# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 18:05:45 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  25  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 OK
;

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   1.370  -1.9447  -0.5083  -0.0750
 02F  C1    C  CH3   0  -0.396   5.0324  -0.1097  -0.1089
 02F  C2    C  CH2   0  -0.118   2.7816   0.5180  -0.1716
 02F  O2    O  O2    0  -0.488   3.7168  -0.4445   0.2491
 02F  C4    C  CH2   0  -0.460   0.3496   1.1020  -0.2148
 02F  C5    C  CH1   0  -0.366  -1.0462   1.0001   0.4140
 02F  N6    N  NH2   0  -0.790  -1.9190   2.1128   0.0648
 02F  OP1   O  O     0  -0.721  -2.1432  -0.6607  -1.5378
 02F  OP2   O  OH1   0  -0.745  -1.1507  -1.7939   0.4850
 02F  OP3   O  OH1   0  -0.744  -3.2775  -0.3978   0.8157
 02F  H1    H  HCH3  0   0.202   5.3580   0.8317   0.3502
 02F  H1A   H  HCH3  0   0.232   5.6914  -0.9056   0.2373
 02F  H1B   H  HCH3  0   0.202   5.1516  -0.0105  -1.1948
 02F  H2    H  HCH2  0   0.194   3.0240   1.5035   0.2535
 02F  H2A   H  HCH2  0   0.194   2.8124   0.6326  -1.2660
 02F  H3    H  HCH2  0   0.237   1.1818  -0.8989  -0.1294
 02F  H3A   H  HCH2  0   0.226   1.3621   0.0228   1.3562
 02F  H4    H  HCH2  0   0.244   0.7019   2.1124   0.0187
 02F  H4A   H  HCH2  0   0.236   0.2561   1.0586  -1.3045
 02F  H5    H  HCH1  0   0.280  -0.9435   0.9828   1.5036
 02F  HN6   H  HNH2  0   0.361  -1.5558   2.9596   0.4841
 02F  HOP2  H  HOH1  0   0.488  -1.0141  -1.8152   1.4409
 02F  HOP3  H  HOH1  0   0.491  -3.9443  -1.0659   0.6054
 02F  H6    H  HNH2  0   0.349  -1.8944   2.2648  -0.9367
 02F  C3    C  CH2   0  -0.480   1.3917   0.0965   0.2646

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   single  1.612  0.020  1.612
 02F  P    OP1   double  1.484  0.020  1.484
 02F  C2   C3    single  1.516  0.020  1.516
 02F  O2   C1    single  1.404  0.020  1.404
 02F  O2   C2    single  1.406  0.020  1.406
 02F  C3   C4    single  1.525  0.020  1.525
 02F  C4   C5    single  1.534  0.020  1.534
 02F  C5   P     single  1.823  0.020  1.823
 02F  N6   C5    single  1.457  0.020  1.457
 02F  P    OP3   single  1.607  0.020  1.607
 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  OP2  HOP2  single  0.850  0.020  0.980
 02F  OP3  HOP3  single  0.850  0.020  0.980
 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  105.72  3.000
 02F  OP3   P    OP1  116.26  3.000
 02F  OP2   P    OP1  109.05  3.000
 02F  OP3   P    C5   101.73  3.000
 02F  OP1   P    C5   114.55  3.000
 02F  OP2   P    C5   108.91  3.000
 02F  H1B   C1   H1A  108.36  3.000
 02F  H1B   C1   H1   107.73  3.000
 02F  H1A   C1   H1   108.32  3.000
 02F  H1B   C1   O2   112.07  3.000
 02F  H1A   C1   O2   108.15  3.000
 02F  H1    C1   O2   112.09  3.000
 02F  H2A   C2   H2   106.53  3.000
 02F  H2A   C2   C3   109.91  3.000
 02F  H2    C2   C3   109.86  3.000
 02F  H2A   C2   O2   110.49  3.000
 02F  H2    C2   O2   110.54  3.000
 02F  C3    C2   O2   109.47  3.000
 02F  C2    O2   C1   112.56  3.000
 02F  H4A   C4   H4   106.04  3.000
 02F  H4A   C4   C5   109.13  3.000
 02F  H4    C4   C5   105.46  3.000
 02F  H4A   C4   C3   110.19  3.000
 02F  H4    C4   C3   108.74  3.000
 02F  C5    C4   C3   116.68  3.000
 02F  H5    C5   N6   107.87  3.000
 02F  H5    C5   C4   108.89  3.000
 02F  N6    C5   C4   113.34  3.000
 02F  H5    C5   P    107.48  3.000
 02F  N6    C5   P    105.81  3.000
 02F  C4    C5   P    113.18  3.000
 02F  H6    N6   HN6  105.97  3.000
 02F  H6    N6   C5   109.69  3.000
 02F  HN6   N6   C5   108.95  3.000
 02F  HOP2  OP2  P    115.54  3.000
 02F  HOP3  OP3  P    113.83  3.000
 02F  H3A   C3   H3   107.06  3.000
 02F  H3A   C3   C4   109.84  3.000
 02F  H3    C3   C4   110.89  3.000
 02F  H3A   C3   C2   109.29  3.000
 02F  H3    C3   C2   109.03  3.000
 02F  C4    C3   C2   110.65  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  -179.31  30.0  3
 02F  Var_02  C5  C4  C3  C2  -166.15  30.0  3
 02F  Var_03  C4  C3  C2  O2  -178.30  30.0  3
 02F  Var_04  H1  C1  O2  C2    61.44  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

