# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 12:39:46 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 4-chloro-N-[(1E)-2-(3-methoxyphenyl)ethanimidoyl]-2-(piperidin-4-yloxy)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(CC(=N)NC(=O)c2ccc(Cl)cc2OC3CCNCC3)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
 7Y6  7Y6  4-chloro-N-[(1E)-2-(3-methoxyphenyl)ethanimidoyl]-2-(piperidin-4-yloxy)benzamide  ligand  52  28  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7Y6
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
 7Y6  CL    CL  CL    0  -0.115  -4.8251   3.5998   0.8340
 7Y6  C12   C   CR6   0  -0.025  -3.4627   2.5363   0.7435
 7Y6  C11   C   CR16  0  -0.242  -2.2098   3.0102   1.0861
 7Y6  C10   C   CR16  0  -0.252  -1.1422   2.1294   1.0059
 7Y6  C13   C   CR16  0  -0.331  -3.6719   1.2315   0.3255
 7Y6  C14   C   CR6   0   0.416  -2.5909   0.3542   0.2505
 7Y6  O2    O   O2    0  -0.470  -2.6757  -0.9033  -0.1897
 7Y6  C15   C   CH1   0   0.015  -3.9421  -1.5136  -0.4420
 7Y6  C19   C   CH2   0  -0.443  -3.6915  -2.7375  -1.3051
 7Y6  C18   C   CH2   0  -0.306  -5.0106  -3.4586  -1.5546
 7Y6  N2    N   NH1   0  -0.594  -5.6183  -3.8319  -0.2900
 7Y6  C17   C   CH2   0  -0.300  -5.9235  -2.6666   0.5197
 7Y6  C16   C   CH2   0  -0.464  -4.6412  -1.9127   0.8500
 7Y6  C9    C   CR6   0  -0.199  -1.3113   0.8100   0.6081
 7Y6  C8    C   C     0   0.531  -0.1497  -0.1323   0.6514
 7Y6  O1    O   O     0  -0.413  -0.1969  -1.1911   1.2320
 7Y6  N     N   N     0  -0.579   2.5536  -1.2180   0.6089
 7Y6  N1    N   NH1   0  -0.689   0.9569   0.3557   0.0058
 7Y6  C7    C   C     0   0.412   2.2525  -0.1533   0.0000
 7Y6  C6    C   CH2   0  -0.646   3.1835   0.7371  -0.8033
 7Y6  C5    C   CR6   0   0.083   4.6102   0.2766  -0.7839
 7Y6  C4    C   CR16  0  -0.310   5.1013  -0.5541  -1.7901
 7Y6  C3    C   CR16  0  -0.228   6.4145  -0.9901  -1.7382
 7Y6  C2    C   CR16  0  -0.391   7.2552  -0.6183  -0.6954
 7Y6  C20   C   CR16  0  -0.370   5.4425   0.6498   0.2606
 7Y6  C1    C   CR6   0   0.397   6.7657   0.2079   0.3136
 7Y6  O     O   O2    0  -0.472   7.4885   0.6291   1.3684
 7Y6  C     C   CH3   0  -0.437   8.8312   0.2009   1.4820
 7Y6  H11   H   HCR6  0   0.283  -2.0633   4.0295   1.4127
 7Y6  H13   H   HCR6  0   0.300  -4.6711   0.9207   0.0588
 7Y6  H10   H   HCR6  0   0.281  -0.1582   2.4815   1.2897
 7Y6  H15   H   HCH1  0   0.228  -4.5808  -0.8254  -1.0114
 7Y6  H191  H   HCH2  0   0.245  -3.2425  -2.4452  -2.2568
 7Y6  H192  H   HCH2  0   0.232  -2.9960  -3.4114  -0.7968
 7Y6  H161  H   HCH2  0   0.236  -3.9749  -2.5554   1.4323
