# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 03:27:29 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (2R)-2-methyl-3-phenylpropyl hydrogen (S)-hexylphosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC[P@@](O)(=O)OC[C@H](C)Cc1ccccc1
#
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
 2HR  2HR  '(2R)-2-methyl-3-phenylpropyl hydrogen (S)-hexylphosphonate'  ligand  46  20  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_2HR
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
 2HR  C6    C  CH3    0  -0.661   8.5013   2.7075   5.6431
 2HR  C5    C  CH2    0  -0.419   7.4083   1.6543   5.5248
 2HR  C4    C  CH2    0  -0.412   6.0537   2.1452   6.0200
 2HR  C3    C  CH2    0  -0.405   4.9484   1.1050   5.8893
 2HR  C2    C  CH2    0  -0.422   3.5962   1.5964   6.3918
 2HR  C1    C  CH2    0  -0.747   2.4847   0.5703   6.2093
 2HR  P     P  P      0   1.288   0.8463   1.0932   6.8322
 2HR  O     O  OP    -1  -0.816  -0.1378  -0.0257   6.6001
 2HR  O1    O  O2     0  -0.623   1.1071   1.2615   8.4580
 2HR  C7    C  CH2    0  -0.138   1.3641   0.1242   9.2552
 2HR  C8    C  CH1    0  -0.264   1.0206   0.4090  10.7089
 2HR  C9    C  CH3    0  -0.659  -0.4678   0.6814  10.8959
 2HR  C10   C  CH2    0  -0.485   1.8557   1.5533  11.3040
 2HR  C11   C  CR6    0   0.125   3.3376   1.3238  11.2060
 2HR  C16   C  CR16   0  -0.309   3.9674   0.3928  12.0318
 2HR  C15   C  CR16   0  -0.241   5.3284   0.1441  11.9212
 2HR  C14   C  CR16   0  -0.275   6.0880   0.8287  10.9797
 2HR  C13   C  CR16   0  -0.240   5.4745   1.7628  10.1567
 2HR  C12   C  CR16   0  -0.303   4.1115   2.0054  10.2705
 2HR  O2    O  O      0  -0.810   0.5319   2.4859   6.3558
 2HR  H61   H  HCH3   0   0.225   9.4546   2.3429   5.2588
 2HR  H62   H  HCH3   0   0.215   8.2411   3.6073   5.0822
 2HR  H63   H  HCH3   0   0.215   8.6563   3.0025   6.6826
 2HR  H51   H  HCH2   0   0.210   7.6969   0.7604   6.0868
 2HR  H52   H  HCH2   0   0.210   7.3177   1.3381   4.4809
 2HR  H41   H  HCH2   0   0.207   6.1429   2.4508   7.0687
 2HR  H42   H  HCH2   0   0.206   5.7690   3.0477   5.4676
 2HR  H31   H  HCH2   0   0.204   5.2337   0.2008   6.4388
 2HR  H32   H  HCH2   0   0.204   4.8585   0.8046   4.8395
 2HR  H21   H  HCH2   0   0.224   3.6827   1.8566   7.4504
 2HR  H22   H  HCH2   0   0.209   3.3244   2.5193   5.8715
 2HR  H11   H  HCH2   0   0.236   2.3641   0.3409   5.1450
 2HR  H12A  H  HCH2   0   0.231   2.7642  -0.3767   6.6833
 2HR  H71   H  HCH2   0   0.206   0.7729  -0.7333   8.9151
 2HR  H72   H  HCH2   0   0.206   2.4206  -0.1605   9.1749
 2HR  H8    H  HCH1   0   0.226   1.2742  -0.5072  11.2557
 2HR  H91   H  HCH3   0   0.225  -1.0715  -0.1435  10.5132
 2HR  H92   H  HCH3   0   0.224  -0.7125   0.8100  11.9516
 2HR  H93   H  HCH3   0   0.222  -0.7738   1.5879  10.3718
 2HR  H101  H  HCH2   0   0.239   1.5728   1.6694  12.3546
 2HR  H102  H  HCH2   0   0.237   1.5918   2.4909  10.8092
 2HR  H16   H  HCR6   0   0.243   3.3837  -0.1423  12.7727
 2HR  H15   H  HCR6   0   0.250   5.7987  -0.5824  12.5720
 2HR  H14   H  HCR6   0   0.251   7.1495   0.6358  10.8910
 2HR  H13   H  HCR6   0   0.250   6.0588   2.3051   9.4238
 2HR  H12   H  HCR6   0   0.240   3.6388   2.7332   9.6216

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
 2HR  C6   C5    single    1.522  0.020  1.522
 2HR  C6   H61   single    0.970  0.020  1.090
 2HR  C6   H62   single    0.970  0.020  1.090
