# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 18:52:15 2022
#   Inital geometry file: a 125 line input string
#   Ligand name: 2-ethyl-2-methanoyl-~{N}-[3-[(4-methylpiperazin-1-yl)methyl]phenyl]butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(CC)(C=O)C(=O)Nc1cccc(CN2CCN(C)CC2)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
 QXN  QXN  2-ethyl-2-methanoyl-~{N}-[3-[(4-methylpiperazin-1-yl)methyl]phenyl]butanamide  ligand  53  24  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_QXN
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
 QXN  C1   C  CT    0  -0.359  35.0789  14.1569  14.5025
 QXN  C2   C  CH2   0  -0.463  35.9209  13.7566  13.2689
 QXN  C3   C  CH3   0  -0.670  35.6796  14.5625  11.9966
 QXN  C4   C  CH2   0  -0.407  35.6204  13.5106  15.7931
 QXN  C5   C  CH3   0  -0.674  35.8160  12.0004  15.7338
 QXN  C6   C  C1    0   0.214  33.6301  13.7689  14.2445
 QXN  C7   C  C     0   0.591  35.0338  15.6757  14.6958
 QXN  N8   N  NH1   0  -0.746  36.2408  16.2826  14.7543
 QXN  C9   C  CR6   0   0.391  36.5486  17.6425  14.8984
 QXN  C10  C  CR16  0  -0.362  37.8819  18.0048  14.7081
 QXN  C11  C  CR16  0  -0.229  38.2680  19.3290  14.8347
 QXN  C12  C  CR16  0  -0.305  37.3386  20.3077  15.1489
 QXN  C13  C  CR6   0   0.115  36.0071  19.9559  15.3469
 QXN  C14  C  CR16  0  -0.377  35.6138  18.6285  15.2202
 QXN  C15  C  CH2   0  -0.334  34.9943  21.0111  15.7107
 QXN  N16  N  NT    0  -0.416  34.9732  22.1008  14.7567
 QXN  C17  C  CH2   0  -0.284  34.2017  23.2268  15.2475
 QXN  C18  C  CH2   0  -0.282  34.2497  24.3760  14.2590
 QXN  N19  N  NT    0  -0.409  33.7520  23.9585  12.9647
 QXN  C20  C  CH2   0  -0.280  34.5204  22.8327  12.4738
 QXN  C21  C  CH2   0  -0.282  34.4763  21.6818  13.4599
 QXN  C22  C  CH3   0  -0.515  33.7361  25.0482  12.0182
 QXN  O24  O  O     0  -0.360  32.9335  13.1651  15.0169
 QXN  O25  O  O     0  -0.448  33.9662  16.2546  14.8058
 QXN  H1   H  HCH2  0   0.264  35.7338  12.7004  13.0611
 QXN  H2   H  HCH2  0   0.254  36.9806  13.8099  13.5357
 QXN  H3   H  HCH3  0   0.246  36.3035  14.1707  11.1936
 QXN  H4   H  HCH3  0   0.233  34.6466  14.5070  11.6538
 QXN  H5   H  HCH3  0   0.230  35.9344  15.6155  12.1174
 QXN  H6   H  HCH2  0   0.241  36.5831  13.9700  16.0292
 QXN  H7   H  HCH2  0   0.246  34.9563  13.7643  16.6221
 QXN  H8   H  HCH3  0   0.238  36.1459  11.6374  16.7072
 QXN  H9   H  HCH3  0   0.230  34.8991  11.4711  15.4804
 QXN  H10  H  HCH3  0   0.229  36.5793  11.7176  15.0095
 QXN  H11  H  H     0   0.209  33.2383  14.0594  13.2541
 QXN  H12  H  HNH1  0   0.422  37.0459  15.6882  14.6204
 QXN  H13  H  HCR6  0   0.268  38.6168  17.2494  14.4548
 QXN  H14  H  HCR6  0   0.256  39.3063  19.5943  14.6827
 QXN  H15  H  HCR6  0   0.244  37.6450  21.3423  15.2374
 QXN  H16  H  HCR6  0   0.274  34.5768  18.3746  15.3722
 QXN  H17  H  HCH2  0   0.250  35.2539  21.4283  16.6886
 QXN  H18  H  HCH2  0   0.214  34.0016  20.5446  15.8264
 QXN  H20  H  HCH2  0   0.236  34.6198  23.5564  16.2016