 7Y6  H162  H   HCH2  0   0.247  -4.8815  -1.0421   1.4642
 7Y6  H181  H   HCH2  0   0.194  -5.6626  -2.8045  -2.1570
 7Y6  H182  H   HCH2  0   0.242  -4.8298  -4.3584  -2.1445
 7Y6  H2    H   HNH1  0   0.355  -6.4686  -4.3506  -0.4665
 7Y6  H171  H   HCH2  0   0.195  -6.6214  -1.9742   0.0188
 7Y6  H172  H   HCH2  0   0.241  -6.4070  -2.9899   1.4429
 7Y6  H1    H   HNH1  0   0.428   0.8181   1.2008  -0.5272
 7Y6  H     H   H     0   0.347   3.5444  -1.4079   0.4952
 7Y6  H61C  H   HCH2  0   0.301   2.8118   0.7780  -1.8316
 7Y6  H62C  H   HCH2  0   0.295   3.1063   1.7559  -0.4121
 7Y6  H4    H   HCR6  0   0.252   4.4586  -0.8541  -2.6085
 7Y6  H20   H   HCR6  0   0.261   5.0700   1.2934   1.0500
 7Y6  H3    H   HCR6  0   0.261   6.8013  -1.6301  -2.5207
 7Y6  HA    H   HCR6  0   0.281   8.2755  -0.9762  -0.6886
 7Y6  HC1   H   HCH3  0   0.229   8.9086  -0.8869   1.5575
 7Y6  HC2   H   HCH3  0   0.229   9.4422   0.5398   0.6413
 7Y6  HC3   H   HCH3  0   0.260   9.2198   0.6434   2.3957

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
 7Y6  CL   C12   single    1.731  0.020  1.731
 7Y6  C12  C11   aromatic  1.383  0.020  1.383
 7Y6  C12  C13   aromatic  1.386  0.020  1.386
 7Y6  C11  C10   aromatic  1.386  0.020  1.386
 7Y6  C10  C9    aromatic  1.388  0.020  1.388
 7Y6  C13  C14   aromatic  1.394  0.020  1.394
 7Y6  C14  O2    single    1.335  0.020  1.335
 7Y6  C14  C9    aromatic  1.405  0.020  1.405
 7Y6  O2   C15   single    1.428  0.020  1.428
 7Y6  C15  C19   single    1.518  0.020  1.518
 7Y6  C15  C16   single    1.522  0.020  1.522
 7Y6  C19  C18   single    1.524  0.020  1.524
 7Y6  C18  N2    single    1.452  0.020  1.452
 7Y6  N2   C17   single    1.451  0.020  1.451
 7Y6  C17  C16   single    1.524  0.020  1.524
 7Y6  C9   C8    single    1.496  0.020  1.496
 7Y6  C8   O1    double    1.209  0.020  1.209
 7Y6  C8   N1    single    1.371  0.020  1.371
 7Y6  N    C7    double    1.263  0.020  1.263
 7Y6  N1   C7    single    1.392  0.020  1.392
 7Y6  C7   C6    single    1.518  0.020  1.518
 7Y6  C6   C5    single    1.499  0.020  1.499
 7Y6  C5   C4    aromatic  1.394  0.020  1.394
 7Y6  C5   C20   aromatic  1.387  0.020  1.387
 7Y6  C4   C3    aromatic  1.385  0.020  1.385
 7Y6  C3   C2    aromatic  1.390  0.020  1.390
 7Y6  C2   C1    aromatic  1.393  0.020  1.393
 7Y6  C20  C1    aromatic  1.396  0.020  1.396
 7Y6  C1   O     single    1.346  0.020  1.346
 7Y6  O    C     single    1.414  0.020  1.414
 7Y6  C11  H11   single    0.930  0.020  1.080
 7Y6  C13  H13   single    0.930  0.020  1.080
