# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 17:36:51 2021
#   Inital geometry file: a 78 line input string
#   Ligand name: 4-(4-methylpiperazin-1-yl)benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)c2ccc(cc2)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
 RXJ  RXJ  4-(4-methylpiperazin-1-yl)benzonitrile  ligand  30  15  .  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_RXJ
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
 RXJ  N1   N  NT    0  -0.520  12.8217  -19.5821  -13.8891
 RXJ  C4   C  CH2   0  -0.285  11.9778  -21.5704  -15.0690
 RXJ  C5   C  CR6   0   0.427  12.6517  -18.5539  -13.0026
 RXJ  C6   C  CR16  0  -0.352  11.4078  -18.3128  -12.3751
 RXJ  C7   C  CR16  0  -0.224  11.2506  -17.3120  -11.4440
 RXJ  C8   C  CR6   0  -0.042  12.3195  -16.4838  -11.0943
 RXJ  C10  C  CR16  0  -0.224  13.5505  -16.6885  -11.7194
 RXJ  N    N  NT    0  -0.412  13.1327  -21.5588  -15.9374
 RXJ  C    C  CH3   0  -0.519  13.3762  -22.8595  -16.5197
 RXJ  C1   C  CH2   0  -0.284  14.2726  -21.0879  -15.1846
 RXJ  C11  C  CR16  0  -0.358  13.7124  -17.6883  -12.6526
 RXJ  C2   C  CH2   0  -0.309  14.0484  -19.6814  -14.6633
 RXJ  C3   C  CH2   0  -0.308  11.6696  -20.1813  -14.5468
 RXJ  C9   C  CSP   0   0.038  12.1540  -15.4520  -10.1335
 RXJ  N2   N  NS    0  -0.273  12.0159  -14.6140   -9.3514
 RXJ  H1   H  HCH2  0   0.248  11.1052  -21.9207  -15.6245
 RXJ  H2   H  HCH2  0   0.199  12.1174  -22.2591  -14.2171
 RXJ  H3   H  HCR6  0   0.275  10.5425  -18.9163  -12.6012
 RXJ  H4   H  HCR6  0   0.275  10.2818  -17.1705  -10.9832
 RXJ  H5   H  HCR6  0   0.275  14.3920  -16.0517  -11.4800
 RXJ  H7   H  HCH3  0   0.235  12.5161  -23.1687  -17.1152
 RXJ  H8   H  HCH3  0   0.235  14.2430  -22.8158  -17.1799
 RXJ  H9   H  HCH3  0   0.194  13.5640  -23.6407  -15.7667
 RXJ  H10  H  HCH2  0   0.198  14.5045  -21.7568  -14.3367
 RXJ  H11  H  HCH2  0   0.248  15.1546  -21.0688  -15.8285
 RXJ  H12  H  HCR6  0   0.277  14.6845  -17.7798  -13.1112
 RXJ  H13  H  HCH2  0   0.260  14.9048  -19.4369  -14.0391
 RXJ  H14  H  HCH2  0   0.232  14.0339  -18.9717  -15.5008
 RXJ  H15  H  HCH2  0   0.233  11.3310  -19.5436  -15.3734
 RXJ  H16  H  HCH2  0   0.262  10.8432  -20.2809  -13.8492

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
 RXJ  C    N    single    1.446  0.020  1.446
 RXJ  N    C1   single    1.445  0.020  1.445
 RXJ  N    C4   single    1.445  0.020  1.445
 RXJ  C1   C2   single    1.517  0.020  1.517
 RXJ  C4   C3   single    1.516  0.020  1.516
 RXJ  C2   N1   single    1.454  0.020  1.454
 RXJ  C3   N1   single    1.456  0.020  1.456
 RXJ  N1   C5   single    1.368  0.020  1.368
 RXJ  C5   C11  aromatic  1.413  0.020  1.413
 RXJ  C5   C6   aromatic  1.414  0.020  1.414
 RXJ  C11  C10  aromatic  1.377  0.020  1.377
 RXJ  C6   C7   aromatic  1.376  0.020  1.376
 RXJ  C10  C8   aromatic  1.396  0.020  1.396
 RXJ  C7   C8   aromatic  1.397  0.020  1.397
 RXJ  C8   C9   single    1.420  0.020  1.420
 RXJ  C9   N2   triple    1.155  0.020  1.155
 RXJ  C4   H1   single    0.970  0.020  1.090
 RXJ  C4   H2   single    0.970  0.020  1.090
 RXJ  C6   H3   single    0.930  0.020  1.080
 RXJ  C7   H4   single    0.930  0.020  1.080
 RXJ  C10  H5   single    0.930  0.020  1.080
 RXJ  C    H7   single    0.970  0.020  1.090
 RXJ  C    H8   single    0.970  0.020  1.090
 RXJ  C    H9   single    0.970  0.020  1.090
 RXJ  C1   H10  single    0.970  0.020  1.090
 RXJ  C1   H11  single    0.970  0.020  1.090
 RXJ  C11  H12  single    0.930  0.020  1.080
 RXJ  C2   H13  single    0.970  0.020  1.090
