# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 03:04:39 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  22  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 OK
;

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  OH1   0  -0.747   3.0547   0.0625  -0.4848
 Q02  P    P  P     0   1.353   1.6630   0.2048   0.3088
 Q02  O1   O  O     0  -0.711   1.6286  -0.3794   1.6715
 Q02  O2   O  OH1   0  -0.742   1.3347   1.7774   0.3885
 Q02  C    C  CH1   0  -0.458   0.5009  -0.5702  -0.8781
 Q02  N    N  NH2   0  -0.783   0.7472  -1.9952  -1.0139
 Q02  C1   C  CR6   0   0.142  -0.9070  -0.2586  -0.4342
 Q02  C6   C  CR16  0  -0.293  -1.5565  -1.0469   0.5123
 Q02  C5   C  CR16  0  -0.242  -2.8448  -0.7345   0.9242
 Q02  C4   C  CR16  0  -0.267  -3.4989   0.3731   0.4012
 Q02  C3   C  CR16  0  -0.241  -2.8567   1.1664  -0.5399
 Q02  C2   C  CR16  0  -0.300  -1.5690   0.8515  -0.9509
 Q02  H1   H  HOH1  0   0.495   3.8400   0.1915   0.0648
 Q02  H2   H  HOH1  0   0.490   1.4493   2.2755  -0.4310
 Q02  H3   H  HCH1  0   0.306   0.6652  -0.1086  -1.8558
 Q02  H4   H  HNH2  0   0.368   1.6112  -2.1536  -1.5157
 Q02  H5   H  HNH2  0   0.358   0.8587  -2.4405  -0.1116
 Q02  H7   H  HCR6  0   0.248  -1.0705  -1.9177   0.9325
 Q02  H8   H  HCR6  0   0.257  -3.3392  -1.3592   1.6569
 Q02  H9   H  HCR6  0   0.257  -4.5041   0.6130   0.7221
 Q02  H10  H  HCR6  0   0.257  -3.3596   2.0281  -0.9595
 Q02  H11  H  HCR6  0   0.251  -1.0804   1.4728  -1.6928

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    double    1.483  0.020  1.483
 Q02  C5  C6   aromatic  1.388  0.020  1.388
 Q02  C5  C4   aromatic  1.389  0.020  1.389
 Q02  C6  C1   aromatic  1.393  0.020  1.393
 Q02  C4  C3   aromatic  1.388  0.020  1.388
 Q02  O   P    single    1.608  0.020  1.608
 Q02  P   O2   single    1.609  0.020  1.609
 Q02  P   C    single    1.833  0.020  1.833
 Q02  C1  C    single    1.509  0.020  1.509
 Q02  C1  C2   aromatic  1.392  0.020  1.392
 Q02  C3  C2   aromatic  1.388  0.020  1.388
 Q02  C   N    single    1.453  0.020  1.453
 Q02  O   H1   single    0.850  0.020  0.980
 Q02  O2  H2   single    0.850  0.020  0.980
 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  H1   O   P   114.23  3.000
 Q02  C    P   O2  108.42  3.000
 Q02  C    P   O1  114.44  3.000
 Q02  O2   P   O1  109.57  3.000
 Q02  C    P   O   101.05  3.000
 Q02  O2   P   O   106.71  3.000
 Q02  O1   P   O   116.02  3.000
 Q02  H2   O2  P   115.97  3.000
 Q02  H3   C   C1  108.42  3.000
 Q02  H3   C   N   107.76  3.000
 Q02  C1   C   N   112.85  3.000
 Q02  H3   C   P   107.77  3.000
 Q02  N    C   P   111.58  3.000
 Q02  C1   C   P   108.29  3.000
 Q02  H5   N   H4  106.21  3.000
 Q02  H5   N   C   111.52  3.000
 Q02  H4   N   C   110.17  3.000
 Q02  C2   C1  C6  118.81  3.000
 Q02  C2   C1  C   119.96  3.000
 Q02  C6   C1  C   121.22  3.000
 Q02  H7   C6  C5  118.85  3.000
 Q02  H7   C6  C1  120.67  3.000
 Q02  C5   C6  C1  120.48  3.000
 Q02  H8   C5  C4  120.02  3.000
 Q02  H8   C5  C6  119.66  3.000
 Q02  C4   C5  C6  120.32  3.000
 Q02  H9   C4  C3  120.27  3.000
 Q02  H9   C4  C5  120.17  3.000
 Q02  C3   C4  C5  119.55  3.000
 Q02  H10  C3  C2  119.79  3.000
 Q02  H10  C3  C4  120.18  3.000
 Q02  C2   C3  C4  120.02  3.000
 Q02  H11  C2  C3  119.40  3.000
 Q02  H11  C2  C1  119.78  3.000
 Q02  C3   C2  C1  120.82  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

