# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 14:55:15 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: diethyl (4-methylbenzyl)phosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCO[P](=O)(Cc1ccc(C)cc1)OCC
#
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
 EBP  EBP  'diethyl (4-methylbenzyl)phosphonate'  ligand  35  16  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EBP
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
 EBP  C1    C  CR6   0   0.096  -0.7501   0.5188  -1.3062
 EBP  C2    C  CR16  0  -0.277  -1.4638  -0.4340  -2.0271
 EBP  C3    C  CR16  0  -0.287  -1.1195  -0.7383  -3.3358
 EBP  C4    C  CR6   0   0.084  -0.0485  -0.1068  -3.9649
 EBP  C5    C  CR16  0  -0.287   0.6672   0.8405  -3.2362
 EBP  C6    C  CR16  0  -0.273   0.3250   1.1473  -1.9271
 EBP  C7    C  CH2   0  -0.811  -1.1060   0.8312   0.1191
 EBP  C8    C  CH3   0  -0.721   0.3048  -0.4174  -5.3905
 EBP  C9    C  CH2   0  -0.171  -1.8126  -0.3670   3.4122
 EBP  C10   C  CH3   0  -0.685  -2.0305   0.4002   4.6931
 EBP  C11   C  CH2   0  -0.172   2.3056  -0.5566   1.7689
 EBP  C12   C  CH3   0  -0.682   3.6207  -0.0471   1.2337
 EBP  P     P  P     0   1.407  -0.2758  -0.2987   1.2585
 EBP  O1    O  O2    0  -0.596  -0.6753   0.1949   2.7376
 EBP  O2    O  O2    0  -0.582   1.2420   0.1886   1.1501
 EBP  O3    O  O     0  -0.714  -0.5239  -1.7412   1.0124
 EBP  H2    H  HCR6  0   0.248  -2.3026  -0.9407  -1.5653
 EBP  H3    H  HCR6  0   0.246  -1.6933  -1.4821  -3.8764
 EBP  H5    H  HCR6  0   0.246   1.5084   1.3461  -3.6961
 EBP  H6    H  HCR6  0   0.247   0.9009   1.8873  -1.3848
 EBP  H71   H  HCH2  0   0.305  -2.1814   0.7247   0.2855
 EBP  H72   H  HCH2  0   0.305  -0.8406   1.8561   0.3851
 EBP  H81   H  HCH3  0   0.248  -0.2524   0.2195  -6.0809
 EBP  H82   H  HCH3  0   0.243   1.3645  -0.2541  -5.5840
 EBP  H83   H  HCH3  0   0.243   0.0705  -1.4509  -5.6444
 EBP  H91   H  HCH2  0   0.234  -1.6295  -1.4224   3.6217
 EBP  H92   H  HCH2  0   0.226  -2.7005  -0.3030   2.7765
 EBP  H101  H  HCH3  0   0.237  -2.8826  -0.0220   5.2257
 EBP  H102  H  HCH3  0   0.236  -1.1610   0.3348   5.3472
 EBP  H103  H  HCH3  0   0.235  -2.2428   1.4514   4.4988
 EBP  H111  H  HCH2  0   0.233   2.2523  -0.4276   2.8522
 EBP  H112  H  HCH2  0   0.232   2.1891  -1.6203   1.5514
 EBP  H121  H  HCH3  0   0.237   4.4368  -0.5939   1.7057
 EBP  H122  H  HCH3  0   0.235   3.6952  -0.1956   0.1566
 EBP  H123  H  HCH3  0   0.235   3.7567   1.0123   1.4500

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
 EBP  C1   C2    aromatic  1.392  0.020  1.392
 EBP  C1   C6    aromatic  1.391  0.020  1.391
 EBP  C1   C7    single    1.502  0.020  1.502
 EBP  C2   C3    aromatic  1.387  0.020  1.387
 EBP  C2   H2    single    0.930  0.020  1.080
 EBP  C3   C4    aromatic  1.393  0.020  1.393
 EBP  C3   H3    single    0.930  0.020  1.080
 EBP  C4   C5    aromatic  1.393  0.020  1.393
 EBP  C4   C8    single    1.501  0.020  1.501
 EBP  C5   C6    aromatic  1.387  0.020  1.387
 EBP  C5   H5    single    0.930  0.020  1.080
 EBP  C6   H6    single    0.930  0.020  1.080
 EBP  C7   P     single    1.807  0.020  1.807
 EBP  C7   H71   single    0.970  0.020  1.090
 EBP  C7   H72   single    0.970  0.020  1.090
 EBP  C8   H81   single    0.970  0.020  1.090
 EBP  C8   H82   single    0.970  0.020  1.090
 EBP  C8   H83   single    0.970  0.020  1.090
 EBP  C9   C10   single    1.509  0.020  1.509
 EBP  C9   O1    single    1.437  0.020  1.437
 EBP  C9   H91   single    0.970  0.020  1.090
 EBP  C9   H92   single    0.970  0.020  1.090
 EBP  C10  H101  single    0.970  0.020  1.090
 EBP  C10  H102  single    0.970  0.020  1.090
 EBP  C10  H103  single    0.970  0.020  1.090
 EBP  C11  C12   single    1.509  0.020  1.509
 EBP  C11  O2    single    1.439  0.020  1.439
 EBP  C11  H111  single    0.970  0.020  1.090
 EBP  C11  H112  single    0.970  0.020  1.090
 EBP  C12  H121  single    0.970  0.020  1.090
 EBP  C12  H122  single    0.970  0.020  1.090
 EBP  C12  H123  single    0.970  0.020  1.090
