# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 00:41:40 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: [(R)-amino(phenyl)methyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](c1ccccc1)[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
 Q02  Q02  '[(R)-amino(phenyl)methyl]phosphonic acid'  ligand  20  12  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Q02
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
 Q02  O    O  OP    -1  -0.905   3.0569   0.0436  -0.6085
 Q02  P    P  P      0   1.159   1.7251   0.4102   0.0655
 Q02  O1   O  O      0  -0.898   1.5934  -0.1132   1.5018
 Q02  O2   O  OP    -1  -0.888   1.3336   1.8810  -0.1115
 Q02  C    C  CH1    0  -0.442   0.4613  -0.6035  -0.9010
 Q02  N    N  NH2    0  -0.810   0.7745  -2.0370  -0.8306
 Q02  C1   C  C      0   0.169  -0.9329  -0.3152  -0.4471
 Q02  C6   C  C1     0  -0.333  -1.6477  -1.1850   0.3756
 Q02  C5   C  C1     0  -0.245  -2.9303  -0.8731   0.8146
 Q02  C4   C  C1     0  -0.289  -3.5322   0.3188   0.4394
 Q02  C3   C  C1     0  -0.253  -2.8330   1.1963  -0.3836
 Q02  C2   C  C1     0  -0.293  -1.5521   0.8847  -0.8116
 Q02  H3   H  HCH1   0   0.203   0.5383  -0.3051  -1.9535
 Q02  H4   H  HNH2   0   0.331   1.6998  -2.1473  -1.2302
 Q02  H5   H  HNH2   0   0.322   0.9196  -2.2593   0.1501
 Q02  H7   H  H      0   0.225  -1.2127  -2.1307   0.6710
 Q02  H8   H  H      0   0.240  -3.4610  -1.5698   1.4523
 Q02  H9   H  H      0   0.240  -4.5323   0.5596   0.7768
 Q02  H10  H  H      0   0.239  -3.2894   2.1293  -0.6920
 Q02  H11  H  H      0   0.225  -1.0168   1.5800  -1.4448

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
 Q02  O1  P    deloc     1.534  0.020  1.534
 Q02  C5  C6   aromatic  1.391  0.020  1.391
 Q02  C5  C4   aromatic  1.387  0.020  1.387
 Q02  C6  C1   aromatic  1.394  0.020  1.394
 Q02  C4  C3   aromatic  1.391  0.020  1.391
 Q02  O   P    deloc     1.537  0.020  1.537
 Q02  P   O2   deloc     1.532  0.020  1.532
 Q02  P   C    single    1.887  0.020  1.887
 Q02  C1  C    single    1.494  0.020  1.494
 Q02  C1  C2   aromatic  1.399  0.020  1.399
 Q02  C3  C2   aromatic  1.386  0.020  1.386
 Q02  C   N    single    1.469  0.020  1.469
 Q02  C   H3   single    0.970  0.020  1.090
 Q02  N   H4   single    0.890  0.020  1.040
 Q02  N   H5   single    0.890  0.020  1.040
 Q02  C6  H7   single    0.930  0.020  1.080
 Q02  C5  H8   single    0.930  0.020  1.080
 Q02  C4  H9   single    0.930  0.020  1.080
 Q02  C3  H10  single    0.930  0.020  1.080
 Q02  C2  H11  single    0.930  0.020  1.080

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
 Q02  C    P   O2  106.58  3.000
 Q02  C    P   O1  103.81  3.000
 Q02  O2   P   O1  114.43  3.000
 Q02  C    P   O   103.16  3.000
 Q02  O2   P   O   113.56  3.000
 Q02  O1   P   O   113.80  3.000
 Q02  H3   C   C1  107.73  3.000
 Q02  H3   C   N   107.25  3.000
 Q02  C1   C   N   111.88  3.000
 Q02  H3   C   P   107.37  3.000
 Q02  N    C   P   110.91  3.000
 Q02  C1   C   P   111.45  3.000
 Q02  H5   N   H4  103.08  3.000
 Q02  H5   N   C   106.87  3.000
 Q02  H4   N   C   106.37  3.000
 Q02  C2   C1  C6  117.52  3.000
 Q02  C2   C1  C   119.96  3.000
 Q02  C6   C1  C   122.49  3.000
 Q02  H7   C6  C5  118.72  3.000
 Q02  H7   C6  C1  120.01  3.000
 Q02  C5   C6  C1  121.26  3.000
 Q02  H8   C5  C4  119.95  3.000
 Q02  H8   C5  C6  119.55  3.000
 Q02  C4   C5  C6  120.50  3.000
 Q02  H9   C4  C3  120.55  3.000
 Q02  H9   C4  C5  120.52  3.000
 Q02  C3   C4  C5  118.93  3.000
 Q02  H10  C3  C2  119.67  3.000
 Q02  H10  C3  C4  119.98  3.000
 Q02  C2   C3  C4  120.35  3.000
 Q02  H11  C2  C3  119.57  3.000
 Q02  H11  C2  C1  118.99  3.000
 Q02  C3   C2  C1  121.44  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
 Q02  CONST_01  C4   C5  C6  C1    0.00  0.0  0
 Q02  CONST_02  C4   C3  C2  C1    0.00  0.0  0
 Q02  CONST_03  C3   C4  C5  C6    0.00  0.0  0
 Q02  CONST_04  C3   C2  C1  C6    0.00  0.0  0
 Q02  CONST_05  C2   C1  C6  C5    0.00  0.0  0
 Q02  CONST_06  C2   C3  C4  C5    0.00  0.0  0
 Q02  CONST_07  C5   C6  C1  C   180.00  0.0  0
 Q02  CONST_08  C3   C2  C1  C   180.00  0.0  0
 Q02  CONST_09  H8   C5  C6  C1  180.00  0.0  0
 Q02  CONST_10  H10  C3  C2  C1  180.00  0.0  0
 Q02  CONST_11  H9   C4  C5  C6  180.00  0.0  0
 Q02  CONST_12  H11  C2  C1  C6  180.00  0.0  0
 Q02  CONST_13  H7   C6  C5  C4  180.00  0.0  0

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
 Q02  chir_01  C  P  C1  N  positiv

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
 Q02  plan-1  C    0.020
 Q02  plan-1  C1   0.020
 Q02  plan-1  C6   0.020
 Q02  plan-1  C5   0.020
 Q02  plan-1  C4   0.020
 Q02  plan-1  C3   0.020
 Q02  plan-1  C2   0.020
 Q02  plan-1  H7   0.020
 Q02  plan-1  H8   0.020
 Q02  plan-1  H9   0.020
 Q02  plan-1  H10  0.020
 Q02  plan-1  H11  0.020

