# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 04:49:20 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (2R)-3-[[(1R)-1-azanylethyl]-hydroxy-phosphoryl]-2-methyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)[P](O)(=O)C[C@H](C)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
 LY0  LY0  '(2R)-3-[[(1R)-1-azanylethyl]-hydroxy-phosphoryl]-2-methyl-propanoic acid'  ligand  24  12  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LY0
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
 LY0  P     P  P      0   1.173  -1.1826  -0.5392  -0.1530
 LY0  C1    C  CH3    0  -0.681  -2.4911   1.7216   0.9153
 LY0  N1    N  NH2    0  -0.799  -3.7792   0.0460  -0.4158
 LY0  C2    C  CH1    0  -0.315  -2.5110   0.7562  -0.2686
 LY0  C4    C  CH2    0  -0.682   0.3323   0.4511   0.1784
 LY0  C5    C  CH1    0  -0.367   1.6361  -0.3194  -0.0124
 LY0  C6    C  C      0   0.421   2.8931   0.5838  -0.0151
 LY0  C7    C  CH3    0  -0.656   1.8004  -1.4269   1.0301
 LY0  O31   O  O      0  -0.830  -1.0239  -1.2117  -1.5055
 LY0  O32   O  OP    -1  -0.831  -1.5395  -1.4085   1.0446
 LY0  O61   O  OC    -1  -0.630   3.9818  -0.0015  -0.2048
 LY0  O62   O  O      0  -0.607   2.7484   1.8092   0.1665
 LY0  H1    H  HCH3   0   0.213  -2.5512   1.1774   1.8603
 LY0  H1A   H  HCH3   0   0.220  -1.5865   2.3311   0.9390
 LY0  H1B   H  HCH3   0   0.221  -3.3440   2.4036   0.8678
 LY0  HN1   H  HNH2   0   0.326  -3.8987  -0.5668   0.3830
 LY0  HN1A  H  HNH2   0   0.334  -4.5447   0.7092  -0.3703
 LY0  H2    H  HCH1   0   0.213  -2.3383   1.3299  -1.1864
 LY0  H4    H  HCH2   0   0.221   0.3149   1.3072  -0.5028
 LY0  H4A   H  HCH2   0   0.213   0.2882   0.8692   1.1886
 LY0  H5    H  HCH1   0   0.209   1.5986  -0.8020  -0.9970
 LY0  H7    H  HCH3   0   0.213   2.7226  -1.9835   0.8705
 LY0  H7A   H  HCH3   0   0.200   1.8327  -1.0068   2.0392
 LY0  H7B   H  HCH3   0   0.221   0.9681  -2.1278   1.0011

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
 LY0  C2   P     single  1.859  0.020  1.859
 LY0  O31  P     deloc   1.519  0.020  1.519
 LY0  P    O32   deloc   1.522  0.020  1.522
 LY0  P    C4    single  1.840  0.020  1.840
 LY0  C1   C2    single  1.528  0.020  1.528
 LY0  C1   H1    single  0.970  0.020  1.090
 LY0  C1   H1A   single  0.970  0.020  1.090
 LY0  C1   H1B   single  0.970  0.020  1.090
 LY0  N1   C2    single  1.461  0.020  1.461
 LY0  N1   HN1   single  0.890  0.020  1.040
 LY0  N1   HN1A  single  0.890  0.020  1.040
 LY0  C2   H2    single  0.970  0.020  1.090
 LY0  C4   C5    single  1.526  0.020  1.526
 LY0  C4   H4    single  0.970  0.020  1.090
 LY0  C4   H4A   single  0.970  0.020  1.090
 LY0  C5   C6    single  1.548  0.020  1.548
 LY0  C5   C7    single  1.530  0.020  1.530
 LY0  C5   H5    single  0.970  0.020  1.090
 LY0  O62  C6    deloc   1.247  0.020  1.247
 LY0  C6   O61   deloc   1.250  0.020  1.250
 LY0  C7   H7    single  0.970  0.020  1.090
 LY0  C7   H7A   single  0.970  0.020  1.090
 LY0  C7   H7B   single  0.970  0.020  1.090

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
 LY0  O32   P   O31  118.18  3.000
 LY0  O32   P   C4   111.02  3.000
 LY0  O31   P   C4   108.22  3.000
 LY0  C4    P   C2   102.97  3.000
 LY0  O32   P   C2   106.22  3.000
 LY0  O31   P   C2   109.14  3.000
 LY0  H1B   C1  H1A  107.42  3.000
 LY0  H1B   C1  H1   107.80  3.000
 LY0  H1A   C1  H1   107.77  3.000
 LY0  H1B   C1  C2   110.51  3.000
 LY0  H1A   C1  C2   112.37  3.000
 LY0  H1    C1  C2   110.79  3.000
 LY0  HN1A  N1  HN1  105.72  3.000
 LY0  HN1A  N1  C2   109.45  3.000
 LY0  HN1   N1  C2   108.47  3.000
 LY0  H2    C2  N1   107.87  3.000
 LY0  H2    C2  C1   108.42  3.000
 LY0  N1    C2  C1   113.36  3.000
 LY0  H2    C2  P    107.71  3.000
 LY0  N1    C2  P    106.73  3.000
 LY0  C1    C2  P    112.51  3.000
 LY0  H4A   C4  H4   105.97  3.000
 LY0  H4A   C4  C5   110.04  3.000
 LY0  H4    C4  C5   109.31  3.000
 LY0  H4A   C4  P    109.80  3.000
 LY0  H4    C4  P    107.21  3.000
 LY0  C5    C4  P    114.15  3.000
 LY0  H5    C5  C7   107.26  3.000
 LY0  H5    C5  C6   106.44  3.000
 LY0  C7    C5  C6   109.66  3.000
 LY0  H5    C5  C4   107.76  3.000
 LY0  C7    C5  C4   111.84  3.000
 LY0  C6    C5  C4   113.54  3.000
 LY0  O62   C6  O61  125.66  3.000
 LY0  O61   C6  C5   115.74  3.000
 LY0  O62   C6  C5   118.61  3.000
 LY0  H7B   C7  H7A  107.12  3.000
 LY0  H7B   C7  H7   108.33  3.000
 LY0  H7A   C7  H7   107.85  3.000
 LY0  H7B   C7  C5   111.47  3.000
 LY0  H7A   C7  C5   110.73  3.000
 LY0  H7    C7  C5   111.17  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
 LY0  Var_01  C5  C4  P  C2  -165.91  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
 LY0  chir_02  C2  P   C1  N1  positiv
 LY0  chir_03  C5  C4  C6  C7  negativ

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
 LY0  plan-1  C5   0.020
 LY0  plan-1  C6   0.020
 LY0  plan-1  O61  0.020
 LY0  plan-1  O62  0.020

