# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 22:43:43 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: cyclobutyl-[4-(2-methoxyphenyl)piperidin-1-yl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccccc1C2CCN(CC2)C(=O)C3CCC3
#
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
 A5W  A5W  cyclobutyl-[4-(2-methoxyphenyl)piperidin-1-yl]methanone  ligand  43  20  .  2021-08-06  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_A5W
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
 A5W  C16  C  C     0  -0.430  -4.6754  -0.6907   1.1223
 A5W  C15  C  C     0  -0.456  -5.9165   0.2158   1.0446
 A5W  C12  C  C     0   0.561  -2.9482  -0.0819  -0.7714
 A5W  C13  C  C     0  -0.420  -3.9097   0.3777   0.3006
 A5W  C14  C  C     0  -0.419  -5.2683   0.9355  -0.1525
 A5W  C11  C  CH2   0  -0.414   0.4896  -0.3183  -1.1903
 A5W  C10  C  CH2   0  -0.315  -0.8033  -1.1126  -1.3270
 A5W  C9   C  CH2   0  -0.320  -1.3367  -0.7388   1.0079
 A5W  C8   C  CH2   0  -0.416  -0.0752   0.0938   1.2040
 A5W  C7   C  CH1   0  -0.313   1.0211  -0.3752   0.2482
 A5W  C4   C  CR16  0  -0.267   3.5858   2.3843   0.9150
 A5W  C5   C  CR16  0  -0.320   2.3853   1.6867   0.8264
 A5W  C6   C  CR6   0   0.062   2.3262   0.3741   0.3772
 A5W  C3   C  CR16  0  -0.258   4.7611   1.7564   0.5458
 A5W  C2   C  CR16  0  -0.381   4.7399   0.4436   0.0886
 A5W  C1   C  CR6   0   0.349   3.5331  -0.2445   0.0003
 A5W  O1   O  O     0  -0.505  -3.2318   0.0435  -1.9577
 A5W  N    N  NT    0  -0.445  -1.7955  -0.6588  -0.3674
 A5W  O    O  O2    0  -0.469   3.4376  -1.5155  -0.4420
 A5W  C    C  CH3   0  -0.434   4.6174  -2.2155  -0.7780
 A5W  H1   H  H     0   0.238  -4.2883  -0.9468   2.1087
 A5W  H2   H  H     0   0.235  -4.8087  -1.6117   0.5518
 A5W  H3   H  H     0   0.233  -6.8813  -0.2641   0.8831
 A5W  H4   H  H     0   0.229  -5.9906   0.8651   1.9180
 A5W  H5   H  H     0   0.277  -3.4188   1.0858   0.9742
 A5W  H6   H  H     0   0.230  -5.5809   0.4987  -1.1003
 A5W  H7   H  H     0   0.233  -5.3694   2.0187  -0.2154
 A5W  H8   H  HCH2  0   0.245   1.2275  -0.7193  -1.8875
 A5W  H9   H  HCH2  0   0.228   0.3117   0.7247  -1.4707
 A5W  H10  H  HCH2  0   0.262  -1.2063  -1.0289  -2.3323
 A5W  H11  H  HCH2  0   0.237  -0.6012  -2.1736  -1.1399
 A5W  H12  H  HCH2  0   0.242  -1.1272  -1.7882   1.2424
 A5W  H13  H  HCH2  0   0.271  -2.1137  -0.4120   1.6925
 A5W  H14  H  HCH2  0   0.228  -0.3276   1.1439   1.0308
 A5W  H15  H  HCH2  0   0.246   0.2567   0.0052   2.2412
 A5W  H16  H  HCH1  0   0.237   1.2070  -1.4292   0.4841
 A5W  H18  H  HCR6  0   0.247   1.4721   2.1880   1.1195
 A5W  H19  H  HCR6  0   0.255   5.7070   2.2787   0.6114
 A5W  H20  H  HCR6  0   0.276   5.6724  -0.0250  -0.1941
 A5W  H21  H  HCH3  0   0.226   5.1481  -1.7498  -1.6127
 A5W  H22  H  HCH3  0   0.227   5.3011  -2.2979   0.0711
 A5W  H23  H  HCH3  0   0.258   4.3086  -3.2144  -1.0760
 A5W  H17  H  HCR6  0   0.248   3.5945   3.4058   1.2717

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
 A5W  C    O    single    1.412  0.020  1.412
 A5W  O    C1   single    1.349  0.020  1.349
 A5W  C2   C1   aromatic  1.392  0.020  1.392
 A5W  C2   C3   aromatic  1.390  0.020  1.390
 A5W  C1   C6   aromatic  1.408  0.020  1.408
 A5W  C7   C6   single    1.510  0.020  1.510
 A5W  C7   C8   single    1.528  0.020  1.528
