520
 ALK  C2  O5  single  1.419  0.020  1.419
 ALK  C5  H1  single  0.970  0.020  1.090
 ALK  C5  H2  single  0.970  0.020  1.090
 ALK  C5  H3  single  0.970  0.020  1.090
 ALK  C3  H4  single  0.970  0.020  1.090
 ALK  C3  H5  single  0.970  0.020  1.090
 ALK  C3  H6  single  0.970  0.020  1.090
 ALK  C2  H7  single  0.970  0.020  1.090
 ALK  O5  H8  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
 ALK  P1  O3  C5  117.63  3.000
 ALK  H3  C5  H2  108.02  3.000
 ALK  H3  C5  H1  108.18  3.000
 ALK  H2  C5  H1  108.06  3.000
 ALK  H3  C5  O3  108.12  3.000
 ALK  H2  C5  O3  112.17  3.000
 ALK  H1  C5  O3  112.15  3.000
 ALK  H6  C3  H5  108.10  3.000
 ALK  H6  C3  H4  107.38  3.000
 ALK  H5  C3  H4  108.20  3.000
 ALK  H6  C3  C2  111.30  3.000
 ALK  H5  C3  C2  111.03  3.000
 ALK  H4  C3  C2  110.69  3.000
 ALK  H7  C2  P1  107.88  3.000
 ALK  H7  C2  O5  110.39  3.000
 ALK  P1  C2  O5  104.96  3.000
 ALK  H7  C2  C3  108.67  3.000
 ALK  O5  C2  C3  111.64  3.000
 ALK  P1  C2  C3  113.21  3.000
 ALK  H8  O5  C2  107.85  3.000
 ALK  O2  P1  O1  119.24  3.000
 ALK  O1  P1  C2  109.95  3.000
 ALK  O2  P1  C2  110.38  3.000
 ALK  C2  P1  O3   96.58  3.000
 ALK  O1  P1  O3  109.04  3.000
 ALK  O2  P1  O3  109.27  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
 ALK  Var_01  O2  P1  O3  C5   59.46  30.0  3
 ALK  Var_02  H1  C5  O3  P1  -61.84  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
 ALK  chir_01  C2  P1  C3  O5  positiv

