# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 05:35:23 2022
#   Inital geometry file: a 66 line input string
#   Ligand name: (1S)-2,2-dimethylcyclopentyl (R)-methylphosphinate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[P@H](=O)O[C@H]1CCCC1(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
 UCY  UCY  '(1S)-2,2-dimethylcyclopentyl (R)-methylphosphinate'  ligand  28  11  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_UCY
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
 UCY  C10  C  CH3   0  -0.927  54.1224  26.0597  21.7331
 UCY  P09  P  P     0   1.007  55.0382  25.9760  23.2752
 UCY  O12  O  O     0  -0.712  54.2261  25.9384  24.5258
 UCY  C02  C  CT    0  -0.080  58.3355  24.7668  23.8219
 UCY  C03  C  CH3   0  -0.658  58.5782  25.9543  24.7531
 UCY  C04  C  CH2   0  -0.435  59.2294  23.5579  24.2158
 UCY  C05  C  CH2   0  -0.454  58.2896  22.4660  24.7348
 UCY  C06  C  CH2   0  -0.463  57.0151  22.7001  23.9366
 UCY  C07  C  CH1   0   0.077  56.8912  24.2127  23.9930
 UCY  O08  O  O2    0  -0.601  55.9613  24.6779  23.0112
 UCY  H1   H  HCH3  0   0.278  53.5092  26.9601  21.7301
 UCY  H2   H  HCH3  0   0.278  54.7990  26.0955  20.8803
 UCY  H3   H  HCH3  0   0.282  53.4691  25.1928  21.6362
 UCY  H5   H  HCH3  0   0.228  59.6809  25.4324  22.2794
 UCY  H6   H  HCH3  0   0.226  58.4090  24.3806  21.6718
 UCY  H7   H  HCH3  0   0.223  58.0526  26.0625  22.0792
 UCY  H8   H  HCH3  0   0.227  58.4138  25.6800  25.7973
 UCY  H9   H  HCH3  0   0.229  59.6053  26.3128  24.6622
 UCY  H10  H  HCH3  0   0.224  57.9178  26.7926  24.5218
 UCY  H11  H  HCH2  0   0.232  59.7585  23.1891  23.3337
 UCY  H12  H  HCH2  0   0.235  59.9930  23.8333  24.9454
 UCY  H13  H  HCH2  0   0.224  58.0911  22.5997  25.8016
 UCY  H14  H  HCH2  0   0.239  58.6965  21.4627  24.6075
 UCY  H15  H  HCH2  0   0.242  56.1385  22.1910  24.3399
 UCY  H16  H  HCH2  0   0.229  57.1479  22.3705  22.9012
 UCY  H17  H  HCH1  0   0.234  56.5247  24.4853  24.9909
 UCY  H18  H  H     0   0.065  55.9283  27.0695  23.2331
 UCY  C01  C  CH3   0  -0.647  58.6230  25.1824  22.3811

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
 UCY  C10  P09  single  1.796  0.020  1.796
 UCY  C01  C02  single  1.527  0.020  1.527
 UCY  O08  P09  single  1.615  0.020  1.615
 UCY  O08  C07  single  1.430  0.020  1.430
 UCY  P09  O12  double  1.492  0.020  1.492
 UCY  C02  C07  single  1.556  0.020  1.556
 UCY  C02  C04  single  1.554  0.020  1.554
 UCY  C02  C03  single  1.528  0.020  1.528
 UCY  C07  C06  single  1.519  0.020  1.519
 UCY  C06  C05  single  1.522  0.020  1.522
 UCY  C04  C05  single  1.531  0.020  1.531
 UCY  C10  H1   single  0.939  0.020  1.096
 UCY  C10  H2   single  0.939  0.020  1.096
 UCY  C10  H3   single  0.939  0.020  1.096
 UCY  C01  H5   single  0.939  0.020  1.096
 UCY  C01  H6   single  0.939  0.020  1.096
 UCY  C01  H7   single  0.939  0.020  1.096
 UCY  C03  H8   single  0.939  0.020  1.096
