# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 03:07:57 2021
#   Inital geometry file: a 126 line input string
#   Ligand name: 2-methyl-4-{4-[2-(4-methyl-3-oxopiperazin-1-yl)-2-oxoethyl]phenoxy}benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1=O)C(=O)Cc2ccc(Oc3ccc(C#N)c(C)c3)cc2
#
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
 O7P  O7P  2-methyl-4-{4-[2-(4-methyl-3-oxopiperazin-1-yl)-2-oxoethyl]phenoxy}benzonitrile  ligand  48  27  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_O7P
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
 O7P  C01  C  CH3   0  -0.745  10.8890   6.6169  10.5269
 O7P  C02  C  CR6   0   0.153   9.9105   7.3030  11.4286
 O7P  C03  C  CR6   0  -0.044  10.3412   8.0266  12.5533
 O7P  C04  C  CSP   0   0.026  11.7300   8.1043  12.8569
 O7P  C06  C  CR16  0  -0.222   9.4239   8.6729  13.3796
 O7P  C07  C  CR16  0  -0.353   8.0699   8.6197  13.1088
 O7P  C08  C  CR6   0   0.405   7.6374   7.9070  11.9941
 O7P  C10  C  CR6   0   0.289   5.3890   8.5836  12.2328
 O7P  C11  C  CR16  0  -0.284   5.3078   9.9243  11.8863
 O7P  C12  C  CR16  0  -0.297   4.3008  10.7023  12.4343
 O7P  C13  C  CR6   0   0.181   3.3727  10.1603  13.3192
 O7P  C14  C  CH2   0  -0.726   2.2826  11.0147  13.8915
 O7P  C15  C  C     0   0.580   2.7337  11.7536  15.1433
 O7P  C17  C  CH2   0  -0.392   0.5996  13.0033  15.0513
 O7P  C18  C  C     0   0.540  -0.4797  13.4237  16.0363
 O7P  C21  C  CH2   0  -0.267   1.1667  13.3333  17.8608
 O7P  C22  C  CH2   0  -0.340   2.2136  13.4876  16.7843
 O7P  C25  C  CR16  0  -0.310   3.4763   8.8146  13.6490
 O7P  C26  C  CR16  0  -0.296   4.4832   8.0212  13.1150
 O7P  C27  C  CR16  0  -0.389   8.5530   7.2565  11.1680
 O7P  N05  N  NS    0  -0.259  12.8556   8.1657  13.1011
 O7P  N16  N  NT    0  -0.475   1.8653  12.6575  15.6532
 O7P  N19  N  NT    0  -0.455  -0.1657  13.5693  17.3297
 O7P  O09  O  O2    0  -0.503   6.3384   7.7752  11.6495
 O7P  O24  O  O     0  -0.479   3.8198  11.5335  15.6534
 O7P  H1   H  HCH3  0   0.259  11.5397   5.9410  11.0832
 O7P  H2   H  HCH3  0   0.265  10.3763   6.0364   9.7624
 O7P  H3   H  HCH3  0   0.262  11.5303   7.3407  10.0212
 O7P  H4   H  HCR6  0   0.285   9.7718   9.2194  14.2457
 O7P  H5   H  HCR6  0   0.292   7.3743   9.1265  13.7635
 O7P  H6   H  HCR6  0   0.278   6.0139  10.3557  11.1877
 O7P  H7   H  HCR6  0   0.258   4.2315  11.7469  12.1559
 O7P  H8   H  HCH2  0   0.298   1.9414  11.7341  13.1427
 O7P  H9   H  HCH2  0   0.304   1.4116  10.3995  14.1366
 O7P  H10  H  HCH2  0   0.300   0.1844  12.1568  14.5073
 O7P  H11  H  HCH2  0   0.284   0.7130  13.8230  14.3319
 O7P  H12  H  HCH3  0   0.249  -0.8033  13.9817  19.2593
 O7P  H13  H  HCH3  0   0.248  -1.7044  14.8399  18.0096
 O7P  H14  H  HCH3  0   0.246  -1.9946  13.1174  18.2866
 O7P  H15  H  HCH2  0   0.251   1.2265  12.3378  18.3108
 O7P  H16  H  HCH2  0   0.261   1.3594  14.0626  18.6483
 O7P  H17  H  HCH2  0   0.260   2.2766  14.5332  16.4648
 O7P  H18  H  HCH2  0   0.283   3.1857  13.1991  17.1729
 O7P  H19  H  HCR6  0   0.259   2.7599   8.3693  14.3286
