# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 12:20:34 2021
#   Inital geometry file: a 126 line input string
#   Ligand name: 1-[cis-4-(3-methylphenyl)cyclohexyl]-4-(pyridin-3-yl)piperazine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(c1)[C@H]2CC[C@H](CC2)N3CCN(CC3)c4cccnc4
#
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
 VUG  VUG  1-[cis-4-(3-methylphenyl)cyclohexyl]-4-(pyridin-3-yl)piperazine  ligand  54  25  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VUG
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
 VUG  C17  C  CR16  0  -0.303  84.3823  116.9635  82.9193
 VUG  C16  C  CR16  0  -0.274  84.6586  116.1822  84.0274
 VUG  C15  C  CR6   0   0.320  85.5699  116.6378  84.9957
 VUG  C14  C  CH2   0  -0.271  85.2241  114.6103  86.3021
 VUG  C13  C  CH2   0  -0.343  85.6126  114.0266  87.6539
 VUG  C12  C  CH2   0  -0.351  86.9726  116.1466  86.9845
 VUG  C11  C  CH2   0  -0.260  86.5690  116.0426  88.4572
 VUG  C10  C  CH1   0  -0.018  85.4456  114.5933  90.0376
 VUG  C18  C  CR16  0  -0.120  85.0167  118.1851  82.7697
 VUG  C19  C  CR16  0  -0.164  86.1602  117.8918  84.7294
 VUG  C20  C  CR16  0  -0.342  83.4058  113.8887  94.6353
 VUG  C21  C  CR16  0  -0.225  83.0648  113.5412  95.9335
 VUG  C22  C  CR16  0  -0.324  83.9903  112.9180  96.7611
 VUG  N01  N  NT    0  -0.442  85.5026  115.0649  88.6585
 VUG  C02  C  CR6   0   0.120  85.2727  112.6390  96.2979
 VUG  N02  N  NT    0  -0.517  85.8359  115.9122  86.1232
 VUG  C03  C  CR16  0  -0.391  85.5971  112.9980  94.9899
 VUG  N03  N  N     0  -0.385  85.8913  118.6283  83.6661
 VUG  C04  C  CR6   0   0.213  84.6837  113.6208  94.1449
 VUG  C05  C  CH1   0  -0.346  85.0647  113.9752  92.7302
 VUG  C06  C  CH2   0  -0.416  84.3671  113.0554  91.7075
 VUG  C07  C  CH2   0  -0.476  84.2398  113.7010  90.3217
 VUG  C08  C  CH2   0  -0.430  84.7619  115.4275  92.3656
 VUG  C09  C  CH2   0  -0.451  85.3822  115.7887  91.0085
 VUG  H1   H  HCR6  0   0.263  83.6813  116.6153  82.1722
 VUG  H2   H  HCR6  0   0.279  84.1681  115.2244  84.1271
 VUG  H3   H  HCH2  0   0.236  84.1356  114.7140  86.2678
 VUG  H4   H  HCH2  0   0.261  84.9223  113.2122  87.8598
 VUG  H5   H  HCH2  0   0.240  87.7701  115.4304  86.7565
 VUG  H6   H  HCH2  0   0.273  87.3957  117.1322  86.8182
 VUG  H7   H  HCH2  0   0.203  87.4774  115.7799  89.0222
 VUG  H8   H  HCH2  0   0.234  86.2398  117.0199  88.8152
 VUG  H9   H  HCH1  0   0.191  86.3582  114.0119  90.2694
 VUG  H10  H  HCR6  0   0.250  84.8208  118.8196  81.9132
 VUG  H11  H  HCR6  0   0.255  86.8810  118.3208  85.4148
 VUG  H13  H  HCR6  0   0.248  82.0692  113.7534  96.3029
 VUG  H14  H  HCR6  0   0.242  83.7127  112.6450  97.7724
 VUG  H15  H  HCH3  0   0.247  86.8709  112.7456  97.7323
 VUG  H16  H  HCH3  0   0.242  85.8253  111.3498  97.9358
 VUG  H17  H  HCH3  0   0.242  87.0018  111.3916  96.6222
 VUG  H18  H  HCR6  0   0.235  86.5937  112.7835  94.6163
 VUG  H19  H  HCH1  0   0.243  86.1471  113.8337  92.6401
 VUG  H20  H  HCH2  0   0.232  83.3689  112.7967  92.0688
 VUG  H21  H  HCH2  0   0.232  84.9204  112.1155  91.6362
 VUG  H22  H  HCH2  0   0.224  83.3329  114.3109  90.2651
 VUG  H23  H  HCH2  0   0.243  84.1220  112.9082  89.5831
