# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 06:23:05 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: N-[4-(4-methylpiperazin-1-yl)phenyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)c2ccc(NC(C)=O)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
 O1A  O1A  N-[4-(4-methylpiperazin-1-yl)phenyl]acetamide  ligand  36  17  .  2021-08-17  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_O1A
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
 O1A  N1   N  NT    0  -0.514   1.7634   0.0398   0.1383
 O1A  C4   C  CH2   0  -0.284   3.9496   1.0886  -0.1752
 O1A  C5   C  CR6   0   0.348   0.3689   0.0966   0.0678
 O1A  C6   C  CR16  0  -0.313  -0.3016   1.2958   0.3468
 O1A  C7   C  CR16  0  -0.332  -1.6782   1.3714   0.3154
 O1A  C8   C  CR6   0   0.339  -2.4636   0.2544   0.0173
 O1A  C10  C  CH3   0  -0.782  -6.2287   0.1351  -0.2327
 O1A  N    N  NT    0  -0.412   4.5664  -0.2120  -0.3292
 O1A  C    C  CH3   0  -0.518   5.9689  -0.1834   0.0158
 O1A  O    O  O     0  -0.482  -4.6236  -1.5381  -0.8025
 O1A  C1   C  CH2   0  -0.277   3.8415  -1.1927   0.4498
 O1A  C11  C  CR16  0  -0.304  -1.8126  -0.9441  -0.2551
 O1A  C12  C  CR16  0  -0.346  -0.4237  -1.0109  -0.2377
 O1A  C2   C  CH2   0  -0.313   2.3872  -1.2621   0.0222
 O1A  C3   C  CH2   0  -0.306   2.4977   1.0529  -0.6078
 O1A  C9   C  C     0   0.508  -4.8318  -0.4198  -0.3598
 O1A  N2   N  NH1   0  -0.732  -3.8547   0.4295   0.0377
 O1A  H1   H  HCH2  0   0.192   4.0068   1.4459   0.8681
 O1A  H2   H  HCH2  0   0.240   4.4807   1.8157  -0.7941
 O1A  H3   H  HCR6  0   0.263   0.2554   2.1843   0.6145
 O1A  H4   H  HCR6  0   0.266  -2.1544   2.3182   0.5442
 O1A  H5   H  HCH3  0   0.267  -6.8756  -0.6119   0.2247
 O1A  H6   H  HCH3  0   0.253  -6.2848   1.0513   0.3517
 O1A  H7   H  HCH3  0   0.273  -6.6238   0.3426  -1.2282
 O1A  H9   H  HCH3  0   0.192   6.1512   0.0887   1.0670
 O1A  H10  H  HCH3  0   0.233   6.4180  -1.1624  -0.1589
 O1A  H11  H  HCH3  0   0.233   6.4920   0.5411  -0.6103
 O1A  H12  H  HCH2  0   0.239   4.2926  -2.1765   0.3017
 O1A  H13  H  HCH2  0   0.192   3.8904  -0.9715   1.5308
 O1A  H14  H  HCR6  0   0.275  -2.3681  -1.8359  -0.4943
 O1A  H15  H  HCR6  0   0.268   0.0293  -1.9629  -0.4788
 O1A  H16  H  HCH2  0   0.250   1.8734  -1.9711   0.6730
 O1A  H17  H  HCH2  0   0.209   2.3293  -1.6536  -1.0051
 O1A  H18  H  HCH2  0   0.213   2.4409   0.8564  -1.6892
 O1A  H19  H  HCH2  0   0.252   2.0657   2.0368  -0.4337
 O1A  H20  H  HNH1  0   0.412  -4.1593   1.3318   0.3693

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
 O1A  O    C9   double    1.221  0.020  1.221
 O1A  C9   C10  single    1.508  0.020  1.508
 O1A  C9   N2   single    1.354  0.020  1.354
 O1A  N2   C8   single    1.402  0.020  1.402
 O1A  C8   C11  aromatic  1.391  0.020  1.391
 O1A  C8   C7   aromatic  1.398  0.020  1.398