 QXN  H21  H  HCH2  0   0.190  33.1493  22.9506  15.4311
 QXN  H22  H  HCH2  0   0.187  35.2850  24.7551  14.1942
 QXN  H23  H  HCH2  0   0.234  33.6314  25.1959  14.6333
 QXN  H25  H  HCH2  0   0.233  34.1020  22.5020  11.5202
 QXN  H26  H  HCH2  0   0.186  35.5734  23.1092  12.2873
 QXN  H27  H  HCH2  0   0.190  33.4426  21.3007  13.5304
 QXN  H28  H  HCH2  0   0.240  35.0937  20.8655  13.0796
 QXN  H29  H  HCH3  0   0.231  33.1105  25.8609  12.3911
 QXN  H30  H  HCH3  0   0.189  34.7364  25.4623  11.8147
 QXN  H31  H  HCH3  0   0.231  33.3162  24.7130  11.0684

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
 QXN  C3   C2   single    1.525  0.020  1.525
 QXN  C22  N19  single    1.443  0.020  1.443
 QXN  C20  N19  single    1.449  0.020  1.449
 QXN  C20  C21  single    1.516  0.020  1.516
 QXN  C2   C1   single    1.546  0.020  1.546
 QXN  N19  C18  single    1.448  0.020  1.448
 QXN  C21  N16  single    1.451  0.020  1.451
 QXN  C18  C17  single    1.517  0.020  1.517
 QXN  C6   C1   single    1.522  0.020  1.522
 QXN  C6   O24  double    1.203  0.020  1.203
 QXN  C1   C7   single    1.532  0.020  1.532
 QXN  C1   C4   single    1.542  0.020  1.542
 QXN  O25  C7   double    1.219  0.020  1.219
 QXN  C7   N8   single    1.352  0.020  1.352
 QXN  N16  C17  single    1.451  0.020  1.451
 QXN  N16  C15  single    1.448  0.020  1.448
 QXN  N8   C9   single    1.402  0.020  1.402
 QXN  C9   C14  aromatic  1.396  0.020  1.396
 QXN  C9   C10  aromatic  1.395  0.020  1.395
 QXN  C5   C4   single    1.524  0.020  1.524
 QXN  C14  C13  aromatic  1.390  0.020  1.390
 QXN  C10  C11  aromatic  1.385  0.020  1.385
 QXN  C13  C15  single    1.507  0.020  1.507
 QXN  C13  C12  aromatic  1.391  0.020  1.391
 QXN  C11  C12  aromatic  1.386  0.020  1.386
 QXN  C2   H1   single    0.970  0.020  1.090
 QXN  C2   H2   single    0.970  0.020  1.090
 QXN  C3   H3   single    0.970  0.020  1.090
 QXN  C3   H4   single    0.970  0.020  1.090
 QXN  C3   H5   single    0.970  0.020  1.090
 QXN  C4   H6   single    0.970  0.020  1.090
 QXN  C4   H7   single    0.970  0.020  1.090
 QXN  C5   H8   single    0.970  0.020  1.090
 QXN  C5   H9   single    0.970  0.020  1.090
 QXN  C5   H10  single    0.970  0.020  1.090
 QXN  C6   H11  single    0.930  0.020  1.080
 QXN  N8   H12  single    0.860  0.020  1.020
 QXN  C10  H13  single    0.930  0.020  1.080
 QXN  C11  H14  single    0.930  0.020  1.080
 QXN  C12  H15  single    0.930  0.020  1.080
 QXN  C14  H16  single    0.930  0.020  1.080
 QXN  C15  H17  single    0.970  0.020  1.090
 QXN  C15  H18  single    0.970  0.020  1.090
 QXN  C17  H20  single    0.970  0.020  1.090
 QXN  C17  H21  single    0.970  0.020  1.090
 QXN  C18  H22  single    0.970  0.020  1.090
 QXN  C18  H23  single    0.970  0.020  1.090
 QXN  C20  H25  single    0.970  0.020  1.090
 QXN  C20  H26  single    0.970  0.020  1.090
 QXN  C21  H27  single    0.970  0.020  1.090
 QXN  C21  H28  single    0.970  0.020  1.090
