# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 08:50:29 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 2-ethyl-7-(piperazin-1-yl)-5H-[1,3,4]thiadiazolo[3,2-a]pyrimidin-5-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC1=NN2C(=O)C=C(N=C2S1)N3CCNCC3
#
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
 NIF  NIF  2-ethyl-7-(piperazin-1-yl)-5H-[1,3,4]thiadiazolo[3,2-a]pyrimidin-5-one  ligand  33  18  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NIF
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
 NIF  C1    C  CR5   0   0.113  -3.3306   0.5042   0.0614
 NIF  N1    N  N     0  -0.191  -2.8588  -0.6715  -0.0984
 NIF  O1    O  O     0  -0.487  -1.3383  -2.9167  -0.3590
 NIF  S1    S  S2    0   0.223  -2.1218   1.7566   0.2614
 NIF  C2    C  CR5   0   0.365  -0.8989   0.5355   0.1115
 NIF  N2    N  NR5   0  -0.417  -1.5085  -0.6601  -0.0737
 NIF  C3    C  C     0   0.588   1.1763  -0.3506   0.0334
 NIF  N3    N  N     0  -0.515   0.3669   0.7404   0.1680
 NIF  C4    C  C1    0  -0.592   0.6389  -1.6240  -0.1383
 NIF  N4    N  NH1   0  -0.577   5.3083   0.5532  -0.1377
 NIF  C5    C  C     0   0.562  -0.7542  -1.8554  -0.2113
 NIF  N5    N  NT    0  -0.501   2.5019  -0.0934   0.0690
 NIF  C6    C  CH2   0  -0.493  -4.7803   0.8366   0.0834
 NIF  C7    C  CH3   0  -0.667  -5.6837  -0.3739  -0.0876
 NIF  C8    C  CH2   0  -0.312   3.4891  -1.1582   0.0131
 NIF  C9    C  CH2   0  -0.319   4.7641  -0.6767  -0.6755
 NIF  C10   C  CH2   0  -0.325   4.2864   1.5823  -0.1080
 NIF  C11   C  CH2   0  -0.314   3.0139   1.1598   0.6124
 NIF  H4    H  H     0   0.275   1.2610  -2.5020  -0.2050
 NIF  H6    H  HCH2  0   0.279  -4.9984   1.3438   1.0267
 NIF  H6A   H  HCH2  0   0.280  -4.9723   1.5730  -0.7013
 NIF  H7    H  HCH3  0   0.237  -5.5065  -0.8765  -1.0372
 NIF  H7A   H  HCH3  0   0.237  -5.5369  -1.0974   0.7128
 NIF  H7B   H  HCH3  0   0.248  -6.7238  -0.0530  -0.0652
 NIF  H8    H  HCH2  0   0.236   3.7191  -1.5084   1.0278
 NIF  H8A   H  HCH2  0   0.263   3.1047  -2.0063  -0.5486
 NIF  H9    H  HCH2  0   0.229   4.5519  -0.5247  -1.7382
 NIF  H9A   H  HCH2  0   0.249   5.5128  -1.4673  -0.6095
 NIF  H10   H  HCH2  0   0.247   4.6827   2.4759   0.3767
 NIF  H10A  H  HCH2  0   0.228   4.0409   1.8562  -1.1386
 NIF  H11   H  HCH2  0   0.274   2.2578   1.9330   0.5203
 NIF  H11A  H  HCH2  0   0.230   3.2254   1.0281   1.6819
 NIF  HN4   H  HNH1  0   0.344   5.6506   0.3902   0.8031

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
 NIF  C1   N1    double  1.277  0.020  1.277
 NIF  C1   S1    single  1.752  0.020  1.752
 NIF  C1   C6    single  1.487  0.020  1.487
 NIF  N1   N2    single  1.351  0.020  1.351
