# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 17:23:42 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (4-amino-1,2,5-oxadiazol-3-yl)[4-(pyridin-2-ylmethyl)piperazin-1-yl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nonc1C(=O)N2CCN(CC2)Cc3ccccn3
#
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
 4GX  4GX  (4-amino-1,2,5-oxadiazol-3-yl)[4-(pyridin-2-ylmethyl)piperazin-1-yl]methanone  ligand  37  21  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4GX
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
 4GX  N1   N  N     0  -0.188  -4.9330  -1.5523  -0.2605
 4GX  N3   N  NT    0  -0.456  -1.1709   1.0771  -0.7977
 4GX  C4   C  CH2   0  -0.281   0.6598   2.2568   0.3105
 4GX  C6   C  CR6   0   0.213   3.7094   0.1299   0.6502
 4GX  C7   C  CR16  0  -0.318   3.9449  -0.1280  -0.6976
 4GX  C8   C  CR16  0  -0.152   5.0110  -0.9403  -1.0464
 4GX  C10  C  CR16  0  -0.081   5.4988  -1.1491   1.2697
 4GX  C9   C  CR16  0  -0.327   5.8122  -1.4653  -0.0425
 4GX  C1   C  CR5   0   0.026  -3.2915  -0.1147  -0.5996
 4GX  C    C  CR5   0   0.377  -4.4146  -0.4614   0.2260
 4GX  C2   C  C     0   0.572  -2.4745   1.1247  -0.4939
 4GX  C12  C  CH2   0  -0.325  -0.3481  -0.1194  -0.9026
 4GX  C3   C  CH2   0  -0.325  -0.3762   2.2968  -0.7981
 4GX  C11  C  CH2   0  -0.280   0.7000  -0.1228   0.1970
 4GX  N5   N  N     0  -0.428   4.4737  -0.3772   1.6129
 4GX  N2   N  N     0  -0.098  -3.2084  -0.9919  -1.5447
 4GX  N4   N  NT    0  -0.429   1.4992   1.0857   0.1567
 4GX  N    N  NH2   0  -0.838  -4.9055   0.2055   1.2901
 4GX  O1   O  O     0  -0.480  -3.0709   2.1398  -0.1570
 4GX  O    O  O     0  -0.215  -4.1886  -1.8622  -1.3543
 4GX  H1   H  HCH2  0   0.252   1.2780   3.1545   0.2449
 4GX  H2   H  HCH2  0   0.208   0.1499   2.2805   1.2879
 4GX  H3   H  HCH2  0   0.223   2.2870   0.7655   2.1101
 4GX  H4   H  HCH2  0   0.265   3.0121   2.0596   1.1729
 4GX  H5   H  HCR6  0   0.264   3.2944   0.2990  -1.4485
 4GX  H6   H  HCR6  0   0.270   5.2154  -1.1591  -2.0865
 4GX  H7   H  HCR6  0   0.260   6.1010  -1.5391   2.0834
 4GX  H8   H  HCR6  0   0.267   6.6567  -2.1026  -0.2658
 4GX  H9   H  HCH2  0   0.281  -0.9500  -1.0186  -0.8277
 4GX  H10  H  HCH2  0   0.254   0.1385  -0.1245  -1.8811
 4GX  H11  H  HCH2  0   0.257   0.1288   2.3670  -1.7653
 4GX  H12  H  HCH2  0   0.275  -1.0218   3.1632  -0.6892
 4GX  H13  H  HCH2  0   0.212   0.2007  -0.2464   1.1734
 4GX  H14  H  HCH2  0   0.257   1.3432  -0.9934   0.0521
 4GX  H16  H  HNH2  0   0.405  -4.3048   0.8747   1.7395
 4GX  H17  H  HNH2  0   0.404  -5.5063  -0.3058   1.9157
 4GX  C5   C  CH2   0  -0.321   2.5977   1.0489   1.0924

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
 4GX  C9   C10  aromatic  1.386  0.020  1.386
 4GX  C9   C8   aromatic  1.388  0.020  1.388
 4GX  C10  N5   aromatic  1.328  0.020  1.328
 4GX  C8   C7   aromatic  1.385  0.020  1.385
 4GX  N5   C6   aromatic  1.330  0.020  1.330
 4GX  C7   C6   aromatic  1.392  0.020  1.392
 4GX  C6   C5   single    1.509  0.020  1.509
 4GX  C5   N4   single    1.443  0.020  1.443
 4GX  N4   C4   single    1.449  0.020  1.449
