# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 02:51:51 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: [(R)-hydroxy(4-methylphenyl)methyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)[C@H](O)[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
 BOY  BOY  '[(R)-hydroxy(4-methylphenyl)methyl]phosphonic acid'  ligand  22  13  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BOY
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
 BOY  CAA   C  CH3    0  -0.723   4.6811  -0.4504   0.5066
 BOY  CAF   C  CR16   0  -0.294   2.5512  -0.9735  -0.7422
 BOY  CAG   C  CR16   0  -0.293   2.5794   0.9390   0.6764
 BOY  CAH   C  CR16   0  -0.292   1.2296  -0.7121  -1.0642
 BOY  CAI   C  CR16   0  -0.312   1.2548   1.2051   0.3472
 BOY  CAJ   C  CR6    0   0.073   3.2543  -0.1535   0.1414
 BOY  CAK   C  CR6    0   0.137   0.5532   0.3851  -0.5308
 BOY  CAL   C  CH1    0  -0.328  -0.8818   0.6329  -0.8776
 BOY  OAC   O  OH1    0  -0.714  -1.2440   1.9935  -0.7333
 BOY  PAM   P  P      0   1.152  -2.0695  -0.3351   0.2493
 BOY  HAA3  H  HCH3   0   0.240   4.7430  -1.2126   1.2869
 BOY  HAA2  H  HCH3   0   0.237   5.2454  -0.8235  -0.3489
 BOY  HAA1  H  HCH3   0   0.237   5.1916   0.4369   0.8810
 BOY  HAF1  H  HCR6   0   0.232   3.0505  -1.8273  -1.1877
 BOY  HAG1  H  HCR6   0   0.231   3.0991   1.6030   1.3592
 BOY  HAH1  H  HCR6   0   0.225   0.7158  -1.3650  -1.7615
 BOY  HAI1  H  HCR6   0   0.227   0.7707   2.0749   0.7717
 BOY  HAL1  H  HCH1   0   0.194  -1.0442   0.3240  -1.9183
 BOY  HAC1  H  HOH1   0   0.423  -1.7152   1.9732   0.1315
 BOY  OAB   O  OP    -1  -0.893  -2.3411   0.7834   1.2887
 BOY  OAD   O  OP    -1  -0.892  -3.2878  -0.6680  -0.6130
 BOY  OAE   O  O      0  -0.867  -1.3309  -1.5480   0.8011

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
 BOY  CAA  CAJ   single    1.502  0.020  1.502
 BOY  CAJ  CAG   aromatic  1.391  0.020  1.391
 BOY  CAJ  CAF   aromatic  1.396  0.020  1.396
 BOY  CAG  CAI   aromatic  1.391  0.020  1.391
 BOY  CAF  CAH   aromatic  1.385  0.020  1.385
 BOY  CAI  CAK   aromatic  1.391  0.020  1.391
 BOY  CAH  CAK   aromatic  1.395  0.020  1.395
 BOY  CAK  CAL   single    1.497  0.020  1.497
 BOY  OAE  PAM   deloc     1.524  0.020  1.524
 BOY  OAC  CAL   single    1.415  0.020  1.415
 BOY  CAL  PAM   single    1.902  0.020  1.902
 BOY  PAM  OAD   deloc     1.529  0.020  1.529
 BOY  PAM  OAB   deloc     1.551  0.020  1.551
 BOY  CAA  HAA3  single    0.970  0.020  1.090
 BOY  CAA  HAA2  single    0.970  0.020  1.090
 BOY  CAA  HAA1  single    0.970  0.020  1.090
 BOY  CAF  HAF1  single    0.930  0.020  1.080
 BOY  CAG  HAG1  single    0.930  0.020  1.080
 BOY  CAH  HAH1  single    0.930  0.020  1.080
 BOY  CAI  HAI1  single    0.930  0.020  1.080
 BOY  CAL  HAL1  single    0.970  0.020  1.090
 BOY  OAC  HAC1  single    0.850  0.020  0.980