 A5W  C7   C11  single    1.535  0.020  1.535
 A5W  C3   C4   aromatic  1.383  0.020  1.383
 A5W  C6   C5   aromatic  1.389  0.020  1.389
 A5W  C8   C9   single    1.524  0.020  1.524
 A5W  C11  C10  single    1.524  0.020  1.524
 A5W  C5   C4   aromatic  1.391  0.020  1.391
 A5W  C9   N    single    1.452  0.020  1.452
 A5W  C10  N    single    1.453  0.020  1.453
 A5W  N    C12  single    1.351  0.020  1.351
 A5W  O1   C12  double    1.226  0.020  1.226
 A5W  C12  C13  single    1.512  0.020  1.512
 A5W  C13  C14  single    1.537  0.020  1.537
 A5W  C13  C16  single    1.550  0.020  1.550
 A5W  C14  C15  single    1.540  0.020  1.540
 A5W  C16  C15  single    1.539  0.020  1.539
 A5W  C16  H1   single    0.970  0.020  1.090
 A5W  C16  H2   single    0.970  0.020  1.090
 A5W  C15  H3   single    0.970  0.020  1.090
 A5W  C15  H4   single    0.970  0.020  1.090
 A5W  C13  H5   single    0.970  0.020  1.090
 A5W  C14  H6   single    0.970  0.020  1.090
 A5W  C14  H7   single    0.970  0.020  1.090
 A5W  C11  H8   single    0.970  0.020  1.090
 A5W  C11  H9   single    0.970  0.020  1.090
 A5W  C10  H10  single    0.970  0.020  1.090
 A5W  C10  H11  single    0.970  0.020  1.090
 A5W  C9   H12  single    0.970  0.020  1.090
 A5W  C9   H13  single    0.970  0.020  1.090
 A5W  C8   H14  single    0.970  0.020  1.090
 A5W  C8   H15  single    0.970  0.020  1.090
 A5W  C7   H16  single    0.970  0.020  1.090
 A5W  C4   H17  single    0.930  0.020  1.080
 A5W  C5   H18  single    0.930  0.020  1.080
 A5W  C3   H19  single    0.930  0.020  1.080
 A5W  C2   H20  single    0.930  0.020  1.080
 A5W  C    H21  single    0.970  0.020  1.090
 A5W  C    H22  single    0.970  0.020  1.090
 A5W  C    H23  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
 A5W  H2   C16  H1   108.55  3.000
 A5W  H2   C16  C13  111.39  3.000
 A5W  H1   C16  C13  117.78  3.000
 A5W  H2   C16  C15  111.85  3.000
 A5W  H1   C16  C15  118.07  3.000
 A5W  C13  C16  C15   88.03  3.000
 A5W  H4   C15  H3   108.70  3.000
 A5W  H4   C15  C14  111.89  3.000
 A5W  H3   C15  C14  117.60  3.000
 A5W  H4   C15  C16  111.41  3.000
 A5W  H3   C15  C16  117.53  3.000
 A5W  C14  C15  C16   88.57  3.000
 A5W  N    C12  O1   122.03  3.000
 A5W  O1   C12  C13  120.52  3.000
 A5W  N    C12  C13  117.42  3.000
 A5W  H5   C13  C14  110.08  3.000
 A5W  H5   C13  C12  110.38  3.000
 A5W  C14  C13  C12  117.61  3.000
 A5W  H5   C13  C16  109.97  3.000
 A5W  C14  C13  C16   88.27  3.000
 A5W  C12  C13  C16  118.72  3.000
 A5W  H7   C14  H6   108.77  3.000
 A5W  H7   C14  C13  117.37  3.000
 A5W  H6   C14  C13  111.39  3.000
 A5W  H7   C14  C15  118.06  3.000
 A5W  H6   C14  C15  111.60  3.000
 A5W  C13  C14  C15   88.47  3.000
 A5W  H9   C11  H8   107.23  3.000
 A5W  H9   C11  C7   109.37  3.000
 A5W  H8   C11  C7   110.55  3.000
 A5W  H9   C11  C10  109.62  3.000
 A5W  H8   C11  C10  108.96  3.000
 A5W  C7   C11  C10  111.02  3.000
 A5W  H11  C10  H10  107.51  3.000
 A5W  H11  C10  N    108.39  3.000
 A5W  H10  C10  N    109.50  3.000
 A5W  H11  C10  C11  109.44  3.000
 A5W  H10  C10  C11  110.96  3.000
 A5W  N    C10  C11  110.94  3.000
 A5W  H13  C9   H12  106.87  3.000
 A5W  H13  C9   N    110.76  3.000
 A5W  H12  C9   N    108.42  3.000
 A5W  H13  C9   C8   110.28  3.000
 A5W  H12  C9   C8   109.72  3.000
 A5W  N    C9   C8   110.69  3.000
 A5W  H15  C8   H14  107.36  3.000
