# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 20:26:02 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 2-(4-methylphenoxy)-1-(4-methylpiperazin-4-ium-1-yl)ethanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[NH+]1CCN(CC1)C(=O)COc2ccc(C)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
 LPZ  LPZ  2-(4-methylphenoxy)-1-(4-methylpiperazin-4-ium-1-yl)ethanone  ligand  39  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LPZ
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
 LPZ  N1   N  NT1   1  -0.522  -4.7439  -0.8008  -0.0353
 LPZ  C4   C  CR6   0   0.364   2.4990   0.3361  -0.0281
 LPZ  C5   C  CR16  0  -0.332   3.5736   1.1684  -0.3414
 LPZ  C6   C  CR16  0  -0.279   4.8597   0.6623  -0.3668
 LPZ  C7   C  CH2   0  -0.325   0.1656   0.1381   0.2912
 LPZ  C8   C  C     0   0.546  -1.0524   1.0473   0.2073
 LPZ  C10  C  CH2   0  -0.307  -3.4723  -1.5785   0.0082
 LPZ  C13  C  CH3   0  -0.532  -5.7507  -1.4503  -0.9081
 LPZ  N    N  NT    0  -0.471  -2.2454   0.4727   0.4885
 LPZ  O    O  O2    0  -0.466   1.2787   0.9211  -0.0281
 LPZ  C1   C  CR6   0   0.075   5.1234  -0.6798  -0.0862
 LPZ  C11  C  CH2   0  -0.315  -4.4858   0.6103  -0.4467
 LPZ  C12  C  CH2   0  -0.337  -3.4659   1.2498   0.4710
 LPZ  C2   C  CR16  0  -0.288   4.0412  -1.4910   0.2282
 LPZ  C3   C  CR16  0  -0.361   2.7380  -1.0024   0.2610
 LPZ  C9   C  CH2   0  -0.346  -2.4539  -0.8975   0.9026
 LPZ  O1   O  O     0  -0.465  -0.9424   2.2190  -0.0950
 LPZ  H1   H  HNT1  0   0.469  -5.1322  -0.7820   0.9107
 LPZ  H2   H  HCR6  0   0.261   3.3930   2.2141  -0.5580
 LPZ  H3   H  HCR6  0   0.249   5.6788   1.3298  -0.6084
 LPZ  H4   H  HCH2  0   0.268   0.2485  -0.2801   1.3024
 LPZ  H5   H  HCH2  0   0.265   0.0527  -0.7026  -0.4051
 LPZ  H6   H  HCH2  0   0.320  -3.7038  -2.5730   0.3833
 LPZ  H7   H  HCH2  0   0.306  -3.1123  -1.6582  -1.0171
 LPZ  H8   H  HCH3  0   0.297  -5.9435  -2.4517  -0.5355
 LPZ  H9   H  HCH3  0   0.297  -6.6632  -0.8619  -0.8862
 LPZ  H10  H  HCH3  0   0.291  -5.3596  -1.4945  -1.9204
 LPZ  H11  H  HCH3  0   0.245   6.7920  -1.5063  -1.1675
 LPZ  H12  H  HCH3  0   0.241   7.2524  -0.4843   0.1828
 LPZ  H13  H  HCH3  0   0.241   6.6360  -2.1093   0.4755
 LPZ  H14  H  HCH2  0   0.305  -4.1354   0.5838  -1.4782
 LPZ  H15  H  HCH2  0   0.317  -5.4318   1.1455  -0.4042
 LPZ  H16  H  HCH2  0   0.280  -3.8682   1.3298   1.4863
 LPZ  H17  H  HCH2  0   0.306  -3.2661   2.2577   0.1182
 LPZ  H18  H  HCR6  0   0.251   4.2049  -2.5375   0.4577
 LPZ  H19  H  HCR6  0   0.276   1.9357  -1.6822   0.5161
 LPZ  H20  H  HCH2  0   0.286  -2.7952  -0.9211   1.9425
 LPZ  H21  H  HCH2  0   0.309  -1.5417  -1.4861   0.8601
 LPZ  C    C  CH3   0  -0.720   6.5220  -1.2231  -0.1479

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
 LPZ  C    C1   single    1.502  0.020  1.502
 LPZ  C1   C2   aromatic  1.389  0.020  1.389
 LPZ  C1   C6   aromatic  1.396  0.020  1.396
 LPZ  C2   C3   aromatic  1.392  0.020  1.392
 LPZ  C6   C5   aromatic  1.382  0.020  1.382
 LPZ  C3   C4   aromatic  1.390  0.020  1.390
