# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 10:50:59 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: 4-[2-(4-methylphenyl)-5-(piperidin-4-ylmethoxy)pyridin-3-yl]benzenecarbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)c2ncc(OCC3CCNCC3)cc2c4ccc(cc4)C#N
#
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
 8WC  8WC  4-[2-(4-methylphenyl)-5-(piperidin-4-ylmethoxy)pyridin-3-yl]benzenecarbonitrile  ligand  54  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8WC
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
 8WC  C4   C  CR16  0  -0.281   3.8394   3.5249  -0.4376
 8WC  C5   C  CR16  0  -0.275   2.5839   2.9583  -0.5759
 8WC  C6   C  CR6   0   0.015   2.2252   1.8279   0.1590
 8WC  N1   N  NH1   0  -0.595  -7.9520  -0.7395   0.6631
 8WC  C7   C  CR6   0   0.193   0.8710   1.2510   0.0055
 8WC  C8   C  CR6   0   0.041   0.6288  -0.1303  -0.1034
 8WC  N2   N  N     0  -0.405  -0.1289   2.1223  -0.0171
 8WC  C9   C  CR6   0   0.015   1.7055  -1.1408  -0.1694
 8WC  C10  C  CR16  0  -0.279   1.6839  -2.2372   0.6910
 8WC  C11  C  CR16  0  -0.225   2.6676  -3.2078   0.6257
 8WC  C12  C  CR6   0  -0.006   3.6866  -3.0885  -0.3172
 8WC  C13  C  CSP   0   0.054   4.7059  -4.0842  -0.3915
 8WC  C14  C  CR16  0  -0.222   3.7142  -2.0015  -1.1919
 8WC  C15  C  CR16  0  -0.264   2.7289  -1.0369  -1.1123
 8WC  N    N  NS    0  -0.251   5.5296  -4.8877  -0.4534
 8WC  C1   C  CR6   0   0.089   4.7769   2.9939   0.4485
 8WC  C16  C  CR16  0  -0.289  -0.6863  -0.5584  -0.1873
 8WC  C17  C  CR6   0   0.342  -1.7265   0.3653  -0.1876
 8WC  C18  C  CH2   0  -0.163  -4.0685   0.7915  -0.2418
 8WC  C19  C  CH1   0  -0.291  -5.3552  -0.0002  -0.3594
 8WC  C2   C  CR16  0  -0.289   4.4081   1.8779   1.1934
 8WC  C20  C  CH2   0  -0.412  -5.5313  -1.0228   0.7629
 8WC  C21  C  CH2   0  -0.295  -6.8799  -1.7181   0.6447
 8WC  C22  C  CH2   0  -0.293  -7.8562   0.1791  -0.4570
 8WC  C23  C  CH2   0  -0.421  -6.5494   0.9550  -0.3811
 8WC  C24  C  CR16  0  -0.198  -1.3853   1.7138  -0.1138
 8WC  C3   C  CR16  0  -0.271   3.1542   1.3007   1.0515
 8WC  H1   H  HCR6  0   0.247   4.0951   4.3969  -1.0284
 8WC  H2   H  HCR6  0   0.247   1.8762   3.3922  -1.2708
 8WC  H5   H  HCR6  0   0.273   0.9026  -2.3257   1.4346
 8WC  H6   H  HCR6  0   0.284   2.6482  -4.0499   1.3038
 8WC  H7   H  HCR6  0   0.283   4.4998  -1.9163  -1.9299
 8WC  H8   H  HCR6  0   0.270   2.7511  -0.1988  -1.7957
 8WC  H12  H  HCR6  0   0.279  -0.9102  -1.6144  -0.2847
 8WC  H13  H  HCH2  0   0.222  -4.0577   1.3578   0.6983
 8WC  H14  H  HCH2  0   0.236  -3.9932   1.5106  -1.0661
 8WC  H15  H  HCH1  0   0.229  -5.3418  -0.5386  -1.3164
 8WC  H16  H  HCR6  0   0.248   5.1086   1.4503   1.9009
