# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 10:09:16 2021
#   Inital geometry file: a 69 line input string
#   Ligand name: 2-({[(1S,3S)-3-fluorocyclohexyl]methyl}amino)ethane-1,1-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(O)CNC[C@H]1CCC[C@H](F)C1
#
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
 WD1  WD1  2-({[(1S,3S)-3-fluorocyclohexyl]methyl}amino)ethane-1,1-diol  ligand  31  13  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WD1
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
 WD1  O1   O  OH1   0  -0.670   4.8794  -0.6198  17.3348
 WD1  C1   C  CH1   0   0.239   3.8938  -0.7943  18.3112
 WD1  O2   O  OH1   0  -0.676   3.9434  -2.0686  18.8961
 WD1  C2   C  CH2   0  -0.302   2.5261  -0.6368  17.6730
 WD1  N1   N  NH1   0  -0.597   2.2811  -1.6203  16.6401
 WD1  C3   C  CH2   0  -0.301   1.0544  -1.4107  15.8970
 WD1  C4   C  CH1   0  -0.237  -0.2523  -1.3664  16.7018
 WD1  C5   C  CH2   0  -0.446  -1.4563  -1.2323  15.7508
 WD1  C6   C  CH2   0  -0.456  -2.0558  -2.5927  15.4164
 WD1  C7   C  CH2   0  -0.484  -2.6088  -3.2756  16.6726
 WD1  C8   C  CH1   0   0.190  -1.8116  -2.9441  17.9289
 WD1  F1   F  F     0  -0.397  -2.3923  -1.8351  18.5752
 WD1  C9   C  CH2   0  -0.517  -0.3745  -2.6047  17.6055
 WD1  H1   H  HOH1  0   0.454   5.7150  -0.4186  17.7679
 WD1  H2   H  HOH1  0   0.455   4.7021  -2.1195  19.4866
 WD1  H3   H  HCH2  0   0.228   2.4752   0.3602  17.2264
 WD1  H4   H  HCH2  0   0.202   1.7851  -0.6472  18.4865
 WD1  H5   H  HNH1  0   0.344   2.2818  -2.5482  17.0443
 WD1  H7   H  HCH2  0   0.222   1.1467  -0.4740  15.3360
 WD1  H8   H  HCH2  0   0.224   0.9817  -2.2080  15.1487
 WD1  H9   H  HCH1  0   0.233  -0.2287  -0.4785  17.3404
 WD1  H10  H  HCH2  0   0.228  -1.1465  -0.7175  14.8366
 WD1  H11  H  HCH2  0   0.228  -2.2273  -0.6039  16.2035
 WD1  H12  H  HCH2  0   0.237  -2.8466  -2.4919  14.6710
 WD1  H13  H  HCH2  0   0.221  -1.2905  -3.2247  14.9562
 WD1  H14  H  HCH2  0   0.240  -3.6515  -2.9940  16.8383
 WD1  H15  H  HCH2  0   0.238  -2.6054  -4.3593  16.5377
 WD1  H16  H  HCH1  0   0.222  -1.8662  -3.7693  18.6423
 WD1  H17  H  HCH2  0   0.231   0.0515  -3.4844  17.1092
 WD1  H18  H  HCH2  0   0.250   0.2006  -2.4698  18.5256
 WD1  H19  H  HCH1  0   0.197   3.9962  -0.0235  19.0883

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
 WD1  C6  C5   single  1.524  0.020  1.524
 WD1  C6  C7   single  1.533  0.020  1.533
 WD1  C3  N1   single  1.449  0.020  1.449
 WD1  C3  C4   single  1.535  0.020  1.535
 WD1  C5  C4   single  1.540  0.020  1.540
 WD1  N1  C2   single  1.447  0.020  1.447
 WD1  C7  C8   single  1.524  0.020  1.524
 WD1  C2  C1   single  1.518  0.020  1.518
 WD1  C4  C9   single  1.538  0.020  1.538
 WD1  C9  C8   single  1.512  0.020  1.512
 WD1  C8  F1   single  1.409  0.020  1.409
 WD1  C1  O1   single  1.398  0.020  1.398
 WD1  C1  O2   single  1.403  0.020  1.403
 WD1  O1  H1   single  0.850  0.020  0.980
 WD1  O2  H2   single  0.850  0.020  0.980
 WD1  C2  H3   single  0.970  0.020  1.090
 WD1  C2  H4   single  0.970  0.020  1.090
