# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 02:47:44 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: (2-amino-2,3-dihydro-1H-inden-2-yl)phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1(Cc2ccccc2C1)[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
 PMI  PMI  '(2-amino-2,3-dihydro-1H-inden-2-yl)phosphonic acid'  ligand  24  14  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PMI
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
 PMI  O14   O  O      0  -0.908  -0.4588  -6.9318  -0.5830
 PMI  P10   P  P      0   1.187   0.9117  -6.3268  -0.2453
 PMI  O12   O  OP    -1  -0.890   0.8797  -5.3522   0.9346
 PMI  O13   O  OP    -1  -0.910   2.0348  -7.3767  -0.1557
 PMI  C8'   C  CT     0  -0.123   1.3964  -5.2964  -1.7400
 PMI  C9'   C  CH2    0  -0.503   0.3056  -4.2539  -2.0586
 PMI  C2'   C  C      0   0.111   0.7304  -3.0249  -1.3142
 PMI  N11   N  NH2    0  -0.830   1.5901  -6.2056  -2.8625
 PMI  C7'   C  CH2    0  -0.510   2.6365  -4.4336  -1.3914
 PMI  C1'   C  C      0   0.133   2.0682  -3.1258  -0.9353
 PMI  C6'   C  C1     0  -0.341   2.6888  -2.0800  -0.2727
 PMI  C5'   C  C1     0  -0.269   1.9595  -0.9305   0.0262
 PMI  C4'   C  C1     0  -0.268   0.6241  -0.8327  -0.3446
 PMI  C3'   C  C1     0  -0.340   0.0051  -1.8813  -1.0230
 PMI  H9'1  H  HCH2   0   0.227  -0.6935  -4.6055  -1.7917
 PMI  H9'2  H  HCH2   0   0.219   0.2822  -4.0386  -3.1361
 PMI  H111  H  HNH2   0   0.312   2.0923  -5.7315  -3.6069
 PMI  H112  H  HNH2   0   0.319   2.1900  -6.9619  -2.5542
 PMI  H7'1  H  HCH2   0   0.214   3.2510  -4.2717  -2.2888
 PMI  H7'2  H  HCH2   0   0.223   3.2893  -4.9083  -0.6553
 PMI  H6'   H  H      0   0.233   3.7307  -2.1515   0.0185
 PMI  H5'   H  H      0   0.240   2.4349  -0.1104   0.5498
 PMI  H4'   H  H      0   0.240   0.0624   0.0620  -0.1052
 PMI  H3'   H  H      0   0.233  -1.0361  -1.7961  -1.3136

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
 PMI  O14  P10   deloc     1.536  0.020  1.536
 PMI  P10  O13   deloc     1.540  0.020  1.540
 PMI  P10  C8'   single    1.879  0.020  1.879
 PMI  P10  O12   deloc     1.531  0.020  1.531
 PMI  C8'  N11   single    1.457  0.020  1.457
 PMI  C8'  C9'   single    1.542  0.020  1.542
 PMI  C8'  C7'   single    1.550  0.020  1.550
 PMI  C9'  C2'   single    1.498  0.020  1.498
 PMI  C9'  H9'1  single    0.970  0.020  1.090
 PMI  C9'  H9'2  single    0.970  0.020  1.090
 PMI  C2'  C3'   aromatic  1.385  0.020  1.385
 PMI  C2'  C1'   aromatic  1.394  0.020  1.394
 PMI  N11  H111  single    0.890  0.020  1.040
 PMI  N11  H112  single    0.890  0.020  1.040
 PMI  C7'  C1'   single    1.497  0.020  1.497
 PMI  C7'  H7'1  single    0.970  0.020  1.090
 PMI  C7'  H7'2  single    0.970  0.020  1.090
 PMI  C1'  C6'   aromatic  1.385  0.020  1.385
 PMI  C6'  C5'   aromatic  1.394  0.020  1.394
 PMI  C6'  H6'   single    0.930  0.020  1.080
 PMI  C5'  C4'   aromatic  1.389  0.020  1.389
 PMI  C5'  H5'   single    0.930  0.020  1.080
