# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 23:21:26 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: [4-(propan-2-yl)piperazin-1-yl](thiophen-2-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)N1CCN(CC1)C(=O)c2sccc2
#
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
 NUY  NUY  '[4-(propan-2-yl)piperazin-1-yl](thiophen-2-yl)methanone'  ligand  34  16  .  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_NUY
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
 NUY  N1   N  NT    0  -0.424  -2.6623   0.1829   0.1670
 NUY  C4   C  CH2   0  -0.274  -1.5182   1.0226  -0.1431
 NUY  C5   C  CH2   0  -0.326  -0.3064   0.6806   0.7111
 NUY  C6   C  CH2   0  -0.323  -1.0984  -1.5770   0.8504
 NUY  C7   C  CH2   0  -0.286  -2.2926  -1.2122  -0.0140
 NUY  C10  C  CR15  0  -0.183   3.0432  -0.2076  -1.4084
 NUY  C1   C  CH3   0  -0.686  -5.0464  -0.3290  -0.2457
 NUY  C11  C  CR15  0  -0.185   4.1951   0.5958  -1.2124
 NUY  C12  C  CR15  0  -0.453   4.3056   1.0432   0.0697
 NUY  C2   C  CH1   0  -0.045  -3.8534   0.5531  -0.6062
 NUY  C3   C  CH3   0  -0.685  -4.2355   2.0124  -0.3714
 NUY  C9   C  CR5   0  -0.327   2.2837  -0.3296  -0.2803
 NUY  N2   N  NT    0  -0.456   0.0402  -0.7231   0.5675
 NUY  O1   O  O     0  -0.476   1.1151  -2.3218  -0.6263
 NUY  S1   S  S2    0   0.243   3.0036   0.5109   1.0412
 NUY  H2   H  HCH2  0   0.195  -1.2319   0.9490  -1.2075
 NUY  H3   H  HCH2  0   0.253  -1.7534   2.0676   0.0548
 NUY  H4   H  HCH2  0   0.270   0.5174   1.3209   0.4090
 NUY  H5   H  HCH2  0   0.248  -0.5221   0.8868   1.7627
 NUY  H6   H  HCH2  0   0.250  -1.3604  -1.4475   1.9047
 NUY  H7   H  HCH2  0   0.266  -0.8304  -2.6189   0.6980
 NUY  H8   H  HCH2  0   0.251  -3.1159  -1.8609   0.2826
 NUY  H9   H  HCH2  0   0.199  -2.0620  -1.4407  -1.0691
 NUY  H11  H  HCH3  0   0.222  -5.2255  -0.3151   0.8313
 NUY  H12  H  HCH3  0   0.235  -5.9426   0.0471  -0.7393
 NUY  H13  H  HCH3  0   0.236  -4.9266  -1.3653  -0.5578
 NUY  H14  H  HCR5  0   0.274   4.9126   0.8228  -1.9873
 NUY  H15  H  HCR5  0   0.304   5.0867   1.6534   0.4966
 NUY  H16  H  HCH1  0   0.190  -3.6533   0.4245  -1.6856
 NUY  H17  H  HCH3  0   0.222  -4.3512   2.2132   0.6957
 NUY  H18  H  HCH3  0   0.236  -3.5117   2.7181  -0.7759
 NUY  H19  H  HCH3  0   0.235  -5.1874   2.2253  -0.8575
 NUY  C8   C  C     0   0.530   1.0875  -1.1992  -0.1406
 NUY  H10  H  HCR5  0   0.273   2.7813  -0.6711  -2.3490

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
 NUY  C11  C10  aromatic  1.418  0.020  1.418
 NUY  C11  C12  aromatic  1.362  0.020  1.362
 NUY  C10  C9   aromatic  1.365  0.020  1.365
 NUY  O1   C8   double    1.224  0.020  1.224
