# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 03:44:36 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 2-(2,4-dichlorophenoxy)-N-[4-(piperidin-1-ylmethyl)phenyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(OCC(=O)Nc2ccc(CN3CCCCC3)cc2)c(Cl)c1
#
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
 GC8  GC8  2-(2,4-dichlorophenoxy)-N-[4-(piperidin-1-ylmethyl)phenyl]acetamide  ligand  48  26  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GC8
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
 GC8  CL1   CL  CL    0  -0.123  -8.6583  -1.4898   0.6705
 GC8  C02   C   CR6   0  -0.071  -7.0105  -1.0109   0.4398
 GC8  C03   C   CR16  0  -0.193  -6.0098  -1.9637   0.4152
 GC8  C04   C   CR16  0  -0.390  -4.6908  -1.5718   0.2310
 GC8  C05   C   CR6   0   0.475  -4.3622  -0.2302   0.0683
 GC8  O06   O   O2    0  -0.442  -3.1233   0.2435  -0.1188
 GC8  C07   C   CH2   0  -0.315  -2.0590  -0.6689  -0.1590
 GC8  C08   C   C     0   0.509  -0.7946   0.1214  -0.4629
 GC8  O09   O   O     0  -0.444  -0.8243   1.2689  -0.8533
 GC8  N10   N   NH1   0  -0.745   0.3236  -0.6155  -0.2728
 GC8  C11   C   CR6   0   0.360   1.6601  -0.2800  -0.5224
 GC8  C12   C   CR16  0  -0.301   2.0936   0.9666  -0.9688
 GC8  C13   C   CR16  0  -0.306   3.4509   1.1858  -1.1751
 GC8  C14   C   CR6   0   0.077   4.4009   0.1991  -0.9545
 GC8  C15   C   CR16  0  -0.270   3.9543  -1.0415  -0.5035
 GC8  C16   C   CR16  0  -0.336   2.6101  -1.2793  -0.2916
 GC8  C17   C   CH2   0  -0.318   5.8639   0.4429  -1.2161
 GC8  N18   N   NT    0  -0.410   6.7073  -0.0662  -0.1562
 GC8  C19   C   CH2   0  -0.276   8.0994  -0.1464  -0.5616
 GC8  C20   C   CH2   0  -0.437   8.9429  -0.8151   0.5132
 GC8  C21   C   CH2   0  -0.439   8.8106  -0.0756   1.8387
 GC8  C22   C   CH2   0  -0.435   7.3402   0.0686   2.2105
 GC8  C23   C   CH2   0  -0.273   6.5554   0.6974   1.0697
 GC8  C24   C   CR6   0  -0.164  -5.3956   0.7124   0.0988
 GC8  CL2   CL  CL    0  -0.093  -5.0089   2.3814  -0.1004
 GC8  C26   C   CR16  0  -0.162  -6.7117   0.3346   0.2828
 GC8  H03   H   HCR6  0   0.290  -6.2411  -3.0125   0.5388
 GC8  H26   H   HCR6  0   0.303  -7.4914   1.0832   0.3011
 GC8  H04   H   HCR6  0   0.304  -3.9282  -2.3374   0.2199
 GC8  H071  H   HCH2  0   0.272  -1.9548  -1.2056   0.7911
 GC8  H072  H   HCH2  0   0.281  -2.1986  -1.4189  -0.9477
 GC8  H10   H   HNH1  0   0.421   0.1859  -1.5544   0.0728
 GC8  H12   H   HCR6  0   0.277   1.3976   1.7694  -1.1473
 GC8  H16   H   HCR6  0   0.268   2.2889  -2.2534   0.0594
 GC8  H13   H   HCR6  0   0.250   3.7695   2.1650  -1.5136
 GC8  H15   H   HCR6  0   0.247   4.6720  -1.8272  -0.3052
 GC8  H171  H   HCH2  0   0.247   6.1492  -0.0664  -2.1426
 GC8  H172  H   HCH2  0   0.207   6.0259   1.5191  -1.4007
 GC8  H191  H   HCH2  0   0.232   8.1568  -0.7182  -1.4916
 GC8  H192  H   HCH2  0   0.181   8.5165   0.8544  -0.7778
 GC8  H231  H   HCH2  0   0.182   6.8889   1.7424   0.9268
 GC8  H232  H   HCH2  0   0.236   5.4958   0.7419   1.3301
 GC8  H201  H   HCH2  0   0.214   8.6114  -1.8510   0.6335
