# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 05:39:58 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: [(1R)-1-amino-2-propylpentyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC(CCC)[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
 Q08  Q08  '[(1R)-1-amino-2-propylpentyl]phosphonic acid'  ligand  33  13  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Q08
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
 Q08  O2   O  OH1   0  -0.745   0.9586   1.8094  -1.0247
 Q08  P    P  P     0   1.375  -0.3482   1.7103  -0.0880
 Q08  O    O  OH1   0  -0.751  -0.2973   3.0074   0.8754
 Q08  O1   O  O     0  -0.709  -1.6474   1.7129  -0.8034
 Q08  C7   C  CH1   0  -0.341   0.0599   0.3077   1.0103
 Q08  N    N  NH2   0  -0.803  -0.9466   0.3529   2.0688
 Q08  C3   C  CH1   0  -0.275   0.1383  -1.0830   0.3415
 Q08  C4   C  CH2   0  -0.399  -1.0239  -1.4570  -0.5861
 Q08  C5   C  CH2   0  -0.420  -2.4150  -1.4978   0.0343
 Q08  C6   C  CH3   0  -0.664  -3.4607  -1.9841  -0.9603
 Q08  C2   C  CH2   0  -0.404   1.4702  -1.3173  -0.3864
 Q08  C1   C  CH2   0  -0.432   2.7162  -1.2939   0.4929
 Q08  C    C  CH3   0  -0.660   3.9730  -1.6650  -0.2833
 Q08  H1   H  HOH1  0   0.491   0.8460   2.3874  -1.7920
 Q08  H2   H  HOH1  0   0.485   0.5423   3.1558   1.3288
 Q08  H3   H  HCH1  0   0.267   1.0610   0.5268   1.4056
 Q08  H4   H  HNH2  0   0.359  -0.9817  -0.5439   2.5365
 Q08  H5   H  HNH2  0   0.357  -0.6791   1.0261   2.7745
 Q08  H7   H  HCH1  0   0.230   0.1235  -1.7890   1.1845
 Q08  H8   H  HCH2  0   0.213  -1.0343  -0.7911  -1.4543
 Q08  H9   H  HCH2  0   0.215  -0.7994  -2.4529  -0.9834
 Q08  H10  H  HCH2  0   0.199  -2.4041  -2.1619   0.9046
 Q08  H11  H  HCH2  0   0.230  -2.6871  -0.5101   0.4028
 Q08  H12  H  HCH3  0   0.224  -4.4511  -2.0355  -0.5063
 Q08  H13  H  HCH3  0   0.214  -3.5274  -1.3138  -1.8194
 Q08  H14  H  HCH3  0   0.212  -3.2190  -2.9797  -1.3387
 Q08  H15  H  HCH2  0   0.219   1.4127  -2.3037  -0.8574
 Q08  H16  H  HCH2  0   0.225   1.5826  -0.6031  -1.2054
 Q08  H17  H  HCH2  0   0.216   2.8597  -0.3072   0.9405
 Q08  H18  H  HCH2  0   0.214   2.5827  -1.9910   1.3260
 Q08  H19  H  HCH3  0   0.227   4.8568  -1.6464   0.3554
 Q08  H20  H  HCH3  0   0.217   3.8947  -2.6674  -0.7086
 Q08  H21  H  HCH3  0   0.217   4.1469  -0.9708  -1.1075

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
 Q08  N   C7   single  1.461  0.020  1.461
 Q08  C6  C5   single  1.523  0.020  1.523
 Q08  C7  C3   single  1.545  0.020  1.545
 Q08  C7  P    single  1.828  0.020  1.828
 Q08  C4  C3   single  1.533  0.020  1.533
 Q08  C4  C5   single  1.524  0.020  1.524
 Q08  O1  P    double  1.483  0.020  1.483
 Q08  C3  C2   single  1.536  0.020  1.536
 Q08  O   P    single  1.617  0.020  1.617
 Q08  P   O2   single  1.611  0.020  1.611
 Q08  C2  C1   single  1.525  0.020  1.525
 Q08  C1  C    single  1.523  0.020  1.523
 Q08  O2  H1   single  0.850  0.020  0.980
 Q08  O   H2   single  0.850  0.020  0.980
 Q08  C7  H3   single  0.970  0.020  1.090
 Q08  N   H4   single  0.890  0.020  1.040
 Q08  N   H5   single  0.890  0.020  1.040