 4GX  N4   C11  single    1.449  0.020  1.449
 4GX  C4   C3   single    1.518  0.020  1.518
 4GX  C11  C12  single    1.519  0.020  1.519
 4GX  C3   N3   single    1.456  0.020  1.456
 4GX  C12  N3   single    1.456  0.020  1.456
 4GX  N3   C2   single    1.339  0.020  1.339
 4GX  N2   C1   aromatic  1.292  0.020  1.292
 4GX  N2   O    aromatic  1.325  0.020  1.325
 4GX  C2   C1   single    1.488  0.020  1.488
 4GX  C2   O1   double    1.225  0.020  1.225
 4GX  C1   C    aromatic  1.436  0.020  1.436
 4GX  O    N1   aromatic  1.359  0.020  1.359
 4GX  C    N1   aromatic  1.302  0.020  1.302
 4GX  C    N    single    1.348  0.020  1.348
 4GX  C4   H1   single    0.970  0.020  1.090
 4GX  C4   H2   single    0.970  0.020  1.090
 4GX  C5   H3   single    0.970  0.020  1.090
 4GX  C5   H4   single    0.970  0.020  1.090
 4GX  C7   H5   single    0.930  0.020  1.080
 4GX  C8   H6   single    0.930  0.020  1.080
 4GX  C10  H7   single    0.930  0.020  1.080
 4GX  C9   H8   single    0.930  0.020  1.080
 4GX  C12  H9   single    0.970  0.020  1.090
 4GX  C12  H10  single    0.970  0.020  1.090
 4GX  C3   H11  single    0.970  0.020  1.090
 4GX  C3   H12  single    0.970  0.020  1.090
 4GX  C11  H13  single    0.970  0.020  1.090
 4GX  C11  H14  single    0.970  0.020  1.090
 4GX  N    H16  single    0.890  0.020  1.040
 4GX  N    H17  single    0.890  0.020  1.040

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
 4GX  O    N1   C    105.88  3.000
 4GX  C3   N3   C12  112.34  3.000
 4GX  C12  N3   C2   126.55  3.000
 4GX  C3   N3   C2   120.10  3.000
 4GX  H2   C4   H1   107.30  3.000
 4GX  H2   C4   N4   112.29  3.000
 4GX  H1   C4   N4   109.28  3.000
 4GX  H2   C4   C3   109.34  3.000
 4GX  H1   C4   C3   108.72  3.000
 4GX  N4   C4   C3   109.83  3.000
 4GX  N5   C6   C7   122.21  3.000
 4GX  C7   C6   C5   121.42  3.000
 4GX  N5   C6   C5   116.34  3.000
 4GX  H5   C7   C8   121.32  3.000
 4GX  H5   C7   C6   119.82  3.000
 4GX  C8   C7   C6   118.86  3.000
 4GX  H6   C8   C9   120.65  3.000
 4GX  H6   C8   C7   120.39  3.000
 4GX  C9   C8   C7   118.96  3.000
 4GX  H7   C10  N5   116.33  3.000
 4GX  H7   C10  C9   120.18  3.000
 4GX  N5   C10  C9   123.49  3.000
 4GX  H8   C9   C10  120.44  3.000
 4GX  H8   C9   C8   121.64  3.000
 4GX  C10  C9   C8   117.92  3.000
 4GX  N2   C1   C2   125.60  3.000
 4GX  C2   C1   C    126.11  3.000
 4GX  N2   C1   C    107.87  3.000
 4GX  N    C    C1   128.24  3.000
 4GX  N    C    N1   124.35  3.000
 4GX  C1   C    N1   107.38  3.000
 4GX  O1   C2   C1   116.26  3.000
 4GX  O1   C2   N3   124.47  3.000
 4GX  C1   C2   N3   119.25  3.000
 4GX  H10  C12  H9   107.76  3.000
 4GX  H10  C12  C11  109.93  3.000
 4GX  H9   C12  C11  109.33  3.000
 4GX  H10  C12  N3   108.66  3.000
 4GX  H9   C12  N3   111.27  3.000
 4GX  C11  C12  N3   109.85  3.000
 4GX  H12  C3   H11  108.19  3.000
 4GX  H12  C3   C4   110.71  3.000
 4GX  H11  C3   C4   109.42  3.000
 4GX  H12  C3   N3   110.11  3.000
 4GX  H11  C3   N3   107.83  3.000
 4GX  C4   C3   N3   110.51  3.000
 4GX  H14  C11  H13  107.13  3.000
 4GX  H14  C11  N4   109.65  3.000