 NIF  O1   C5    double  1.220  0.020  1.220
 NIF  S1   C2    single  1.735  0.020  1.735
 NIF  C2   N2    single  1.355  0.020  1.355
 NIF  C2   N3    double  1.284  0.020  1.284
 NIF  N2   C5    single  1.420  0.020  1.420
 NIF  C3   N3    single  1.365  0.020  1.365
 NIF  C3   C4    double  1.393  0.020  1.393
 NIF  C3   N5    single  1.351  0.020  1.351
 NIF  C4   C5    single  1.414  0.020  1.414
 NIF  N4   C9    single  1.448  0.020  1.448
 NIF  N4   C10   single  1.451  0.020  1.451
 NIF  N5   C8    single  1.453  0.020  1.453
 NIF  N5   C11   single  1.459  0.020  1.459
 NIF  C6   C7    single  1.520  0.020  1.520
 NIF  C8   C9    single  1.527  0.020  1.527
 NIF  C10  C11   single  1.522  0.020  1.522
 NIF  C4   H4    single  0.930  0.020  1.080
 NIF  N4   HN4   single  0.890  0.020  1.040
 NIF  C6   H6    single  0.970  0.020  1.090
 NIF  C6   H6A   single  0.970  0.020  1.090
 NIF  C7   H7    single  0.970  0.020  1.090
 NIF  C7   H7A   single  0.970  0.020  1.090
 NIF  C7   H7B   single  0.970  0.020  1.090
 NIF  C8   H8    single  0.970  0.020  1.090
 NIF  C8   H8A   single  0.970  0.020  1.090
 NIF  C9   H9    single  0.970  0.020  1.090
 NIF  C9   H9A   single  0.970  0.020  1.090
 NIF  C10  H10   single  0.970  0.020  1.090
 NIF  C10  H10A  single  0.970  0.020  1.090
 NIF  C11  H11   single  0.970  0.020  1.090
 NIF  C11  H11A  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
 NIF  C6    C1   S1   120.73  3.000
 NIF  C6    C1   N1   124.59  3.000
 NIF  S1    C1   N1   114.68  3.000
 NIF  N2    N1   C1   111.06  3.000
 NIF  C2    S1   C1    88.47  3.000
 NIF  N3    C2   N2   126.21  3.000
 NIF  N3    C2   S1   125.39  3.000
 NIF  N2    C2   S1   108.41  3.000
 NIF  C5    N2   C2   121.13  3.000
 NIF  C5    N2   N1   121.48  3.000
 NIF  C2    N2   N1   117.38  3.000
 NIF  N5    C3   C4   123.78  3.000
 NIF  N5    C3   N3   115.28  3.000
 NIF  C4    C3   N3   120.94  3.000
 NIF  C3    N3   C2   116.92  3.000
 NIF  H4    C4   C5   115.59  3.000
 NIF  H4    C4   C3   121.98  3.000
 NIF  C5    C4   C3   122.42  3.000
 NIF  HN4   N4   C10  109.44  3.000
 NIF  HN4   N4   C9   109.55  3.000
 NIF  C10   N4   C9   110.20  3.000
 NIF  C4    C5   N2   112.37  3.000
 NIF  C4    C5   O1   128.32  3.000
 NIF  N2    C5   O1   119.31  3.000
 NIF  C11   N5   C8   113.91  3.000
 NIF  C11   N5   C3   121.19  3.000
 NIF  C8    N5   C3   121.75  3.000
 NIF  H6A   C6   H6   105.78  3.000
 NIF  H6A   C6   C7   110.57  3.000
 NIF  H6    C6   C7   110.37  3.000
 NIF  H6A   C6   C1   108.13  3.000
 NIF  H6    C6   C1   108.12  3.000
 NIF  C7    C6   C1   113.55  3.000
 NIF  H7B   C7   H7A  108.03  3.000
