# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 16:25:28 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: (R)-({[(4-iodophenyl)acetyl]amino}methyl)phosphinic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P@@H](=O)CNC(=O)Cc1ccc(I)cc1
#
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
 IPP  IPP  '(R)-({[(4-iodophenyl)acetyl]amino}methyl)phosphinic acid'  ligand  25  15  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IPP
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
 IPP  P    P  P      0   0.963  -0.9260   0.0497  -4.6222
 IPP  O1P  O  OP    -1  -0.812  -0.7693   0.2105  -6.1175
 IPP  O2P  O  O      0  -0.788  -1.1925  -1.3103  -4.0173
 IPP  C    C  CH2    0  -0.576   0.5650   0.7995  -3.8191
 IPP  N    N  NH1    0  -0.615   0.6225   0.5262  -2.4053
 IPP  C1   C  C      0   0.543   1.2409  -0.5455  -1.8898
 IPP  O1   O  O      0  -0.494   1.9778  -1.2791  -2.5333
 IPP  C2   C  CH2    0  -0.651   0.9928  -0.7810  -0.4110
 IPP  C1'  C  CR6    0   0.127   0.5612  -2.1964  -0.1407
 IPP  C2'  C  CR16   0  -0.279  -0.4715  -2.7724  -0.8789
 IPP  C3'  C  CR16   0  -0.218  -0.9074  -4.0611  -0.6102
 IPP  C4'  C  CR6    0  -0.235  -0.3027  -4.7832   0.4104
 IPP  I    I  I      0   0.043  -0.9585  -6.7402   0.8266
 IPP  C5'  C  CR16   0  -0.210   0.7288  -4.2355   1.1551
 IPP  C6'  C  CR16   0  -0.313   1.1532  -2.9428   0.8706
 IPP  H    H  H      0  -0.057  -1.9363   0.9556  -4.1592
 IPP  H1   H  HCH2   0   0.260   1.4595   0.4061  -4.3031
 IPP  H2   H  HCH2   0   0.261   0.5587   1.8796  -3.9799
 IPP  HN   H  HNH1   0   0.399  -0.0117   1.0352  -1.8121
 IPP  H21  H  HCH2   0   0.286   1.9200  -0.5650   0.1252
 IPP  H22  H  HCH2   0   0.275   0.2413  -0.0903  -0.0202
 IPP  H2'  H  HCR6   0   0.277  -0.9354  -2.2197  -1.6895
 IPP  H3'  H  HCR6   0   0.276  -1.7089  -4.4879  -1.1979
 IPP  H5'  H  HCR6   0   0.277   1.2087  -4.7950   1.9464
 IPP  H6'  H  HCR6   0   0.262   1.9618  -2.5183   1.4533

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
 IPP  P    O1P  deloc     1.512  0.020  1.512
 IPP  P    O2P  deloc     1.512  0.020  1.512
 IPP  P    C    single    1.852  0.020  1.852
 IPP  P    H    single    1.209  0.020  1.412
 IPP  C    N    single    1.441  0.020  1.441
 IPP  C    H1   single    0.970  0.020  1.090
 IPP  C    H2   single    0.970  0.020  1.090
 IPP  N    C1   single    1.340  0.020  1.340
 IPP  N    HN   single    0.860  0.020  1.020
 IPP  C1   O1   double    1.223  0.020  1.223
 IPP  C1   C2   single    1.518  0.020  1.518
 IPP  C2   C1'  single    1.504  0.020  1.504
 IPP  C2   H21  single    0.970  0.020  1.090
 IPP  C2   H22  single    0.970  0.020  1.090
 IPP  C1'  C2'  aromatic  1.394  0.020  1.394
 IPP  C1'  C6'  aromatic  1.389  0.020  1.389
 IPP  C2'  C3'  aromatic  1.387  0.020  1.387
 IPP  C2'  H2'  single    0.930  0.020  1.080
 IPP  C3'  C4'  aromatic  1.389  0.020  1.389
 IPP  C3'  H3'  single    0.930  0.020  1.080
 IPP  C4'  I    single    2.106  0.020  2.106
 IPP  C4'  C5'  aromatic  1.385  0.020  1.385
 IPP  C5'  C6'  aromatic  1.390  0.020  1.390
 IPP  C5'  H5'  single    0.930  0.020  1.080
 IPP  C6'  H6'  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