 QXN  C22  H29  single    0.970  0.020  1.090
 QXN  C22  H30  single    0.970  0.020  1.090
 QXN  C22  H31  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
 QXN  C7   C1   C6   104.25  3.000
 QXN  C7   C1   C4   108.69  3.000
 QXN  C6   C1   C4   111.68  3.000
 QXN  C4   C1   C2   111.60  3.000
 QXN  C7   C1   C2   111.93  3.000
 QXN  C6   C1   C2   108.49  3.000
 QXN  H2   C2   H1   105.03  3.000
 QXN  H2   C2   C3   109.32  3.000
 QXN  H1   C2   C3   108.97  3.000
 QXN  H2   C2   C1   108.68  3.000
 QXN  H1   C2   C1   107.98  3.000
 QXN  C3   C2   C1   116.27  3.000
 QXN  H5   C3   H4   107.80  3.000
 QXN  H5   C3   H3   107.17  3.000
 QXN  H4   C3   H3   107.01  3.000
 QXN  H5   C3   C2   112.39  3.000
 QXN  H4   C3   C2   112.67  3.000
 QXN  H3   C3   C2   109.52  3.000
 QXN  H7   C4   H6   105.90  3.000
 QXN  H7   C4   C5   109.74  3.000
 QXN  H6   C4   C5   108.18  3.000
 QXN  H7   C4   C1   108.94  3.000
 QXN  H6   C4   C1   108.31  3.000
 QXN  C5   C4   C1   115.34  3.000
 QXN  H10  C5   H9   108.00  3.000
 QXN  H10  C5   H8   107.17  3.000
 QXN  H9   C5   H8   107.51  3.000
 QXN  H10  C5   C4   111.90  3.000
 QXN  H9   C5   C4   112.51  3.000
 QXN  H8   C5   C4   109.52  3.000
 QXN  H11  C6   O24  120.19  3.000
 QXN  H11  C6   C1   115.01  3.000
 QXN  O24  C6   C1   124.78  3.000
 QXN  O25  C7   N8   124.36  3.000
 QXN  N8   C7   C1   115.10  3.000
 QXN  O25  C7   C1   120.53  3.000
 QXN  H12  N8   C9   114.18  3.000
 QXN  H12  N8   C7   116.22  3.000
 QXN  C9   N8   C7   129.49  3.000
 QXN  C14  C9   C10  119.21  3.000
 QXN  C10  C9   N8   116.61  3.000
 QXN  C14  C9   N8   124.18  3.000
 QXN  H13  C10  C11  119.91  3.000
 QXN  H13  C10  C9   119.93  3.000
 QXN  C11  C10  C9   120.16  3.000
 QXN  H14  C11  C12  120.14  3.000
 QXN  H14  C11  C10  119.26  3.000
 QXN  C12  C11  C10  120.59  3.000
 QXN  H15  C12  C13  120.05  3.000
 QXN  H15  C12  C11  120.24  3.000
 QXN  C13  C12  C11  119.70  3.000
 QXN  C15  C13  C14  120.03  3.000
 QXN  C15  C13  C12  120.03  3.000
 QXN  C14  C13  C12  119.94  3.000
 QXN  H16  C14  C13  118.94  3.000
 QXN  H16  C14  C9   120.66  3.000
 QXN  C13  C14  C9   120.39  3.000
 QXN  H18  C15  H17  106.32  3.000
 QXN  H18  C15  N16  111.98  3.000
 QXN  H17  C15  N16  107.77  3.000
 QXN  H18  C15  C13  109.51  3.000
 QXN  H17  C15  C13  108.85  3.000
 QXN  N16  C15  C13  112.18  3.000
 QXN  C21  N16  C17  110.15  3.000
 QXN  C17  N16  C15  111.65  3.000
 QXN  C21  N16  C15  112.12  3.000
 QXN  H21  C17  H20  107.17  3.000
 QXN  H21  C17  C18  109.16  3.000
 QXN  H20  C17  C18  109.17  3.000
 QXN  H21  C17  N16  111.67  3.000
 QXN  H20  C17  N16  109.04  3.000
 QXN  C18  C17  N16  110.54  3.000
 QXN  H23  C18  H22  107.04  3.000
 QXN  H23  C18  N19  109.15  3.000
 QXN  H22  C18  N19  111.63  3.000
 QXN  H23  C18  C17  109.11  3.000
 QXN  H22  C18  C17  109.14  3.000
 QXN  N19  C18  C17  110.68  3.000
 QXN  C22  N19  C20  111.74  3.000
 QXN  C20  N19  C18  110.16  3.000
 QXN  C22  N19  C18  111.85  3.000
 QXN  H26  C20  H25  107.07  3.000