 RXJ  C2   H14  single    0.970  0.020  1.090
 RXJ  C3   H15  single    0.970  0.020  1.090
 RXJ  C3   H16  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
 RXJ  C3   N1   C2   113.52  3.000
 RXJ  C3   N1   C5   120.25  3.000
 RXJ  C2   N1   C5   120.08  3.000
 RXJ  H2   C4   H1   107.05  3.000
 RXJ  H2   C4   C3   109.36  3.000
 RXJ  H1   C4   C3   107.86  3.000
 RXJ  H2   C4   N    111.57  3.000
 RXJ  H1   C4   N    109.60  3.000
 RXJ  C3   C4   N    111.24  3.000
 RXJ  C11  C5   C6   116.49  3.000
 RXJ  C6   C5   N1   121.67  3.000
 RXJ  C11  C5   N1   121.84  3.000
 RXJ  H3   C6   C7   117.19  3.000
 RXJ  H3   C6   C5   121.15  3.000
 RXJ  C7   C6   C5   121.66  3.000
 RXJ  H4   C7   C8   120.06  3.000
 RXJ  H4   C7   C6   119.06  3.000
 RXJ  C8   C7   C6   120.88  3.000
 RXJ  C9   C8   C10  120.84  3.000
 RXJ  C9   C8   C7   120.75  3.000
 RXJ  C10  C8   C7   118.42  3.000
 RXJ  H5   C10  C11  119.06  3.000
 RXJ  H5   C10  C8   120.03  3.000
 RXJ  C11  C10  C8   120.91  3.000
 RXJ  C1   N    C    111.73  3.000
 RXJ  C1   N    C4   108.66  3.000
 RXJ  C    N    C4   111.68  3.000
 RXJ  H9   C    H8   107.87  3.000
 RXJ  H9   C    H7   107.85  3.000
 RXJ  H8   C    H7   107.91  3.000
 RXJ  H9   C    N    113.06  3.000
 RXJ  H8   C    N    109.98  3.000
 RXJ  H7   C    N    110.01  3.000
 RXJ  H11  C1   H10  107.07  3.000
 RXJ  H11  C1   C2   107.81  3.000
 RXJ  H10  C1   C2   109.19  3.000
 RXJ  H11  C1   N    109.61  3.000
 RXJ  H10  C1   N    111.61  3.000
 RXJ  C2   C1   N    111.39  3.000
 RXJ  H12  C11  C10  117.10  3.000
 RXJ  H12  C11  C5   121.28  3.000
 RXJ  C10  C11  C5   121.61  3.000
 RXJ  H14  C2   H13  107.63  3.000
 RXJ  H14  C2   C1   109.83  3.000
 RXJ  H13  C2   C1   106.82  3.000
 RXJ  H14  C2   N1   110.55  3.000
 RXJ  H13  C2   N1   110.08  3.000
 RXJ  C1   C2   N1   111.78  3.000
 RXJ  H16  C3   H15  107.59  3.000
 RXJ  H16  C3   C4   106.98  3.000
 RXJ  H15  C3   C4   109.62  3.000
 RXJ  H16  C3   N1   110.47  3.000
 RXJ  H15  C3   N1   110.20  3.000
 RXJ  C4   C3   N1   111.84  3.000
 RXJ  N2   C9   C8   180.00  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
 RXJ  CONST_01  C8   C10  C11  C5     0.00   0.0  0
 RXJ  CONST_02  C8   C7   C6   C5     0.00   0.0  0
 RXJ  CONST_03  C10  C11  C5   C6     0.00   0.0  0
 RXJ  CONST_04  C10  C8   C7   C6     0.00   0.0  0
 RXJ  CONST_05  C11  C5   C6   C7     0.00   0.0  0
 RXJ  CONST_06  C11  C10  C8   C7     0.00   0.0  0
 RXJ  CONST_07  C10  C11  C5   N1   180.00   0.0  0
 RXJ  CONST_08  C7   C6   C5   N1   180.00   0.0  0
 RXJ  CONST_09  C9   C8   C7   C6   180.00   0.0  0
 RXJ  CONST_10  C9   C8   C10  C11  180.00   0.0  0
 RXJ  CONST_11  H12  C11  C5   N1     0.00   0.0  0
 RXJ  CONST_12  H3   C6   C5   N1     0.00   0.0  0
 RXJ  CONST_13  H5   C10  C11  C5   180.00   0.0  0
 RXJ  CONST_14  H4   C7   C6   C5   180.00   0.0  0
 RXJ  Var_01    N    C1   C2   N1    54.57  30.0  1
 RXJ  Var_02    N    C4   C3   N1   -54.78  30.0  1
 RXJ  Var_03    C2   C1   N    C4   -60.53  30.0  1
 RXJ  Var_04    C2   N1   C3   C4    48.32  30.0  1
 RXJ  Var_05    C1   C2   N1   C5   159.37  30.0  1
 RXJ  Var_06    C3   C4   N    C1    60.59  30.0  1
 RXJ  Var_07    H7   C    N    C4    60.44  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
 RXJ  plan-1  N1   0.020
 RXJ  plan-1  C5   0.020
 RXJ  plan-1  C6   0.020
 RXJ  plan-1  C7   0.020
 RXJ  plan-1  C8   0.020
 RXJ  plan-1  C10  0.020
 RXJ  plan-1  C11  0.020
 RXJ  plan-1  C9   0.020
 RXJ  plan-1  N2   0.020
 RXJ  plan-1  H3   0.020
 RXJ  plan-1  H4   0.020
 RXJ  plan-1  H5   0.020
 RXJ  plan-1  H12  0.020