 8WC  H17  H  HCH2  0   0.235  -4.7369  -1.7705   0.7370
 8WC  H18  H  HCH2  0   0.212  -5.4693  -0.5167   1.7326
 8WC  H19  H  HCH2  0   0.231  -7.0160  -2.4084   1.4798
 8WC  H20  H  HCH2  0   0.185  -6.8815  -2.3270  -0.2752
 8WC  H21  H  HCH2  0   0.186  -7.9013  -0.3364  -1.4313
 8WC  H22  H  HCH2  0   0.232  -8.7022   0.8682  -0.4234
 8WC  H23  H  HCH2  0   0.217  -6.5476   1.5702   0.5249
 8WC  H24  H  HCH2  0   0.233  -6.4766   1.6358  -1.2330
 8WC  H25  H  HCR6  0   0.279  -2.1372   2.4936  -0.1274
 8WC  H26  H  HCR6  0   0.253   2.9024   0.4397   1.6575
 8WC  C    C  CH3   0  -0.725   6.1341   3.6170   0.5917
 8WC  O    O  O2    0  -0.470  -2.9730  -0.1142  -0.2786
 8WC  H3   H  HNH1  0   0.351  -8.8439  -1.2159   0.6334
 8WC  H9   H  HCH3  0   0.247   6.0600   4.6542   0.9224
 8WC  H10  H  HCH3  0   0.244   6.7473   3.0799   1.3139
 8WC  H11  H  HCH3  0   0.247   6.6688   3.6243  -0.3595

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
 8WC  C    C1   single    1.500  0.020  1.500
 8WC  C1   C4   aromatic  1.395  0.020  1.395
 8WC  C1   C2   aromatic  1.392  0.020  1.392
 8WC  C4   C5   aromatic  1.384  0.020  1.384
 8WC  N    C13  triple    1.152  0.020  1.152
 8WC  C13  C12  single    1.427  0.020  1.427
 8WC  C2   C3   aromatic  1.388  0.020  1.388
 8WC  C5   C6   aromatic  1.395  0.020  1.395
 8WC  C12  C14  aromatic  1.396  0.020  1.396
 8WC  C12  C11  aromatic  1.393  0.020  1.393
 8WC  C14  C15  aromatic  1.381  0.020  1.381
 8WC  C11  C10  aromatic  1.383  0.020  1.383
 8WC  C3   C6   aromatic  1.392  0.020  1.392
 8WC  C6   C7   single    1.480  0.020  1.480
 8WC  C15  C9   aromatic  1.395  0.020  1.395
 8WC  C10  C9   aromatic  1.394  0.020  1.394
 8WC  C9   C8   single    1.478  0.020  1.478
 8WC  C7   C8   aromatic  1.407  0.020  1.407
 8WC  C7   N2   aromatic  1.326  0.020  1.326
 8WC  C8   C16  aromatic  1.386  0.020  1.386
 8WC  N2   C24  aromatic  1.325  0.020  1.325
 8WC  C16  C17  aromatic  1.391  0.020  1.391
 8WC  C24  C17  aromatic  1.393  0.020  1.393
 8WC  C17  O    single    1.339  0.020  1.339
 8WC  O    C18  single    1.422  0.020  1.422
 8WC  C19  C18  single    1.515  0.020  1.515
 8WC  C19  C23  single    1.529  0.020  1.529
 8WC  C19  C20  single    1.529  0.020  1.529
 8WC  C21  C20  single    1.522  0.020  1.522
 8WC  C21  N1   single    1.452  0.020  1.452
 8WC  C22  C23  single    1.522  0.020  1.522
 8WC  C22  N1   single    1.452  0.020  1.452
 8WC  C4   H1   single    0.930  0.020  1.080
 8WC  C5   H2   single    0.930  0.020  1.080
 8WC  N1   H3   single    0.890  0.020  1.040
 8WC  C10  H5   single    0.930  0.020  1.080
 8WC  C11  H6   single    0.930  0.020  1.080
 8WC  C14  H7   single    0.930  0.020  1.080
