# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 07:31:15 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 4-acetyl-N-ethylpiperazine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=O)N1CCN(CC1)C(C)=O
#
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
 K3D  K3D  4-acetyl-N-ethylpiperazine-1-carboxamide  ligand  31  14  .  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_K3D
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
 K3D  N1   N  NT    0  -0.500   0.5666  -0.3639  -0.7032
 K3D  C4   C  CH2   0  -0.296  -1.0290   1.1919   0.3095
 K3D  C5   C  CH2   0  -0.306  -1.4966  -1.1885   0.3378
 K3D  C6   C  CH2   0  -0.309  -0.4576  -1.3863  -0.7582
 K3D  C8   C  CH3   0  -0.808  -4.3424  -0.6819   0.2019
 K3D  N    N  NH1   0  -0.677   2.7152   0.3344  -0.1587
 K3D  C    C  CH3   0  -0.692   4.8625   1.3599   0.3521
 K3D  O    O  O     0  -0.543   2.0723  -1.7980   0.2157
 K3D  C1   C  CH2   0  -0.256   4.0825   0.0633   0.2424
 K3D  C2   C  C     0   0.735   1.7993  -0.6722  -0.1892
 K3D  C3   C  CH2   0  -0.329   0.0104   0.9745  -0.7843
 K3D  N2   N  NT    0  -0.449  -2.0420   0.1545   0.2687
 K3D  O1   O  O     0  -0.508  -3.7486   1.6243   0.1621
 K3D  H1   H  HCH2  0   0.245  -0.5328   1.1765   1.2862
 K3D  H2   H  HCH2  0   0.270  -1.4967   2.1648   0.1871
 K3D  H3   H  HCH2  0   0.277  -2.2788  -1.9331   0.2251
 K3D  H4   H  HCH2  0   0.247  -1.0343  -1.3464   1.3184
 K3D  H5   H  HCH2  0   0.247  -0.9520  -1.3326  -1.7334
 K3D  H6   H  HCH2  0   0.269  -0.0090  -2.3716  -0.6686
 K3D  H7   H  HCH3  0   0.265  -4.1987  -1.3443  -0.6522
 K3D  H8   H  HCH3  0   0.267  -4.2595  -1.2897   1.1039
 K3D  H9   H  HCH3  0   0.269  -5.3503  -0.2776   0.1550
 K3D  H10  H  HNH1  0   0.393   2.5991   1.1085  -0.7925
 K3D  H11  H  HCH3  0   0.240   5.8881   1.1551   0.6565
 K3D  H12  H  HCH3  0   0.229   4.9016   1.8849  -0.6042
 K3D  H13  H  HCH3  0   0.231   4.4174   2.0290   1.0889
 K3D  H14  H  HCH2  0   0.234   4.0731  -0.4431   1.2077
 K3D  H15  H  HCH2  0   0.220   4.5802  -0.6096  -0.4638
 K3D  H16  H  HCH2  0   0.263   0.7752   1.7398  -0.6864
 K3D  H17  H  HCH2  0   0.252  -0.4531   1.1095  -1.7656
 K3D  C7   C  C     0   0.521  -3.3574   0.4642   0.2073

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
 K3D  O   C2   double  1.227  0.020  1.227
 K3D  C1  N    single  1.450  0.020  1.450
 K3D  C1  C    single  1.517  0.020  1.517
 K3D  C3  C4   single  1.524  0.020  1.524
 K3D  C3  N1   single  1.452  0.020  1.452
 K3D  C2  N    single  1.361  0.020  1.361
 K3D  C2  N1   single  1.371  0.020  1.371
 K3D  C8  C7   single  1.511  0.020  1.511
 K3D  C4  N2   single  1.451  0.020  1.451
 K3D  N1  C6   single  1.448  0.020  1.448
 K3D  N2  C7   single  1.353  0.020  1.353
 K3D  N2  C5   single  1.451  0.020  1.451
 K3D  C7  O1   double  1.225  0.020  1.225
 K3D  C6  C5   single  1.523  0.020  1.523
 K3D  C4  H1   single  0.970  0.020  1.090
 K3D  C4  H2   single  0.970  0.020  1.090
 K3D  C5  H3   single  0.970  0.020  1.090
 K3D  C5  H4   single  0.970  0.020  1.090
 K3D  C6  H5   single  0.970  0.020  1.090
 K3D  C6  H6   single  0.970  0.020  1.090
 K3D  C8  H7   single  0.970  0.020  1.090
 K3D  C8  H8   single  0.970  0.020  1.090
 K3D  C8  H9   single  0.970  0.020  1.090
 K3D  N   H10  single  0.890  0.020  1.040
 K3D  C   H11  single  0.970  0.020  1.090
 K3D  C   H12  single  0.970  0.020  1.090
 K3D  C   H13  single  0.970  0.020  1.090
