# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 11:55:45 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: (1R)-1,2,2-trimethylpropyl (R)-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
 GD7  GD7  '(1R)-1,2,2-trimethylpropyl (R)-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_GD7
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
 GD7  C1   C  CH3   0  -0.650  -2.1588  -0.7036   1.3356
 GD7  C2   C  CH3   0  -0.655  -3.0269   0.2398  -0.8062
 GD7  C3   C  CH3   0  -0.651  -1.4000  -1.6429  -0.8475
 GD7  C4   C  CH3   0  -0.681  -0.9017   2.0036   0.4490
 GD7  C5   C  CH1   0   0.073  -0.6445   0.6507  -0.1882
 GD7  C6   C  CT    0  -0.105  -1.8022  -0.3615  -0.1117
 GD7  OH   O  O2    0  -0.601   0.5073   0.0634   0.4486
 GD7  P1   P  P     0   1.004   1.9231   0.0444  -0.3166
 GD7  O11  O  O     0  -0.722   2.5552   1.3760  -0.5499
 GD7  H11  H  HCH3  0   0.226  -2.4945   0.1730   1.8923
 GD7  H12  H  HCH3  0   0.229  -2.9737  -1.4298   1.3567
 GD7  H13  H  HCH3  0   0.231  -1.3158  -1.1411   1.8712
 GD7  H21  H  HCH3  0   0.227  -2.7995   0.5529  -1.8280
 GD7  H22  H  HCH3  0   0.234  -3.8282  -0.4992  -0.8593
 GD7  H23  H  HCH3  0   0.231  -3.4169   1.1049  -0.2691
 GD7  H31  H  HCH3  0   0.231  -0.5608  -2.1470  -0.3662
 GD7  H32  H  HCH3  0   0.231  -2.2346  -2.3459  -0.8624
 GD7  H33  H  HCH3  0   0.223  -1.1225  -1.4418  -1.8852
 GD7  H42  H  HCH3  0   0.236  -1.7264   2.5167  -0.0434
 GD7  H43  H  HCH3  0   0.233  -1.1421   1.9156   1.5087
 GD7  H5   H  HCH1  0   0.229  -0.4281   0.8105  -1.2547
 GD7  H71  H  HCH3  0   0.277   2.3357  -2.0345   0.8351
 GD7  H72  H  HCH3  0   0.281   3.8246  -1.2894   0.2303
 GD7  H73  H  HCH3  0   0.284   3.0468  -0.6463   1.6830
 GD7  HP1  H  H     0   0.069   1.6441  -0.6469  -1.5149
 GD7  H41  H  HCH3  0   0.244  -0.0193   2.6358   0.3509
 GD7  C7   C  CH3   0  -0.928   2.8646  -1.0916   0.7052

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
 GD7  C1  C6   single  1.529  0.020  1.529
 GD7  C1  H11  single  0.939  0.020  1.096
 GD7  C1  H12  single  0.939  0.020  1.096
 GD7  C1  H13  single  0.939  0.020  1.096
 GD7  C2  C6   single  1.531  0.020  1.531
 GD7  C2  H21  single  0.939  0.020  1.096
 GD7  C2  H22  single  0.939  0.020  1.096
 GD7  C2  H23  single  0.939  0.020  1.096
 GD7  C3  C6   single  1.531  0.020  1.531
 GD7  C3  H31  single  0.939  0.020  1.096
 GD7  C3  H32  single  0.939  0.020  1.096
 GD7  C3  H33  single  0.939  0.020  1.096
 GD7  C4  C5   single  1.517  0.020  1.517
 GD7  C4  H41  single  0.970  0.020  1.090
 GD7  C4  H42  single  0.939  0.020  1.096
 GD7  C4  H43  single  0.939  0.020  1.096
 GD7  C5  C6   single  1.540  0.020  1.540
 GD7  C5  OH   single  1.441  0.020  1.441
 GD7  C5  H5   single  0.939  0.020  1.096
 GD7  C7  P1   single  1.795  0.020  1.795
 GD7  C7  H71  single  0.939  0.020  1.096
 GD7  C7  H72  single  0.939  0.020  1.096
 GD7  C7  H73  single  0.939  0.020  1.096
 GD7  OH  P1   single  1.610  0.020  1.610
 GD7  P1  O11  double  1.492  0.020  1.492
 GD7  P1  HP1  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
 GD7  H13  C1  H12  107.50  3.000
 GD7  H13  C1  H11  108.03  3.000
 GD7  H12  C1  H11  107.15  3.000
 GD7  H13  C1  C6   111.98  3.000
 GD7  H12  C1  C6   109.95  3.000
 GD7  H11  C1  C6   112.01  3.000
 GD7  H23  C2  H22  107.37  3.000
 GD7  H23  C2  H21  107.93  3.000
 GD7  H22  C2  H21  107.54  3.000
 GD7  H23  C2  C6   111.98  3.000
 GD7  H22  C2  C6   110.09  3.000
 GD7  H21  C2  C6   111.73  3.000
 GD7  H33  C3  H32  107.44  3.000
 GD7  H33  C3  H31  107.98  3.000
 GD7  H32  C3  H31  107.26  3.000
 GD7  H33  C3  C6   111.65  3.000
 GD7  H32  C3  C6   110.16  3.000
 GD7  H31  C3  C6   112.13  3.000
 GD7  H43  C4  H42  108.09  3.000
 GD7  H43  C4  H41  108.23  3.000
 GD7  H42  C4  H41  107.41  3.000
 GD7  H43  C4  C5   111.94  3.000
 GD7  H42  C4  C5   111.02  3.000
 GD7  H41  C4  C5   110.01  3.000
 GD7  H5   C5  OH   109.30  3.000
 GD7  H5   C5  C6   106.95  3.000
 GD7  OH   C5  C6   108.13  3.000
 GD7  H5   C5  C4   108.12  3.000
 GD7  OH   C5  C4   108.25  3.000
 GD7  C6   C5  C4   115.96  3.000
 GD7  C5   C6  C3   109.19  3.000
 GD7  C5   C6  C2   108.71  3.000
 GD7  C3   C6  C2   108.71  3.000
 GD7  C5   C6  C1   111.68  3.000
 GD7  C3   C6  C1   109.19  3.000
 GD7  C2   C6  C1   109.30  3.000
 GD7  P1   OH  C5   119.85  3.000
 GD7  HP1  P1  O11  112.84  3.000
 GD7  HP1  P1  OH   103.62  3.000
 GD7  O11  P1  OH   115.87  3.000
 GD7  HP1  P1  C7   106.09  3.000
 GD7  O11  P1  C7   115.57  3.000
 GD7  OH   P1  C7   101.44  3.000
 GD7  H73  C7  H72  108.55  3.000
 GD7  H73  C7  H71  109.15  3.000
 GD7  H72  C7  H71  108.84  3.000
 GD7  H73  C7  P1   109.88  3.000
 GD7  H72  C7  P1   109.21  3.000
 GD7  H71  C7  P1   111.17  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
 GD7  Var_01  C7   P1  OH  C5  -167.54  30.0  3
 GD7  Var_02  H21  C2  C6  C1   176.70  30.0  3
 GD7  Var_03  H31  C3  C6  C1   -57.86  30.0  3
 GD7  Var_04  H11  C1  C6  C2   -58.75  30.0  3
 GD7  Var_05  H71  C7  P1  OH    53.37  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
 GD7  chir_01  C5  C4  C6  OH   positiv
 GD7  chir_02  P1  C7  OH  O11  both

