# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 11:37:03 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: (1R)-1,2,2-trimethylpropyl (S)-methylphosphinate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O[P@@H](C)=O)C(C)(C)C
#
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
 GD8  GD8  '(1R)-1,2,2-trimethylpropyl (S)-methylphosphinate'  ligand  27  10  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GD8
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
 GD8  C7   C  CH3   0  -0.655   3.0332  -0.3788   0.6425
 GD8  C4   C  CT    0  -0.110   1.7617  -0.4040  -0.2097
 GD8  C6   C  CH3   0  -0.651   2.0875   0.0689  -1.6272
 GD8  C5   C  CH3   0  -0.638   1.2402  -1.8434  -0.2629
 GD8  C2   C  CH1   0   0.075   0.7049   0.4906   0.4625
 GD8  C3   C  CH3   0  -0.679   1.0773   1.9535   0.6223
 GD8  O2   O  O2    0  -0.603  -0.5097   0.4188  -0.3134
 GD8  P    P  P     0   1.015  -1.9178   0.1738   0.4302
 GD8  C1   C  CH3   0  -0.929  -3.0707   0.3620  -0.9317
 GD8  O1   O  O     0  -0.723  -2.0322  -1.0969   1.2048
 GD8  H7   H  HCH3  0   0.230   3.5038   0.6051   0.6539
 GD8  H7A  H  HCH3  0   0.227   2.8304  -0.6648   1.6777
 GD8  H7B  H  HCH3  0   0.234   3.7663  -1.0829   0.2452
 GD8  H6   H  HCH3  0   0.228   2.8269  -0.5951  -2.0791
 GD8  H6A  H  HCH3  0   0.230   1.2060   0.0612  -2.2688
 GD8  H6B  H  HCH3  0   0.226   2.5084   1.0755  -1.6390
 GD8  H5   H  HCH3  0   0.222   0.9401  -2.1956   0.7266
 GD8  H5A  H  HCH3  0   0.230   0.3821  -1.9449  -0.9272
 GD8  H5B  H  HCH3  0   0.223   2.0210  -2.5107  -0.6328
 GD8  H2   H  HCH1  0   0.230   0.5214   0.0704   1.4608
 GD8  H3   H  HCH3  0   0.240   0.2572   2.5068   1.0817
 GD8  H3A  H  HCH3  0   0.238   1.9417   2.0656   1.2748
 GD8  H3B  H  HCH3  0   0.235   1.3077   2.4263  -0.3325
 GD8  H1   H  HCH3  0   0.282  -2.9294  -0.4432  -1.6520
 GD8  H1A  H  HCH3  0   0.280  -4.0882   0.3095  -0.5459
 GD8  H1B  H  HCH3  0   0.278  -2.9350   1.3196  -1.4320
 GD8  H1P  H  H     0   0.065  -2.0884   1.3192   1.2361

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
 GD8  C7  C4   single  1.531  0.020  1.531
 GD8  C4  C6   single  1.529  0.020  1.529
 GD8  C4  C5   single  1.532  0.020  1.532
 GD8  C4  C2   single  1.539  0.020  1.539
 GD8  C2  C3   single  1.518  0.020  1.518
 GD8  C2  O2   single  1.443  0.020  1.443
 GD8  O2  P    single  1.611  0.020  1.611
 GD8  P   C1   single  1.794  0.020  1.794
 GD8  P   O1   double  1.493  0.020  1.493
 GD8  C7  H7   single  0.939  0.020  1.096
 GD8  C7  H7A  single  0.939  0.020  1.096
 GD8  C7  H7B  single  0.939  0.020  1.096
 GD8  C6  H6   single  0.939  0.020  1.096