 A5W  H15  C8   C7   110.54  3.000
 A5W  H14  C8   C7   111.17  3.000
 A5W  H15  C8   C9   109.22  3.000
 A5W  H14  C8   C9   108.25  3.000
 A5W  C7   C8   C9   110.22  3.000
 A5W  H16  C7   C6   108.19  3.000
 A5W  H16  C7   C8   106.39  3.000
 A5W  C6   C7   C8   114.47  3.000
 A5W  H16  C7   C11  107.23  3.000
 A5W  C8   C7   C11  109.05  3.000
 A5W  C6   C7   C11  111.16  3.000
 A5W  H17  C4   C3   120.65  3.000
 A5W  H17  C4   C5   120.09  3.000
 A5W  C3   C4   C5   119.26  3.000
 A5W  H18  C5   C6   119.31  3.000
 A5W  H18  C5   C4   118.60  3.000
 A5W  C6   C5   C4   122.09  3.000
 A5W  C1   C6   C5   117.75  3.000
 A5W  C5   C6   C7   122.23  3.000
 A5W  C1   C6   C7   120.00  3.000
 A5W  H19  C3   C2   119.26  3.000
 A5W  H19  C3   C4   120.50  3.000
 A5W  C2   C3   C4   120.24  3.000
 A5W  H20  C2   C1   121.12  3.000
 A5W  H20  C2   C3   118.82  3.000
 A5W  C1   C2   C3   120.06  3.000
 A5W  O    C1   C2   123.22  3.000
 A5W  C2   C1   C6   120.60  3.000
 A5W  O    C1   C6   116.17  3.000
 A5W  C9   N    C10  113.11  3.000
 A5W  C10  N    C12  121.24  3.000
 A5W  C9   N    C12  125.20  3.000
 A5W  C    O    C1   119.06  3.000
 A5W  H23  C    H22  108.74  3.000
 A5W  H23  C    H21  108.65  3.000
 A5W  H22  C    H21  108.75  3.000
 A5W  H23  C    O    106.46  3.000
 A5W  H22  C    O    112.03  3.000
 A5W  H21  C    O    112.09  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
 A5W  CONST_01  C1   C2   C3   C4     0.00   0.0  0
 A5W  CONST_02  C1   C6   C5   C4     0.00   0.0  0
 A5W  CONST_03  C2   C1   C6   C5     0.00   0.0  0
 A5W  CONST_04  C2   C3   C4   C5     0.00   0.0  0
 A5W  CONST_05  C3   C2   C1   C6     0.00   0.0  0
 A5W  CONST_06  C3   C4   C5   C6     0.00   0.0  0
 A5W  CONST_07  C2   C1   C6   C7   180.00   0.0  0
 A5W  CONST_08  C4   C5   C6   C7   180.00   0.0  0
 A5W  CONST_09  O    C1   C6   C7     0.00   0.0  0
 A5W  CONST_10  O    C1   C6   C5   180.00   0.0  0
 A5W  CONST_11  O    C1   C2   C3   180.00   0.0  0
 A5W  CONST_12  C9   N    C12  C13    0.00   0.0  0
 A5W  CONST_13  C10  N    C12  C13  180.00   0.0  0
 A5W  CONST_14  H18  C5   C6   C7     0.00   0.0  0
 A5W  CONST_15  H20  C2   C3   C4   180.00   0.0  0
 A5W  CONST_16  H19  C3   C4   C5   180.00   0.0  0
 A5W  CONST_17  H17  C4   C5   C6   180.00   0.0  0
 A5W  CONST_18  O1   C12  N    C10    0.00   0.0  0
 A5W  CONST_19  O1   C12  N    C9   180.00   0.0  0
 A5W  Var_01    C13  C14  C15  C16  -19.46  30.0  1
 A5W  Var_02    C9   N    C10  C11  -57.25  30.0  1
 A5W  Var_03    C8   C9   N    C10   58.60  30.0  1
 A5W  Var_04    N    C9   C8   C7   -57.56  30.0  1
 A5W  Var_05    N    C10  C11  C7    55.07  30.0  1
 A5W  Var_06    H21  C    O    C1   -62.98  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
 A5W  chir_01  C13  C12  C14  C16  negativ
 A5W  chir_02  C7   C6   C8   C11  negativ

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
 A5W  plan-1  C12  0.020
 A5W  plan-1  C13  0.020
 A5W  plan-1  C10  0.020
 A5W  plan-1  C9   0.020
 A5W  plan-1  O1   0.020
 A5W  plan-1  N    0.020
 A5W  plan-2  C7   0.020
 A5W  plan-2  C4   0.020
 A5W  plan-2  C5   0.020
 A5W  plan-2  C6   0.020
 A5W  plan-2  C3   0.020
 A5W  plan-2  C2   0.020
 A5W  plan-2  C1   0.020
 A5W  plan-2  O    0.020
 A5W  plan-2  H18  0.020
 A5W  plan-2  H19  0.020
 A5W  plan-2  H20  0.020
 A5W  plan-2  H17  0.020