 7Y6  C10  H10   single    0.930  0.020  1.080
 7Y6  C15  H15   single    0.970  0.020  1.090
 7Y6  C19  H191  single    0.970  0.020  1.090
 7Y6  C19  H192  single    0.970  0.020  1.090
 7Y6  C16  H161  single    0.970  0.020  1.090
 7Y6  C16  H162  single    0.970  0.020  1.090
 7Y6  C18  H181  single    0.970  0.020  1.090
 7Y6  C18  H182  single    0.970  0.020  1.090
 7Y6  N2   H2    single    0.890  0.020  1.040
 7Y6  C17  H171  single    0.970  0.020  1.090
 7Y6  C17  H172  single    0.970  0.020  1.090
 7Y6  N1   H1    single    0.860  0.020  1.020
 7Y6  N    H     single    0.860  0.020  1.020
 7Y6  C6   H61C  single    0.970  0.020  1.090
 7Y6  C6   H62C  single    0.970  0.020  1.090
 7Y6  C4   H4    single    0.930  0.020  1.080
 7Y6  C20  H20   single    0.930  0.020  1.080
 7Y6  C3   H3    single    0.930  0.020  1.080
 7Y6  C2   HA    single    0.930  0.020  1.080
 7Y6  C    HC1   single    0.970  0.020  1.090
 7Y6  C    HC2   single    0.970  0.020  1.090
 7Y6  C    HC3   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
 7Y6  C13   C12  C11   122.29  3.000
 7Y6  C13   C12  CL    118.39  3.000
 7Y6  C11   C12  CL    119.32  3.000
 7Y6  H11   C11  C10   120.83  3.000
 7Y6  H11   C11  C12   121.41  3.000
 7Y6  C10   C11  C12   117.76  3.000
 7Y6  H10   C10  C9    119.65  3.000
 7Y6  H10   C10  C11   118.56  3.000
 7Y6  C9    C10  C11   121.77  3.000
 7Y6  H13   C13  C14   121.54  3.000
 7Y6  H13   C13  C12   119.02  3.000
 7Y6  C14   C13  C12   119.44  3.000
 7Y6  C9    C14  O2    116.58  3.000
 7Y6  C9    C14  C13   119.24  3.000
 7Y6  O2    C14  C13   124.14  3.000
 7Y6  C15   O2   C14   121.14  3.000
 7Y6  H15   C15  C16   109.71  3.000
 7Y6  H15   C15  C19   107.84  3.000
 7Y6  C16   C15  C19   110.30  3.000
 7Y6  H15   C15  O2    109.85  3.000
 7Y6  C16   C15  O2    111.68  3.000
 7Y6  C19   C15  O2    107.37  3.000
 7Y6  H192  C19  H191  107.96  3.000
 7Y6  H192  C19  C18   109.57  3.000
 7Y6  H191  C19  C18   109.87  3.000
 7Y6  H192  C19  C15   109.72  3.000
 7Y6  H191  C19  C15   110.33  3.000
 7Y6  C18   C19  C15   109.37  3.000
 7Y6  H182  C18  H181  106.96  3.000
 7Y6  H182  C18  N2    109.16  3.000
 7Y6  H181  C18  N2    112.39  3.000
 7Y6  H182  C18  C19   109.60  3.000
 7Y6  H181  C18  C19   108.70  3.000
 7Y6  N2    C18  C19   109.97  3.000
 7Y6  H2    N2   C17   109.41  3.000
 7Y6  H2    N2   C18   109.38  3.000
 7Y6  C17   N2   C18   111.56  3.000
 7Y6  H172  C17  H171  106.85  3.000
 7Y6  H172  C17  C16   109.64  3.000
 7Y6  H171  C17  C16   108.67  3.000
 7Y6  H172  C17  N2    109.11  3.000
 7Y6  H171  C17  N2    112.56  3.000