 O7P  H20  H  HCR6  0   0.273   4.5541   6.9726  13.3744
 O7P  H21  H  HCR6  0   0.277   8.1898   6.7121  10.3049
 O7P  O23  O  O     0  -0.512  -1.6082  13.6232  15.6039
 O7P  C20  C  CH3   0  -0.517  -1.2289  13.8930  18.2634

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
 O7P  C01  C02  single    1.497  0.020  1.497
 O7P  C02  C03  aromatic  1.405  0.020  1.405
 O7P  C02  C27  aromatic  1.383  0.020  1.383
 O7P  C03  C04  single    1.424  0.020  1.424
 O7P  C03  C06  aromatic  1.394  0.020  1.394
 O7P  C04  N05  triple    1.153  0.020  1.153
 O7P  C06  C07  aromatic  1.382  0.020  1.382
 O7P  C07  C08  aromatic  1.392  0.020  1.392
 O7P  C08  C27  aromatic  1.394  0.020  1.394
 O7P  C08  O09  single    1.350  0.020  1.350
 O7P  C10  C11  aromatic  1.387  0.020  1.387
 O7P  C10  C26  aromatic  1.384  0.020  1.384
 O7P  C10  O09  single    1.377  0.020  1.377
 O7P  C11  C12  aromatic  1.386  0.020  1.386
 O7P  C12  C13  aromatic  1.392  0.020  1.392
 O7P  C13  C14  single    1.499  0.020  1.499
 O7P  C13  C25  aromatic  1.389  0.020  1.389
 O7P  C15  N16  single    1.353  0.020  1.353
 O7P  C15  O24  double    1.220  0.020  1.220
 O7P  C17  C18  single    1.520  0.020  1.520
 O7P  C17  N16  single    1.444  0.020  1.444
 O7P  C18  N19  single    1.339  0.020  1.339
 O7P  C18  O23  double    1.225  0.020  1.225
 O7P  C20  N19  single    1.451  0.020  1.451
 O7P  C21  C22  single    1.510  0.020  1.510
 O7P  C21  N19  single    1.454  0.020  1.454
 O7P  C22  N16  single    1.446  0.020  1.446
 O7P  C25  C26  aromatic  1.389  0.020  1.389
 O7P  C14  C15  single    1.522  0.020  1.522
 O7P  C01  H1   single    0.970  0.020  1.090
 O7P  C01  H2   single    0.970  0.020  1.090
 O7P  C01  H3   single    0.970  0.020  1.090
 O7P  C06  H4   single    0.930  0.020  1.080
 O7P  C07  H5   single    0.930  0.020  1.080
 O7P  C11  H6   single    0.930  0.020  1.080
 O7P  C12  H7   single    0.930  0.020  1.080
 O7P  C14  H8   single    0.970  0.020  1.090
 O7P  C14  H9   single    0.970  0.020  1.090
 O7P  C17  H10  single    0.970  0.020  1.090
 O7P  C17  H11  single    0.970  0.020  1.090
 O7P  C20  H12  single    0.970  0.020  1.090
 O7P  C20  H13  single    0.970  0.020  1.090
 O7P  C20  H14  single    0.970  0.020  1.090
 O7P  C21  H15  single    0.970  0.020  1.090
 O7P  C21  H16  single    0.970  0.020  1.090
 O7P  C22  H17  single    0.970  0.020  1.090
 O7P  C22  H18  single    0.970  0.020  1.090
 O7P  C25  H19  single    0.930  0.020  1.080
 O7P  C26  H20  single    0.930  0.020  1.080
 O7P  C27  H21  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
 O7P  H3   C01  H2   107.77  3.000
 O7P  H3   C01  H1   107.26  3.000
 O7P  H2   C01  H1   107.99  3.000
 O7P  H3   C01  C02  111.05  3.000
 O7P  H2   C01  C02  111.07  3.000
 O7P  H1   C01  C02  111.51  3.000
 O7P  C27  C02  C03  117.97  3.000
 O7P  C27  C02  C01  120.84  3.000
 O7P  C03  C02  C01  121.18  3.000
 O7P  C06  C03  C04  119.36  3.000
 O7P  C06  C03  C02  120.78  3.000
 O7P  C04  C03  C02  119.86  3.000
 O7P  N05  C04  C03  180.00  3.000
