# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 22:55:41 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: [(1R)-1-amino-3-methylbutyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)[P](O)(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
 PLE  PLE  '[(1R)-1-amino-3-methylbutyl]phosphonic acid'  peptide  22  10  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PLE
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
 PLE  C1   C  CH3    0  -0.651   3.5858   0.7099  -0.8002
 PLE  C2   C  CH1    0  -0.214   2.5790  -0.1417  -0.0323
 PLE  C3   C  CH3    0  -0.657   2.8904  -0.1147   1.4608
 PLE  C4   C  CH2    0  -0.401   1.1528   0.3296  -0.3232
 PLE  C5   C  CH1    0  -0.351   0.0290  -0.5359   0.2281
 PLE  N1   N  NH2    0  -0.808   0.1189  -1.8913  -0.3415
 PLE  P1   P  P      0   1.156  -1.6479   0.2306  -0.0490
 PLE  O1   O  OP    -1  -0.913  -1.6302   1.5733   0.6994
 PLE  O2   O  O      0  -0.916  -1.7783   0.3751  -1.5757
 PLE  H1   H  HCH3   0   0.216   4.6132   0.3912  -0.6110
 PLE  H2   H  HCH3   0   0.217   3.4158   0.6533  -1.8775
 PLE  H3   H  HCH3   0   0.205   3.5104   1.7619  -0.5116
 PLE  H4   H  HCH1   0   0.200   2.6743  -1.1761  -0.3795
 PLE  H5   H  HCH3   0   0.223   2.2419  -0.7859   2.0247
 PLE  H6   H  HCH3   0   0.216   3.9213  -0.4155   1.6580
 PLE  H7   H  HCH3   0   0.204   2.7566   0.8926   1.8653
 PLE  H8   H  HCH2   0   0.193   1.0268   1.3440   0.0703
 PLE  H9   H  HCH2   0   0.190   1.0149   0.4138  -1.4082
 PLE  H10  H  HCH1   0   0.175   0.1685  -0.6353   1.3136
 PLE  H11  H  HNH2   0   0.319  -0.6917  -2.4023  -0.0067
 PLE  H12  H  HNH2   0   0.311  -0.0550  -1.7962  -1.3380
 PLE  O3   O  OP    -1  -0.914  -2.6343  -0.7906   0.5482

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
 PLE  C1  C2   single  1.526  0.020  1.526
 PLE  C2  C3   single  1.526  0.020  1.526
 PLE  C2  C4   single  1.530  0.020  1.530
 PLE  C4  C5   single  1.522  0.020  1.522
 PLE  C5  N1   single  1.473  0.020  1.473
 PLE  C5  P1   single  1.864  0.020  1.864
 PLE  P1  O1   deloc   1.537  0.020  1.537
 PLE  P1  O2   deloc   1.539  0.020  1.539
 PLE  C1  H1   single  0.970  0.020  1.090
 PLE  C1  H2   single  0.970  0.020  1.090
 PLE  C1  H3   single  0.970  0.020  1.090
 PLE  C2  H4   single  0.970  0.020  1.090
 PLE  C3  H5   single  0.970  0.020  1.090
 PLE  C3  H6   single  0.970  0.020  1.090
 PLE  C3  H7   single  0.970  0.020  1.090
 PLE  C4  H8   single  0.970  0.020  1.090
 PLE  C4  H9   single  0.970  0.020  1.090
 PLE  C5  H10  single  0.970  0.020  1.090
 PLE  N1  H11  single  0.890  0.020  1.040
 PLE  N1  H12  single  0.890  0.020  1.040
 PLE  P1  O3   deloc   1.540  0.020  1.540

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
 PLE  H3   C1  H2   107.42  3.000
 PLE  H3   C1  H1   107.45  3.000
 PLE  H2   C1  H1   107.59  3.000
 PLE  H3   C1  C2   111.02  3.000
 PLE  H2   C1  C2   111.39  3.000
 PLE  H1   C1  C2   111.76  3.000
 PLE  H4   C2  C4   108.17  3.000
 PLE  H4   C2  C3   108.01  3.000
 PLE  C4   C2  C3   111.77  3.000
 PLE  H4   C2  C1   108.07  3.000
 PLE  C4   C2  C1   110.33  3.000
 PLE  C3   C2  C1   110.36  3.000
 PLE  H7   C3  H6   107.61  3.000
 PLE  H7   C3  H5   107.64  3.000
 PLE  H6   C3  H5   107.37  3.000
 PLE  H7   C3  C2   110.69  3.000
 PLE  H6   C3  C2   111.38  3.000
 PLE  H5   C3  C2   111.95  3.000
 PLE  H9   C4  H8   105.65  3.000
 PLE  H9   C4  C5   108.01  3.000
 PLE  H8   C4  C5   108.16  3.000
 PLE  H9   C4  C2   109.20  3.000
 PLE  H8   C4  C2   108.92  3.000
 PLE  C5   C4  C2   116.38  3.000
 PLE  H10  C5  P1   107.34  3.000
 PLE  H10  C5  N1   106.92  3.000
 PLE  P1   C5  N1   112.07  3.000
 PLE  H10  C5  C4   108.40  3.000
 PLE  P1   C5  C4   112.12  3.000
 PLE  N1   C5  C4   109.77  3.000
 PLE  H12  N1  H11  103.53  3.000
 PLE  H12  N1  C5   106.42  3.000
 PLE  H11  N1  C5   106.68  3.000
 PLE  O3   P1  O2   113.11  3.000
 PLE  O3   P1  O1   113.44  3.000
 PLE  O2   P1  O1   113.69  3.000
 PLE  O3   P1  C5   104.23  3.000
 PLE  O2   P1  C5   105.20  3.000
 PLE  O1   P1  C5   106.04  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
 PLE  Var_01  C5  C4  C2  C1   172.33  30.0  3
 PLE  Var_02  H5  C3  C2  C1  -174.87  30.0  3
 PLE  Var_03  H1  C1  C2  C3    56.12  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
 PLE  chir_01  C5  C4  N1  P1  positiv