 K3D  C1  H14  single  0.970  0.020  1.090
 K3D  C1  H15  single  0.970  0.020  1.090
 K3D  C3  H16  single  0.970  0.020  1.090
 K3D  C3  H17  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
 K3D  C3   N1  C2   124.95  3.000
 K3D  C2   N1  C6   119.44  3.000
 K3D  C3   N1  C6   112.20  3.000
 K3D  H2   C4  H1   107.94  3.000
 K3D  H2   C4  N2   109.67  3.000
 K3D  H1   C4  N2   109.34  3.000
 K3D  H2   C4  C3   109.90  3.000
 K3D  H1   C4  C3   109.20  3.000
 K3D  N2   C4  C3   110.73  3.000
 K3D  H4   C5  H3   107.35  3.000
 K3D  H4   C5  N2   109.54  3.000
 K3D  H3   C5  N2   111.03  3.000
 K3D  H4   C5  C6   109.73  3.000
 K3D  H3   C5  C6   109.13  3.000
 K3D  N2   C5  C6   110.02  3.000
 K3D  H6   C6  H5   107.72  3.000
 K3D  H6   C6  C5   109.89  3.000
 K3D  H5   C6  C5   109.06  3.000
 K3D  H6   C6  N1   110.19  3.000
 K3D  H5   C6  N1   108.58  3.000
 K3D  C5   C6  N1   111.31  3.000
 K3D  H9   C8  H8   108.26  3.000
 K3D  H9   C8  H7   108.32  3.000
 K3D  H8   C8  H7   107.40  3.000
 K3D  H9   C8  C7   108.82  3.000
 K3D  H8   C8  C7   111.72  3.000
 K3D  H7   C8  C7   112.19  3.000
 K3D  H10  N   C2   118.46  3.000
 K3D  H10  N   C1   115.24  3.000
 K3D  C2   N   C1   120.15  3.000
 K3D  H13  C   H12  108.15  3.000
 K3D  H13  C   H11  108.11  3.000
 K3D  H12  C   H11  107.55  3.000
 K3D  H13  C   C1   111.31  3.000
 K3D  H12  C   C1   111.48  3.000
 K3D  H11  C   C1   110.10  3.000
 K3D  H15  C1  H14  106.83  3.000
 K3D  H15  C1  C    109.76  3.000
 K3D  H14  C1  C    109.72  3.000
 K3D  H15  C1  N    111.40  3.000
 K3D  H14  C1  N    108.88  3.000
 K3D  C    C1  N    110.18  3.000
 K3D  O    C2  N    121.42  3.000
 K3D  N    C2  N1   116.57  3.000
 K3D  O    C2  N1   122.01  3.000
 K3D  H17  C3  H16  106.99  3.000
 K3D  H17  C3  C4   109.71  3.000
 K3D  H16  C3  C4   108.35  3.000
 K3D  H17  C3  N1   109.05  3.000
 K3D  H16  C3  N1   112.01  3.000
 K3D  C4   C3  N1   110.65  3.000
 K3D  C7   N2  C5   125.42  3.000
 K3D  C5   N2  C4   113.46  3.000
 K3D  C7   N2  C4   121.10  3.000
 K3D  O1   C7  N2   121.94  3.000
 K3D  O1   C7  C8   120.65  3.000
 K3D  N2   C7  C8   117.41  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
 K3D  CONST_01  C8   C7  N2  C4   180.00   0.0  0
 K3D  CONST_02  O1   C7  N2  C4     0.00   0.0  0
 K3D  CONST_03  C8   C7  N2  C5     0.00   0.0  0
 K3D  CONST_04  O1   C7  N2  C5   180.00   0.0  0
 K3D  CONST_05  O    C2  N1  C6     0.00   0.0  0
 K3D  CONST_07  N    C2  N1  C6   180.00   0.0  0
 K3D  CONST_09  C1   N   C2  N1   180.00   0.0  0
 K3D  CONST_11  C1   N   C2  O      0.00   0.0  0
 K3D  Var_01    N2   C4  C3  N1   -53.94  30.0  1
 K3D  Var_02    N2   C5  C6  N1    54.35  30.0  1
 K3D  Var_03    C6   N1  C3  C4    55.76  30.0  1
 K3D  Var_04    C6   C5  N2  C4   -54.58  30.0  1
 K3D  Var_05    C3   C4  N2  C5    54.76  30.0  1
 K3D  Var_06    C3   N1  C6  C5   -56.33  30.0  1
 K3D  Var_07    H7   C8  C7  N2   -60.44  30.0  3
 K3D  Var_08    C2   N   C1  C   -173.41  30.0  3
 K3D  Var_09    H11  C   C1  N    179.81  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
 K3D  plan-1  N1   0.020
 K3D  plan-1  C6   0.020
 K3D  plan-1  N    0.020
 K3D  plan-1  O    0.020
 K3D  plan-1  C1   0.020
 K3D  plan-1  C2   0.020
 K3D  plan-1  C3   0.020
 K3D  plan-1  H10  0.020
 K3D  plan-2  C4   0.020
 K3D  plan-2  C5   0.020
 K3D  plan-2  C8   0.020
 K3D  plan-2  N2   0.020
 K3D  plan-2  O1   0.020
 K3D  plan-2  C7   0.020