 UCY  C03  H9   single  0.939  0.020  1.096
 UCY  C03  H10  single  0.939  0.020  1.096
 UCY  C04  H11  single  0.939  0.020  1.096
 UCY  C04  H12  single  0.939  0.020  1.096
 UCY  C05  H13  single  0.939  0.020  1.096
 UCY  C05  H14  single  0.939  0.020  1.096
 UCY  C06  H15  single  0.939  0.020  1.096
 UCY  C06  H16  single  0.939  0.020  1.096
 UCY  C07  H17  single  0.939  0.020  1.096
 UCY  P09  H18  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
 UCY  H3   C10  H2   109.21  3.000
 UCY  H3   C10  H1   108.65  3.000
 UCY  H2   C10  H1   108.69  3.000
 UCY  H3   C10  P09  110.18  3.000
 UCY  H2   C10  P09  110.92  3.000
 UCY  H1   C10  P09  109.14  3.000
 UCY  H18  P09  O08  104.93  3.000
 UCY  H18  P09  O12  112.84  3.000
 UCY  O08  P09  O12  115.35  3.000
 UCY  H18  P09  C10  105.07  3.000
 UCY  O12  P09  C10  116.33  3.000
 UCY  O08  P09  C10  100.88  3.000
 UCY  C07  C02  C04  103.23  3.000
 UCY  C04  C02  C03  111.01  3.000
 UCY  C07  C02  C03  110.91  3.000
 UCY  C03  C02  C01  109.48  3.000
 UCY  C04  C02  C01  110.04  3.000
 UCY  C07  C02  C01  112.05  3.000
 UCY  H10  C03  H9   107.42  3.000
 UCY  H10  C03  H8   107.71  3.000
 UCY  H9   C03  H8   107.68  3.000
 UCY  H10  C03  C02  111.80  3.000
 UCY  H9   C03  C02  110.72  3.000
 UCY  H8   C03  C02  111.32  3.000
 UCY  H12  C04  H11  106.62  3.000
 UCY  H12  C04  C05  112.51  3.000
 UCY  H11  C04  C05  109.27  3.000
 UCY  H12  C04  C02  112.05  3.000
 UCY  H11  C04  C02  109.66  3.000
 UCY  C05  C04  C02  106.71  3.000
 UCY  H14  C05  H13  107.12  3.000
 UCY  H14  C05  C06  113.14  3.000
 UCY  H13  C05  C06  109.93  3.000
 UCY  H14  C05  C04  112.80  3.000
 UCY  H13  C05  C04  110.78  3.000
 UCY  C06  C05  C04  103.09  3.000
 UCY  H16  C06  H15  107.86  3.000
 UCY  H16  C06  C07  110.18  3.000
 UCY  H15  C06  C07  112.68  3.000
 UCY  H16  C06  C05  110.37  3.000
 UCY  H15  C06  C05  114.02  3.000
 UCY  C07  C06  C05  101.66  3.000
 UCY  H17  C07  O08  109.04  3.000
 UCY  H17  C07  C06  107.96  3.000
 UCY  O08  C07  C06  110.58  3.000
 UCY  H17  C07  C02  108.75  3.000
 UCY  C06  C07  C02  105.95  3.000
 UCY  O08  C07  C02  114.34  3.000
 UCY  C07  O08  P09  121.40  3.000
 UCY  H7   C01  H6   108.07  3.000
 UCY  H7   C01  H5   107.22  3.000
 UCY  H6   C01  H5   107.31  3.000
 UCY  H7   C01  C02  112.47  3.000
 UCY  H6   C01  C02  112.11  3.000
 UCY  H5   C01  C02  109.43  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
 UCY  Var_01  C06  C05  C04  C02   31.03  30.0  1
 UCY  Var_02  C07  C06  C05  C04  -43.38  30.0  1
 UCY  Var_03  C07  C02  C04  C05   -6.41  30.0  1
 UCY  Var_04  H5   C01  C02  C04  -57.99  30.0  3
 UCY  Var_05  H8   C03  C02  C04  -56.38  30.0  3
 UCY  Var_06  H18  P09  O08  C07   70.75  30.0  3
 UCY  Var_07  H1   C10  P09  O12   59.57  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
 UCY  chir_02  C07  O08  C02  C06  positiv
 UCY  chir_03  P09  C10  O08  O12  both