 NUY  C12  S1   aromatic  1.709  0.020  1.709
 NUY  C9   C8   single    1.485  0.020  1.485
 NUY  C9   S1   aromatic  1.724  0.020  1.724
 NUY  C8   N2   single    1.351  0.020  1.351
 NUY  N2   C6   single    1.451  0.020  1.451
 NUY  N2   C5   single    1.453  0.020  1.453
 NUY  C6   C7   single    1.519  0.020  1.519
 NUY  C5   C4   single    1.522  0.020  1.522
 NUY  C7   N1   single    1.455  0.020  1.455
 NUY  C4   N1   single    1.453  0.020  1.453
 NUY  N1   C2   single    1.467  0.020  1.467
 NUY  C2   C1   single    1.527  0.020  1.527
 NUY  C2   C3   single    1.527  0.020  1.527
 NUY  C4   H2   single    0.970  0.020  1.090
 NUY  C4   H3   single    0.970  0.020  1.090
 NUY  C5   H4   single    0.970  0.020  1.090
 NUY  C5   H5   single    0.970  0.020  1.090
 NUY  C6   H6   single    0.970  0.020  1.090
 NUY  C6   H7   single    0.970  0.020  1.090
 NUY  C7   H8   single    0.970  0.020  1.090
 NUY  C7   H9   single    0.970  0.020  1.090
 NUY  C10  H10  single    0.930  0.020  1.080
 NUY  C1   H11  single    0.970  0.020  1.090
 NUY  C1   H12  single    0.970  0.020  1.090
 NUY  C1   H13  single    0.970  0.020  1.090
 NUY  C11  H14  single    0.930  0.020  1.080
 NUY  C12  H15  single    0.930  0.020  1.080
 NUY  C2   H16  single    0.970  0.020  1.090
 NUY  C3   H17  single    0.970  0.020  1.090
 NUY  C3   H18  single    0.970  0.020  1.090
 NUY  C3   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
 NUY  C2   N1   C7   112.50  3.000
 NUY  C2   N1   C4   112.39  3.000
 NUY  C7   N1   C4   109.13  3.000
 NUY  H3   C4   H2   107.15  3.000
 NUY  H3   C4   C5   106.60  3.000
 NUY  H2   C4   C5   108.64  3.000
 NUY  H3   C4   N1   110.23  3.000
 NUY  H2   C4   N1   111.79  3.000
 NUY  C5   C4   N1   112.18  3.000
 NUY  H5   C5   H4   107.82  3.000
 NUY  H5   C5   N2   108.93  3.000
 NUY  H4   C5   N2   111.16  3.000
 NUY  H5   C5   C4   109.91  3.000
 NUY  H4   C5   C4   108.38  3.000
 NUY  N2   C5   C4   110.59  3.000
 NUY  H7   C6   H6   107.92  3.000
 NUY  H7   C6   N2   110.08  3.000
 NUY  H6   C6   N2   107.83  3.000
 NUY  H7   C6   C7   110.14  3.000
 NUY  H6   C6   C7   109.37  3.000
 NUY  N2   C6   C7   111.39  3.000
 NUY  H9   C7   H8   107.15  3.000
 NUY  H9   C7   C6   109.27  3.000
 NUY  H8   C7   C6   107.24  3.000
 NUY  H9   C7   N1   111.75  3.000
 NUY  H8   C7   N1   110.19  3.000
 NUY  C6   C7   N1   111.06  3.000
 NUY  H10  C10  C9   123.08  3.000
 NUY  H10  C10  C11  124.06  3.000
 NUY  C9   C10  C11  112.85  3.000
 NUY  H13  C1   H12  106.80  3.000
 NUY  H13  C1   H11  108.23  3.000
 NUY  H12  C1   H11  107.90  3.000
 NUY  H13  C1   C2   113.34  3.000
 NUY  H12  C1   C2   109.64  3.000
