# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 07:05:33 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: (2R)-2-{[(R)-[(1R)-1-aminoethyl](hydroxy)phosphoryl]methyl}butanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)[P](O)(=O)C[C@H](CC(O)=O)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
 P8D  P8D  '(2R)-2-{[(R)-[(1R)-1-aminoethyl](hydroxy)phosphoryl]methyl}butanedioic acid'  ligand  26  15  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_P8D
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
 P8D  C1    C  CH3    0  -0.660   4.4950  -0.4195   0.3333
 P8D  N1    N  NH2    0  -0.802   3.3807   0.3081  -1.7110
 P8D  C2    C  CH1    0  -0.334   3.2411  -0.5387  -0.5232
 P8D  P3    P  P      0   1.164   1.7398  -0.1300   0.4930
 P8D  C4    C  CH2    0  -0.685   0.3604  -0.5518  -0.6444
 P8D  C5    C  CH1    0  -0.325  -1.0189  -0.2457  -0.0634
 P8D  C6    C  C      0   0.425  -1.3176   1.2654  -0.0359
 P8D  C7    C  CH2    0  -0.515  -2.1125  -0.9536  -0.8770
 P8D  C8    C  C      0   0.389  -3.5142  -0.7291  -0.2945
 P8D  O31   O  O      0  -0.823   1.7723   1.3655   0.7596
 P8D  O32   O  OP    -1  -0.836   1.6805  -1.0727   1.6858
 P8D  O61   O  OC    -1  -0.635  -1.7470   1.7488   1.0325
 P8D  O62   O  O      0  -0.629  -1.1596   1.8887  -1.1068
 P8D  O81   O  OC    -1  -0.626  -4.3074  -0.0166  -0.9443
 P8D  O82   O  O      0  -0.632  -3.7557  -1.2806   0.8017
 P8D  H1    H  HCH3   0   0.211   4.6133   0.5997   0.7085
 P8D  H1A   H  HCH3   0   0.220   4.4511  -1.0855   1.1946
 P8D  H1B   H  HCH3   0   0.219   5.3867  -0.6676  -0.2454
 P8D  HN1   H  HNH2   0   0.341   2.6066   0.1372  -2.3419
 P8D  HN1A  H  HNH2   0   0.328   3.2732   1.2743  -1.4199
 P8D  H2    H  HCH1   0   0.215   3.1542  -1.5760  -0.8667
 P8D  H4    H  HCH2   0   0.214   0.4727  -0.0242  -1.5950
 P8D  H4A   H  HCH2   0   0.209   0.4413  -1.6223  -0.8663
 P8D  H5    H  HCH1   0   0.183  -1.0665  -0.6324   0.9587
 P8D  H7    H  HCH2   0   0.184  -2.0584  -0.6070  -1.9120
 P8D  H7A   H  HCH2   0   0.198  -1.8954  -2.0281  -0.8875

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
 P8D  C1  C2    single  1.523  0.020  1.523
 P8D  C1  H1    single  0.970  0.020  1.090
 P8D  C1  H1A   single  0.970  0.020  1.090
 P8D  C1  H1B   single  0.970  0.020  1.090
 P8D  N1  C2    single  1.465  0.020  1.465
 P8D  N1  HN1   single  0.890  0.020  1.040
 P8D  N1  HN1A  single  0.890  0.020  1.040
 P8D  C2  P3    single  1.858  0.020  1.858
 P8D  C2  H2    single  0.970  0.020  1.090
 P8D  P3  C4    single  1.837  0.020  1.837
 P8D  P3  O31   deloc   1.519  0.020  1.519
 P8D  P3  O32   deloc   1.522  0.020  1.522
 P8D  C4  C5    single  1.528  0.020  1.528
 P8D  C4  H4    single  0.970  0.020  1.090
 P8D  C4  H4A   single  0.970  0.020  1.090
 P8D  C5  C6    single  1.541  0.020  1.541
 P8D  C5  C7    single  1.536  0.020  1.536
 P8D  C5  H5    single  0.970  0.020  1.090
 P8D  C6  O61   deloc   1.249  0.020  1.249
 P8D  C6  O62   deloc   1.249  0.020  1.249
 P8D  C7  C8    single  1.534  0.020  1.534
 P8D  C7  H7    single  0.970  0.020  1.090
 P8D  C7  H7A   single  0.970  0.020  1.090
 P8D  C8  O81   deloc   1.249  0.020  1.249
 P8D  C8  O82   deloc   1.251  0.020  1.251

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
 P8D  H1B   C1  H1A  108.25  3.000
 P8D  H1B   C1  H1   107.80  3.000
 P8D  H1A   C1  H1   107.64  3.000
 P8D  H1B   C1  C2   110.89  3.000
 P8D  H1A   C1  C2   111.31  3.000
 P8D  H1    C1  C2   110.81  3.000
 P8D  HN1A  N1  HN1  104.97  3.000
 P8D  HN1A  N1  C2   107.91  3.000
 P8D  HN1   N1  C2   109.54  3.000
 P8D  H2    C2  P3   108.39  3.000
 P8D  H2    C2  N1   107.48  3.000
 P8D  P3    C2  N1   113.15  3.000
 P8D  H2    C2  C1   108.39  3.000
 P8D  P3    C2  C1   109.90  3.000
 P8D  N1    C2  C1   109.40  3.000
 P8D  O32   P3  O31  118.24  3.000
 P8D  O32   P3  C4   108.29  3.000
 P8D  O31   P3  C4   110.53  3.000
 P8D  O32   P3  C2   108.91  3.000
 P8D  O31   P3  C2   107.16  3.000
 P8D  C4    P3  C2   102.56  3.000
 P8D  H4A   C4  H4   106.72  3.000
 P8D  H4A   C4  C5   109.83  3.000
 P8D  H4    C4  C5   109.08  3.000
 P8D  H4A   C4  P3   107.11  3.000
 P8D  H4    C4  P3   110.52  3.000
 P8D  C5    C4  P3   113.36  3.000
 P8D  H5    C5  C7   107.52  3.000
 P8D  H5    C5  C6   108.76  3.000
 P8D  C7    C5  C6   108.87  3.000
 P8D  H5    C5  C4   108.90  3.000
 P8D  C7    C5  C4   110.43  3.000
 P8D  C6    C5  C4   112.24  3.000
 P8D  O62   C6  O61  125.72  3.000
 P8D  O62   C6  C5   116.72  3.000
 P8D  O61   C6  C5   117.49  3.000
 P8D  H7A   C7  H7   106.97  3.000
 P8D  H7A   C7  C8   109.14  3.000
 P8D  H7    C7  C8   111.00  3.000
 P8D  H7A   C7  C5   108.41  3.000
 P8D  H7    C7  C5   108.68  3.000
 P8D  C8    C7  C5   112.45  3.000
 P8D  O82   C8  O81  125.81  3.000
 P8D  O82   C8  C7   116.40  3.000
 P8D  O81   C8  C7   117.79  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
 P8D  Var_01  C5   C4  P3  C2  -177.47  30.0  3
 P8D  Var_02  O81  C8  C7  C5   110.54  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
 P8D  chir_01  C2  C1  N1  P3  positiv
 P8D  chir_03  C5  C7  C6  C4  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
 P8D  plan-1  C5   0.020
 P8D  plan-1  C6   0.020
 P8D  plan-1  O61  0.020
 P8D  plan-1  O62  0.020
 P8D  plan-2  C7   0.020
 P8D  plan-2  C8   0.020
 P8D  plan-2  O81  0.020
 P8D  plan-2  O82  0.020