 GC8  H202  H   HCH2  0   0.229   9.9853  -0.8471   0.1882
 GC8  H211  H   HCH2  0   0.230   9.3618  -0.5924   2.6275
 GC8  H212  H   HCH2  0   0.209   9.2580   0.9197   1.7421
 GC8  H221  H   HCH2  0   0.214   6.9160  -0.9151   2.4327
 GC8  H222  H   HCH2  0   0.227   7.2252   0.6798   3.1085

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
 GC8  CL1  C02   single    1.731  0.020  1.731
 GC8  C02  C03   aromatic  1.382  0.020  1.382
 GC8  C02  C26   aromatic  1.387  0.020  1.387
 GC8  C03  C04   aromatic  1.388  0.020  1.388
 GC8  C04  C05   aromatic  1.391  0.020  1.391
 GC8  C05  O06   single    1.339  0.020  1.339
 GC8  C05  C24   aromatic  1.399  0.020  1.399
 GC8  O06  C07   single    1.402  0.020  1.402
 GC8  C07  C08   single    1.522  0.020  1.522
 GC8  C08  O09   double    1.212  0.020  1.212
 GC8  C08  N10   single    1.353  0.020  1.353
 GC8  N10  C11   single    1.400  0.020  1.400
 GC8  C11  C12   aromatic  1.393  0.020  1.393
 GC8  C11  C16   aromatic  1.398  0.020  1.398
 GC8  C12  C13   aromatic  1.390  0.020  1.390
 GC8  C13  C14   aromatic  1.387  0.020  1.387
 GC8  C14  C15   aromatic  1.394  0.020  1.394
 GC8  C14  C17   single    1.506  0.020  1.506
 GC8  C15  C16   aromatic  1.381  0.020  1.381
 GC8  C17  N18   single    1.447  0.020  1.447
 GC8  N18  C19   single    1.452  0.020  1.452
 GC8  N18  C23   single    1.452  0.020  1.452
 GC8  C19  C20   single    1.521  0.020  1.521
 GC8  C20  C21   single    1.524  0.020  1.524
 GC8  C21  C22   single    1.524  0.020  1.524
 GC8  C22  C23   single    1.521  0.020  1.521
 GC8  C24  CL2   single    1.725  0.020  1.725
 GC8  C24  C26   aromatic  1.381  0.020  1.381
 GC8  C03  H03   single    0.930  0.020  1.080
 GC8  C26  H26   single    0.930  0.020  1.080
 GC8  C04  H04   single    0.930  0.020  1.080
 GC8  C07  H071  single    0.970  0.020  1.090
 GC8  C07  H072  single    0.970  0.020  1.090
 GC8  N10  H10   single    0.860  0.020  1.020
 GC8  C12  H12   single    0.930  0.020  1.080
 GC8  C16  H16   single    0.930  0.020  1.080
 GC8  C13  H13   single    0.930  0.020  1.080
 GC8  C15  H15   single    0.930  0.020  1.080
 GC8  C17  H171  single    0.970  0.020  1.090
 GC8  C17  H172  single    0.970  0.020  1.090
 GC8  C19  H191  single    0.970  0.020  1.090
 GC8  C19  H192  single    0.970  0.020  1.090
 GC8  C23  H231  single    0.970  0.020  1.090
 GC8  C23  H232  single    0.970  0.020  1.090
 GC8  C20  H201  single    0.970  0.020  1.090
 GC8  C20  H202  single    0.970  0.020  1.090
 GC8  C21  H211  single    0.970  0.020  1.090
 GC8  C21  H212  single    0.970  0.020  1.090
 GC8  C22  H221  single    0.970  0.020  1.090
 GC8  C22  H222  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
 GC8  C26   C02  C03   120.71  3.000
 GC8  C26   C02  CL1   119.23  3.000
 GC8  C03   C02  CL1   120.05  3.000
 GC8  H03   C03  C04   119.49  3.000
 GC8  H03   C03  C02   120.79  3.000
 GC8  C04   C03  C02   119.72  3.000
 GC8  H04   C04  C05   121.03  3.000
 GC8  H04   C04  C03   118.15  3.000
 GC8  C05   C04  C03   120.82  3.000