 VUG  H24  H  HCH2  0   0.239  85.1376  116.1057  93.1345
 VUG  H25  H  HCH2  0   0.224  83.6781  115.5719  92.3313
 VUG  H26  H  HCH2  0   0.233  86.3841  116.1934  91.1654
 VUG  H27  H  HCH2  0   0.229  84.7878  116.5821  90.5475
 VUG  H28  H  HCH2  0   0.225  85.5099  113.9098  85.5057
 VUG  H29  H  HCH2  0   0.212  86.6165  113.5741  87.6188
 VUG  H12  H  HCR6  0   0.241  82.6696  114.3712  94.0027
 VUG  C01  C  CH3   0  -0.724  86.2931  111.9934  97.1909

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
 VUG  C18  C17  aromatic  1.385  0.020  1.385
 VUG  C18  N03  aromatic  1.328  0.020  1.328
 VUG  C17  C16  aromatic  1.384  0.020  1.384
 VUG  N03  C19  aromatic  1.321  0.020  1.321
 VUG  C16  C15  aromatic  1.406  0.020  1.406
 VUG  C19  C15  aromatic  1.411  0.020  1.411
 VUG  C15  N02  single    1.367  0.020  1.367
 VUG  N02  C14  single    1.450  0.020  1.450
 VUG  N02  C12  single    1.445  0.020  1.445
 VUG  C14  C13  single    1.523  0.020  1.523
 VUG  C12  C11  single    1.531  0.020  1.531
 VUG  C13  N01  single    1.449  0.020  1.449
 VUG  C11  N01  single    1.461  0.020  1.461
 VUG  N01  C10  single    1.459  0.020  1.459
 VUG  C10  C07  single    1.527  0.020  1.527
 VUG  C10  C09  single    1.541  0.020  1.541
 VUG  C07  C06  single    1.534  0.020  1.534
 VUG  C09  C08  single    1.535  0.020  1.535
 VUG  C06  C05  single    1.542  0.020  1.542
 VUG  C08  C05  single    1.528  0.020  1.528
 VUG  C05  C04  single    1.507  0.020  1.507
 VUG  C04  C03  aromatic  1.391  0.020  1.391
 VUG  C04  C20  aromatic  1.395  0.020  1.395
 VUG  C03  C02  aromatic  1.395  0.020  1.395
 VUG  C20  C21  aromatic  1.386  0.020  1.386
 VUG  C02  C01  single    1.502  0.020  1.502
 VUG  C02  C22  aromatic  1.392  0.020  1.392
 VUG  C21  C22  aromatic  1.389  0.020  1.389
 VUG  C17  H1   single    0.930  0.020  1.080
 VUG  C16  H2   single    0.930  0.020  1.080
 VUG  C14  H3   single    0.970  0.020  1.090
 VUG  C13  H4   single    0.970  0.020  1.090
 VUG  C12  H5   single    0.970  0.020  1.090
 VUG  C12  H6   single    0.970  0.020  1.090
 VUG  C11  H7   single    0.970  0.020  1.090
 VUG  C11  H8   single    0.970  0.020  1.090
 VUG  C10  H9   single    0.970  0.020  1.090
 VUG  C18  H10  single    0.930  0.020  1.080
 VUG  C19  H11  single    0.930  0.020  1.080
 VUG  C20  H12  single    0.930  0.020  1.080
 VUG  C21  H13  single    0.930  0.020  1.080
 VUG  C22  H14  single    0.930  0.020  1.080
 VUG  C01  H15  single    0.970  0.020  1.090
 VUG  C01  H16  single    0.970  0.020  1.090
 VUG  C01  H17  single    0.970  0.020  1.090
 VUG  C03  H18  single    0.930  0.020  1.080
 VUG  C05  H19  single    0.970  0.020  1.090
 VUG  C06  H20  single    0.970  0.020  1.090
 VUG  C06  H21  single    0.970  0.020  1.090
 VUG  C07  H22  single    0.970  0.020  1.090
 VUG  C07  H23  single    0.970  0.020  1.090
 VUG  C08  H24  single    0.970  0.020  1.090
 VUG  C08  H25  single    0.970  0.020  1.090
 VUG  C09  H26  single    0.970  0.020  1.090
 VUG  C09  H27  single    0.970  0.020  1.090
 VUG  C14  H28  single    0.970  0.020  1.090
 VUG  C13  H29  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
