# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 09:29:04 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: [(1S)-1-amino-4-methoxybutyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCC[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
 02F  02F  '[(1S)-1-amino-4-methoxybutyl]phosphonic acid'  ligand  23  11  .  2021-07-27  2021-07-27  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_02F
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
 02F  P    P  P      0   1.165  -2.0326  -0.4634  -0.1107
 02F  C1   C  CH3    0  -0.394   4.9768  -0.2028  -0.1737
 02F  C2   C  CH2    0  -0.118   2.7388   0.4815  -0.1984
 02F  O2   O  O2     0  -0.489   3.6878  -0.4134   0.3363
 02F  C4   C  CH2    0  -0.437   0.3193   1.1593  -0.1458
 02F  C5   C  CH1    0  -0.323  -1.0702   1.0308   0.4909
 02F  N6   N  NH2    0  -0.809  -1.8963   2.2157   0.2467
 02F  OP1  O  O      0  -0.912  -2.3421  -0.1163  -1.5789
 02F  OP2  O  OP    -1  -0.889  -1.1095  -1.6811   0.0468
 02F  OP3  O  OP    -1  -0.911  -3.2793  -0.5379   0.7795
 02F  H1   H  HCH3   0   0.198   5.3533   0.8028   0.0529
 02F  H1A  H  HCH3   0   0.229   5.6478  -0.9296   0.2844
 02F  H1B  H  HCH3   0   0.199   5.0195  -0.3353  -1.2622
 02F  H2   H  HCH2   0   0.181   3.0403   1.5211   0.0046
 02F  H2A  H  HCH2   0   0.183   2.6926   0.3795  -1.2938
 02F  H3   H  HCH2   0   0.235   1.0659  -0.8176   0.2049
 02F  H3A  H  HCH2   0   0.197   1.4350   0.3234   1.4916
 02F  H4   H  HCH2   0   0.186   0.6746   2.1889   0.0037
 02F  H4A  H  HCH2   0   0.192   0.2245   1.0303  -1.2305
 02F  H5   H  HCH1   0   0.163  -0.9275   0.9401   1.5777
 02F  HN6  H  HNH2   0   0.314  -1.3239   3.0514   0.3096
 02F  H6   H  HNH2   0   0.313  -2.2153   2.1716  -0.7145
 02F  C3   C  CH2    0  -0.472   1.3761   0.2083   0.4032

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
 02F  P   OP2  deloc   1.536  0.020  1.536
 02F  P   OP1  deloc   1.540  0.020  1.540
 02F  C2  C3   single  1.514  0.020  1.514
 02F  O2  C1   single  1.402  0.020  1.402
 02F  O2  C2   single  1.410  0.020  1.410
 02F  C3  C4   single  1.524  0.020  1.524
 02F  C4  C5   single  1.534  0.020  1.534
 02F  C5  P    single  1.876  0.020  1.876
 02F  N6  C5   single  1.465  0.020  1.465
 02F  P   OP3  deloc   1.534  0.020  1.534
 02F  C1  H1   single  0.970  0.020  1.090
 02F  C1  H1A  single  0.970  0.020  1.090
 02F  C1  H1B  single  0.970  0.020  1.090
 02F  C2  H2   single  0.970  0.020  1.090
 02F  C2  H2A  single  0.970  0.020  1.090
 02F  C3  H3   single  0.970  0.020  1.090
 02F  C3  H3A  single  0.970  0.020  1.090
 02F  C4  H4   single  0.970  0.020  1.090
 02F  C4  H4A  single  0.970  0.020  1.090
 02F  C5  H5   single  0.970  0.020  1.090
 02F  N6  HN6  single  0.890  0.020  1.040
 02F  N6  H6   single  0.890  0.020  1.040

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
 02F  OP3  P   OP2  112.98  3.000
 02F  OP3  P   OP1  113.64  3.000
 02F  OP2  P   OP1  113.40  3.000
 02F  OP3  P   C5   105.63  3.000
 02F  OP1  P   C5   103.25  3.000
 02F  OP2  P   C5   106.86  3.000
 02F  H1B  C1  H1A  108.21  3.000
 02F  H1B  C1  H1   107.58  3.000
 02F  H1A  C1  H1   108.24  3.000
 02F  H1B  C1  O2   112.24  3.000
 02F  H1A  C1  O2   108.24  3.000
 02F  H1   C1  O2   112.20  3.000
 02F  H2A  C2  H2   106.40  3.000
 02F  H2A  C2  C3   109.92  3.000
 02F  H2   C2  C3   110.08  3.000
 02F  H2A  C2  O2   110.29  3.000
 02F  H2   C2  O2   110.18  3.000
 02F  C3   C2  O2   109.91  3.000
 02F  C2   O2  C1   112.68  3.000
 02F  H4A  C4  H4   105.83  3.000
 02F  H4A  C4  C5   108.81  3.000
 02F  H4   C4  C5   108.35  3.000
 02F  H4A  C4  C3   110.05  3.000
 02F  H4   C4  C3   108.14  3.000
 02F  C5   C4  C3   115.24  3.000
 02F  H5   C5  N6   107.73  3.000
 02F  H5   C5  C4   107.43  3.000
 02F  N6   C5  C4   111.95  3.000
 02F  H5   C5  P    108.52  3.000
 02F  N6   C5  P    107.54  3.000
 02F  C4   C5  P    113.47  3.000
 02F  H6   N6  HN6  105.79  3.000
 02F  H6   N6  C5   107.47  3.000
 02F  HN6  N6  C5   109.74  3.000
 02F  H3A  C3  H3   107.15  3.000
 02F  H3A  C3  C4   109.23  3.000
 02F  H3   C3  C4   108.93  3.000
 02F  H3A  C3  C2   109.10  3.000
 02F  H3   C3  C2   110.71  3.000
 02F  C4   C3  C2   111.61  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
 02F  Var_01  C3  C2  O2  C1  -179.45  30.0  3
 02F  Var_02  C5  C4  C3  C2  -175.29  30.0  3
 02F  Var_03  C4  C3  C2  O2   179.81  30.0  3
 02F  Var_04  H1  C1  O2  C2    60.70  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
 02F  chir_01  C5  C4  P  N6  positiv

