# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 11:55:44 2022
#   Inital geometry file: a 58 line input string
#   Ligand name: [(R)-(2,4-dichlorophenyl)(sulfanyl)methyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)[C@H](S)c1ccc(Cl)cc1Cl
#
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
 SDF  SDF  '[(R)-(2,4-dichlorophenyl)(sulfanyl)methyl]phosphonic acid'  ligand  19  14  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SDF
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
 SDF  C1   C   C      0   0.313   0.1309   0.0167   0.4853
 SDF  P1   P   P      0   1.209  -2.3276   0.3292  -0.7981
 SDF  S1   S   S2     0  -0.283  -1.9110   0.7446   2.2088
 SDF  CL1  CL  CL     0  -0.141   0.3411  -2.6363  -0.1054
 SDF  C2   C   C      0  -0.123   0.9588  -1.0203   0.0556
 SDF  CL2  CL  CL     0  -0.137   4.5225   0.6746  -0.4848
 SDF  C3   C   C1     0  -0.163   2.3035  -0.8381  -0.2379
 SDF  C4   C   C      0  -0.076   2.8431   0.4298  -0.1249
 SDF  C5   C   C1     0  -0.198   2.0599   1.4984   0.2807
 SDF  C6   C   C1     0  -0.312   0.7256   1.2772   0.5725
 SDF  C7   C   CH1    0  -0.736  -1.3237  -0.1654   0.7492
 SDF  O13  O   OP    -1  -0.869  -1.5945  -0.3774  -1.9328
 SDF  H3   H   H      0   0.288   2.9151  -1.6732  -0.5511
 SDF  H5   H   H      0   0.272   2.4809   2.4911   0.3659
 SDF  H6   H   H      0   0.247   0.1215   2.1122   0.8988
 SDF  H61  H   HSH1   0   0.207  -2.2684   1.8541   1.5473
 SDF  H7   H   HCH1   0   0.257  -1.5390  -1.2132   0.9554
 SDF  O11  O   OP    -1  -0.883  -3.7325  -0.1973  -0.5148
 SDF  O12  O   O      0  -0.874  -2.2147   1.8575  -0.8187

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
 SDF  C1   C7   single    1.490  0.020  1.490
 SDF  C1   C6   aromatic  1.397  0.020  1.397
 SDF  P1   O11  deloc     1.527  0.020  1.527
 SDF  P1   O13  deloc     1.525  0.020  1.525
 SDF  S1   C7   single    1.818  0.020  1.818
 SDF  CL1  C2   single    1.738  0.020  1.738
 SDF  C2   C1   aromatic  1.395  0.020  1.395
 SDF  CL2  C4   single    1.735  0.020  1.735
 SDF  C3   C2   aromatic  1.388  0.020  1.388
 SDF  C3   C4   aromatic  1.383  0.020  1.383
 SDF  C3   H3   single    0.930  0.020  1.080
 SDF  C4   C5   aromatic  1.386  0.020  1.386
 SDF  C5   C6   aromatic  1.384  0.020  1.384
 SDF  C5   H5   single    0.930  0.020  1.080
 SDF  C6   H6   single    0.930  0.020  1.080
 SDF  C7   P1   single    1.910  0.020  1.910
 SDF  O12  P1   deloc     1.533  0.020  1.533
 SDF  S1   H61  single    1.200  0.020  1.300
 SDF  C7   H7   single    0.970  0.020  1.090

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
 SDF  C7   C1  C6   121.01  3.000
 SDF  C6   C1  C2   115.95  3.000
 SDF  C7   C1  C2   122.91  3.000
 SDF  O13  P1  O12  114.63  3.000
 SDF  O12  P1  O11  114.46  3.000
 SDF  O13  P1  O11  114.88  3.000
 SDF  O12  P1  C7   103.32  3.000
 SDF  O13  P1  C7   103.31  3.000
 SDF  O11  P1  C7   104.12  3.000
 SDF  H61  S1  C7    95.98  3.000
 SDF  C3   C2  CL1  116.54  3.000
 SDF  C3   C2  C1   122.85  3.000
 SDF  CL1  C2  C1   120.60  3.000
 SDF  H3   C3  C4   120.74  3.000
 SDF  H3   C3  C2   120.51  3.000
 SDF  C4   C3  C2   118.75  3.000
 SDF  C5   C4  C3   120.71  3.000
 SDF  C5   C4  CL2  119.94  3.000
 SDF  C3   C4  CL2  119.35  3.000
 SDF  H5   C5  C6   120.36  3.000
 SDF  H5   C5  C4   120.73  3.000
 SDF  C6   C5  C4   118.92  3.000
 SDF  H6   C6  C5   118.63  3.000
 SDF  H6   C6  C1   118.56  3.000
 SDF  C5   C6  C1   122.81  3.000
 SDF  H7   C7  S1   105.41  3.000
 SDF  H7   C7  P1   107.38  3.000
 SDF  S1   C7  P1   110.56  3.000
 SDF  H7   C7  C1   110.12  3.000
 SDF  P1   C7  C1   109.77  3.000
 SDF  S1   C7  C1   113.37  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
 SDF  CONST_01  C4   C5  C6  C1     0.00  0.0  0
 SDF  CONST_02  C4   C3  C2  C1     0.00  0.0  0
 SDF  CONST_03  C5   C6  C1  C2     0.00  0.0  0
 SDF  CONST_04  C5   C4  C3  C2     0.00  0.0  0
 SDF  CONST_05  C6   C1  C2  C3     0.00  0.0  0
 SDF  CONST_06  C6   C5  C4  C3     0.00  0.0  0
 SDF  CONST_07  C6   C1  C2  CL1  180.00  0.0  0
 SDF  CONST_08  C4   C3  C2  CL1  180.00  0.0  0
 SDF  CONST_09  CL2  C4  C3  C2   180.00  0.0  0
 SDF  CONST_10  C6   C5  C4  CL2  180.00  0.0  0
 SDF  CONST_11  C7   C1  C2  C3   180.00  0.0  0
 SDF  CONST_12  C7   C1  C6  C5   180.00  0.0  0
 SDF  CONST_13  H5   C5  C6  C1   180.00  0.0  0
 SDF  CONST_14  H3   C3  C2  C1   180.00  0.0  0
 SDF  CONST_15  H6   C6  C1  C2   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
 SDF  chir_01  C7  C1  S1  P1  negativ

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
 SDF  plan-1  C1   0.020
 SDF  plan-1  CL1  0.020
 SDF  plan-1  C2   0.020
 SDF  plan-1  CL2  0.020
 SDF  plan-1  C3   0.020
 SDF  plan-1  C4   0.020
 SDF  plan-1  C5   0.020
 SDF  plan-1  C6   0.020
 SDF  plan-1  C7   0.020
 SDF  plan-1  H3   0.020
 SDF  plan-1  H5   0.020
 SDF  plan-1  H6   0.020