 7Y6  C16   C17  N2    109.95  3.000
 7Y6  H162  C16  H161  107.64  3.000
 7Y6  H162  C16  C17   109.34  3.000
 7Y6  H161  C16  C17   109.72  3.000
 7Y6  H162  C16  C15   111.67  3.000
 7Y6  H161  C16  C15   109.03  3.000
 7Y6  C17   C16  C15   109.41  3.000
 7Y6  C8    C9   C14   120.68  3.000
 7Y6  C8    C9   C10   119.71  3.000
 7Y6  C14   C9   C10   119.49  3.000
 7Y6  N1    C8   O1    124.73  3.000
 7Y6  N1    C8   C9    112.88  3.000
 7Y6  O1    C8   C9    122.36  3.000
 7Y6  H     N    C7    109.65  3.000
 7Y6  H1    N1   C7    115.61  3.000
 7Y6  H1    N1   C8    115.84  3.000
 7Y6  C7    N1   C8    128.54  3.000
 7Y6  C6    C7   N1    111.01  3.000
 7Y6  C6    C7   N     127.11  3.000
 7Y6  N1    C7   N     121.88  3.000
 7Y6  H62C  C6   H61C  106.10  3.000
 7Y6  H62C  C6   C5    110.40  3.000
 7Y6  H61C  C6   C5    110.30  3.000
 7Y6  H62C  C6   C7    108.28  3.000
 7Y6  H61C  C6   C7    108.11  3.000
 7Y6  C5    C6   C7    113.36  3.000
 7Y6  C20   C5   C4    119.51  3.000
 7Y6  C20   C5   C6    119.88  3.000
 7Y6  C4    C5   C6    120.59  3.000
 7Y6  H4    C4   C3    120.26  3.000
 7Y6  H4    C4   C5    120.10  3.000
 7Y6  C3    C4   C5    119.64  3.000
 7Y6  H3    C3   C2    118.97  3.000
 7Y6  H3    C3   C4    119.86  3.000
 7Y6  C2    C3   C4    121.17  3.000
 7Y6  HA    C2   C1    121.56  3.000
 7Y6  HA    C2   C3    119.14  3.000
 7Y6  C1    C2   C3    119.31  3.000
 7Y6  H20   C20  C1    119.06  3.000
 7Y6  H20   C20  C5    120.12  3.000
 7Y6  C1    C20  C5    120.82  3.000
 7Y6  O     C1   C20   116.08  3.000
 7Y6  O     C1   C2    124.36  3.000
 7Y6  C20   C1   C2    119.56  3.000
 7Y6  C     O    C1    118.56  3.000
 7Y6  HC3   C    HC2   108.69  3.000
 7Y6  HC3   C    HC1   108.76  3.000
 7Y6  HC2   C    HC1   108.79  3.000
 7Y6  HC3   C    O     106.49  3.000
 7Y6  HC2   C    O     112.03  3.000
 7Y6  HC1   C    O     111.97  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
 7Y6  CONST_01  C9   C10  C11  C12    0.00   0.0  0
 7Y6  CONST_02  C9   C14  C13  C12    0.00   0.0  0
 7Y6  CONST_03  C14  C13  C12  C11    0.00   0.0  0
 7Y6  CONST_04  C14  C9   C10  C11    0.00   0.0  0
 7Y6  CONST_05  C13  C12  C11  C10    0.00   0.0  0
 7Y6  CONST_06  C13  C14  C9   C10    0.00   0.0  0
 7Y6  CONST_07  C2   C3   C4   C5     0.00   0.0  0
 7Y6  CONST_08  C2   C1   C20  C5     0.00   0.0  0
 7Y6  CONST_09  C1   C20  C5   C4     0.00   0.0  0
 7Y6  CONST_10  C1   C2   C3   C4     0.00   0.0  0
 7Y6  CONST_11  C20  C5   C4   C3     0.00   0.0  0
 7Y6  CONST_12  C20  C1   C2   C3     0.00   0.0  0
 7Y6  CONST_13  C10  C11  C12  CL   180.00   0.0  0