 O1A  C11  C12  aromatic  1.391  0.020  1.391
 O1A  C7   C6   aromatic  1.379  0.020  1.379
 O1A  C12  C5   aromatic  1.396  0.020  1.396
 O1A  C6   C5   aromatic  1.402  0.020  1.402
 O1A  C5   N1   single    1.397  0.020  1.397
 O1A  N1   C2   single    1.448  0.020  1.448
 O1A  N1   C3   single    1.457  0.020  1.457
 O1A  C2   C1   single    1.517  0.020  1.517
 O1A  C3   C4   single    1.515  0.020  1.515
 O1A  C1   N    single    1.447  0.020  1.447
 O1A  C4   N    single    1.448  0.020  1.448
 O1A  N    C    single    1.445  0.020  1.445
 O1A  C4   H1   single    0.970  0.020  1.090
 O1A  C4   H2   single    0.970  0.020  1.090
 O1A  C6   H3   single    0.930  0.020  1.080
 O1A  C7   H4   single    0.930  0.020  1.080
 O1A  C10  H5   single    0.970  0.020  1.090
 O1A  C10  H6   single    0.970  0.020  1.090
 O1A  C10  H7   single    0.970  0.020  1.090
 O1A  C    H9   single    0.970  0.020  1.090
 O1A  C    H10  single    0.970  0.020  1.090
 O1A  C    H11  single    0.970  0.020  1.090
 O1A  C1   H12  single    0.970  0.020  1.090
 O1A  C1   H13  single    0.970  0.020  1.090
 O1A  C11  H14  single    0.930  0.020  1.080
 O1A  C12  H15  single    0.930  0.020  1.080
 O1A  C2   H16  single    0.970  0.020  1.090
 O1A  C2   H17  single    0.970  0.020  1.090
 O1A  C3   H18  single    0.970  0.020  1.090
 O1A  C3   H19  single    0.970  0.020  1.090
 O1A  N2   H20  single    0.860  0.020  1.020

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
 O1A  C3   N1   C2   111.53  3.000
 O1A  C3   N1   C5   116.67  3.000
 O1A  C2   N1   C5   117.53  3.000
 O1A  H2   C4   H1   107.14  3.000
 O1A  H2   C4   C3   108.64  3.000
 O1A  H1   C4   C3   109.08  3.000
 O1A  H2   C4   N    109.30  3.000
 O1A  H1   C4   N    111.66  3.000
 O1A  C3   C4   N    110.90  3.000
 O1A  C12  C5   C6   116.79  3.000
 O1A  C6   C5   N1   120.13  3.000
 O1A  C12  C5   N1   123.06  3.000
 O1A  H3   C6   C7   118.32  3.000
 O1A  H3   C6   C5   120.35  3.000
 O1A  C7   C6   C5   121.32  3.000
 O1A  H4   C7   C8   119.74  3.000
 O1A  H4   C7   C6   118.79  3.000
 O1A  C8   C7   C6   121.46  3.000
 O1A  N2   C8   C11  125.09  3.000
 O1A  C11  C8   C7   117.87  3.000
 O1A  N2   C8   C7   117.04  3.000
 O1A  H7   C10  H6   108.14  3.000
 O1A  H7   C10  H5   107.37  3.000
 O1A  H6   C10  H5   108.74  3.000
 O1A  H7   C10  C9   109.18  3.000
 O1A  H6   C10  C9   113.74  3.000
 O1A  H5   C10  C9   109.47  3.000
 O1A  C1   N    C    111.79  3.000
 O1A  C    N    C4   111.74  3.000
 O1A  C1   N    C4   109.77  3.000
 O1A  H11  C    H10  107.85  3.000
 O1A  H11  C    H9   107.72  3.000
 O1A  H10  C    H9   107.84  3.000
 O1A  H11  C    N    109.97  3.000
 O1A  H10  C    N    110.09  3.000
 O1A  H9   C    N    113.18  3.000
 O1A  H13  C1   H12  107.14  3.000
 O1A  H13  C1   C2   109.11  3.000
 O1A  H12  C1   C2   108.45  3.000
 O1A  H13  C1   N    111.65  3.000