 GD8  C6  H6A  single  0.939  0.020  1.096
 GD8  C6  H6B  single  0.939  0.020  1.096
 GD8  C5  H5   single  0.939  0.020  1.096
 GD8  C5  H5A  single  0.939  0.020  1.096
 GD8  C5  H5B  single  0.939  0.020  1.096
 GD8  C2  H2   single  0.939  0.020  1.096
 GD8  C3  H3   single  0.939  0.020  1.096
 GD8  C3  H3A  single  0.939  0.020  1.096
 GD8  C3  H3B  single  0.939  0.020  1.096
 GD8  C1  H1   single  0.939  0.020  1.096
 GD8  C1  H1A  single  0.939  0.020  1.096
 GD8  C1  H1B  single  0.939  0.020  1.096
 GD8  P   H1P  single  1.209  0.020  1.412

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
 GD8  H7B  C7  H7A  107.50  3.000
 GD8  H7B  C7  H7   107.21  3.000
 GD8  H7A  C7  H7   107.83  3.000
 GD8  H7B  C7  C4   110.16  3.000
 GD8  H7A  C7  C4   111.64  3.000
 GD8  H7   C7  C4   112.27  3.000
 GD8  C2   C4  C5   109.12  3.000
 GD8  C2   C4  C6   111.80  3.000
 GD8  C5   C4  C6   109.32  3.000
 GD8  C2   C4  C7   108.52  3.000
 GD8  C5   C4  C7   108.52  3.000
 GD8  C6   C4  C7   109.51  3.000
 GD8  H6B  C6  H6A  108.18  3.000
 GD8  H6B  C6  H6   107.18  3.000
 GD8  H6A  C6  H6   107.44  3.000
 GD8  H6B  C6  C4   112.17  3.000
 GD8  H6A  C6  C4   111.77  3.000
 GD8  H6   C6  C4   109.87  3.000
 GD8  H5B  C5  H5A  107.44  3.000
 GD8  H5B  C5  H5   107.84  3.000
 GD8  H5A  C5  H5   107.81  3.000
 GD8  H5B  C5  C4   110.03  3.000
 GD8  H5A  C5  C4   112.13  3.000
 GD8  H5   C5  C4   111.41  3.000
 GD8  H2   C2  O2   109.21  3.000
 GD8  H2   C2  C3   108.30  3.000
 GD8  O2   C2  C3   108.12  3.000
 GD8  H2   C2  C4   106.82  3.000
 GD8  O2   C2  C4   108.31  3.000
 GD8  C3   C2  C4   115.95  3.000
 GD8  H3B  C3  H3A  108.21  3.000
 GD8  H3B  C3  H3   107.92  3.000
 GD8  H3A  C3  H3   106.99  3.000
 GD8  H3B  C3  C2   112.19  3.000
 GD8  H3A  C3  C2   110.92  3.000
 GD8  H3   C3  C2   110.41  3.000
 GD8  P    O2  C2   119.67  3.000
 GD8  H1P  P   O1   112.67  3.000
 GD8  H1P  P   C1   105.71  3.000
 GD8  O1   P   C1   115.72  3.000
 GD8  H1P  P   O2   104.24  3.000
 GD8  O1   P   O2   115.85  3.000
 GD8  C1   P   O2   101.26  3.000
 GD8  H1B  C1  H1A  108.75  3.000
 GD8  H1B  C1  H1   109.27  3.000
 GD8  H1A  C1  H1   108.64  3.000
 GD8  H1B  C1  P    111.15  3.000
 GD8  H1A  C1  P    109.05  3.000
 GD8  H1   C1  P    109.94  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
 GD8  Var_01  C1  P   O2  C2  173.72  30.0  3
 GD8  Var_02  H6  C6  C4  C7   60.57  30.0  3
 GD8  Var_03  H5  C5  C4  C7   64.02  30.0  3
 GD8  Var_04  H7  C7  C4  C6   56.00  30.0  3
 GD8  Var_05  H1  C1  P   O2   66.16  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
 GD8  chir_01  C2  C4  C3  O2  negativ
 GD8  chir_02  P   O2  C1  O1  both