 NIF  H7B   C7   H7   108.03  3.000
 NIF  H7A   C7   H7   108.21  3.000
 NIF  H7B   C7   C6   109.31  3.000
 NIF  H7A   C7   C6   111.49  3.000
 NIF  H7    C7   C6   111.65  3.000
 NIF  H8A   C8   H8   107.62  3.000
 NIF  H8A   C8   C9   107.95  3.000
 NIF  H8    C8   C9   110.03  3.000
 NIF  H8A   C8   N5   110.56  3.000
 NIF  H8    C8   N5   109.91  3.000
 NIF  C9    C8   N5   110.71  3.000
 NIF  H9A   C9   H9   107.01  3.000
 NIF  H9A   C9   C8   108.50  3.000
 NIF  H9    C9   C8   108.66  3.000
 NIF  H9A   C9   N4   109.58  3.000
 NIF  H9    C9   N4   108.39  3.000
 NIF  C8    C9   N4   114.46  3.000
 NIF  H10A  C10  H10  107.15  3.000
 NIF  H10A  C10  C11  109.13  3.000
 NIF  H10   C10  C11  108.70  3.000
 NIF  H10A  C10  N4   108.44  3.000
 NIF  H10   C10  N4   109.53  3.000
 NIF  C11   C10  N4   113.69  3.000
 NIF  H11A  C11  H11  107.59  3.000
 NIF  H11A  C11  C10  109.47  3.000
 NIF  H11   C11  C10  110.16  3.000
 NIF  H11A  C11  N5   109.10  3.000
 NIF  H11   C11  N5   109.62  3.000
 NIF  C10   C11  N5   110.83  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
 NIF  CONST_01  S1   C2   N2   N1     0.00   0.0  0
 NIF  CONST_02  N3   C2   N2   N1   180.00   0.0  0
 NIF  CONST_03  C4   C5   N2   N1   180.00   0.0  0
 NIF  CONST_04  C5   N2   C2   S1   180.00   0.0  0
 NIF  CONST_05  C3   N3   C2   S1   180.00   0.0  0
 NIF  CONST_06  C4   C5   N2   C2     0.00   0.0  0
 NIF  CONST_07  C4   C3   N3   C2     0.00   0.0  0
 NIF  CONST_08  N5   C3   N3   C2   180.00   0.0  0
 NIF  CONST_09  C3   N3   C2   N2     0.00   0.0  0
 NIF  CONST_10  C5   N2   C2   N3     0.00   0.0  0
 NIF  CONST_11  C8   N5   C3   N3   180.00   0.0  0
 NIF  CONST_13  C8   N5   C3   C4     0.00   0.0  0
 NIF  CONST_15  O1   C5   N2   N1     0.00   0.0  0
 NIF  CONST_16  C2   N2   C5   O1   180.00   0.0  0
 NIF  Var_01    C9   C8   N5   C3   148.96  30.0  1
 NIF  Var_02    C10  C11  N5   C3  -147.81  30.0  1
 NIF  Var_03    N5   C8   C9   N4    51.71  30.0  1
 NIF  Var_04    N5   C11  C10  N4   -53.20  30.0  1
 NIF  Var_05    C10  N4   C9   C8   -52.78  30.0  1
 NIF  Var_06    C11  C10  N4   C9    53.37  30.0  1
 NIF  Var_07    C7   C6   C1   N1     0.73  30.0  3
 NIF  Var_08    H7   C7   C6   C1   -60.31  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
 NIF  plan-1  C1   0.020
 NIF  plan-1  N1   0.020
 NIF  plan-1  O1   0.020
 NIF  plan-1  S1   0.020
 NIF  plan-1  C2   0.020
 NIF  plan-1  N2   0.020
 NIF  plan-1  C3   0.020
 NIF  plan-1  N3   0.020
 NIF  plan-1  C4   0.020
 NIF  plan-1  C5   0.020
 NIF  plan-1  N5   0.020
 NIF  plan-1  C6   0.020
 NIF  plan-1  C8   0.020
 NIF  plan-1  C11  0.020
 NIF  plan-1  H4   0.020