 GC8  C24   C05  O06   116.61  3.000
 GC8  C24   C05  C04   118.22  3.000
 GC8  O06   C05  C04   125.17  3.000
 GC8  C07   O06  C05   118.41  3.000
 GC8  H072  C07  H071  107.48  3.000
 GC8  H072  C07  C08   108.49  3.000
 GC8  H071  C07  C08   110.39  3.000
 GC8  H072  C07  O06   111.64  3.000
 GC8  H071  C07  O06   111.46  3.000
 GC8  C08   C07  O06   107.36  3.000
 GC8  N10   C08  O09   125.53  3.000
 GC8  N10   C08  C07   112.08  3.000
 GC8  O09   C08  C07   122.38  3.000
 GC8  H10   N10  C11   114.45  3.000
 GC8  H10   N10  C08   116.22  3.000
 GC8  C11   N10  C08   129.30  3.000
 GC8  C16   C11  C12   118.76  3.000
 GC8  C16   C11  N10   116.61  3.000
 GC8  C12   C11  N10   124.64  3.000
 GC8  H12   C12  C13   119.25  3.000
 GC8  H12   C12  C11   121.25  3.000
 GC8  C13   C12  C11   119.50  3.000
 GC8  H13   C13  C14   119.40  3.000
 GC8  H13   C13  C12   118.41  3.000
 GC8  C14   C13  C12   122.19  3.000
 GC8  C17   C14  C15   120.77  3.000
 GC8  C17   C14  C13   121.49  3.000
 GC8  C15   C14  C13   117.72  3.000
 GC8  H15   C15  C16   119.48  3.000
 GC8  H15   C15  C14   119.53  3.000
 GC8  C16   C15  C14   120.98  3.000
 GC8  H16   C16  C15   119.52  3.000
 GC8  H16   C16  C11   119.63  3.000
 GC8  C15   C16  C11   120.85  3.000
 GC8  H172  C17  H171  105.89  3.000
 GC8  H172  C17  N18   112.33  3.000
 GC8  H171  C17  N18   107.71  3.000
 GC8  H172  C17  C14   109.23  3.000
 GC8  H171  C17  C14   108.95  3.000
 GC8  N18   C17  C14   112.45  3.000
 GC8  C23   N18  C19   111.41  3.000
 GC8  C23   N18  C17   111.86  3.000
 GC8  C19   N18  C17   111.94  3.000
 GC8  H192  C19  H191  106.69  3.000
 GC8  H192  C19  C20   109.08  3.000
 GC8  H191  C19  C20   110.00  3.000
 GC8  H192  C19  N18   111.49  3.000
 GC8  H191  C19  N18   108.46  3.000
 GC8  C20   C19  N18   111.02  3.000
 GC8  H202  C20  H201  107.10  3.000
 GC8  H202  C20  C21   110.85  3.000
 GC8  H201  C20  C21   109.73  3.000
 GC8  H202  C20  C19   109.38  3.000
 GC8  H201  C20  C19   109.02  3.000
 GC8  C21   C20  C19   110.68  3.000
 GC8  H212  C21  H211  106.70  3.000
 GC8  H212  C21  C22   109.25  3.000
 GC8  H211  C21  C22   110.83  3.000
 GC8  H212  C21  C20   109.20  3.000
 GC8  H211  C21  C20   110.78  3.000
 GC8  C22   C21  C20   110.00  3.000
 GC8  H222  C22  H221  107.18  3.000
 GC8  H222  C22  C23   109.33  3.000
 GC8  H221  C22  C23   108.91  3.000
 GC8  H222  C22  C21   110.80  3.000
 GC8  H221  C22  C21   109.79  3.000
 GC8  C23   C22  C21   110.74  3.000
 GC8  H232  C23  H231  106.56  3.000
 GC8  H232  C23  C22   109.80  3.000
 GC8  H231  C23  C22   109.39  3.000
 GC8  H232  C23  N18   108.91  3.000
 GC8  H231  C23  N18   110.86  3.000
 GC8  C22   C23  N18   111.21  3.000
 GC8  C26   C24  CL2   119.58  3.000
 GC8  C26   C24  C05   121.49  3.000
 GC8  CL2   C24  C05   118.94  3.000
 GC8  H26   C26  C24   120.00  3.000
 GC8  H26   C26  C02   120.96  3.000
 GC8  C24   C26  C02   119.05  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
 GC8  CONST_01  C05  C04  C03  C02     0.00   0.0  0
 GC8  CONST_02  C05  C24  C26  C02     0.00   0.0  0