 EBP  P    O1    single    1.610  0.020  1.610
 EBP  P    O2    single    1.598  0.020  1.598
 EBP  P    O3    double    1.484  0.020  1.484

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
 EBP  C7    C1   C6    120.84  3.000
 EBP  C7    C1   C2    120.82  3.000
 EBP  C6    C1   C2    118.31  3.000
 EBP  H2    C2   C3    119.46  3.000
 EBP  H2    C2   C1    119.76  3.000
 EBP  C3    C2   C1    120.77  3.000
 EBP  H3    C3   C4    119.52  3.000
 EBP  H3    C3   C2    119.33  3.000
 EBP  C4    C3   C2    121.16  3.000
 EBP  C8    C4   C5    121.10  3.000
 EBP  C8    C4   C3    121.06  3.000
 EBP  C5    C4   C3    117.83  3.000
 EBP  H5    C5   C6    119.25  3.000
 EBP  H5    C5   C4    119.60  3.000
 EBP  C6    C5   C4    121.14  3.000
 EBP  H6    C6   C5    119.49  3.000
 EBP  H6    C6   C1    119.73  3.000
 EBP  C5    C6   C1    120.78  3.000
 EBP  H72   C7   H71   107.07  3.000
 EBP  H72   C7   P     108.77  3.000
 EBP  H71   C7   P     107.17  3.000
 EBP  H72   C7   C1    111.64  3.000
 EBP  H71   C7   C1    110.93  3.000
 EBP  P     C7   C1    111.07  3.000
 EBP  H83   C8   H82   108.05  3.000
 EBP  H83   C8   H81   107.23  3.000
 EBP  H82   C8   H81   107.25  3.000
 EBP  H83   C8   C4    111.53  3.000
 EBP  H82   C8   C4    111.50  3.000
 EBP  H81   C8   C4    111.07  3.000
 EBP  H92   C9   H91   107.72  3.000
 EBP  H92   C9   O1    110.29  3.000
 EBP  H91   C9   O1    109.60  3.000
 EBP  H92   C9   C10   110.27  3.000
 EBP  H91   C9   C10   110.66  3.000
 EBP  O1    C9   C10   108.30  3.000
 EBP  H103  C10  H102  108.68  3.000
 EBP  H103  C10  H101  107.96  3.000
 EBP  H102  C10  H101  107.89  3.000
 EBP  H103  C10  C9    111.54  3.000
 EBP  H102  C10  C9    111.33  3.000
 EBP  H101  C10  C9    109.32  3.000
 EBP  H112  C11  H111  107.90  3.000
 EBP  H112  C11  O2    109.89  3.000
 EBP  H111  C11  O2    109.23  3.000
 EBP  H112  C11  C12   110.57  3.000
 EBP  H111  C11  C12   110.76  3.000
 EBP  O2    C11  C12   108.48  3.000
 EBP  H123  C12  H122  108.67  3.000
 EBP  H123  C12  H121  107.96  3.000
 EBP  H122  C12  H121  107.97  3.000
 EBP  H123  C12  C11   111.52  3.000
 EBP  H122  C12  C11   111.36  3.000
 EBP  H121  C12  C11   109.25  3.000
 EBP  O3    P    O2    116.36  3.000
 EBP  O3    P    O1    114.13  3.000
 EBP  O2    P    O1    101.81  3.000
 EBP  O3    P    C7    115.24  3.000
 EBP  O2    P    C7    101.71  3.000
 EBP  O1    P    C7    105.88  3.000
 EBP  P     O1   C9    120.53  3.000
 EBP  P     O2   C11   121.00  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
 EBP  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 EBP  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 EBP  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 EBP  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 EBP  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 EBP  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 EBP  CONST_07  C8    C4   C3   C2   180.00   0.0  0
 EBP  CONST_08  C7    C1   C2   C3   180.00   0.0  0
 EBP  CONST_09  C7    C1   C6   C5   180.00   0.0  0
 EBP  CONST_10  C8    C4   C5   C6   180.00   0.0  0
 EBP  CONST_11  H3    C3   C2   C1   180.00   0.0  0
 EBP  CONST_12  H5    C5   C6   C1   180.00   0.0  0
 EBP  CONST_13  H6    C6   C1   C2   180.00   0.0  0
 EBP  CONST_14  H2    C2   C3   C4   180.00   0.0  0
 EBP  Var_01    P     C7   C1   C2    86.42  30.0  2
 EBP  Var_02    H81   C8   C4   C3    88.00  30.0  2
 EBP  Var_03    O1    P    C7   C1   176.93  30.0  3
 EBP  Var_04    H91   C9   O1   P     65.84  30.0  1
 EBP  Var_05    H111  C11  O2   P    -72.21  30.0  1
 EBP  Var_06    H101  C10  C9   O1  -179.23  30.0  3
 EBP  Var_07    H121  C12  C11  O2   179.18  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
 EBP  plan-1  C1  0.020
 EBP  plan-1  C2  0.020
 EBP  plan-1  C3  0.020
 EBP  plan-1  C4  0.020
 EBP  plan-1  C5  0.020
 EBP  plan-1  C6  0.020
 EBP  plan-1  C7  0.020
 EBP  plan-1  C8  0.020
 EBP  plan-1  H2  0.020
 EBP  plan-1  H3  0.020
 EBP  plan-1  H5  0.020
 EBP  plan-1  H6  0.020