 2HR  C6   H63   single    0.970  0.020  1.090
 2HR  C5   C4    single    1.524  0.020  1.524
 2HR  C5   H51   single    0.970  0.020  1.090
 2HR  C5   H52   single    0.970  0.020  1.090
 2HR  C4   C3    single    1.523  0.020  1.523
 2HR  C4   H41   single    0.970  0.020  1.090
 2HR  C4   H42   single    0.970  0.020  1.090
 2HR  C3   C2    single    1.524  0.020  1.524
 2HR  C3   H31   single    0.970  0.020  1.090
 2HR  C3   H32   single    0.970  0.020  1.090
 2HR  C2   C1    single    1.524  0.020  1.524
 2HR  C2   H21   single    0.970  0.020  1.090
 2HR  C2   H22   single    0.970  0.020  1.090
 2HR  C1   P     single    1.829  0.020  1.829
 2HR  C1   H11   single    0.970  0.020  1.090
 2HR  C1   H12A  single    0.970  0.020  1.090
 2HR  P    O     deloc     1.508  0.020  1.508
 2HR  P    O1    single    1.655  0.020  1.655
 2HR  P    O2    deloc     1.505  0.020  1.505
 2HR  O1   C7    single    1.412  0.020  1.412
 2HR  C7   C8    single    1.521  0.020  1.521
 2HR  C7   H71   single    0.970  0.020  1.090
 2HR  C7   H72   single    0.970  0.020  1.090
 2HR  C8   C9    single    1.525  0.020  1.525
 2HR  C8   C10   single    1.537  0.020  1.537
 2HR  C8   H8    single    0.970  0.020  1.090
 2HR  C9   H91   single    0.970  0.020  1.090
 2HR  C9   H92   single    0.970  0.020  1.090
 2HR  C9   H93   single    0.970  0.020  1.090
 2HR  C10  C11   single    1.503  0.020  1.503
 2HR  C10  H101  single    0.970  0.020  1.090
 2HR  C10  H102  single    0.970  0.020  1.090
 2HR  C11  C16   aromatic  1.395  0.020  1.395
 2HR  C11  C12   aromatic  1.392  0.020  1.392
 2HR  C16  C15   aromatic  1.388  0.020  1.388
 2HR  C16  H16   single    0.930  0.020  1.080
 2HR  C15  C14   aromatic  1.390  0.020  1.390
 2HR  C15  H15   single    0.930  0.020  1.080
 2HR  C14  C13   aromatic  1.388  0.020  1.388
 2HR  C14  H14   single    0.930  0.020  1.080
 2HR  C13  C12   aromatic  1.389  0.020  1.389
 2HR  C13  H13   single    0.930  0.020  1.080
 2HR  C12  H12   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
 2HR  H63   C6   H62   107.48  3.000
 2HR  H63   C6   H61   107.56  3.000
 2HR  H62   C6   H61   107.63  3.000
 2HR  H63   C6   C5    111.28  3.000
 2HR  H62   C6   C5    111.05  3.000
 2HR  H61   C6   C5    111.64  3.000
 2HR  H52   C5   H51   106.00  3.000
 2HR  H52   C5   C4    109.24  3.000
 2HR  H51   C5   C4    109.31  3.000
 2HR  H52   C5   C6    109.48  3.000
 2HR  H51   C5   C6    109.62  3.000
 2HR  C4    C5   C6    112.96  3.000
 2HR  H42   C4   H41   105.89  3.000
 2HR  H42   C4   C3    109.30  3.000
 2HR  H41   C4   C3    109.37  3.000
 2HR  H42   C4   C5    109.42  3.000
 2HR  H41   C4   C5    109.18  3.000
 2HR  C3    C4   C5    113.40  3.000
 2HR  H32   C3   H31   106.00  3.000
 2HR  H32   C3   C2    109.36  3.000
 2HR  H31   C3   C2    109.37  3.000
 2HR  H32   C3   C4    109.21  3.000
 2HR  H31   C3   C4    109.36  3.000
 2HR  C2    C3   C4    113.29  3.000
 2HR  H22   C2   H21   106.22  3.000
 2HR  H22   C2   C1    109.27  3.000
 2HR  H21   C2   C1    109.50  3.000
 2HR  H22   C2   C3    109.61  3.000
 2HR  H21   C2   C3    109.02  3.000
 2HR  C1    C2   C3    113.00  3.000
 2HR  H12A  C1   H11   105.52  3.000
 2HR  H12A  C1   P     109.17  3.000
 2HR  H11   C1   P     106.98  3.000
 2HR  H12A  C1   C2    110.14  3.000
 2HR  H11   C1   C2    109.74  3.000
 2HR  P     C1   C2    114.84  3.000