 GC8  CONST_03  C24  C26  C02  C03     0.00   0.0  0
 GC8  CONST_04  C24  C05  C04  C03     0.00   0.0  0
 GC8  CONST_05  C26  C02  C03  C04     0.00   0.0  0
 GC8  CONST_06  C26  C24  C05  C04     0.00   0.0  0
 GC8  CONST_07  C14  C13  C12  C11     0.00   0.0  0
 GC8  CONST_08  C14  C15  C16  C11     0.00   0.0  0
 GC8  CONST_09  C15  C16  C11  C12     0.00   0.0  0
 GC8  CONST_10  C15  C14  C13  C12     0.00   0.0  0
 GC8  CONST_11  C16  C11  C12  C13     0.00   0.0  0
 GC8  CONST_12  C16  C15  C14  C13     0.00   0.0  0
 GC8  CONST_13  C04  C03  C02  CL1   180.00   0.0  0
 GC8  CONST_14  C24  C26  C02  CL1   180.00   0.0  0
 GC8  CONST_15  CL2  C24  C26  C02   180.00   0.0  0
 GC8  CONST_16  O06  C05  C04  C03   180.00   0.0  0
 GC8  CONST_17  CL2  C24  C05  C04   180.00   0.0  0
 GC8  CONST_18  C26  C24  C05  O06   180.00   0.0  0
 GC8  CONST_19  C13  C12  C11  N10   180.00   0.0  0
 GC8  CONST_20  C15  C16  C11  N10   180.00   0.0  0
 GC8  CONST_21  C17  C14  C13  C12   180.00   0.0  0
 GC8  CONST_22  C17  C14  C15  C16   180.00   0.0  0
 GC8  CONST_23  H04  C04  C03  C02   180.00   0.0  0
 GC8  CONST_24  H26  C26  C02  C03   180.00   0.0  0
 GC8  CONST_25  H03  C03  C04  C05   180.00   0.0  0
 GC8  CONST_26  H13  C13  C12  C11   180.00   0.0  0
 GC8  CONST_27  H15  C15  C16  C11   180.00   0.0  0
 GC8  CONST_28  H16  C16  C11  C12   180.00   0.0  0
 GC8  CONST_29  H12  C12  C13  C14   180.00   0.0  0
 GC8  CONST_30  C12  C11  N10  C08     0.00   0.0  0
 GC8  CONST_31  C16  C11  N10  C08   180.00   0.0  0
 GC8  CONST_32  H10  N10  C11  C12   180.00   0.0  0
 GC8  CONST_33  C11  N10  C08  C07   180.00   0.0  0
 GC8  CONST_34  C11  N10  C08  O09     0.00   0.0  0
 GC8  Var_01    C21  C20  C19  N18   -56.69  30.0  1
 GC8  Var_02    C21  C22  C23  N18    56.21  30.0  1
 GC8  Var_03    C22  C23  N18  C19   -59.53  30.0  1
 GC8  Var_04    C22  C21  C20  C19    53.32  30.0  1
 GC8  Var_05    C23  N18  C19  C20    59.72  30.0  1
 GC8  Var_06    C23  C22  C21  C20   -53.05  30.0  1
 GC8  Var_07    N18  C17  C14  C13   135.94  30.0  2
 GC8  Var_08    C19  N18  C17  C14   165.01  30.0  3
 GC8  Var_09    C24  C05  O06  C07  -179.85  30.0  2
 GC8  Var_10    C08  C07  O06  C05   176.68  30.0  3
 GC8  Var_11    O09  C08  C07  O06   -13.16  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
 GC8  plan-1  CL1  0.020
 GC8  plan-1  C02  0.020
 GC8  plan-1  C03  0.020
 GC8  plan-1  C04  0.020
 GC8  plan-1  C05  0.020
 GC8  plan-1  O06  0.020
 GC8  plan-1  C24  0.020
 GC8  plan-1  CL2  0.020
 GC8  plan-1  C26  0.020
 GC8  plan-1  H03  0.020
 GC8  plan-1  H26  0.020
 GC8  plan-1  H04  0.020
 GC8  plan-2  N10  0.020
 GC8  plan-2  C11  0.020
 GC8  plan-2  C12  0.020
 GC8  plan-2  C13  0.020
 GC8  plan-2  C14  0.020
 GC8  plan-2  C15  0.020
 GC8  plan-2  C16  0.020
 GC8  plan-2  C17  0.020
 GC8  plan-2  H12  0.020
 GC8  plan-2  H16  0.020
 GC8  plan-2  H13  0.020
 GC8  plan-2  H15  0.020
 GC8  plan-3  C07  0.020
 GC8  plan-3  C08  0.020
 GC8  plan-3  O09  0.020
 GC8  plan-3  N10  0.020
 GC8  plan-3  C11  0.020
 GC8  plan-3  H10  0.020