 O1A  H12  C1   N    109.30  3.000
 O1A  C2   C1   N    111.06  3.000
 O1A  H14  C11  C12  118.54  3.000
 O1A  H14  C11  C8   121.02  3.000
 O1A  C12  C11  C8   120.43  3.000
 O1A  H15  C12  C11  117.25  3.000
 O1A  H15  C12  C5   120.63  3.000
 O1A  C11  C12  C5   122.12  3.000
 O1A  H17  C2   H16  107.50  3.000
 O1A  H17  C2   C1   109.24  3.000
 O1A  H16  C2   C1   108.24  3.000
 O1A  H17  C2   N1   111.83  3.000
 O1A  H16  C2   N1   109.49  3.000
 O1A  C1   C2   N1   110.43  3.000
 O1A  H19  C3   H18  107.34  3.000
 O1A  H19  C3   C4   108.26  3.000
 O1A  H18  C3   C4   109.52  3.000
 O1A  H19  C3   N1   110.28  3.000
 O1A  H18  C3   N1   110.68  3.000
 O1A  C4   C3   N1   110.67  3.000
 O1A  N2   C9   O    123.91  3.000
 O1A  N2   C9   C10  114.38  3.000
 O1A  O    C9   C10  121.71  3.000
 O1A  H20  N2   C9   116.09  3.000
 O1A  H20  N2   C8   114.60  3.000
 O1A  C9   N2   C8   129.28  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
 O1A  CONST_01  C8   C11  C12  C5      0.00   0.0  0
 O1A  CONST_02  C8   C7   C6   C5      0.00   0.0  0
 O1A  CONST_03  C11  C8   C7   C6      0.00   0.0  0
 O1A  CONST_04  C11  C12  C5   C6      0.00   0.0  0
 O1A  CONST_05  C12  C11  C8   C7      0.00   0.0  0
 O1A  CONST_06  C12  C5   C6   C7      0.00   0.0  0
 O1A  CONST_07  C11  C12  C5   N1    180.00   0.0  0
 O1A  CONST_08  C7   C6   C5   N1    180.00   0.0  0
 O1A  CONST_09  N2   C8   C7   C6    180.00   0.0  0
 O1A  CONST_10  N2   C8   C11  C12   180.00   0.0  0
 O1A  CONST_11  H15  C12  C5   N1      0.00   0.0  0
 O1A  CONST_12  H3   C6   C5   N1      0.00   0.0  0
 O1A  CONST_13  H14  C11  C12  C5    180.00   0.0  0
 O1A  CONST_14  H4   C7   C6   C5    180.00   0.0  0
 O1A  CONST_15  C9   N2   C8   C7    180.00   0.0  0
 O1A  CONST_16  C9   N2   C8   C11     0.00   0.0  0
 O1A  CONST_17  H20  N2   C8   C7      0.00   0.0  0
 O1A  CONST_18  O    C9   N2   C8      0.00   0.0  0
 O1A  CONST_19  C10  C9   N2   C8    180.00   0.0  0
 O1A  Var_01    N    C1   C2   N1    -57.04  30.0  1
 O1A  Var_02    N    C4   C3   N1     56.57  30.0  1
 O1A  Var_03    C5   N1   C3   C4    165.95  30.0  1
 O1A  Var_04    C2   C1   N    C4     58.50  30.0  1
 O1A  Var_05    C1   C2   N1   C5   -166.31  30.0  1
 O1A  Var_06    C3   C4   N    C1    -58.23  30.0  1
 O1A  Var_07    H9   C    N    C4     62.16  30.0  3
 O1A  Var_08    H5   C10  C9   O      46.72  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
 O1A  plan-1  N1   0.020
 O1A  plan-1  C5   0.020
 O1A  plan-1  C6   0.020
 O1A  plan-1  C7   0.020
 O1A  plan-1  C8   0.020
 O1A  plan-1  C11  0.020
 O1A  plan-1  C12  0.020
 O1A  plan-1  N2   0.020
 O1A  plan-1  H3   0.020
 O1A  plan-1  H4   0.020
 O1A  plan-1  H14  0.020
 O1A  plan-1  H15  0.020
 O1A  plan-2  C8   0.020
 O1A  plan-2  C10  0.020
 O1A  plan-2  O    0.020
 O1A  plan-2  C9   0.020
 O1A  plan-2  N2   0.020
 O1A  plan-2  H20  0.020