 4GX  H13  C11  N4   111.56  3.000
 4GX  H14  C11  C12  108.19  3.000
 4GX  H13  C11  C12  109.18  3.000
 4GX  N4   C11  C12  111.00  3.000
 4GX  C10  N5   C6   118.56  3.000
 4GX  O    N2   C1   107.06  3.000
 4GX  C11  N4   C5   112.35  3.000
 4GX  C11  N4   C4   110.58  3.000
 4GX  C5   N4   C4   113.12  3.000
 4GX  H17  N    H16  114.63  3.000
 4GX  H17  N    C    117.15  3.000
 4GX  H16  N    C    117.68  3.000
 4GX  N2   O    N1   111.79  3.000
 4GX  H4   C5   H3   106.04  3.000
 4GX  H4   C5   N4   108.18  3.000
 4GX  H3   C5   N4   113.02  3.000
 4GX  H4   C5   C6   107.75  3.000
 4GX  H3   C5   C6   108.79  3.000
 4GX  N4   C5   C6   112.72  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
 4GX  CONST_01  C1   N2   O    N1     0.00   0.0  0
 4GX  CONST_02  N2   C1   C    N1     0.00   0.0  0
 4GX  CONST_03  C9   C10  N5   C6     0.00   0.0  0
 4GX  CONST_04  C9   C8   C7   C6     0.00   0.0  0
 4GX  CONST_05  C10  C9   C8   C7     0.00   0.0  0
 4GX  CONST_06  C10  N5   C6   C7     0.00   0.0  0
 4GX  CONST_07  N5   C10  C9   C8     0.00   0.0  0
 4GX  CONST_08  N5   C6   C7   C8     0.00   0.0  0
 4GX  CONST_09  O    N1   C    C1     0.00   0.0  0
 4GX  CONST_10  O    N2   C1   C      0.00   0.0  0
 4GX  CONST_11  N2   O    N1   C      0.00   0.0  0
 4GX  CONST_12  C2   C1   C    N1   180.00   0.0  0
 4GX  CONST_13  C10  N5   C6   C5   180.00   0.0  0
 4GX  CONST_14  C8   C7   C6   C5   180.00   0.0  0
 4GX  CONST_15  O    N2   C1   C2   180.00   0.0  0
 4GX  CONST_16  N    C    C1   N2   180.00   0.0  0
 4GX  CONST_17  O    N1   C    N    180.00   0.0  0
 4GX  CONST_18  C3   N3   C2   C1   180.00   0.0  0
 4GX  CONST_20  H7   C10  N5   C6   180.00   0.0  0
 4GX  CONST_21  H6   C8   C7   C6   180.00   0.0  0
 4GX  CONST_22  H8   C9   C8   C7   180.00   0.0  0
 4GX  CONST_23  H5   C7   C8   C9   180.00   0.0  0
 4GX  CONST_25  O1   C2   N3   C3     0.00   0.0  0
 4GX  Var_01    N4   C4   C3   N3    57.01  30.0  1
 4GX  Var_02    N4   C11  C12  N3   -55.82  30.0  1
 4GX  Var_03    C12  C11  N4   C4    58.96  30.0  1
 4GX  Var_04    C12  N3   C3   C4   -55.72  30.0  1
 4GX  Var_05    C11  N4   C4   C3   -59.02  30.0  1
 4GX  Var_06    C11  C12  N3   C3    54.62  30.0  1
 4GX  Var_07    N2   C1   C2   N3   -40.80  30.0  2
 4GX  Var_08    C6   C5   N4   C4  -160.29  30.0  2
 4GX  Var_09    N4   C5   C6   C7    27.94  30.0  2

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
 4GX  plan-1  N1   0.020
 4GX  plan-1  C1   0.020
 4GX  plan-1  C    0.020
 4GX  plan-1  C2   0.020
 4GX  plan-1  N2   0.020
 4GX  plan-1  N    0.020
 4GX  plan-1  O    0.020
 4GX  plan-2  C6   0.020
 4GX  plan-2  C7   0.020
 4GX  plan-2  C8   0.020
 4GX  plan-2  C10  0.020
 4GX  plan-2  C9   0.020
 4GX  plan-2  N5   0.020
 4GX  plan-2  H5   0.020
 4GX  plan-2  H6   0.020
 4GX  plan-2  H7   0.020
 4GX  plan-2  H8   0.020
 4GX  plan-2  C5   0.020
 4GX  plan-3  N3   0.020
 4GX  plan-3  C1   0.020
 4GX  plan-3  C2   0.020
 4GX  plan-3  C12  0.020
 4GX  plan-3  C3   0.020
 4GX  plan-3  O1   0.020
 4GX  plan-4  C    0.020
 4GX  plan-4  N    0.020
 4GX  plan-4  H16  0.020
 4GX  plan-4  H17  0.020