 O7P  H4   C06  C07  119.45  3.000
 O7P  H4   C06  C03  119.83  3.000
 O7P  C07  C06  C03  120.72  3.000
 O7P  H5   C07  C08  121.66  3.000
 O7P  H5   C07  C06  119.58  3.000
 O7P  C08  C07  C06  118.76  3.000
 O7P  O09  C08  C27  115.78  3.000
 O7P  O09  C08  C07  123.59  3.000
 O7P  C27  C08  C07  120.62  3.000
 O7P  O09  C10  C26  118.87  3.000
 O7P  O09  C10  C11  120.14  3.000
 O7P  C26  C10  C11  120.91  3.000
 O7P  H6   C11  C12  120.36  3.000
 O7P  H6   C11  C10  120.53  3.000
 O7P  C12  C11  C10  119.11  3.000
 O7P  H7   C12  C13  119.75  3.000
 O7P  H7   C12  C11  119.09  3.000
 O7P  C13  C12  C11  121.15  3.000
 O7P  C25  C13  C14  121.05  3.000
 O7P  C25  C13  C12  118.57  3.000
 O7P  C14  C13  C12  120.38  3.000
 O7P  H9   C14  H8   105.97  3.000
 O7P  H9   C14  C15  108.95  3.000
 O7P  H8   C14  C15  109.66  3.000
 O7P  H9   C14  C13  110.12  3.000
 O7P  H8   C14  C13  109.92  3.000
 O7P  C15  C14  C13  112.04  3.000
 O7P  O24  C15  N16  122.29  3.000
 O7P  O24  C15  C14  121.34  3.000
 O7P  N16  C15  C14  116.36  3.000
 O7P  H11  C17  H10  107.04  3.000
 O7P  H11  C17  N16  111.21  3.000
 O7P  H10  C17  N16  110.89  3.000
 O7P  H11  C17  C18  106.96  3.000
 O7P  H10  C17  C18  105.55  3.000
 O7P  N16  C17  C18  114.74  3.000
 O7P  O23  C18  N19  122.64  3.000
 O7P  O23  C18  C17  118.05  3.000
 O7P  N19  C18  C17  119.31  3.000
 O7P  H16  C21  H15  107.57  3.000
 O7P  H16  C21  N19  108.50  3.000
 O7P  H15  C21  N19  110.37  3.000
 O7P  H16  C21  C22  108.91  3.000
 O7P  H15  C21  C22  110.39  3.000
 O7P  N19  C21  C22  111.01  3.000
 O7P  H18  C22  H17  107.85  3.000
 O7P  H18  C22  N16  110.07  3.000
 O7P  H17  C22  N16  109.50  3.000
 O7P  H18  C22  C21  109.78  3.000
 O7P  H17  C22  C21  110.22  3.000
 O7P  N16  C22  C21  109.41  3.000
 O7P  H19  C25  C26  119.07  3.000
 O7P  H19  C25  C13  119.85  3.000
 O7P  C26  C25  C13  121.08  3.000
 O7P  H20  C26  C25  120.59  3.000
 O7P  H20  C26  C10  120.23  3.000
 O7P  C25  C26  C10  119.18  3.000
 O7P  H21  C27  C08  119.11  3.000
 O7P  H21  C27  C02  119.75  3.000
 O7P  C08  C27  C02  121.15  3.000
 O7P  C22  N16  C17  113.57  3.000
 O7P  C22  N16  C15  121.59  3.000
 O7P  C17  N16  C15  124.44  3.000
 O7P  C21  N19  C20  118.20  3.000
 O7P  C21  N19  C18  123.38  3.000
 O7P  C20  N19  C18  118.29  3.000
 O7P  C10  O09  C08  119.86  3.000
 O7P  H14  C20  H13  108.46  3.000
 O7P  H14  C20  H12  108.28  3.000
 O7P  H13  C20  H12  108.26  3.000
 O7P  H14  C20  N19  111.69  3.000
 O7P  H13  C20  N19  111.33  3.000
 O7P  H12  C20  N19  108.72  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
 O7P  CONST_01  C07  C06  C03  C02     0.00   0.0  0
 O7P  CONST_02  C07  C08  C27  C02     0.00   0.0  0
 O7P  CONST_03  C08  C27  C02  C03     0.00   0.0  0
 O7P  CONST_04  C08  C07  C06  C03     0.00   0.0  0
 O7P  CONST_05  C27  C02  C03  C06     0.00   0.0  0
 O7P  CONST_06  C27  C08  C07  C06     0.00   0.0  0
 O7P  CONST_07  C13  C12  C11  C10     0.00   0.0  0
 O7P  CONST_08  C13  C25  C26  C10     0.00   0.0  0
