# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 22:16:15 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 1-[(2,5-dihydrothiophen-3-yl)methyl]piperidin-4-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1CCN(CC1)CC2=CCSC2
#
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
 NUG  NUG  1-[(2,5-dihydrothiophen-3-yl)methyl]piperidin-4-ol  ligand  30  13  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NUG
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
 NUG  N1   N  NT    0  -0.418   0.7962   0.6867   0.1177
 NUG  C4   C  CH2   0  -0.324  -0.3535   1.3468   0.7014
 NUG  C5   C  CR5   0   0.115  -1.6224   0.5881   0.4624
 NUG  C6   C  CR15  0  -0.260  -2.5320   0.3039   1.3873
 NUG  C7   C  CH2   0  -0.570  -3.7797  -0.3887   0.9472
 NUG  C8   C  CH2   0  -0.581  -1.9399   0.1465  -0.9357
 NUG  C10  C  CH2   0  -0.459   3.1054   0.9073  -0.6801
 NUG  C1   C  CH1   0   0.066   3.4783  -0.4040  -0.0128
 NUG  C2   C  CH2   0  -0.476   2.2430  -1.2888   0.0890
 NUG  C3   C  CH2   0  -0.287   1.1136  -0.5563   0.7970
 NUG  C9   C  CH2   0  -0.289   1.9484   1.5667   0.0554
 NUG  O1   O  OH1   0  -0.675   4.5181  -1.0068  -0.7548
 NUG  S1   S  S2    0  -0.054  -3.6004  -0.6082  -0.8592
 NUG  H2   H  HCH2  0   0.213  -0.2306   1.5344   1.7809
 NUG  H3   H  HCH2  0   0.249  -0.4524   2.3285   0.2250
 NUG  H5   H  HCR5  0   0.257  -2.4061   0.5590   2.4334
 NUG  H7   H  HCH2  0   0.270  -3.9049  -1.3566   1.4370
 NUG  H8   H  HCH2  0   0.270  -4.6711   0.2030   1.1656
 NUG  H9   H  HCH2  0   0.268  -1.9368   0.9894  -1.6307
 NUG  H10  H  HCH2  0   0.273  -1.2122  -0.5788  -1.3037
 NUG  H11  H  HCH2  0   0.238   3.9598   1.5882  -0.6936
 NUG  H12  H  HCH2  0   0.221   2.8150   0.7200  -1.7187
 NUG  H13  H  HCH1  0   0.186   3.8209  -0.1786   1.0104
 NUG  H14  H  HCH2  0   0.222   1.9178  -1.5754  -0.9158
 NUG  H15  H  HCH2  0   0.235   2.4759  -2.2088   0.6334
 NUG  H16  H  HCH2  0   0.193   1.3924  -0.3765   1.8511
 NUG  H17  H  HCH2  0   0.244   0.2250  -1.1905   0.8171
 NUG  H18  H  HCH2  0   0.241   1.6601   2.4821  -0.4664
 NUG  H19  H  HCH2  0   0.190   2.2817   1.8716   1.0633
 NUG  H20  H  HOH1  0   0.446   4.7580  -1.8307  -0.3190

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
 NUG  C7   S1   single  1.829  0.020  1.829
 NUG  C7   C6   single  1.493  0.020  1.493
 NUG  S1   C8   single  1.826  0.020  1.826
 NUG  C6   C5   double  1.328  0.020  1.328
 NUG  C8   C5   single  1.500  0.020  1.500
 NUG  C5   C4   single  1.498  0.020  1.498
 NUG  C2   C3   single  1.521  0.020  1.521
 NUG  C2   C1   single  1.523  0.020  1.523
 NUG  C3   N1   single  1.452  0.020  1.452
 NUG  N1   C4   single  1.448  0.020  1.448
 NUG  N1   C9   single  1.451  0.020  1.451
 NUG  O1   C1   single  1.413  0.020  1.413
 NUG  C1   C10  single  1.518  0.020  1.518
 NUG  C10  C9   single  1.521  0.020  1.521
 NUG  C4   H2   single  0.970  0.020  1.090
 NUG  C4   H3   single  0.970  0.020  1.090
 NUG  C6   H5   single  0.930  0.020  1.080
 NUG  C7   H7   single  0.970  0.020  1.090
 NUG  C7   H8   single  0.970  0.020  1.090
 NUG  C8   H9   single  0.970  0.020  1.090
 NUG  C8   H10  single  0.970  0.020  1.090
 NUG  C10  H11  single  0.970  0.020  1.090
 NUG  C10  H12  single  0.970  0.020  1.090
 NUG  C1   H13  single  0.970  0.020  1.090
 NUG  C2   H14  single  0.970  0.020  1.090
 NUG  C2   H15  single  0.970  0.020  1.090
 NUG  C3   H16  single  0.970  0.020  1.090
 NUG  C3   H17  single  0.970  0.020  1.090
 NUG  C9   H18  single  0.970  0.020  1.090
 NUG  C9   H19  single  0.970  0.020  1.090
 NUG  O1   H20  single  0.850  0.020  0.980