 VUG  H1   C17  C18  120.41  3.000
 VUG  H1   C17  C16  120.04  3.000
 VUG  C18  C17  C16  119.55  3.000
 VUG  H2   C16  C15  121.20  3.000
 VUG  H2   C16  C17  118.93  3.000
 VUG  C15  C16  C17  119.88  3.000
 VUG  N02  C15  C19  123.08  3.000
 VUG  N02  C15  C16  121.49  3.000
 VUG  C19  C15  C16  115.42  3.000
 VUG  H28  C14  H3   107.26  3.000
 VUG  H28  C14  N02  111.93  3.000
 VUG  H3   C14  N02  109.33  3.000
 VUG  H28  C14  C13  109.44  3.000
 VUG  H3   C14  C13  108.54  3.000
 VUG  N02  C14  C13  110.25  3.000
 VUG  H29  C13  H4   106.07  3.000
 VUG  H29  C13  N01  112.68  3.000
 VUG  H4   C13  N01  110.93  3.000
 VUG  H29  C13  C14  111.20  3.000
 VUG  H4   C13  C14  107.05  3.000
 VUG  N01  C13  C14  108.75  3.000
 VUG  H6   C12  H5   106.13  3.000
 VUG  H6   C12  N02  111.25  3.000
 VUG  H5   C12  N02  110.02  3.000
 VUG  H6   C12  C11  108.17  3.000
 VUG  H5   C12  C11  110.35  3.000
 VUG  N02  C12  C11  110.80  3.000
 VUG  H8   C11  H7   107.10  3.000
 VUG  H8   C11  N01  109.50  3.000
 VUG  H7   C11  N01  111.82  3.000
 VUG  H8   C11  C12  109.53  3.000
 VUG  H7   C11  C12  107.00  3.000
 VUG  N01  C11  C12  111.75  3.000
 VUG  H9   C10  C09  108.03  3.000
 VUG  H9   C10  C07  107.78  3.000
 VUG  C09  C10  C07  107.67  3.000
 VUG  H9   C10  N01  109.61  3.000
 VUG  C09  C10  N01  110.27  3.000
 VUG  C07  C10  N01  113.31  3.000
 VUG  H10  C18  N03  117.19  3.000
 VUG  H10  C18  C17  121.27  3.000
 VUG  N03  C18  C17  121.54  3.000
 VUG  H11  C19  N03  115.08  3.000
 VUG  H11  C19  C15  120.72  3.000
 VUG  N03  C19  C15  124.20  3.000
 VUG  H12  C20  C04  120.17  3.000
 VUG  H12  C20  C21  119.40  3.000
 VUG  C04  C20  C21  120.43  3.000
 VUG  H13  C21  C22  119.82  3.000
 VUG  H13  C21  C20  119.76  3.000
 VUG  C22  C21  C20  120.42  3.000
 VUG  H14  C22  C02  119.74  3.000
 VUG  H14  C22  C21  119.89  3.000
 VUG  C02  C22  C21  120.37  3.000
 VUG  C10  N01  C11  112.04  3.000
 VUG  C10  N01  C13  115.27  3.000
 VUG  C11  N01  C13  109.19  3.000
 VUG  C03  C02  C01  120.68  3.000
 VUG  C01  C02  C22  120.96  3.000
 VUG  C03  C02  C22  118.35  3.000
 VUG  C12  N02  C14  113.83  3.000
 VUG  C12  N02  C15  123.96  3.000
 VUG  C14  N02  C15  119.76  3.000
 VUG  H18  C03  C04  118.82  3.000
 VUG  H18  C03  C02  119.04  3.000
 VUG  C04  C03  C02  122.14  3.000
 VUG  C19  N03  C18  119.41  3.000
 VUG  C05  C04  C03  120.61  3.000
 VUG  C03  C04  C20  118.29  3.000
 VUG  C05  C04  C20  121.09  3.000
 VUG  H19  C05  C08  107.40  3.000
 VUG  H19  C05  C06  108.38  3.000
 VUG  C08  C05  C06  108.61  3.000
 VUG  H19  C05  C04  107.25  3.000
 VUG  C08  C05  C04  113.42  3.000
 VUG  C06  C05  C04  111.58  3.000
 VUG  H21  C06  H20  106.29  3.000
 VUG  H21  C06  C07  110.18  3.000
 VUG  H20  C06  C07  108.81  3.000
 VUG  H21  C06  C05  109.10  3.000
 VUG  H20  C06  C05  109.58  3.000
 VUG  C07  C06  C05  112.67  3.000
 VUG  H23  C07  H22  106.30  3.000
 VUG  H23  C07  C06  108.36  3.000
 VUG  H22  C07  C06  110.49  3.000
 VUG  H23  C07  C10  112.61  3.000
 VUG  H22  C07  C10  108.62  3.000
 VUG  C06  C07  C10  110.40  3.000
 VUG  H25  C08  H24  106.32  3.000
 VUG  H25  C08  C09  109.97  3.000
 VUG  H24  C08  C09  109.72  3.000
 VUG  H25  C08  C05  109.23  3.000