 IPP  H    P    C     99.87  3.000
 IPP  H    P    O2P  108.35  3.000
 IPP  C    P    O2P  109.42  3.000
 IPP  H    P    O1P  108.98  3.000
 IPP  C    P    O1P  107.60  3.000
 IPP  O2P  P    O1P  120.63  3.000
 IPP  H2   C    H1   107.23  3.000
 IPP  H2   C    N    109.40  3.000
 IPP  H1   C    N    109.53  3.000
 IPP  H2   C    P    109.39  3.000
 IPP  H1   C    P    108.78  3.000
 IPP  N    C    P    112.38  3.000
 IPP  HN   N    C1   117.93  3.000
 IPP  HN   N    C    117.20  3.000
 IPP  C1   N    C    123.18  3.000
 IPP  C2   C1   O1   121.20  3.000
 IPP  C2   C1   N    115.05  3.000
 IPP  O1   C1   N    123.73  3.000
 IPP  H22  C2   H21  106.44  3.000
 IPP  H22  C2   C1'  109.46  3.000
 IPP  H21  C2   C1'  109.96  3.000
 IPP  H22  C2   C1   111.26  3.000
 IPP  H21  C2   C1   107.98  3.000
 IPP  C1'  C2   C1   111.59  3.000
 IPP  C6'  C1'  C2'  118.63  3.000
 IPP  C6'  C1'  C2   120.93  3.000
 IPP  C2'  C1'  C2   120.41  3.000
 IPP  H2'  C2'  C3'  118.93  3.000
 IPP  H2'  C2'  C1'  120.12  3.000
 IPP  C3'  C2'  C1'  120.94  3.000
 IPP  H3'  C3'  C4'  121.11  3.000
 IPP  H3'  C3'  C2'  119.63  3.000
 IPP  C4'  C3'  C2'  119.26  3.000
 IPP  C5'  C4'  I    119.55  3.000
 IPP  C5'  C4'  C3'  120.91  3.000
 IPP  I    C4'  C3'  119.53  3.000
 IPP  H5'  C5'  C6'  119.70  3.000
 IPP  H5'  C5'  C4'  121.28  3.000
 IPP  C6'  C5'  C4'  119.02  3.000
 IPP  H6'  C6'  C5'  118.83  3.000
 IPP  H6'  C6'  C1'  119.94  3.000
 IPP  C5'  C6'  C1'  121.23  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
 IPP  CONST_01  C4'  C3'  C2'  C1'     0.00   0.0  0
 IPP  CONST_02  C4'  C5'  C6'  C1'     0.00   0.0  0
 IPP  CONST_03  C5'  C6'  C1'  C2'     0.00   0.0  0
 IPP  CONST_04  C5'  C4'  C3'  C2'     0.00   0.0  0
 IPP  CONST_05  C6'  C1'  C2'  C3'     0.00   0.0  0
 IPP  CONST_06  C6'  C5'  C4'  C3'     0.00   0.0  0
 IPP  CONST_07  C3'  C2'  C1'  C2    180.00   0.0  0
 IPP  CONST_08  C5'  C6'  C1'  C2    180.00   0.0  0
 IPP  CONST_09  I    C4'  C3'  C2'   180.00   0.0  0
 IPP  CONST_10  C6'  C5'  C4'  I     180.00   0.0  0
 IPP  CONST_11  H3'  C3'  C2'  C1'   180.00   0.0  0
 IPP  CONST_12  H5'  C5'  C6'  C1'   180.00   0.0  0
 IPP  CONST_13  H6'  C6'  C1'  C2'   180.00   0.0  0
 IPP  CONST_14  H2'  C2'  C3'  C4'   180.00   0.0  0
 IPP  CONST_15  O1   C1   N    C       0.00   0.0  0
 IPP  CONST_16  C2   C1   N    C     180.00   0.0  0
 IPP  CONST_17  HN   N    C1   O1    180.00   0.0  0
 IPP  Var_01    C2'  C1'  C2   C1    -49.85  30.0  2
 IPP  Var_02    C1'  C2   C1   N     129.27  30.0  3
 IPP  Var_03    C1   N    C    P      90.45  30.0  3
 IPP  Var_04    N    C    P    O1P  -171.23  30.0  3

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
 IPP  plan-1  C2   0.020
 IPP  plan-1  C1'  0.020
 IPP  plan-1  C2'  0.020
 IPP  plan-1  C3'  0.020
 IPP  plan-1  C4'  0.020
 IPP  plan-1  I    0.020
 IPP  plan-1  C5'  0.020
 IPP  plan-1  C6'  0.020
 IPP  plan-1  H2'  0.020
 IPP  plan-1  H3'  0.020
 IPP  plan-1  H5'  0.020
 IPP  plan-1  H6'  0.020
 IPP  plan-2  C    0.020
 IPP  plan-2  N    0.020
 IPP  plan-2  C1   0.020
 IPP  plan-2  O1   0.020
 IPP  plan-2  C2   0.020
 IPP  plan-2  HN   0.020