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
 NUG  C9   N1   C3   111.45  3.000
 NUG  C9   N1   C4   111.79  3.000
 NUG  C3   N1   C4   112.03  3.000
 NUG  H3   C4   H2   106.46  3.000
 NUG  H3   C4   C5   107.94  3.000
 NUG  H2   C4   C5   109.69  3.000
 NUG  H3   C4   N1   107.74  3.000
 NUG  H2   C4   N1   112.56  3.000
 NUG  C5   C4   N1   112.17  3.000
 NUG  C8   C5   C6   116.18  3.000
 NUG  C8   C5   C4   118.50  3.000
 NUG  C6   C5   C4   125.28  3.000
 NUG  H5   C6   C7   119.37  3.000
 NUG  H5   C6   C5   122.83  3.000
 NUG  C7   C6   C5   117.79  3.000
 NUG  H8   C7   H7   107.28  3.000
 NUG  H8   C7   S1   110.04  3.000
 NUG  H7   C7   S1   110.36  3.000
 NUG  H8   C7   C6   111.83  3.000
 NUG  H7   C7   C6   112.00  3.000
 NUG  S1   C7   C6   105.36  3.000
 NUG  H10  C8   H9   107.24  3.000
 NUG  H10  C8   S1   110.24  3.000
 NUG  H9   C8   S1   110.37  3.000
 NUG  H10  C8   C5   111.64  3.000
 NUG  H9   C8   C5   111.42  3.000
 NUG  S1   C8   C5   105.97  3.000
 NUG  H12  C10  H11  107.60  3.000
 NUG  H12  C10  C9   109.34  3.000
 NUG  H11  C10  C9   109.30  3.000
 NUG  H12  C10  C1   109.54  3.000
 NUG  H11  C10  C1   110.59  3.000
 NUG  C9   C10  C1   110.41  3.000
 NUG  H13  C1   O1   110.25  3.000
 NUG  H13  C1   C2   107.99  3.000
 NUG  O1   C1   C2   112.59  3.000
 NUG  H13  C1   C10  107.93  3.000
 NUG  O1   C1   C10  108.58  3.000
 NUG  C2   C1   C10  109.39  3.000
 NUG  H15  C2   H14  107.45  3.000
 NUG  H15  C2   C3   109.35  3.000
 NUG  H14  C2   C3   109.44  3.000
 NUG  H15  C2   C1   110.44  3.000
 NUG  H14  C2   C1   109.38  3.000
 NUG  C3   C2   C1   110.71  3.000
 NUG  H17  C3   H16  106.40  3.000
 NUG  H17  C3   C2   109.47  3.000
 NUG  H16  C3   C2   109.57  3.000
 NUG  H17  C3   N1   109.15  3.000
 NUG  H16  C3   N1   111.23  3.000
 NUG  C2   C3   N1   110.91  3.000
 NUG  H19  C9   H18  106.51  3.000
 NUG  H19  C9   C10  109.35  3.000
 NUG  H18  C9   C10  109.45  3.000
 NUG  H19  C9   N1   111.58  3.000
 NUG  H18  C9   N1   108.61  3.000
 NUG  C10  C9   N1   111.21  3.000
 NUG  H20  O1   C1   108.12  3.000
 NUG  C8   S1   C7    94.65  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
 NUG  Var_01  C1  C2   C3  N1    56.86  30.0  1
 NUG  Var_02  C1  C10  C9  N1   -57.16  30.0  1
 NUG  Var_03  S1  C7   C6  C5    -0.35  30.0  1
 NUG  Var_04  S1  C8   C5  C6     2.43  30.0  1
 NUG  Var_05  C8  C5   C6  C7    -1.42  30.0  1
 NUG  Var_06  C3  N1   C9  C10   59.26  30.0  1
 NUG  Var_07  C9  N1   C3  C2   -58.97  30.0  1
 NUG  Var_08  C6  C5   C4  N1   132.30  30.0  1

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
 NUG  chir_01  C1  C2  O1  C10  negativ

