# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 18:16:46 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (2R)-3-[(R)-[(1S)-1-aminoethyl](hydroxy)phosphoryl]-2-methylpropanoic 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
 2D8  2D8  '(2R)-3-[(R)-[(1S)-1-aminoethyl](hydroxy)phosphoryl]-2-methylpropanoic acid'  ligand  26  12  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_2D8
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
 2D8  C4   C  CH2   0  -0.746   0.3763  -0.4823  -0.1744
 2D8  C5   C  CH1   0  -0.371   1.6369   0.3485   0.0526
 2D8  C6   C  C     0   0.571   2.8603  -0.5411  -0.0017
 2D8  C7   C  CH3   0  -0.675   1.7940   1.4837  -0.9667
 2D8  N1   N  NH2   0  -0.790  -2.5443  -1.7654  -0.7737
 2D8  P    P  P     0   1.235  -1.1609   0.4501   0.1212
 2D8  C1   C  CH3   0  -0.665  -3.8337  -0.1294   0.5140
 2D8  C2   C  CH1   0  -0.335  -2.4845  -0.8084   0.3164
 2D8  O31  O  O     0  -0.721  -1.0763   1.4356   1.2401
 2D8  O32  O  OH1   0  -0.766  -1.5181   1.2125  -1.2706
 2D8  O61  O  OH1   0  -0.593   3.9205   0.0504   0.5358
 2D8  O62  O  O     0  -0.437   2.8976  -1.6429  -0.4895
 2D8  H1   H  HCH2  0   0.288   0.3687  -0.9195  -1.1760
 2D8  H2   H  HCH2  0   0.299   0.3521  -1.3209   0.5277
 2D8  H3   H  HCH1  0   0.287   1.5968   0.7918   1.0516
 2D8  H4   H  HCH3  0   0.252   0.9792   2.1985  -0.8704
 2D8  H5   H  HCH3  0   0.255   2.7218   2.0326  -0.8157
 2D8  H6   H  HCH3  0   0.237   1.7893   1.0965  -1.9867
 2D8  H8   H  HNH2  0   0.365  -1.7029  -2.3231  -0.8352
 2D8  H10  H  HCH3  0   0.248  -4.5927  -0.8840   0.7198
 2D8  H11  H  HCH3  0   0.240  -3.8123   0.5680   1.3504
 2D8  H12  H  HCH3  0   0.231  -4.1388   0.4191  -0.3784
 2D8  H13  H  HCH1  0   0.274  -2.2338  -1.3557   1.2304
 2D8  H14  H  HOH1  0   0.485  -1.1703   0.8115  -2.0756
 2D8  H15  H  HOH1  0   0.481   4.6993  -0.5194   0.4470
 2D8  H7   H  HNH2  0   0.348  -2.6743  -1.3065  -1.6664

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
 2D8  C1   C2   single  1.523  0.020  1.523
 2D8  C2   N1   single  1.452  0.020  1.452
 2D8  C2   P    single  1.837  0.020  1.837
 2D8  O62  C6   double  1.206  0.020  1.206
 2D8  C4   P    single  1.822  0.020  1.822
 2D8  C4   C5   single  1.527  0.020  1.527
 2D8  P    O31  double  1.493  0.020  1.493
 2D8  P    O32  single  1.627  0.020  1.627
 2D8  C6   C5   single  1.514  0.020  1.514
 2D8  C6   O61  single  1.328  0.020  1.328
 2D8  C7   C5   single  1.534  0.020  1.534
 2D8  C4   H1   single  0.970  0.020  1.090
 2D8  C4   H2   single  0.970  0.020  1.090
 2D8  C5   H3   single  0.970  0.020  1.090
 2D8  C7   H4   single  0.970  0.020  1.090
 2D8  C7   H5   single  0.970  0.020  1.090
 2D8  C7   H6   single  0.970  0.020  1.090
 2D8  N1   H7   single  0.890  0.020  1.040
 2D8  N1   H8   single  0.890  0.020  1.040
 2D8  C1   H10  single  0.970  0.020  1.090
 2D8  C1   H11  single  0.970  0.020  1.090
 2D8  C1   H12  single  0.970  0.020  1.090
 2D8  C2   H13  single  0.970  0.020  1.090
 2D8  O32  H14  single  0.850  0.020  0.980
 2D8  O61  H15  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
 2D8  H2   C4   H1   106.34  3.000
 2D8  H2   C4   P    105.63  3.000
 2D8  H1   C4   P    110.34  3.000
 2D8  H2   C4   C5   109.87  3.000
 2D8  H1   C4   C5   111.09  3.000
 2D8  P    C4   C5   113.20  3.000
 2D8  H3   C5   C7   108.11  3.000
 2D8  H3   C5   C6   107.50  3.000
 2D8  C7   C5   C6   109.17  3.000
 2D8  H3   C5   C4   109.04  3.000
 2D8  C7   C5   C4   112.86  3.000
 2D8  C6   C5   C4   110.01  3.000
 2D8  O62  C6   O61  123.11  3.000
 2D8  O61  C6   C5   111.66  3.000
 2D8  O62  C6   C5   125.22  3.000
 2D8  H6   C7   H5   108.20  3.000
 2D8  H6   C7   H4   108.22  3.000
 2D8  H5   C7   H4   107.13  3.000
 2D8  H6   C7   C5   111.00  3.000
 2D8  H5   C7   C5   111.61  3.000
 2D8  H4   C7   C5   110.53  3.000
 2D8  H8   N1   H7   107.65  3.000
 2D8  H8   N1   C2   112.02  3.000
 2D8  H7   N1   C2   111.63  3.000
 2D8  O32  P    O31  110.14  3.000
 2D8  O32  P    C2   104.70  3.000
 2D8  O31  P    C2   114.41  3.000
 2D8  O32  P    C4   106.64  3.000
 2D8  O31  P    C4   114.30  3.000
 2D8  C2   P    C4   105.94  3.000
 2D8  H12  C1   H11  108.16  3.000
 2D8  H12  C1   H10  107.93  3.000
 2D8  H11  C1   H10  108.17  3.000
 2D8  H12  C1   C2   111.45  3.000
 2D8  H11  C1   C2   111.57  3.000
 2D8  H10  C1   C2   109.43  3.000
 2D8  H13  C2   C1   108.51  3.000
 2D8  H13  C2   P    105.44  3.000
 2D8  C1   C2   P    110.28  3.000
 2D8  H13  C2   N1   107.87  3.000
 2D8  P    C2   N1   113.67  3.000
 2D8  C1   C2   N1   110.78  3.000
 2D8  H14  O32  P    116.12  3.000
 2D8  H15  O61  C6   110.04  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
 2D8  CONST_01  H15  O61  C6  C5   180.00   0.0  0
 2D8  Var_01    C2   P    C4  C5  -162.71  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
 2D8  chir_01  C5  C4  C6   C7   negativ
 2D8  chir_03  C2  C1  N1   P    negativ
 2D8  chir_04  P   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
 2D8  plan-1  C5   0.020
 2D8  plan-1  C6   0.020
 2D8  plan-1  O61  0.020
 2D8  plan-1  O62  0.020
 2D8  plan-1  H15  0.020