 VUG  H24  C08  C05  110.74  3.000
 VUG  C09  C08  C05  110.77  3.000
 VUG  H27  C09  H26  106.88  3.000
 VUG  H27  C09  C08  108.89  3.000
 VUG  H26  C09  C08  109.32  3.000
 VUG  H27  C09  C10  108.64  3.000
 VUG  H26  C09  C10  109.89  3.000
 VUG  C08  C09  C10  113.02  3.000
 VUG  H17  C01  H16  108.04  3.000
 VUG  H17  C01  H15  107.16  3.000
 VUG  H16  C01  H15  107.16  3.000
 VUG  H17  C01  C02  111.65  3.000
 VUG  H16  C01  C02  111.63  3.000
 VUG  H15  C01  C02  110.99  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
 VUG  CONST_01  C19  N03  C18  C17     0.00   0.0  0
 VUG  CONST_02  C19  C15  C16  C17     0.00   0.0  0
 VUG  CONST_03  N03  C18  C17  C16     0.00   0.0  0
 VUG  CONST_04  N03  C19  C15  C16     0.00   0.0  0
 VUG  CONST_05  C18  C17  C16  C15     0.00   0.0  0
 VUG  CONST_06  C18  N03  C19  C15     0.00   0.0  0
 VUG  CONST_07  C02  C03  C04  C20     0.00   0.0  0
 VUG  CONST_08  C02  C22  C21  C20     0.00   0.0  0
 VUG  CONST_09  C03  C04  C20  C21     0.00   0.0  0
 VUG  CONST_10  C03  C02  C22  C21     0.00   0.0  0
 VUG  CONST_11  C04  C03  C02  C22     0.00   0.0  0
 VUG  CONST_12  C04  C20  C21  C22     0.00   0.0  0
 VUG  CONST_13  N02  C15  C16  C17   180.00   0.0  0
 VUG  CONST_14  C05  C04  C20  C21   180.00   0.0  0
 VUG  CONST_15  C05  C04  C03  C02   180.00   0.0  0
 VUG  CONST_16  N03  C19  C15  N02   180.00   0.0  0
 VUG  CONST_17  C01  C02  C22  C21   180.00   0.0  0
 VUG  CONST_18  C04  C03  C02  C01   180.00   0.0  0
 VUG  CONST_19  H10  C18  C17  C16   180.00   0.0  0
 VUG  CONST_20  H11  C19  C15  C16   180.00   0.0  0
 VUG  CONST_21  H1   C17  C16  C15   180.00   0.0  0
 VUG  CONST_22  H2   C16  C17  C18   180.00   0.0  0
 VUG  CONST_23  H18  C03  C04  C20   180.00   0.0  0
 VUG  CONST_24  H14  C22  C21  C20   180.00   0.0  0
 VUG  CONST_25  H12  C20  C21  C22   180.00   0.0  0
 VUG  CONST_26  H13  C21  C22  C02   180.00   0.0  0
 VUG  Var_01    C14  N02  C15  C16     3.29  30.0  2
 VUG  Var_02    C13  C14  N02  C15  -177.25  30.0  1
 VUG  Var_03    C11  C12  N02  C15   138.43  30.0  1
 VUG  Var_04    C11  N01  C13  C14   -70.52  30.0  1
 VUG  Var_05    C12  C11  N01  C13    29.92  30.0  1
 VUG  Var_06    C05  C06  C07  C10    34.03  30.0  1
 VUG  Var_07    C05  C08  C09  C10    31.50  30.0  1
 VUG  Var_08    N02  C14  C13  N01    44.17  30.0  1
 VUG  Var_09    N02  C12  C11  N01    32.52  30.0  1
 VUG  Var_10    H15  C01  C02  C22   -90.01  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
 VUG  chir_01  C10  N01  C07  C09  positiv
 VUG  chir_02  C05  C06  C08  C04  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
 VUG  plan-1  C17  0.020
 VUG  plan-1  C16  0.020
 VUG  plan-1  C15  0.020
 VUG  plan-1  C18  0.020
 VUG  plan-1  C19  0.020
 VUG  plan-1  N02  0.020
 VUG  plan-1  N03  0.020
 VUG  plan-1  H1   0.020
 VUG  plan-1  H2   0.020
 VUG  plan-1  H10  0.020
 VUG  plan-1  H11  0.020
 VUG  plan-2  C20  0.020
 VUG  plan-2  C21  0.020
 VUG  plan-2  C22  0.020
 VUG  plan-2  C02  0.020
 VUG  plan-2  C03  0.020
 VUG  plan-2  C04  0.020
 VUG  plan-2  C05  0.020
 VUG  plan-2  H13  0.020
 VUG  plan-2  H14  0.020
 VUG  plan-2  H18  0.020
 VUG  plan-2  H12  0.020
 VUG  plan-2  C01  0.020