 NUY  H11  C1   C2   110.71  3.000
 NUY  H14  C11  C12  123.51  3.000
 NUY  H14  C11  C10  124.03  3.000
 NUY  C12  C11  C10  112.46  3.000
 NUY  H15  C12  S1   120.16  3.000
 NUY  H15  C12  C11  128.07  3.000
 NUY  S1   C12  C11  111.76  3.000
 NUY  H16  C2   C3   107.86  3.000
 NUY  H16  C2   C1   107.74  3.000
 NUY  C3   C2   C1   108.68  3.000
 NUY  H16  C2   N1   109.77  3.000
 NUY  C3   C2   N1   111.30  3.000
 NUY  C1   C2   N1   111.35  3.000
 NUY  H19  C3   H18  106.75  3.000
 NUY  H19  C3   H17  107.91  3.000
 NUY  H18  C3   H17  108.32  3.000
 NUY  H19  C3   C2   109.68  3.000
 NUY  H18  C3   C2   113.33  3.000
 NUY  H17  C3   C2   110.65  3.000
 NUY  S1   C9   C10  110.94  3.000
 NUY  S1   C9   C8   123.35  3.000
 NUY  C10  C9   C8   125.31  3.000
 NUY  C8   N2   C6   120.21  3.000
 NUY  C6   N2   C5   111.22  3.000
 NUY  C8   N2   C5   125.26  3.000
 NUY  C9   S1   C12   91.96  3.000
 NUY  O1   C8   N2   123.29  3.000
 NUY  N2   C8   C9   117.86  3.000
 NUY  O1   C8   C9   118.79  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
 NUY  CONST_01  S1   C12  C11  C10     0.00   0.0  0
 NUY  CONST_02  C12  S1   C9   C10     0.00   0.0  0
 NUY  CONST_03  S1   C9   C10  C11     0.00   0.0  0
 NUY  CONST_04  C9   S1   C12  C11     0.00   0.0  0
 NUY  CONST_05  C9   C10  C11  C12     0.00   0.0  0
 NUY  CONST_06  C11  C10  C9   C8    180.00   0.0  0
 NUY  CONST_07  C12  S1   C9   C8    180.00   0.0  0
 NUY  CONST_09  C9   C8   N2   C6    180.00   0.0  0
 NUY  CONST_10  H15  C12  C11  C10   180.00   0.0  0
 NUY  CONST_11  H10  C10  C11  C12   180.00   0.0  0
 NUY  CONST_12  H14  C11  C10  C9    180.00   0.0  0
 NUY  CONST_14  O1   C8   N2   C6      0.00   0.0  0
 NUY  Var_01    N2   C6   C7   N1    -57.12  30.0  1
 NUY  Var_02    N2   C5   C4   N1     56.21  30.0  1
 NUY  Var_03    C6   N2   C5   C4    -54.20  30.0  1
 NUY  Var_04    C6   C7   N1   C4     57.27  30.0  1
 NUY  Var_05    C7   C6   N2   C5     55.20  30.0  1
 NUY  Var_06    C7   N1   C4   C5    -57.36  30.0  1
 NUY  Var_07    N2   C8   C9   C10  -141.26  30.0  2
 NUY  Var_08    C1   C2   N1   C4   -179.09  30.0  3
 NUY  Var_09    H11  C1   C2   N1     54.00  30.0  3
 NUY  Var_10    H17  C3   C2   N1    -54.15  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 NUY  plan-1  C10  0.020
 NUY  plan-1  C11  0.020
 NUY  plan-1  C12  0.020
 NUY  plan-1  C9   0.020
 NUY  plan-1  S1   0.020
 NUY  plan-1  H14  0.020
 NUY  plan-1  H15  0.020
 NUY  plan-1  C8   0.020
 NUY  plan-1  H10  0.020
 NUY  plan-2  C5   0.020
 NUY  plan-2  C6   0.020
 NUY  plan-2  C9   0.020
 NUY  plan-2  N2   0.020
 NUY  plan-2  O1   0.020
 NUY  plan-2  C8   0.020