 QXN  H26  C20  C21  109.12  3.000
 QXN  H25  C20  C21  109.07  3.000
 QXN  H26  C20  N19  111.61  3.000
 QXN  H25  C20  N19  109.14  3.000
 QXN  C21  C20  N19  110.74  3.000
 QXN  H28  C21  H27  107.07  3.000
 QXN  H28  C21  C20  108.94  3.000
 QXN  H27  C21  C20  109.32  3.000
 QXN  H28  C21  N16  109.48  3.000
 QXN  H27  C21  N16  111.31  3.000
 QXN  C20  C21  N16  110.62  3.000
 QXN  H31  C22  H30  107.71  3.000
 QXN  H31  C22  H29  107.80  3.000
 QXN  H30  C22  H29  107.69  3.000
 QXN  H31  C22  N19  110.06  3.000
 QXN  H30  C22  N19  113.26  3.000
 QXN  H29  C22  N19  110.15  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
 QXN  CONST_01  C12  C13  C14  C9      0.00   0.0  0
 QXN  CONST_02  C12  C11  C10  C9      0.00   0.0  0
 QXN  CONST_03  C13  C14  C9   C10     0.00   0.0  0
 QXN  CONST_04  C13  C12  C11  C10     0.00   0.0  0
 QXN  CONST_05  C14  C9   C10  C11     0.00   0.0  0
 QXN  CONST_06  C14  C13  C12  C11     0.00   0.0  0
 QXN  CONST_07  C13  C14  C9   N8    180.00   0.0  0
 QXN  CONST_08  C11  C10  C9   N8    180.00   0.0  0
 QXN  CONST_09  C15  C13  C14  C9    180.00   0.0  0
 QXN  CONST_10  C15  C13  C12  C11   180.00   0.0  0
 QXN  CONST_11  H14  C11  C10  C9    180.00   0.0  0
 QXN  CONST_12  H16  C14  C9   C10   180.00   0.0  0
 QXN  CONST_13  H15  C12  C11  C10   180.00   0.0  0
 QXN  CONST_14  H13  C10  C11  C12   180.00   0.0  0
 QXN  CONST_15  C14  C9   N8   C7      0.00   0.0  0
 QXN  CONST_16  C10  C9   N8   C7    180.00   0.0  0
 QXN  CONST_17  H12  N8   C9   C10     0.00   0.0  0
 QXN  CONST_18  C9   N8   C7   C1    180.00   0.0  0
 QXN  CONST_19  O25  C7   N8   C9      0.00   0.0  0
 QXN  Var_01    N19  C20  C21  N16   -57.49  30.0  1
 QXN  Var_02    N19  C18  C17  N16    57.76  30.0  1
 QXN  Var_03    C20  N19  C18  C17   -57.42  30.0  1
 QXN  Var_04    C20  C21  N16  C17    57.27  30.0  1
 QXN  Var_05    C21  C20  N19  C18    57.29  30.0  1
 QXN  Var_06    C21  N16  C17  C18   -57.38  30.0  1
 QXN  Var_07    N16  C15  C13  C12    55.07  30.0  2
 QXN  Var_08    H29  C22  N19  C18   -58.81  30.0  3
 QXN  Var_09    O24  C6   C1   C2    131.58  30.0  2
 QXN  Var_10    O25  C7   C1   C2    127.09  30.0  3
 QXN  Var_11    C5   C4   C1   C2    -52.21  30.0  3
 QXN  Var_12    C6   C1   C2   C3     69.51  30.0  3
 QXN  Var_13    H3   C3   C2   C1   -178.26  30.0  3
 QXN  Var_14    H8   C5   C4   C1   -176.83  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
 QXN  plan-1  N8   0.020
 QXN  plan-1  C9   0.020
 QXN  plan-1  C10  0.020
 QXN  plan-1  C11  0.020
 QXN  plan-1  C12  0.020
 QXN  plan-1  C13  0.020
 QXN  plan-1  C14  0.020
 QXN  plan-1  C15  0.020
 QXN  plan-1  H13  0.020
 QXN  plan-1  H14  0.020
 QXN  plan-1  H15  0.020
 QXN  plan-1  H16  0.020
 QXN  plan-2  C1   0.020
 QXN  plan-2  C7   0.020
 QXN  plan-2  N8   0.020
 QXN  plan-2  C9   0.020
 QXN  plan-2  O25  0.020
 QXN  plan-2  H12  0.020
 QXN  plan-3  C1   0.020
 QXN  plan-3  C6   0.020
 QXN  plan-3  O24  0.020
 QXN  plan-3  H11  0.020