 8WC  C15  H8   single    0.930  0.020  1.080
 8WC  C    H9   single    0.970  0.020  1.090
 8WC  C    H10  single    0.970  0.020  1.090
 8WC  C    H11  single    0.970  0.020  1.090
 8WC  C16  H12  single    0.930  0.020  1.080
 8WC  C18  H13  single    0.970  0.020  1.090
 8WC  C18  H14  single    0.970  0.020  1.090
 8WC  C19  H15  single    0.970  0.020  1.090
 8WC  C2   H16  single    0.930  0.020  1.080
 8WC  C20  H17  single    0.970  0.020  1.090
 8WC  C20  H18  single    0.970  0.020  1.090
 8WC  C21  H19  single    0.970  0.020  1.090
 8WC  C21  H20  single    0.970  0.020  1.090
 8WC  C22  H21  single    0.970  0.020  1.090
 8WC  C22  H22  single    0.970  0.020  1.090
 8WC  C23  H23  single    0.970  0.020  1.090
 8WC  C23  H24  single    0.970  0.020  1.090
 8WC  C24  H25  single    0.930  0.020  1.080
 8WC  C3   H26  single    0.930  0.020  1.080

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
 8WC  H1   C4   C1   119.60  3.000
 8WC  H1   C4   C5   119.26  3.000
 8WC  C1   C4   C5   121.14  3.000
 8WC  H2   C5   C6   119.66  3.000
 8WC  H2   C5   C4   119.53  3.000
 8WC  C6   C5   C4   120.81  3.000
 8WC  C3   C6   C7   121.98  3.000
 8WC  C7   C6   C5   119.76  3.000
 8WC  C3   C6   C5   118.23  3.000
 8WC  H3   N1   C22  109.48  3.000
 8WC  H3   N1   C21  109.47  3.000
 8WC  C22  N1   C21  111.60  3.000
 8WC  N2   C7   C8   120.92  3.000
 8WC  N2   C7   C6   115.82  3.000
 8WC  C8   C7   C6   123.26  3.000
 8WC  C16  C8   C9   118.52  3.000
 8WC  C16  C8   C7   118.14  3.000
 8WC  C9   C8   C7   123.32  3.000
 8WC  C24  N2   C7   120.91  3.000
 8WC  C15  C9   C10  119.14  3.000
 8WC  C10  C9   C8   119.93  3.000
 8WC  C15  C9   C8   120.90  3.000
 8WC  H5   C10  C11  119.23  3.000
 8WC  H5   C10  C9   119.98  3.000
 8WC  C11  C10  C9   120.78  3.000
 8WC  H6   C11  C12  120.27  3.000
 8WC  H6   C11  C10  120.26  3.000
 8WC  C12  C11  C10  119.46  3.000
 8WC  C14  C12  C13  119.79  3.000
 8WC  C14  C12  C11  120.35  3.000
 8WC  C13  C12  C11  119.86  3.000
 8WC  N    C13  C12  180.00  3.000
 8WC  H7   C14  C15  120.17  3.000
 8WC  H7   C14  C12  120.23  3.000
 8WC  C15  C14  C12  119.59  3.000
 8WC  H8   C15  C14  119.35  3.000
 8WC  H8   C15  C9   119.98  3.000
 8WC  C14  C15  C9   120.67  3.000
 8WC  C2   C1   C    121.45  3.000
 8WC  C2   C1   C4   117.85  3.000
 8WC  C    C1   C4   120.70  3.000
 8WC  H12  C16  C17  119.51  3.000
 8WC  H12  C16  C8   120.17  3.000
 8WC  C17  C16  C8   120.30  3.000
 8WC  C24  C17  C16  117.37  3.000
 8WC  C24  C17  O    125.35  3.000
 8WC  C16  C17  O    117.28  3.000
 8WC  H14  C18  H13  107.75  3.000
 8WC  H14  C18  C19  110.03  3.000
 8WC  H13  C18  C19  110.15  3.000
 8WC  H14  C18  O    110.20  3.000