 LPZ  C5   C4   aromatic  1.395  0.020  1.395
 LPZ  C4   O    single    1.353  0.020  1.353
 LPZ  O    C7   single    1.398  0.020  1.398
 LPZ  O1   C8   double    1.215  0.020  1.215
 LPZ  C7   C8   single    1.522  0.020  1.522
 LPZ  C8   N    single    1.354  0.020  1.354
 LPZ  N    C12  single    1.447  0.020  1.447
 LPZ  N    C9   single    1.447  0.020  1.447
 LPZ  C11  C12  single    1.514  0.020  1.514
 LPZ  C11  N1   single    1.492  0.020  1.492
 LPZ  C10  C9   single    1.517  0.020  1.517
 LPZ  C10  N1   single    1.491  0.020  1.491
 LPZ  C13  N1   single    1.482  0.020  1.482
 LPZ  N1   H1   single    0.890  0.020  1.040
 LPZ  C5   H2   single    0.930  0.020  1.080
 LPZ  C6   H3   single    0.930  0.020  1.080
 LPZ  C7   H4   single    0.970  0.020  1.090
 LPZ  C7   H5   single    0.970  0.020  1.090
 LPZ  C10  H6   single    0.970  0.020  1.090
 LPZ  C10  H7   single    0.970  0.020  1.090
 LPZ  C13  H8   single    0.970  0.020  1.090
 LPZ  C13  H9   single    0.970  0.020  1.090
 LPZ  C13  H10  single    0.970  0.020  1.090
 LPZ  C    H11  single    0.970  0.020  1.090
 LPZ  C    H12  single    0.970  0.020  1.090
 LPZ  C    H13  single    0.970  0.020  1.090
 LPZ  C11  H14  single    0.970  0.020  1.090
 LPZ  C11  H15  single    0.970  0.020  1.090
 LPZ  C12  H16  single    0.970  0.020  1.090
 LPZ  C12  H17  single    0.970  0.020  1.090
 LPZ  C2   H18  single    0.930  0.020  1.080
 LPZ  C3   H19  single    0.930  0.020  1.080
 LPZ  C9   H20  single    0.970  0.020  1.090
 LPZ  C9   H21  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
 LPZ  H1   N1   C11  107.65  3.000
 LPZ  H1   N1   C13  107.14  3.000
 LPZ  C11  N1   C13  111.68  3.000
 LPZ  H1   N1   C10  107.84  3.000
 LPZ  C13  N1   C10  111.58  3.000
 LPZ  C11  N1   C10  110.71  3.000
 LPZ  C3   C4   O    124.84  3.000
 LPZ  O    C4   C5   115.90  3.000
 LPZ  C3   C4   C5   119.26  3.000
 LPZ  H2   C5   C6   120.33  3.000
 LPZ  H2   C5   C4   119.50  3.000
 LPZ  C6   C5   C4   120.16  3.000
 LPZ  H3   C6   C1   119.60  3.000
 LPZ  H3   C6   C5   118.80  3.000
 LPZ  C1   C6   C5   121.60  3.000
 LPZ  H5   C7   H4   107.49  3.000
 LPZ  H5   C7   O    111.48  3.000
 LPZ  H4   C7   O    111.33  3.000
 LPZ  H5   C7   C8   109.90  3.000
 LPZ  H4   C7   C8   109.81  3.000
 LPZ  O    C7   C8   106.85  3.000
 LPZ  O1   C8   N    122.74  3.000
 LPZ  N    C8   C7   116.11  3.000
 LPZ  O1   C8   C7   121.15  3.000
 LPZ  H7   C10  H6   109.14  3.000
 LPZ  H7   C10  C9   111.46  3.000
 LPZ  H6   C10  C9   110.49  3.000
 LPZ  H7   C10  N1   107.00  3.000
 LPZ  H6   C10  N1   107.78  3.000
 LPZ  C9   C10  N1   110.83  3.000
 LPZ  H10  C13  H9   110.09  3.000
 LPZ  H10  C13  H8   110.26  3.000
 LPZ  H9   C13  H8   110.10  3.000
 LPZ  H10  C13  N1   108.78  3.000
 LPZ  H9   C13  N1   108.75  3.000
 LPZ  H8   C13  N1   108.82  3.000
 LPZ  C9   N    C12  112.99  3.000
 LPZ  C9   N    C8   126.06  3.000
 LPZ  C12  N    C8   120.85  3.000
 LPZ  C7   O    C4   118.42  3.000
 LPZ  C2   C1   C    121.59  3.000
 LPZ  C2   C1   C6   117.38  3.000
 LPZ  C    C1   C6   121.02  3.000