 WD1  N1  H5   single  0.890  0.020  1.040
 WD1  C3  H7   single  0.970  0.020  1.090
 WD1  C3  H8   single  0.970  0.020  1.090
 WD1  C4  H9   single  0.970  0.020  1.090
 WD1  C5  H10  single  0.970  0.020  1.090
 WD1  C5  H11  single  0.970  0.020  1.090
 WD1  C6  H12  single  0.970  0.020  1.090
 WD1  C6  H13  single  0.970  0.020  1.090
 WD1  C7  H14  single  0.970  0.020  1.090
 WD1  C7  H15  single  0.970  0.020  1.090
 WD1  C8  H16  single  0.970  0.020  1.090
 WD1  C9  H17  single  0.970  0.020  1.090
 WD1  C9  H18  single  0.970  0.020  1.090
 WD1  C1  H19  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
 WD1  H1   O1  C1   108.89  3.000
 WD1  H19  C1  C2   107.97  3.000
 WD1  H19  C1  O2   109.81  3.000
 WD1  C2   C1  O2   107.55  3.000
 WD1  H19  C1  O1   109.90  3.000
 WD1  O2   C1  O1   112.31  3.000
 WD1  C2   C1  O1   109.18  3.000
 WD1  H2   O2  C1   109.36  3.000
 WD1  H4   C2  H3   106.20  3.000
 WD1  H4   C2  N1   114.04  3.000
 WD1  H3   C2  N1   108.68  3.000
 WD1  H4   C2  C1   107.15  3.000
 WD1  H3   C2  C1   107.96  3.000
 WD1  N1   C2  C1   112.47  3.000
 WD1  H5   N1  C3   109.75  3.000
 WD1  H5   N1  C2   109.75  3.000
 WD1  C3   N1  C2   114.26  3.000
 WD1  H8   C3  H7   106.14  3.000
 WD1  H8   C3  C4   108.81  3.000
 WD1  H7   C3  C4   108.39  3.000
 WD1  H8   C3  N1   107.51  3.000
 WD1  H7   C3  N1   108.35  3.000
 WD1  C4   C3  N1   117.12  3.000
 WD1  H9   C4  C9   108.19  3.000
 WD1  H9   C4  C5   107.86  3.000
 WD1  C9   C4  C5   111.77  3.000
 WD1  H9   C4  C3   108.12  3.000
 WD1  C9   C4  C3   110.63  3.000
 WD1  C5   C4  C3   110.14  3.000
 WD1  H11  C5  H10  105.98  3.000
 WD1  H11  C5  C6   109.07  3.000
 WD1  H10  C5  C6   110.37  3.000
 WD1  H11  C5  C4   110.23  3.000
 WD1  H10  C5  C4   109.61  3.000
 WD1  C6   C5  C4   111.43  3.000
 WD1  H13  C6  H12  105.83  3.000
 WD1  H13  C6  C7   109.86  3.000
 WD1  H12  C6  C7   109.84  3.000
 WD1  H13  C6  C5   109.45  3.000
 WD1  H12  C6  C5   110.64  3.000
 WD1  C7   C6  C5   111.09  3.000
 WD1  H15  C7  H14  106.11  3.000
 WD1  H15  C7  C8   108.42  3.000
 WD1  H14  C7  C8   108.54  3.000
 WD1  H15  C7  C6   109.86  3.000
 WD1  H14  C7  C6   110.71  3.000
 WD1  C8   C7  C6   112.94  3.000
 WD1  H16  C8  C9   110.91  3.000
 WD1  H16  C8  F1   105.93  3.000
 WD1  C9   C8  F1   108.25  3.000
 WD1  H16  C8  C7   110.36  3.000
 WD1  F1   C8  C7   109.49  3.000
 WD1  C9   C8  C7   111.69  3.000
 WD1  H18  C9  H17  106.00  3.000
 WD1  H18  C9  C8   110.34  3.000
 WD1  H17  C9  C8   106.62  3.000
 WD1  H18  C9  C4   110.70  3.000
 WD1  H17  C9  C4   110.44  3.000
 WD1  C8   C9  C4   112.46  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
 WD1  Var_01  C7  C6  C5  C4    63.01  30.0  1
 WD1  Var_02  C8  C7  C6  C5   -32.95  30.0  1
 WD1  Var_03  C4  C3  N1  C2   -57.42  30.0  1
 WD1  Var_04  N1  C2  C1  O1    61.24  30.0  2
 WD1  Var_05  C3  N1  C2  C1  -173.10  30.0  2

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
 WD1  chir_01  C4  C3  C5  C9  negativ
 WD1  chir_02  C8  F1  C7  C9  negativ