 8WC  H13  C18  O    110.08  3.000
 8WC  C19  C18  O    108.62  3.000
 8WC  H15  C19  C23  107.66  3.000
 8WC  H15  C19  C20  108.26  3.000
 8WC  C23  C19  C20  109.77  3.000
 8WC  H15  C19  C18  108.27  3.000
 8WC  C20  C19  C18  112.98  3.000
 8WC  C23  C19  C18  109.75  3.000
 8WC  H16  C2   C3   119.13  3.000
 8WC  H16  C2   C1   119.65  3.000
 8WC  C3   C2   C1   121.22  3.000
 8WC  H18  C20  H17  107.24  3.000
 8WC  H18  C20  C21  109.27  3.000
 8WC  H17  C20  C21  109.28  3.000
 8WC  H18  C20  C19  109.53  3.000
 8WC  H17  C20  C19  110.92  3.000
 8WC  C21  C20  C19  110.54  3.000
 8WC  H20  C21  H19  106.78  3.000
 8WC  H20  C21  C20  108.56  3.000
 8WC  H19  C21  C20  109.87  3.000
 8WC  H20  C21  N1   112.43  3.000
 8WC  H19  C21  N1   108.93  3.000
 8WC  C20  C21  N1   110.21  3.000
 8WC  H22  C22  H21  106.89  3.000
 8WC  H22  C22  C23  110.00  3.000
 8WC  H21  C22  C23  108.51  3.000
 8WC  H22  C22  N1   108.94  3.000
 8WC  H21  C22  N1   112.52  3.000
 8WC  C23  C22  N1   109.92  3.000
 8WC  H24  C23  H23  107.15  3.000
 8WC  H24  C23  C22  109.63  3.000
 8WC  H23  C23  C22  109.22  3.000
 8WC  H24  C23  C19  110.37  3.000
 8WC  H23  C23  C19  109.75  3.000
 8WC  C22  C23  C19  110.66  3.000
 8WC  H25  C24  C17  121.74  3.000
 8WC  H25  C24  N2   115.93  3.000
 8WC  C17  C24  N2   122.32  3.000
 8WC  H26  C3   C2   118.94  3.000
 8WC  H26  C3   C6   120.32  3.000
 8WC  C2   C3   C6   120.74  3.000
 8WC  H11  C    H10  107.79  3.000
 8WC  H11  C    H9   106.92  3.000
 8WC  H10  C    H9   107.82  3.000
 8WC  H11  C    C1   111.28  3.000
 8WC  H10  C    C1   111.58  3.000
 8WC  H9   C    C1   111.24  3.000
 8WC  C18  O    C17  119.17  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
 8WC  CONST_01  C3   C2   C1   C4      0.00   0.0  0
 8WC  CONST_02  C3   C6   C5   C4      0.00   0.0  0
 8WC  CONST_03  C7   C6   C5   C4    180.00   0.0  0
 8WC  CONST_04  C2   C1   C4   C5      0.00   0.0  0
 8WC  CONST_05  C2   C3   C6   C5      0.00   0.0  0
 8WC  CONST_08  C1   C4   C5   C6      0.00   0.0  0
 8WC  CONST_09  C1   C2   C3   C6      0.00   0.0  0
 8WC  CONST_10  C9   C8   C7   C6      0.00   0.0  0
 8WC  CONST_11  C16  C8   C7   C6    180.00   0.0  0
 8WC  CONST_12  C24  N2   C7   C6    180.00   0.0  0
 8WC  CONST_13  C2   C3   C6   C7    180.00   0.0  0
 8WC  CONST_16  C17  C16  C8   C7      0.00   0.0  0
 8WC  CONST_17  C17  C24  N2   C7      0.00   0.0  0
 8WC  CONST_18  C14  C15  C9   C8    180.00   0.0  0
 8WC  CONST_19  C11  C10  C9   C8    180.00   0.0  0
 8WC  CONST_21  C24  N2   C7   C8      0.00   0.0  0
 8WC  CONST_22  C24  C17  C16  C8      0.00   0.0  0
 8WC  CONST_24  C9   C8   C7   N2    180.00   0.0  0
 8WC  CONST_25  C16  C8   C7   N2      0.00   0.0  0