 Q08  C3  H7   single  0.970  0.020  1.090
 Q08  C4  H8   single  0.970  0.020  1.090
 Q08  C4  H9   single  0.970  0.020  1.090
 Q08  C5  H10  single  0.970  0.020  1.090
 Q08  C5  H11  single  0.970  0.020  1.090
 Q08  C6  H12  single  0.970  0.020  1.090
 Q08  C6  H13  single  0.970  0.020  1.090
 Q08  C6  H14  single  0.970  0.020  1.090
 Q08  C2  H15  single  0.970  0.020  1.090
 Q08  C2  H16  single  0.970  0.020  1.090
 Q08  C1  H17  single  0.970  0.020  1.090
 Q08  C1  H18  single  0.970  0.020  1.090
 Q08  C   H19  single  0.970  0.020  1.090
 Q08  C   H20  single  0.970  0.020  1.090
 Q08  C   H21  single  0.970  0.020  1.090

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
 Q08  H1   O2  P    113.80  3.000
 Q08  C7   P   O1   119.14  3.000
 Q08  O1   P   O    108.28  3.000
 Q08  C7   P   O    104.51  3.000
 Q08  O    P   O2   105.76  3.000
 Q08  O1   P   O2   115.47  3.000
 Q08  C7   P   O2   102.44  3.000
 Q08  H2   O   P    115.51  3.000
 Q08  H3   C7  C3   106.80  3.000
 Q08  H3   C7  N    111.16  3.000
 Q08  C3   C7  N    112.10  3.000
 Q08  H3   C7  P    105.47  3.000
 Q08  C3   C7  P    116.23  3.000
 Q08  N    C7  P    104.94  3.000
 Q08  H5   N   H4   106.05  3.000
 Q08  H5   N   C7   110.12  3.000
 Q08  H4   N   C7   109.35  3.000
 Q08  H7   C3  C2   106.09  3.000
 Q08  H7   C3  C4   107.28  3.000
 Q08  C2   C3  C4   109.47  3.000
 Q08  H7   C3  C7   104.20  3.000
 Q08  C2   C3  C7   112.73  3.000
 Q08  C4   C3  C7   116.29  3.000
 Q08  H9   C4  H8   105.51  3.000
 Q08  H9   C4  C5   108.09  3.000
 Q08  H8   C4  C5   109.31  3.000
 Q08  H9   C4  C3   106.61  3.000
 Q08  H8   C4  C3   109.80  3.000
 Q08  C5   C4  C3   116.88  3.000
 Q08  H11  C5  H10  106.48  3.000
 Q08  H11  C5  C6   109.83  3.000
 Q08  H10  C5  C6   109.41  3.000
 Q08  H11  C5  C4   109.98  3.000
 Q08  H10  C5  C4   109.32  3.000
 Q08  C6   C5  C4   111.68  3.000
 Q08  H14  C6  H13  107.50  3.000
 Q08  H14  C6  H12  107.59  3.000
 Q08  H13  C6  H12  107.52  3.000
 Q08  H14  C6  C5   111.43  3.000
 Q08  H13  C6  C5   111.09  3.000
 Q08  H12  C6  C5   111.51  3.000
 Q08  H16  C2  H15  105.78  3.000
 Q08  H16  C2  C1   109.76  3.000
 Q08  H15  C2  C1   107.74  3.000
 Q08  H16  C2  C3   110.18  3.000
 Q08  H15  C2  C3   107.21  3.000
 Q08  C1   C2  C3   115.65  3.000
 Q08  H18  C1  H17  106.22  3.000
 Q08  H18  C1  C    109.47  3.000
 Q08  H17  C1  C    108.69  3.000
 Q08  H18  C1  C2   109.23  3.000
 Q08  H17  C1  C2   110.93  3.000
 Q08  C    C1  C2   112.12  3.000
 Q08  H21  C   H20  107.53  3.000
 Q08  H21  C   H19  107.59  3.000
 Q08  H20  C   H19  107.58  3.000
 Q08  H21  C   C1   111.18  3.000
 Q08  H20  C   C1   111.29  3.000
 Q08  H19  C   C1   111.47  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
 Q08  Var_01  C5   C4  C3  C7   -60.09  30.0  1
 Q08  Var_02  C1   C2  C3  C7    62.09  30.0  3
 Q08  Var_03  C6   C5  C4  C3  -175.61  30.0  3
 Q08  Var_04  C    C1  C2  C3   174.55  30.0  3
 Q08  Var_05  H12  C6  C5  C4   178.60  30.0  3
 Q08  Var_06  H19  C   C1  C2  -179.92  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
 Q08  chir_01  C7  N  C3  P  negativ

