# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 15 12:28:18 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  26  12  .  2021-08-13  2021-08-13  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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   1.253  -1.1295  -0.4877  -0.1439
 LY0  C1    C  CH3   0  -0.690  -2.4665   1.7654   0.8726
 LY0  N1    N  NH2   0  -0.786  -3.7190   0.0076  -0.4203
 LY0  C2    C  CH1   0  -0.338  -2.4767   0.7467  -0.2666
 LY0  C4    C  CH2   0  -0.742   0.3930   0.4498   0.1911
 LY0  C5    C  CH1   0  -0.374   1.6680  -0.3572  -0.0427
 LY0  C6    C  C     0   0.572   2.8755   0.5530   0.0277
 LY0  C7    C  CH3   0  -0.669   1.8431  -1.5027   0.9623
 LY0  O31   O  O     0  -0.717  -1.0220  -1.4099  -1.3106
 LY0  O32   O  OH1   0  -0.763  -1.4750  -1.3458   1.1923
 LY0  O61   O  OH1   0  -0.593   3.9522  -0.0202  -0.4970
 LY0  O62   O  O     0  -0.437   2.8887   1.6552   0.5160
 LY0  H1    H  HCH3  0   0.227  -2.5968   1.2882   1.8461
 LY0  H1A   H  HCH3  0   0.241  -1.5480   2.3522   0.9032
 LY0  H1B   H  HCH3  0   0.256  -3.2940   2.4630   0.7392
 LY0  HN1   H  HNH2  0   0.347  -3.9999  -0.3855   0.4699
 LY0  HN1A  H  HNH2  0   0.361  -4.4554   0.6504  -0.6840
 LY0  H2    H  HCH1  0   0.277  -2.2839   1.2738  -1.2066
 LY0  H4    H  HCH2  0   0.297   0.3648   1.3064  -0.4890
 LY0  H4A   H  HCH2  0   0.287   0.3674   0.8600   1.2037
 LY0  H5    H  HCH1  0   0.287   1.6386  -0.7868  -1.0480
 LY0  H7    H  HCH3  0   0.253   2.7758  -2.0392   0.7983
 LY0  H7A   H  HCH3  0   0.236   1.8396  -1.1267   1.9863
 LY0  H7B   H  HCH3  0   0.253   1.0343  -2.2236   0.8648
 LY0  HO32  H  HOH1  0   0.482  -1.3589  -0.8845   2.0321
 LY0  HO61  H  HOH1  0   0.481   4.7196   0.5634  -0.3993

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  1.831  0.020  1.831
 LY0  O31  P     double  1.491  0.020  1.491
 LY0  P    O32   single  1.625  0.020  1.625
 LY0  P    C4    single  1.819  0.020  1.819
 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  1.454  0.020  1.454
 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  1.527  0.020  1.527
 LY0  C4   H4    single  0.970  0.020  1.090
 LY0  C4   H4A   single  0.970  0.020  1.090
 LY0  C5   C6    single  1.514  0.020  1.514
 LY0  C5   C7    single  1.534  0.020  1.534
 LY0  C5   H5    single  0.970  0.020  1.090
 LY0  O62  C6    double  1.206  0.020  1.206
 LY0  C6   O61   single  1.328  0.020  1.328
 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
 LY0  O32  HO32  single  0.850  0.020  0.980
 LY0  O61  HO61  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
 LY0  O32   P    O31  109.40  3.000
 LY0  O32   P    C4   107.38  3.000
 LY0  O31   P    C4   113.73  3.000
 LY0  C4    P    C2   106.30  3.000
 LY0  O32   P    C2   104.75  3.000
 LY0  O31   P    C2   114.68  3.000
 LY0  H1B   C1   H1A  107.36  3.000
 LY0  H1B   C1   H1   107.34  3.000
 LY0  H1A   C1   H1   108.10  3.000
 LY0  H1B   C1   C2   109.28  3.000
 LY0  H1A   C1   C2   112.66  3.000
 LY0  H1    C1   C2   111.87  3.000
 LY0  HN1A  N1   HN1  105.88  3.000
 LY0  HN1A  N1   C2   109.04  3.000
 LY0  HN1   N1   C2   109.96  3.000
 LY0  H2    C2   N1   107.73  3.000
 LY0  H2    C2   C1   108.54  3.000
 LY0  N1    C2   C1   115.05  3.000
 LY0  H2    C2   P    104.63  3.000
 LY0  N1    C2   P    107.04  3.000
 LY0  C1    C2   P    113.23  3.000
 LY0  H4A   C4   H4   106.34  3.000
 LY0  H4A   C4   C5   111.09  3.000
 LY0  H4    C4   C5   109.89  3.000
 LY0  H4A   C4   P    110.15  3.000
 LY0  H4    C4   P    105.51  3.000
 LY0  C5    C4   P    113.47  3.000
 LY0  H5    C5   C7   108.18  3.000
 LY0  H5    C5   C6   107.48  3.000
 LY0  C7    C5   C6   109.12  3.000
 LY0  H5    C5   C4   109.02  3.000
 LY0  C7    C5   C4   112.94  3.000
 LY0  C6    C5   C4   109.95  3.000
 LY0  O62   C6   O61  123.08  3.000
 LY0  O61   C6   C5   111.65  3.000
 LY0  O62   C6   C5   125.26  3.000
 LY0  H7B   C7   H7A  108.07  3.000
 LY0  H7B   C7   H7   107.27  3.000
 LY0  H7A   C7   H7   108.31  3.000
 LY0  H7B   C7   C5   110.56  3.000
 LY0  H7A   C7   C5   110.93  3.000
 LY0  H7    C7   C5   111.54  3.000
 LY0  HO32  O32  P    115.94  3.000
 LY0  HO61  O61  C6   110.02  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  CONST_01  HO61  O61  C6  C5   180.00   0.0  0
 LY0  Var_01    C5    C4   P   C2  -164.52  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
 LY0  chir_04  P   O31  O32  C4  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
 LY0  plan-1  C5    0.020
 LY0  plan-1  C6    0.020
 LY0  plan-1  O61   0.020
 LY0  plan-1  O62   0.020
 LY0  plan-1  HO61  0.020