 8WC  CONST_26  C16  C17  C24  N2      0.00   0.0  0
 8WC  CONST_27  C12  C14  C15  C9      0.00   0.0  0
 8WC  CONST_28  C12  C11  C10  C9      0.00   0.0  0
 8WC  CONST_29  C17  C16  C8   C9    180.00   0.0  0
 8WC  CONST_30  C14  C12  C11  C10     0.00   0.0  0
 8WC  CONST_31  C14  C15  C9   C10     0.00   0.0  0
 8WC  CONST_33  C15  C14  C12  C11     0.00   0.0  0
 8WC  CONST_34  C15  C9   C10  C11     0.00   0.0  0
 8WC  CONST_36  C    C1   C4   C5    180.00   0.0  0
 8WC  CONST_37  O    C17  C16  C8    180.00   0.0  0
 8WC  CONST_38  O    C17  C24  N2    180.00   0.0  0
 8WC  CONST_39  C13  C12  C11  C10   180.00   0.0  0
 8WC  CONST_40  C15  C14  C12  C13   180.00   0.0  0
 8WC  CONST_41  C3   C2   C1   C     180.00   0.0  0
 8WC  CONST_42  H16  C2   C1   C4    180.00   0.0  0
 8WC  CONST_43  H26  C3   C6   C5    180.00   0.0  0
 8WC  CONST_44  H1   C4   C5   C6    180.00   0.0  0
 8WC  CONST_45  H2   C5   C6   C7      0.00   0.0  0
 8WC  CONST_46  H12  C16  C8   C7    180.00   0.0  0
 8WC  CONST_47  H25  C24  N2   C7    180.00   0.0  0
 8WC  CONST_48  H8   C15  C9   C8      0.00   0.0  0
 8WC  CONST_49  H5   C10  C9   C8      0.00   0.0  0
 8WC  CONST_50  H7   C14  C15  C9    180.00   0.0  0
 8WC  CONST_51  H6   C11  C10  C9    180.00   0.0  0
 8WC  Var_01    C19  C20  C21  N1    -57.07  30.0  1
 8WC  Var_02    C19  C23  C22  N1     57.33  30.0  1
 8WC  Var_03    C22  N1   C21  C20    61.62  30.0  1
 8WC  Var_04    C23  C22  N1   C21   -61.64  30.0  1
 8WC  Var_05    C19  C18  O    C17  -179.90  30.0  3
 8WC  Var_06    C24  C17  O    C18    -2.93  30.0  2
 8WC  Var_07    H9   C    C1   C4     60.07  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
 8WC  chir_01  C19  C18  C23  C20  positiv

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
 8WC  plan-1  C6   0.020
 8WC  plan-1  C7   0.020
 8WC  plan-1  C8   0.020
 8WC  plan-1  N2   0.020
 8WC  plan-1  C9   0.020
 8WC  plan-1  C16  0.020
 8WC  plan-1  C17  0.020
 8WC  plan-1  C24  0.020
 8WC  plan-1  H12  0.020
 8WC  plan-1  H25  0.020
 8WC  plan-1  O    0.020
 8WC  plan-2  C8   0.020
 8WC  plan-2  C9   0.020
 8WC  plan-2  C10  0.020
 8WC  plan-2  C11  0.020
 8WC  plan-2  C12  0.020
 8WC  plan-2  C13  0.020
 8WC  plan-2  C14  0.020
 8WC  plan-2  C15  0.020
 8WC  plan-2  N    0.020
 8WC  plan-2  H5   0.020
 8WC  plan-2  H6   0.020
 8WC  plan-2  H7   0.020
 8WC  plan-2  H8   0.020
 8WC  plan-3  C4   0.020
 8WC  plan-3  C5   0.020
 8WC  plan-3  C6   0.020
 8WC  plan-3  C7   0.020
 8WC  plan-3  C1   0.020
 8WC  plan-3  C2   0.020
 8WC  plan-3  C3   0.020
 8WC  plan-3  H1   0.020
 8WC  plan-3  H2   0.020
 8WC  plan-3  H16  0.020
 8WC  plan-3  H26  0.020
 8WC  plan-3  C    0.020