 2HR  O2    P    O1    104.46  3.000
 2HR  O2    P    O     120.10  3.000
 2HR  O1    P    O     109.24  3.000
 2HR  O2    P    C1    110.11  3.000
 2HR  O1    P    C1    102.85  3.000
 2HR  O     P    C1    108.66  3.000
 2HR  C7    O1   P     120.08  3.000
 2HR  H72   C7   H71   107.08  3.000
 2HR  H72   C7   C8    109.64  3.000
 2HR  H71   C7   C8    108.75  3.000
 2HR  H72   C7   O1    110.05  3.000
 2HR  H71   C7   O1    110.91  3.000
 2HR  C8    C7   O1    110.34  3.000
 2HR  H8    C8   C10   107.66  3.000
 2HR  H8    C8   C9    108.30  3.000
 2HR  C10   C8   C9    110.49  3.000
 2HR  H8    C8   C7    105.54  3.000
 2HR  C10   C8   C7    112.76  3.000
 2HR  C9    C8   C7    111.79  3.000
 2HR  H93   C9   H92   107.70  3.000
 2HR  H93   C9   H91   107.72  3.000
 2HR  H92   C9   H91   107.71  3.000
 2HR  H93   C9   C8    111.31  3.000
 2HR  H92   C9   C8    111.01  3.000
 2HR  H91   C9   C8    111.22  3.000
 2HR  H102  C10  H101  106.34  3.000
 2HR  H102  C10  C11   109.86  3.000
 2HR  H101  C10  C11   109.50  3.000
 2HR  H102  C10  C8    109.42  3.000
 2HR  H101  C10  C8    108.08  3.000
 2HR  C11   C10  C8    113.39  3.000
 2HR  C12   C11  C16   118.26  3.000
 2HR  C12   C11  C10   121.14  3.000
 2HR  C16   C11  C10   120.57  3.000
 2HR  H16   C16  C15   119.59  3.000
 2HR  H16   C16  C11   119.39  3.000
 2HR  C15   C16  C11   121.01  3.000
 2HR  H15   C15  C14   120.01  3.000
 2HR  H15   C15  C16   119.88  3.000
 2HR  C14   C15  C16   120.11  3.000
 2HR  H14   C14  C13   120.31  3.000
 2HR  H14   C14  C15   120.24  3.000
 2HR  C13   C14  C15   119.44  3.000
 2HR  H13   C13  C12   119.83  3.000
 2HR  H13   C13  C14   120.00  3.000
 2HR  C12   C13  C14   120.17  3.000
 2HR  H12   C12  C13   119.75  3.000
 2HR  H12   C12  C11   119.25  3.000
 2HR  C13   C12  C11   120.99  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
 2HR  CONST_01  C14  C15  C16  C11     0.00   0.0  0
 2HR  CONST_02  C14  C13  C12  C11     0.00   0.0  0
 2HR  CONST_03  C13  C12  C11  C16     0.00   0.0  0
 2HR  CONST_04  C13  C14  C15  C16     0.00   0.0  0
 2HR  CONST_05  C12  C11  C16  C15     0.00   0.0  0
 2HR  CONST_06  C12  C13  C14  C15     0.00   0.0  0
 2HR  CONST_07  C15  C16  C11  C10   180.00   0.0  0
 2HR  CONST_08  C13  C12  C11  C10   180.00   0.0  0
 2HR  CONST_09  H15  C15  C16  C11   180.00   0.0  0
 2HR  CONST_10  H13  C13  C12  C11   180.00   0.0  0
 2HR  CONST_11  H12  C12  C11  C16   180.00   0.0  0
 2HR  CONST_12  H14  C14  C15  C16   180.00   0.0  0
 2HR  CONST_13  H16  C16  C15  C14   180.00   0.0  0
 2HR  Var_01    C16  C11  C10  C8    -73.51  30.0  2
 2HR  Var_02    C3   C4   C5   C6    179.24  30.0  3
 2HR  Var_03    C2   C3   C4   C5    179.71  30.0  3
 2HR  Var_04    C1   C2   C3   C4    177.82  30.0  3
 2HR  Var_05    P    C1   C2   C3    178.62  30.0  3
 2HR  Var_06    O    P    C1   C2   -179.23  30.0  3
 2HR  Var_07    C8   C7   O1   P    -157.25  30.0  3
 2HR  Var_08    H61  C6   C5   C4   -178.50  30.0  3

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
 2HR  chir_02  C8  C7  C9  C10  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
 2HR  plan-1  C10  0.020
 2HR  plan-1  C11  0.020
 2HR  plan-1  C16  0.020
 2HR  plan-1  C15  0.020
 2HR  plan-1  C14  0.020
 2HR  plan-1  C13  0.020
 2HR  plan-1  C12  0.020
 2HR  plan-1  H16  0.020
 2HR  plan-1  H15  0.020
 2HR  plan-1  H14  0.020
 2HR  plan-1  H13  0.020
 2HR  plan-1  H12  0.020