 7Y6  CONST_14  C14  C13  C12  CL   180.00   0.0  0
 7Y6  CONST_15  O2   C14  C13  C12  180.00   0.0  0
 7Y6  CONST_16  C8   C9   C10  C11  180.00   0.0  0
 7Y6  CONST_17  O2   C14  C9   C10  180.00   0.0  0
 7Y6  CONST_18  C8   C9   C14  C13  180.00   0.0  0
 7Y6  CONST_19  C3   C4   C5   C6   180.00   0.0  0
 7Y6  CONST_20  C1   C20  C5   C6   180.00   0.0  0
 7Y6  CONST_21  O    C1   C20  C5   180.00   0.0  0
 7Y6  CONST_22  O    C1   C2   C3   180.00   0.0  0
 7Y6  CONST_23  H10  C10  C11  C12  180.00   0.0  0
 7Y6  CONST_24  H13  C13  C12  C11  180.00   0.0  0
 7Y6  CONST_25  H11  C11  C12  C13  180.00   0.0  0
 7Y6  CONST_26  H3   C3   C4   C5   180.00   0.0  0
 7Y6  CONST_27  H20  C20  C5   C4   180.00   0.0  0
 7Y6  CONST_28  HA   C2   C3   C4   180.00   0.0  0
 7Y6  CONST_29  H4   C4   C3   C2   180.00   0.0  0
 7Y6  CONST_30  C7   N1   C8   C9   180.00   0.0  0
 7Y6  CONST_31  H1   N1   C8   C9     0.00   0.0  0
 7Y6  CONST_32  C7   N1   C8   O1     0.00   0.0  0
 7Y6  CONST_33  N    C7   N1   C8     0.00   0.0  0
 7Y6  CONST_34  C6   C7   N1   C8   180.00   0.0  0
 7Y6  CONST_35  H    N    C7   N1   180.00   0.0  0
 7Y6  Var_01    N2   C18  C19  C15  -57.98  30.0  1
 7Y6  Var_02    N2   C17  C16  C15   57.76  30.0  1
 7Y6  Var_03    C17  N2   C18  C19   61.68  30.0  1
 7Y6  Var_04    C16  C17  N2   C18  -61.58  30.0  1
 7Y6  Var_05    C9   C14  O2   C15  173.15  30.0  3
 7Y6  Var_06    O1   C8   C9   C10  126.31  30.0  2
 7Y6  Var_07    C4   C5   C6   C7    93.38  30.0  2
 7Y6  Var_08    C5   C6   C7   N     -2.69  30.0  3
 7Y6  Var_09    HC1  C    O    C1   -60.75  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
 7Y6  chir_01  C15  O2  C19  C16  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
 7Y6  plan-1  CL   0.020
 7Y6  plan-1  C12  0.020
 7Y6  plan-1  C11  0.020
 7Y6  plan-1  C10  0.020
 7Y6  plan-1  C13  0.020
 7Y6  plan-1  C14  0.020
 7Y6  plan-1  O2   0.020
 7Y6  plan-1  C9   0.020
 7Y6  plan-1  C8   0.020
 7Y6  plan-1  H11  0.020
 7Y6  plan-1  H13  0.020
 7Y6  plan-1  H10  0.020
 7Y6  plan-2  C6   0.020
 7Y6  plan-2  C5   0.020
 7Y6  plan-2  C4   0.020
 7Y6  plan-2  C3   0.020
 7Y6  plan-2  C2   0.020
 7Y6  plan-2  C20  0.020
 7Y6  plan-2  C1   0.020
 7Y6  plan-2  O    0.020
 7Y6  plan-2  H4   0.020
 7Y6  plan-2  H20  0.020
 7Y6  plan-2  H3   0.020
 7Y6  plan-2  HA   0.020
 7Y6  plan-3  C9   0.020
 7Y6  plan-3  C8   0.020
 7Y6  plan-3  O1   0.020
 7Y6  plan-3  N    0.020
 7Y6  plan-3  N1   0.020
 7Y6  plan-3  C7   0.020
 7Y6  plan-3  C6   0.020
 7Y6  plan-3  H1   0.020
 7Y6  plan-3  H    0.020