 O7P  CONST_09  C25  C26  C10  C11     0.00   0.0  0
 O7P  CONST_10  C25  C13  C12  C11     0.00   0.0  0
 O7P  CONST_11  C26  C10  C11  C12     0.00   0.0  0
 O7P  CONST_12  C26  C25  C13  C12     0.00   0.0  0
 O7P  CONST_13  C21  N19  C18  C17     0.00   0.0  0
 O7P  CONST_14  C06  C03  C02  C01   180.00   0.0  0
 O7P  CONST_15  C08  C27  C02  C01   180.00   0.0  0
 O7P  CONST_16  O09  C08  C27  C02   180.00   0.0  0
 O7P  CONST_17  C27  C02  C03  C04   180.00   0.0  0
 O7P  CONST_18  C07  C06  C03  C04   180.00   0.0  0
 O7P  CONST_19  O09  C08  C07  C06   180.00   0.0  0
 O7P  CONST_20  C14  C13  C12  C11   180.00   0.0  0
 O7P  CONST_21  O09  C10  C11  C12   180.00   0.0  0
 O7P  CONST_22  C26  C25  C13  C14   180.00   0.0  0
 O7P  CONST_23  O09  C10  C26  C25   180.00   0.0  0
 O7P  CONST_24  C20  N19  C18  C17   180.00   0.0  0
 O7P  CONST_25  O23  C18  N19  C21   180.00   0.0  0
 O7P  CONST_26  H4   C06  C03  C02   180.00   0.0  0
 O7P  CONST_27  H21  C27  C02  C03   180.00   0.0  0
 O7P  CONST_28  H5   C07  C06  C03   180.00   0.0  0
 O7P  CONST_29  H7   C12  C11  C10   180.00   0.0  0
 O7P  CONST_30  H19  C25  C26  C10   180.00   0.0  0
 O7P  CONST_31  H20  C26  C10  C11   180.00   0.0  0
 O7P  CONST_32  H6   C11  C12  C13   180.00   0.0  0
 O7P  CONST_33  C17  N16  C15  C14     0.00   0.0  0
 O7P  CONST_34  C22  N16  C15  C14   180.00   0.0  0
 O7P  CONST_35  O24  C15  N16  C17   180.00   0.0  0
 O7P  CONST_36  O24  C15  N16  C22     0.00   0.0  0
 O7P  CONST_37  O23  C18  N19  C20     0.00   0.0  0
 O7P  Var_01    C21  C22  N16  C17    61.00  30.0  1
 O7P  Var_02    C22  N16  C17  C18   -37.31  30.0  1
 O7P  Var_03    C22  C21  N19  C18    23.93  30.0  1
 O7P  Var_04    N19  C18  C17  N16     6.33  30.0  1
 O7P  Var_05    N19  C21  C22  N16   -52.78  30.0  1
 O7P  Var_06    C11  C10  O09  C08    72.59  30.0  2
 O7P  Var_07    C27  C08  O09  C10  -167.16  30.0  2
 O7P  Var_08    C15  C14  C13  C12   -86.16  30.0  2
 O7P  Var_09    N16  C15  C14  C13   173.32  30.0  3
 O7P  Var_10    H1   C01  C02  C03    54.53  30.0  2
 O7P  Var_11    H12  C20  N19  C18  -179.58  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
 O7P  plan-1  C01  0.020
 O7P  plan-1  C02  0.020
 O7P  plan-1  C03  0.020
 O7P  plan-1  C04  0.020
 O7P  plan-1  C06  0.020
 O7P  plan-1  C07  0.020
 O7P  plan-1  C08  0.020
 O7P  plan-1  C27  0.020
 O7P  plan-1  N05  0.020
 O7P  plan-1  O09  0.020
 O7P  plan-1  H4   0.020
 O7P  plan-1  H5   0.020
 O7P  plan-1  H21  0.020
 O7P  plan-2  C10  0.020
 O7P  plan-2  C11  0.020
 O7P  plan-2  C12  0.020
 O7P  plan-2  C13  0.020
 O7P  plan-2  C14  0.020
 O7P  plan-2  C25  0.020
 O7P  plan-2  C26  0.020
 O7P  plan-2  O09  0.020
 O7P  plan-2  H6   0.020
 O7P  plan-2  H7   0.020
 O7P  plan-2  H19  0.020
 O7P  plan-2  H20  0.020
 O7P  plan-3  C14  0.020
 O7P  plan-3  C15  0.020
 O7P  plan-3  C17  0.020
 O7P  plan-3  C22  0.020
 O7P  plan-3  N16  0.020
 O7P  plan-3  O24  0.020
 O7P  plan-4  C17  0.020
 O7P  plan-4  C18  0.020
 O7P  plan-4  C21  0.020
 O7P  plan-4  N19  0.020
 O7P  plan-4  O23  0.020
 O7P  plan-4  C20  0.020