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
 BOY  HAA1  CAA  HAA2  107.79  3.000
 BOY  HAA1  CAA  HAA3  107.22  3.000
 BOY  HAA2  CAA  HAA3  107.00  3.000
 BOY  HAA1  CAA  CAJ   111.56  3.000
 BOY  HAA2  CAA  CAJ   111.60  3.000
 BOY  HAA3  CAA  CAJ   111.43  3.000
 BOY  HAF1  CAF  CAJ   119.38  3.000
 BOY  HAF1  CAF  CAH   119.49  3.000
 BOY  CAJ   CAF  CAH   121.13  3.000
 BOY  HAG1  CAG  CAJ   119.36  3.000
 BOY  HAG1  CAG  CAI   119.22  3.000
 BOY  CAJ   CAG  CAI   121.42  3.000
 BOY  HAH1  CAH  CAK   119.31  3.000
 BOY  HAH1  CAH  CAF   119.20  3.000
 BOY  CAK   CAH  CAF   121.48  3.000
 BOY  HAI1  CAI  CAK   119.71  3.000
 BOY  HAI1  CAI  CAG   119.15  3.000
 BOY  CAK   CAI  CAG   121.14  3.000
 BOY  CAG   CAJ  CAF   117.42  3.000
 BOY  CAF   CAJ  CAA   121.08  3.000
 BOY  CAG   CAJ  CAA   121.50  3.000
 BOY  CAL   CAK  CAI   122.15  3.000
 BOY  CAL   CAK  CAH   120.43  3.000
 BOY  CAI   CAK  CAH   117.41  3.000
 BOY  HAL1  CAL  PAM   109.03  3.000
 BOY  HAL1  CAL  OAC   109.23  3.000
 BOY  PAM   CAL  OAC   105.61  3.000
 BOY  HAL1  CAL  CAK   108.35  3.000
 BOY  PAM   CAL  CAK   112.16  3.000
 BOY  OAC   CAL  CAK   112.39  3.000
 BOY  HAC1  OAC  CAL   101.07  3.000
 BOY  OAE   PAM  OAD   114.65  3.000
 BOY  OAD   PAM  OAB   113.29  3.000
 BOY  OAE   PAM  OAB   114.60  3.000
 BOY  OAB   PAM  CAL    98.01  3.000
 BOY  OAD   PAM  CAL   105.91  3.000
 BOY  OAE   PAM  CAL   108.48  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
 BOY  CONST_01  CAI   CAG  CAJ  CAF    0.00   0.0  0
 BOY  CONST_02  CAI   CAK  CAH  CAF    0.00   0.0  0
 BOY  CONST_03  CAH   CAF  CAJ  CAG    0.00   0.0  0
 BOY  CONST_04  CAH   CAK  CAI  CAG    0.00   0.0  0
 BOY  CONST_05  CAK   CAI  CAG  CAJ    0.00   0.0  0
 BOY  CONST_06  CAK   CAH  CAF  CAJ    0.00   0.0  0
 BOY  CONST_07  CAI   CAG  CAJ  CAA  180.00   0.0  0
 BOY  CONST_08  CAH   CAF  CAJ  CAA  180.00   0.0  0
 BOY  CONST_09  CAL   CAK  CAH  CAF  180.00   0.0  0
 BOY  CONST_10  CAL   CAK  CAI  CAG  180.00   0.0  0
 BOY  CONST_11  HAG1  CAG  CAJ  CAF  180.00   0.0  0
 BOY  CONST_12  HAF1  CAF  CAJ  CAG  180.00   0.0  0
 BOY  CONST_13  HAI1  CAI  CAK  CAH  180.00   0.0  0
 BOY  CONST_14  HAH1  CAH  CAK  CAI  180.00   0.0  0
 BOY  Var_01    HAA3  CAA  CAJ  CAF  -81.50  30.0  2

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
 BOY  chir_01  CAL  CAK  OAC  PAM  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
 BOY  plan-1  CAA   0.020
 BOY  plan-1  CAF   0.020
 BOY  plan-1  CAG   0.020
 BOY  plan-1  CAH   0.020
 BOY  plan-1  CAI   0.020
 BOY  plan-1  CAJ   0.020
 BOY  plan-1  CAK   0.020
 BOY  plan-1  CAL   0.020
 BOY  plan-1  HAF1  0.020
 BOY  plan-1  HAG1  0.020
 BOY  plan-1  HAH1  0.020
 BOY  plan-1  HAI1  0.020