 LPZ  H15  C11  H14  109.18  3.000
 LPZ  H15  C11  C12  110.76  3.000
 LPZ  H14  C11  C12  111.56  3.000
 LPZ  H15  C11  N1   107.70  3.000
 LPZ  H14  C11  N1   107.07  3.000
 LPZ  C12  C11  N1   110.42  3.000
 LPZ  H17  C12  H16  107.51  3.000
 LPZ  H17  C12  C11  108.60  3.000
 LPZ  H16  C12  C11  110.21  3.000
 LPZ  H17  C12  N    110.31  3.000
 LPZ  H16  C12  N    109.75  3.000
 LPZ  C11  C12  N    110.41  3.000
 LPZ  H18  C2   C3   118.38  3.000
 LPZ  H18  C2   C1   119.63  3.000
 LPZ  C3   C2   C1   122.00  3.000
 LPZ  H19  C3   C2   118.63  3.000
 LPZ  H19  C3   C4   121.77  3.000
 LPZ  C2   C3   C4   119.60  3.000
 LPZ  H21  C9   H20  106.70  3.000
 LPZ  H21  C9   N    112.39  3.000
 LPZ  H20  C9   N    109.72  3.000
 LPZ  H21  C9   C10  107.30  3.000
 LPZ  H20  C9   C10  109.94  3.000
 LPZ  N    C9   C10  110.68  3.000
 LPZ  H13  C    H12  107.91  3.000
 LPZ  H13  C    H11  107.30  3.000
 LPZ  H12  C    H11  107.06  3.000
 LPZ  H13  C    C1   111.60  3.000
 LPZ  H12  C    C1   111.49  3.000
 LPZ  H11  C    C1   111.25  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
 LPZ  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 LPZ  CONST_02  C1   C6   C5   C4      0.00   0.0  0
 LPZ  CONST_03  C2   C1   C6   C5      0.00   0.0  0
 LPZ  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 LPZ  CONST_05  C3   C2   C1   C6      0.00   0.0  0
 LPZ  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 LPZ  CONST_07  C    C1   C6   C5    180.00   0.0  0
 LPZ  CONST_08  O    C4   C5   C6    180.00   0.0  0
 LPZ  CONST_09  C3   C2   C1   C     180.00   0.0  0
 LPZ  CONST_10  C2   C3   C4   O     180.00   0.0  0
 LPZ  CONST_11  H18  C2   C3   C4    180.00   0.0  0
 LPZ  CONST_12  H3   C6   C5   C4    180.00   0.0  0
 LPZ  CONST_13  H19  C3   C4   C5    180.00   0.0  0
 LPZ  CONST_14  H2   C5   C6   C1    180.00   0.0  0
 LPZ  CONST_15  C12  N    C8   C7    180.00   0.0  0
 LPZ  CONST_16  C9   N    C8   C7      0.00   0.0  0
 LPZ  CONST_17  O1   C8   N    C12     0.00   0.0  0
 LPZ  CONST_18  O1   C8   N    C9    180.00   0.0  0
 LPZ  Var_01    N    C12  C11  N1     56.33  30.0  1
 LPZ  Var_02    N    C9   C10  N1    -54.72  30.0  1
 LPZ  Var_03    C12  N    C9   C10    56.91  30.0  1
 LPZ  Var_04    C9   N    C12  C11   -57.79  30.0  1
 LPZ  Var_05    C3   C4   O    C7      0.37  30.0  3
 LPZ  Var_06    H11  C    C1   C6    -84.36  30.0  2
 LPZ  Var_07    C8   C7   O    C4   -179.81  30.0  3
 LPZ  Var_08    O    C7   C8   N    -179.82  30.0  2

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
 LPZ  chir_01  N1  C11  C10  C13  positiv

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
 LPZ  plan-1  C4   0.020
 LPZ  plan-1  C5   0.020
 LPZ  plan-1  C6   0.020
 LPZ  plan-1  O    0.020
 LPZ  plan-1  C1   0.020
 LPZ  plan-1  C2   0.020
 LPZ  plan-1  C3   0.020
 LPZ  plan-1  H2   0.020
 LPZ  plan-1  H3   0.020
 LPZ  plan-1  H18  0.020
 LPZ  plan-1  H19  0.020
 LPZ  plan-1  C    0.020
 LPZ  plan-2  C7   0.020
 LPZ  plan-2  C8   0.020
 LPZ  plan-2  N    0.020
 LPZ  plan-2  C12  0.020
 LPZ  plan-2  C9   0.020
 LPZ  plan-2  O1   0.020

