# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 23 09:12:41 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  26  14  .  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_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  -0.718  -0.3731  -7.0274  -0.3910
 PMI  P10   P  P     0   1.395   0.9095  -6.2921  -0.2443
 PMI  O12   O  OH1   0  -0.741   0.9365  -5.2358   0.9658
 PMI  O13   O  OH1   0  -0.755   2.1893  -7.2468  -0.0192
 PMI  C8'   C  CR5   0  -0.154   1.4460  -5.2844  -1.6736
 PMI  C9'   C  CH2   0  -0.520   0.3230  -4.2705  -1.9999
 PMI  C2'   C  CR56  0   0.109   0.7348  -3.0249  -1.2738
 PMI  N11   N  NH2   0  -0.814   1.6040  -6.2482  -2.7474
 PMI  C7'   C  CH2   0  -0.506   2.6741  -4.3927  -1.3500
 PMI  C1'   C  CR56  0   0.117   2.0750  -3.0918  -0.9060
 PMI  C6'   C  CR16  0  -0.326   2.6757  -2.0368  -0.2404
 PMI  C5'   C  CR16  0  -0.261   1.9179  -0.9081   0.0591
 PMI  C4'   C  CR16  0  -0.261   0.5785  -0.8419  -0.3074
 PMI  C3'   C  CR16  0  -0.325  -0.0213  -1.9029  -0.9802
 PMI  HO12  H  HOH1  0   0.491   0.4130  -5.5061   1.7325
 PMI  HO13  H  HOH1  0   0.491   1.9682  -8.1081   0.3594
 PMI  H9'1  H  HCH2  0   0.266  -0.6781  -4.6217  -1.7417
 PMI  H9'2  H  HCH2  0   0.272   0.3155  -4.0918  -3.0814
 PMI  H111  H  HNH2  0   0.357   1.7093  -5.7578  -3.6279
 PMI  H112  H  HNH2  0   0.358   2.4488  -6.7919  -2.6218
 PMI  H7'1  H  HCH2  0   0.267   3.2427  -4.2544  -2.2764
 PMI  H7'2  H  HCH2  0   0.262   3.3670  -4.8302  -0.6288
 PMI  H6'   H  HCR6  0   0.246   3.7181  -2.0868   0.0512
 PMI  H5'   H  HCR6  0   0.251   2.3731  -0.0783   0.5845
 PMI  H4'   H  HCR6  0   0.251  -0.0031   0.0379  -0.0629
 PMI  H3'   H  HCR6  0   0.247  -1.0660  -1.8476  -1.2616

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   double    1.486  0.020  1.486
 PMI  P10  O13   single    1.612  0.020  1.612
 PMI  P10  C8'   single    1.829  0.020  1.829
 PMI  P10  O12   single    1.607  0.020  1.607
 PMI  O12  HO12  single    0.850  0.020  0.980
 PMI  O13  HO13  single    0.850  0.020  0.980
 PMI  C8'  N11   single    1.452  0.020  1.452
 PMI  C8'  C9'   single    1.548  0.020  1.548
 PMI  C8'  C7'   single    1.552  0.020  1.552
 PMI  C9'  C2'   single    1.499  0.020  1.499
 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  1.384  0.020  1.384
 PMI  C2'  C1'   aromatic  1.391  0.020  1.391
 PMI  N11  H111  single    0.890  0.020  1.040
 PMI  N11  H112  single    0.890  0.020  1.040
 PMI  C7'  C1'   single    1.499  0.020  1.499
 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  1.392  0.020  1.392
 PMI  C6'  H6'   single    0.930  0.020  1.080
 PMI  C5'  C4'   aromatic  1.390  0.020  1.390
 PMI  C5'  H5'   single    0.930  0.020  1.080
 PMI  C4'  C3'   aromatic  1.392  0.020  1.392
 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   101.68  3.000
 PMI  C8'   P10  O12   102.79  3.000
 PMI  O13   P10  O12   105.71  3.000
 PMI  O12   P10  O14   114.48  3.000
 PMI  C8'   P10  O14   116.66  3.000
 PMI  O13   P10  O14   113.95  3.000
 PMI  HO12  O12  P10   113.85  3.000
 PMI  HO13  O13  P10   113.63  3.000
 PMI  C7'   C8'  N11   116.72  3.000
 PMI  C7'   C8'  C9'   103.99  3.000
 PMI  N11   C8'  C9'   110.97  3.000
 PMI  C7'   C8'  P10   112.69  3.000
 PMI  C9'   C8'  P10   108.23  3.000
 PMI  N11   C8'  P10   104.14  3.000
 PMI  H9'2  C9'  H9'1  106.23  3.000
 PMI  H9'2  C9'  C2'   110.13  3.000
 PMI  H9'1  C9'  C2'   113.86  3.000
 PMI  H9'2  C9'  C8'   108.65  3.000
 PMI  H9'1  C9'  C8'   113.87  3.000
 PMI  C2'   C9'  C8'   104.05  3.000
 PMI  C3'   C2'  C1'   120.59  3.000
 PMI  C1'   C2'  C9'   110.65  3.000
 PMI  C3'   C2'  C9'   128.75  3.000
 PMI  H112  N11  H111  106.31  3.000
 PMI  H112  N11  C8'   110.83  3.000
 PMI  H111  N11  C8'   109.44  3.000
 PMI  H7'2  C7'  H7'1  106.24  3.000
 PMI  H7'2  C7'  C1'   113.93  3.000
 PMI  H7'1  C7'  C1'   110.38  3.000
 PMI  H7'2  C7'  C8'   114.19  3.000
 PMI  H7'1  C7'  C8'   107.87  3.000
 PMI  C1'   C7'  C8'   104.13  3.000
 PMI  C6'   C1'  C7'   129.06  3.000
 PMI  C6'   C1'  C2'   120.55  3.000
 PMI  C7'   C1'  C2'   110.38  3.000
 PMI  H6'   C6'  C5'   120.21  3.000
 PMI  H6'   C6'  C1'   120.77  3.000
 PMI  C5'   C6'  C1'   119.02  3.000
 PMI  H5'   C5'  C4'   119.77  3.000
 PMI  H5'   C5'  C6'   119.80  3.000
 PMI  C4'   C5'  C6'   120.42  3.000
 PMI  H4'   C4'  C3'   119.80  3.000
 PMI  H4'   C4'  C5'   119.79  3.000
 PMI  C3'   C4'  C5'   120.41  3.000
 PMI  H3'   C3'  C4'   120.14  3.000
 PMI  H3'   C3'  C2'   120.86  3.000
 PMI  C4'   C3'  C2'   119.00  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'  -164.90  30.0  1
 PMI  Var_02    C2'  C1'  C7'  C8'   -15.78  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