 PMI  C4'  C3'   aromatic  1.394  0.020  1.394
 PMI  C4'  H4'   single    0.930  0.020  1.080
 PMI  C3'  H3'   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
 PMI  C8'   P10  O13   103.42  3.000
 PMI  C8'   P10  O12   105.63  3.000
 PMI  O13   P10  O12   113.86  3.000
 PMI  O12   P10  O14   113.68  3.000
 PMI  C8'   P10  O14   105.74  3.000
 PMI  O13   P10  O14   113.27  3.000
 PMI  C7'   C8'  N11   114.46  3.000
 PMI  C7'   C8'  C9'   103.65  3.000
 PMI  N11   C8'  C9'   110.89  3.000
 PMI  C7'   C8'  P10   109.43  3.000
 PMI  C9'   C8'  P10   110.65  3.000
 PMI  N11   C8'  P10   107.75  3.000
 PMI  H9'2  C9'  H9'1  106.45  3.000
 PMI  H9'2  C9'  C2'   109.42  3.000
 PMI  H9'1  C9'  C2'   113.70  3.000
 PMI  H9'2  C9'  C8'   110.49  3.000
 PMI  H9'1  C9'  C8'   112.26  3.000
 PMI  C2'   C9'  C8'   104.56  3.000
 PMI  C3'   C2'  C1'   120.34  3.000
 PMI  C1'   C2'  C9'   110.35  3.000
 PMI  C3'   C2'  C9'   129.29  3.000
 PMI  H112  N11  H111  106.18  3.000
 PMI  H112  N11  C8'   108.05  3.000
 PMI  H111  N11  C8'   109.82  3.000
 PMI  H7'2  C7'  H7'1  106.26  3.000
 PMI  H7'2  C7'  C1'   113.65  3.000
 PMI  H7'1  C7'  C1'   109.40  3.000
 PMI  H7'2  C7'  C8'   112.81  3.000
 PMI  H7'1  C7'  C8'   110.21  3.000
 PMI  C1'   C7'  C8'   104.54  3.000
 PMI  C6'   C1'  C7'   129.44  3.000
 PMI  C6'   C1'  C2'   120.36  3.000
 PMI  C7'   C1'  C2'   110.16  3.000
 PMI  H6'   C6'  C5'   119.97  3.000
 PMI  H6'   C6'  C1'   120.62  3.000
 PMI  C5'   C6'  C1'   119.40  3.000
 PMI  H5'   C5'  C4'   119.84  3.000
 PMI  H5'   C5'  C6'   119.91  3.000
 PMI  C4'   C5'  C6'   120.25  3.000
 PMI  H4'   C4'  C3'   119.91  3.000
 PMI  H4'   C4'  C5'   119.84  3.000
 PMI  C3'   C4'  C5'   120.25  3.000
 PMI  H3'   C3'  C4'   119.85  3.000
 PMI  H3'   C3'  C2'   120.75  3.000
 PMI  C4'   C3'  C2'   119.40  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
 PMI  CONST_01  C5'  C4'  C3'  C2'     0.00   0.0  0
 PMI  CONST_02  C5'  C6'  C1'  C2'     0.00   0.0  0
 PMI  CONST_03  C4'  C3'  C2'  C1'     0.00   0.0  0
 PMI  CONST_04  C4'  C5'  C6'  C1'     0.00   0.0  0
 PMI  CONST_05  C3'  C2'  C1'  C6'     0.00   0.0  0
 PMI  CONST_06  C3'  C4'  C5'  C6'     0.00   0.0  0
 PMI  CONST_07  H3'  C3'  C2'  C9'     0.00   0.0  0
 PMI  CONST_08  H4'  C4'  C3'  C2'   180.00   0.0  0
 PMI  CONST_09  H6'  C6'  C1'  C2'   180.00   0.0  0
 PMI  CONST_10  H5'  C5'  C6'  C1'   180.00   0.0  0
 PMI  Var_01    C3'  C2'  C9'  C8'  -165.70  30.0  1
 PMI  Var_02    C2'  C1'  C7'  C8'   -15.67  30.0  1

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
 PMI  chir_01  C8'  N11  C9'  C7'  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
 PMI  plan-1  C9'  0.020
 PMI  plan-1  C2'  0.020
 PMI  plan-1  C7'  0.020
 PMI  plan-1  C1'  0.020
 PMI  plan-1  C6'  0.020
 PMI  plan-1  C5'  0.020
 PMI  plan-1  C4'  0.020
 PMI  plan-1  C3'  0.020
 PMI  plan-1  H6'  0.020
 PMI  plan-1  H5'  0.020
 PMI  plan-1  H4'  0.020
 PMI  plan-1  H3'  0.020

