# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 15:26:21 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: cyclohexyl (S)-methylphosphonofluoridate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[P@](F)(=O)OC1CCCCC1
#
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
 WW2  WW2  'cyclohexyl (S)-methylphosphonofluoridate'  ligand  25  11  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_WW2
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
 WW2  C1   C  CH2   0  -0.450  -1.4357  -1.2408  -0.2432
 WW2  F1   F  F     0  -0.431   2.2420   1.2139   0.7622
 WW2  O1   O  O     0  -0.696   1.8871  -1.2609   1.1359
 WW2  P1   P  P     0   1.429   1.9108  -0.2048   0.1036
 WW2  C2   C  CH2   0  -0.446  -2.8226  -1.2360   0.3973
 WW2  O2   O  O2    0  -0.601   0.5510   0.0835  -0.6643
 WW2  C3   C  CH2   0  -0.432  -3.6506  -0.0481  -0.0814
 WW2  C4   C  CH2   0  -0.448  -2.9181   1.2667   0.1648
 WW2  C5   C  CH2   0  -0.448  -1.5307   1.2632  -0.4747
 WW2  C6   C  CH1   0   0.053  -0.7276   0.0753   0.0212
 WW2  C7   C  CH3   0  -0.950   3.1177  -0.3308  -1.2013
 WW2  H1   H  HCH2  0   0.243  -0.8394  -2.0691   0.1464
 WW2  H1A  H  HCH2  0   0.226  -1.5300  -1.3861  -1.3243
 WW2  H2   H  HCH2  0   0.238  -3.3308  -2.1747   0.1684
 WW2  H2A  H  HCH2  0   0.219  -2.7214  -1.1960   1.4868
 WW2  H3   H  HCH2  0   0.214  -3.8521  -0.1562  -1.1524
 WW2  H3A  H  HCH2  0   0.233  -4.6208  -0.0375   0.4202
 WW2  H4   H  HCH2  0   0.239  -3.4962   2.1063  -0.2264
 WW2  H4A  H  HCH2  0   0.219  -2.8213   1.4337   1.2426
 WW2  H5   H  HCH2  0   0.227  -1.6269   1.2049  -1.5637
 WW2  H5A  H  HCH2  0   0.244  -1.0045   2.1921  -0.2431
 WW2  H6   H  HCH1  0   0.233  -0.5666   0.1841   1.1005
 WW2  H7   H  HCH3  0   0.295   2.9520  -1.2487  -1.7630
 WW2  H7A  H  HCH3  0   0.293   3.0579   0.5180  -1.8795
 WW2  H7B  H  HCH3  0   0.295   4.1153  -0.3698  -0.7664

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
 WW2  C1  C2   single  1.528  0.020  1.528
 WW2  C1  C6   single  1.518  0.020  1.518
 WW2  C1  H1   single  0.970  0.020  1.090
 WW2  C1  H1A  single  0.970  0.020  1.090
 WW2  P1  F1   single  1.599  0.020  1.599
 WW2  O1  P1   double  1.477  0.020  1.477
 WW2  O2  P1   single  1.588  0.020  1.588
 WW2  P1  C7   single  1.782  0.020  1.782
 WW2  C2  C3   single  1.525  0.020  1.525
 WW2  C2  H2   single  0.970  0.020  1.090
 WW2  C2  H2A  single  0.970  0.020  1.090
 WW2  O2  C6   single  1.451  0.020  1.451
 WW2  C3  C4   single  1.525  0.020  1.525
 WW2  C3  H3   single  0.970  0.020  1.090
 WW2  C3  H3A  single  0.970  0.020  1.090
 WW2  C5  C4   single  1.528  0.020  1.528
 WW2  C4  H4   single  0.970  0.020  1.090
 WW2  C4  H4A  single  0.970  0.020  1.090
 WW2  C6  C5   single  1.517  0.020  1.517
 WW2  C5  H5   single  0.970  0.020  1.090
 WW2  C5  H5A  single  0.970  0.020  1.090
 WW2  C6  H6   single  0.970  0.020  1.090
 WW2  C7  H7   single  0.970  0.020  1.090
 WW2  C7  H7A  single  0.970  0.020  1.090
 WW2  C7  H7B  single  0.970  0.020  1.090

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
 WW2  H1A  C1  H1   107.37  3.000
 WW2  H1A  C1  C6   109.10  3.000
 WW2  H1   C1  C6   109.92  3.000
 WW2  H1A  C1  C2   109.65  3.000
 WW2  H1   C1  C2   110.39  3.000
 WW2  C6   C1  C2   110.35  3.000
 WW2  C7   P1  O2   103.81  3.000
 WW2  C7   P1  O1   118.17  3.000
 WW2  O2   P1  O1   117.01  3.000
 WW2  C7   P1  F1   102.95  3.000
 WW2  O2   P1  F1   102.44  3.000
 WW2  O1   P1  F1   110.48  3.000
 WW2  H2A  C2  H2   106.44  3.000
 WW2  H2A  C2  C3   109.52  3.000
 WW2  H2   C2  C3   110.56  3.000
 WW2  H2A  C2  C1   109.47  3.000
 WW2  H2   C2  C1   109.39  3.000
 WW2  C3   C2  C1   111.34  3.000
 WW2  C6   O2  P1   121.67  3.000
 WW2  H3A  C3  H3   106.66  3.000
 WW2  H3A  C3  C4   110.13  3.000
 WW2  H3   C3  C4   109.35  3.000
 WW2  H3A  C3  C2   110.22  3.000
 WW2  H3   C3  C2   109.27  3.000
 WW2  C4   C3  C2   111.10  3.000
 WW2  H4A  C4  H4   106.39  3.000
 WW2  H4A  C4  C5   109.40  3.000
 WW2  H4   C4  C5   109.43  3.000
 WW2  H4A  C4  C3   109.44  3.000
 WW2  H4   C4  C3   110.53  3.000
 WW2  C5   C4  C3   111.51  3.000
 WW2  H5A  C5  H5   107.36  3.000
 WW2  H5A  C5  C6   109.97  3.000
 WW2  H5   C5  C6   109.26  3.000
 WW2  H5A  C5  C4   110.29  3.000
 WW2  H5   C5  C4   109.68  3.000
 WW2  C6   C5  C4   110.23  3.000
 WW2  H6   C6  C5   108.77  3.000
 WW2  H6   C6  O2   109.58  3.000
 WW2  C5   C6  O2   107.91  3.000
 WW2  H6   C6  C1   109.03  3.000
 WW2  C5   C6  C1   112.03  3.000
 WW2  O2   C6  C1   109.50  3.000
 WW2  H7B  C7  H7A  109.10  3.000
 WW2  H7B  C7  H7   108.37  3.000
 WW2  H7A  C7  H7   109.13  3.000
 WW2  H7B  C7  P1   109.31  3.000
 WW2  H7A  C7  P1   111.35  3.000
 WW2  H7   C7  P1   109.53  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
 WW2  Var_01  C4  C3  C2  C1   -55.15  30.0  1
 WW2  Var_02  C5  C4  C3  C2    55.19  30.0  1
 WW2  Var_03  C6  C1  C2  C3    55.56  30.0  1
 WW2  Var_04  C6  C5  C4  C3   -55.48  30.0  1
 WW2  Var_05  C7  P1  O2  C6   171.43  30.0  3
 WW2  Var_06  H7  C7  P1  F1  -176.95  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
 WW2  chir_02  C6  C1  O2  C5  negativ
 WW2  chir_03  P1  O1  O2  C7  both

