# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 21 22:15:53 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  29  15  .  2021-08-20  2021-08-20  
;
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  -0.665   4.4687  -0.2883   0.2784
 P8D  N1    N  NH2   0  -0.790   3.3367  -0.1012  -1.8813
 P8D  C2    C  CH1   0  -0.335   3.2151  -0.6090  -0.5252
 P8D  P3    P  P     0   1.234   1.7333   0.0688   0.3226
 P8D  C4    C  CH2   0  -0.740   0.3106  -0.4243  -0.7005
 P8D  C5    C  CH1   0  -0.357  -1.0584  -0.2986  -0.0168
 P8D  C6    C  C     0   0.555  -1.3017   1.1362   0.4065
 P8D  C7    C  CH2   0  -0.568  -2.1341  -0.7496  -0.9982
 P8D  C8    C  C     0   0.557  -3.5195  -0.6750  -0.4206
 P8D  O31   O  O     0  -0.717   1.8037   1.5382   0.5759
 P8D  O32   O  OH1   0  -0.756   1.5832  -0.7302   1.7247
 P8D  O61   O  OH1   0  -0.582  -1.1618   1.3211   1.7079
 P8D  O62   O  O     0  -0.446  -1.5711   2.0186  -0.3704
 P8D  O81   O  OH1   0  -0.591  -4.4273  -1.1832  -1.2418
 P8D  O82   O  O     0  -0.437  -3.7849  -0.2024   0.6570
 P8D  H1    H  HCH3  0   0.234   4.6229   0.7889   0.3547
 P8D  H1A   H  HCH3  0   0.238   4.4170  -0.6941   1.2880
 P8D  H1B   H  HCH3  0   0.250   5.3381  -0.7208  -0.2160
 P8D  HN1   H  HNH2  0   0.364   2.5756  -0.4131  -2.4700
 P8D  HN1A  H  HNH2  0   0.353   3.3321   0.9115  -1.8929
 P8D  H2    H  HCH1  0   0.274   3.0969  -1.6959  -0.5806
 P8D  H4    H  HCH2  0   0.291   0.3339   0.1866  -1.6061
 P8D  H4A   H  HCH2  0   0.298   0.4530  -1.4622  -1.0153
 P8D  H5    H  HCH1  0   0.290  -1.0760  -0.9456   0.8614
 P8D  H7    H  HCH2  0   0.295  -2.1070  -0.1425  -1.9077
 P8D  H7A   H  HCH2  0   0.303  -1.9351  -1.7764  -1.3143
 P8D  H12   H  HOH1  0   0.487   1.5813  -1.6934   1.6537
 P8D  H13   H  HOH1  0   0.478  -1.2782   2.2591   1.9227
 P8D  H16   H  HOH1  0   0.483  -5.3106  -1.1104  -0.8496

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  1.453  0.020  1.453
 P8D  N1   HN1   single  0.890  0.020  1.040
 P8D  N1   HN1A  single  0.890  0.020  1.040
 P8D  C2   P3    single  1.837  0.020  1.837
 P8D  C2   H2    single  0.970  0.020  1.090
 P8D  P3   C4    single  1.820  0.020  1.820
 P8D  P3   O31   double  1.493  0.020  1.493
 P8D  P3   O32   single  1.621  0.020  1.621
 P8D  C4   C5    single  1.535  0.020  1.535
 P8D  C4   H4    single  0.970  0.020  1.090
 P8D  C4   H4A   single  0.970  0.020  1.090
 P8D  C5   C6    single  1.516  0.020  1.516
 P8D  C5   C7    single  1.524  0.020  1.524
 P8D  C5   H5    single  0.970  0.020  1.090
 P8D  C6   O61   single  1.322  0.020  1.322
 P8D  C6   O62   double  1.206  0.020  1.206
 P8D  C7   C8    single  1.503  0.020  1.503
 P8D  C7   H7    single  0.970  0.020  1.090
 P8D  C7   H7A   single  0.970  0.020  1.090
 P8D  C8   O81   single  1.325  0.020  1.325
 P8D  C8   O82   double  1.206  0.020  1.206
 P8D  O32  H12   single  0.850  0.020  0.980
 P8D  O61  H13   single  0.850  0.020  0.980
 P8D  O81  H16   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
 P8D  H1B   C1   H1A  108.09  3.000
 P8D  H1B   C1   H1   108.11  3.000
 P8D  H1A   C1   H1   108.04  3.000
 P8D  H1B   C1   C2   109.50  3.000
 P8D  H1A   C1   C2   111.81  3.000
 P8D  H1    C1   C2   111.17  3.000
 P8D  HN1A  N1   HN1  107.35  3.000
 P8D  HN1A  N1   C2   111.09  3.000
 P8D  HN1   N1   C2   111.86  3.000
 P8D  H2    C2   P3   107.61  3.000
 P8D  H2    C2   N1   107.99  3.000
 P8D  P3    C2   N1   111.67  3.000
 P8D  H2    C2   C1   108.94  3.000
 P8D  P3    C2   C1   110.04  3.000
 P8D  N1    C2   C1   110.48  3.000
 P8D  O32   P3   O31  110.05  3.000
 P8D  O32   P3   C4   106.28  3.000
 P8D  O31   P3   C4   113.51  3.000
 P8D  O32   P3   C2   106.98  3.000
 P8D  O31   P3   C2   113.79  3.000
 P8D  C4    P3   C2   105.73  3.000
 P8D  H4A   C4   H4   106.81  3.000
 P8D  H4A   C4   C5   108.78  3.000
 P8D  H4    C4   C5   110.02  3.000
 P8D  H4A   C4   P3   108.48  3.000
 P8D  H4    C4   P3   107.32  3.000
 P8D  C5    C4   P3   115.11  3.000
 P8D  H5    C5   C7   109.35  3.000
 P8D  H5    C5   C6   109.51  3.000
 P8D  C7    C5   C6   110.28  3.000
 P8D  H5    C5   C4   108.92  3.000
 P8D  C7    C5   C4   108.56  3.000
 P8D  C6    C5   C4   110.18  3.000
 P8D  O62   C6   O61  123.74  3.000
 P8D  O62   C6   C5   123.27  3.000
 P8D  O61   C6   C5   112.98  3.000
 P8D  H7A   C7   H7   106.05  3.000
 P8D  H7A   C7   C8   109.01  3.000
 P8D  H7    C7   C8   108.35  3.000
 P8D  H7A   C7   C5   109.62  3.000
 P8D  H7    C7   C5   110.71  3.000
 P8D  C8    C7   C5   112.85  3.000
 P8D  O82   C8   O81  123.58  3.000
 P8D  O82   C8   C7   124.44  3.000
 P8D  O81   C8   C7   111.98  3.000
 P8D  H12   O32  P3   115.35  3.000
 P8D  H13   O61  C6   109.92  3.000
 P8D  H16   O81  C8   110.16  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  CONST_01  H13  O61  C6  C5   180.00   0.0  0
 P8D  CONST_02  H16  O81  C8  C7   180.00   0.0  0
 P8D  Var_01    C5   C4   P3  C2   164.53  30.0  3
 P8D  Var_02    O81  C8   C7  C5  -174.30  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
 P8D  chir_04  P3  C4  O31  O32  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
 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-1  H13  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
 P8D  plan-2  H16  0.020

