# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 05:40:46 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  24  13  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.722   4.6544  -0.4101   0.5195
 BOY  CAF   C  CR16  0  -0.284   2.5757  -0.9621  -0.7927
 BOY  CAG   C  CR16  0  -0.283   2.5024   0.8857   0.7152
 BOY  CAH   C  CR16  0  -0.274   1.2498  -0.7397  -1.1294
 BOY  CAI   C  CR16  0  -0.296   1.1736   1.1085   0.3842
 BOY  CAJ   C  CR6   0   0.088   3.2262  -0.1541   0.1376
 BOY  CAK   C  CR6   0   0.076   0.5311   0.3001  -0.5479
 BOY  CAL   C  CH1   0  -0.305  -0.9180   0.5049  -0.9119
 BOY  OAC   O  OH1   0  -0.645  -1.3154   1.8427  -1.0599
 BOY  PAM   P  P     0   1.351  -1.9636  -0.3858   0.3048
 BOY  HAA3  H  HCH3  0   0.250   4.7163  -1.1453   1.3247
 BOY  HAA2  H  HCH3  0   0.245   5.2290  -0.8017  -0.3196
 BOY  HAA1  H  HCH3  0   0.245   5.1439   0.4975   0.8709
 BOY  HAF1  H  HCR6  0   0.250   3.1159  -1.7730  -1.2667
 BOY  HAG1  H  HCR6  0   0.251   2.9828   1.5356   1.4372
 BOY  HAH1  H  HCR6  0   0.254   0.7731  -1.3779  -1.8640
 BOY  HAI1  H  HCR6  0   0.242   0.6587   1.9286   0.8704
 BOY  HAL1  H  HCH1  0   0.302  -1.1066   0.0212  -1.8748
 BOY  H1    H  HOH1  0   0.494  -2.4284   1.2329   1.7462
 BOY  HAC1  H  HOH1  0   0.459  -1.0885   2.3511  -0.2750
 BOY  H2    H  HOH1  0   0.497  -4.1231  -0.6738   0.1201
 BOY  OAB   O  OH1   0  -0.751  -1.8575   0.4577   1.6732
 BOY  OAD   O  OH1   0  -0.745  -3.4358  -0.1188  -0.2745
 BOY  OAE   O  O     0  -0.700  -1.5777  -1.7965   0.5327

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    1.500  0.020  1.500
 BOY  CAJ  CAG   aromatic  1.392  0.020  1.392
 BOY  CAJ  CAF   aromatic  1.393  0.020  1.393
 BOY  CAG  CAI   aromatic  1.387  0.020  1.387
 BOY  CAF  CAH   aromatic  1.386  0.020  1.386
 BOY  CAI  CAK   aromatic  1.391  0.020  1.391
 BOY  CAH  CAK   aromatic  1.391  0.020  1.391
 BOY  CAK  CAL   single    1.508  0.020  1.508
 BOY  OAE  PAM   double    1.480  0.020  1.480
 BOY  OAC  CAL   single    1.403  0.020  1.403
 BOY  CAL  PAM   single    1.835  0.020  1.835
 BOY  PAM  OAD   single    1.604  0.020  1.604
 BOY  PAM  OAB   single    1.611  0.020  1.611
 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  OAB  H1    single    0.850  0.020  0.980
 BOY  OAC  HAC1  single    0.850  0.020  0.980
 BOY  OAD  H2    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  108.11  3.000
 BOY  HAA1  CAA  HAA3  107.31  3.000
 BOY  HAA2  CAA  HAA3  107.22  3.000
 BOY  HAA1  CAA  CAJ   111.57  3.000
 BOY  HAA2  CAA  CAJ   111.54  3.000
 BOY  HAA3  CAA  CAJ   110.88  3.000
 BOY  HAF1  CAF  CAJ   119.55  3.000
 BOY  HAF1  CAF  CAH   119.40  3.000
 BOY  CAJ   CAF  CAH   121.05  3.000
 BOY  HAG1  CAG  CAJ   119.59  3.000
 BOY  HAG1  CAG  CAI   119.16  3.000
 BOY  CAJ   CAG  CAI   121.25  3.000
 BOY  HAH1  CAH  CAK   119.75  3.000
 BOY  HAH1  CAH  CAF   119.41  3.000
 BOY  CAK   CAH  CAF   120.84  3.000
 BOY  HAI1  CAI  CAK   121.40  3.000
 BOY  HAI1  CAI  CAG   118.01  3.000
 BOY  CAK   CAI  CAG   120.59  3.000
 BOY  CAG   CAJ  CAF   117.86  3.000
 BOY  CAF   CAJ  CAA   121.03  3.000
 BOY  CAG   CAJ  CAA   121.11  3.000
 BOY  CAL   CAK  CAI   121.77  3.000
 BOY  CAL   CAK  CAH   119.80  3.000
 BOY  CAI   CAK  CAH   118.41  3.000
 BOY  HAL1  CAL  PAM   105.71  3.000
 BOY  HAL1  CAL  OAC   106.25  3.000
 BOY  PAM   CAL  OAC   111.80  3.000
 BOY  HAL1  CAL  CAK   108.54  3.000
 BOY  PAM   CAL  CAK   108.76  3.000
 BOY  OAC   CAL  CAK   115.28  3.000
 BOY  HAC1  OAC  CAL   110.54  3.000
 BOY  OAE   PAM  OAD   116.96  3.000
 BOY  OAD   PAM  OAB   106.26  3.000
 BOY  OAE   PAM  OAB   110.55  3.000
 BOY  OAB   PAM  CAL   105.76  3.000
 BOY  OAD   PAM  CAL   101.69  3.000
 BOY  OAE   PAM  CAL   114.60  3.000
 BOY  H1    OAB  PAM   116.47  3.000
 BOY  H2    OAD  PAM   114.15  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  -86.04  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

