# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 16:13:14 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 4-amino-N-(cyclohexylmethyl)-1,2,5-oxadiazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nonc1C(=O)NCC2CCCCC2
#
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
 4GY  4GY  4-amino-N-(cyclohexylmethyl)-1,2,5-oxadiazole-3-carboxamide  ligand  32  16  .  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_4GY
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
 4GY  N1   N  NH2   0  -0.840   4.0633  -1.0440   1.0664
 4GY  N3   N  N     0  -0.189   4.2889   0.9708  -0.1198
 4GY  C6   C  CR5   0   0.036   2.2575   0.1124  -0.2143
 4GY  C7   C  C     0   0.570   1.0889  -0.7714   0.0205
 4GY  C10  C  CH2   0  -0.252  -1.2397  -1.2338  -0.6299
 4GY  C13  C  CH2   0  -0.432  -4.9604  -0.2034  -0.4941
 4GY  C15  C  CH2   0  -0.430  -3.6204   1.4994   0.7818
 4GY  C2   C  CR5   0   0.376   3.5827  -0.0353   0.3146
 4GY  O4   O  O     0  -0.211   3.4453   1.7107  -0.8896
 4GY  N5   N  N     0  -0.106   2.2338   1.1855  -0.9337
 4GY  O8   O  O     0  -0.479   1.1759  -1.6566   0.8622
 4GY  N9   N  NH1   0  -0.640   0.0137  -0.5145  -0.7242
 4GY  C11  C  CH1   0  -0.267  -2.4376  -0.2936  -0.5461
 4GY  C12  C  CH2   0  -0.420  -3.7328  -1.1044  -0.5785
 4GY  C14  C  CH2   0  -0.430  -4.9111   0.6876   0.7429
 4GY  C16  C  CH2   0  -0.413  -2.3935   0.5960   0.6956
 4GY  H1   H  HNH2  0   0.406   3.3860  -1.5900   1.5717
 4GY  H2   H  HNH2  0   0.402   4.9389  -0.8940   1.5399
 4GY  H3   H  HCH2  0   0.252  -1.3448  -1.8901  -1.4990
 4GY  H4   H  HCH2  0   0.246  -1.2046  -1.8727   0.2524
 4GY  H6   H  HCH2  0   0.228  -5.8703  -0.8083  -0.4921
 4GY  H7   H  HCH2  0   0.210  -3.6101   2.2038  -0.0568
 4GY  H8   H  HCH2  0   0.227  -3.5772   2.1014   1.6928
 4GY  H9   H  HNH1  0   0.411   0.0740   0.2168  -1.4173
 4GY  H10  H  HCH1  0   0.222  -2.4263   0.3544  -1.4344
 4GY  H11  H  HCH2  0   0.211  -3.7373  -1.8051   0.2649
 4GY  H12  H  HCH2  0   0.229  -3.7713  -1.7112  -1.4879
 4GY  H13  H  HCH2  0   0.226  -5.7792   1.3509   0.7668
 4GY  H14  H  HCH2  0   0.208  -4.9701   0.0630   1.6415
 4GY  H15  H  HCH2  0   0.229  -1.4832   1.2010   0.6982
 4GY  H16  H  HCH2  0   0.208  -2.3481  -0.0412   1.5878
 4GY  H5   H  HCH2  0   0.210  -5.0058   0.4244  -1.3911

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
 4GY  C14  C13  single    1.525  0.020  1.525
 4GY  C14  C15  single    1.525  0.020  1.525
 4GY  C13  C12  single    1.525  0.020  1.525
 4GY  C15  C16  single    1.526  0.020  1.526
 4GY  C12  C11  single    1.528  0.020  1.528
 4GY  C16  C11  single    1.528  0.020  1.528
 4GY  C11  C10  single    1.525  0.020  1.525
 4GY  C10  N9   single    1.448  0.020  1.448
 4GY  N9   C7   single    1.333  0.020  1.333
 4GY  N5   C6   aromatic  1.292  0.020  1.292
 4GY  N5   O4   aromatic  1.321  0.020  1.321
 4GY  C7   C6   single    1.484  0.020  1.484
 4GY  C7   O8   double    1.225  0.020  1.225
 4GY  C6   C2   aromatic  1.434  0.020  1.434
 4GY  O4   N3   aromatic  1.361  0.020  1.361
 4GY  C2   N3   aromatic  1.304  0.020  1.304
 4GY  C2   N1   single    1.347  0.020  1.347
 4GY  N1   H1   single    0.890  0.020  1.040
 4GY  N1   H2   single    0.890  0.020  1.040
 4GY  C10  H3   single    0.970  0.020  1.090
 4GY  C10  H4   single    0.970  0.020  1.090
 4GY  C13  H5   single    0.970  0.020  1.090
 4GY  C13  H6   single    0.970  0.020  1.090
 4GY  C15  H7   single    0.970  0.020  1.090
 4GY  C15  H8   single    0.970  0.020  1.090
 4GY  N9   H9   single    0.860  0.020  1.020
 4GY  C11  H10  single    0.970  0.020  1.090
 4GY  C12  H11  single    0.970  0.020  1.090
 4GY  C12  H12  single    0.970  0.020  1.090
 4GY  C14  H13  single    0.970  0.020  1.090
 4GY  C14  H14  single    0.970  0.020  1.090
 4GY  C16  H15  single    0.970  0.020  1.090
 4GY  C16  H16  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
 4GY  H2   N1   H1   115.48  3.000
 4GY  H2   N1   C2   117.48  3.000
 4GY  H1   N1   C2   116.53  3.000
 4GY  O4   N3   C2   105.80  3.000
 4GY  N5   C6   C2   107.92  3.000
 4GY  C2   C6   C7   127.44  3.000
 4GY  N5   C6   C7   124.63  3.000
 4GY  N9   C7   O8   125.50  3.000
 4GY  O8   C7   C6   118.90  3.000
 4GY  N9   C7   C6   115.60  3.000
 4GY  H4   C10  H3   107.13  3.000
 4GY  H4   C10  C11  110.01  3.000
 4GY  H3   C10  C11  109.75  3.000
 4GY  H4   C10  N9   108.42  3.000
 4GY  H3   C10  N9   109.23  3.000
 4GY  C11  C10  N9   112.16  3.000
 4GY  H6   C13  H5   106.51  3.000
 4GY  H6   C13  C14  110.42  3.000
 4GY  H5   C13  C14  109.30  3.000
 4GY  H6   C13  C12  110.08  3.000
 4GY  H5   C13  C12  109.06  3.000
 4GY  C14  C13  C12  111.34  3.000
 4GY  H8   C15  H7   106.48  3.000
 4GY  H8   C15  C16  109.96  3.000
 4GY  H7   C15  C16  109.26  3.000
 4GY  H8   C15  C14  110.36  3.000
 4GY  H7   C15  C14  109.32  3.000
 4GY  C16  C15  C14  111.33  3.000
 4GY  C6   C2   N3   107.34  3.000
 4GY  N3   C2   N1   124.80  3.000
 4GY  C6   C2   N1   127.78  3.000
 4GY  N5   O4   N3   111.79  3.000
 4GY  O4   N5   C6   107.14  3.000
 4GY  H9   N9   C10  117.15  3.000
 4GY  H9   N9   C7   118.37  3.000
 4GY  C10  N9   C7   124.47  3.000
 4GY  H10  C11  C16  108.24  3.000
 4GY  H10  C11  C12  107.71  3.000
 4GY  C16  C11  C12  110.52  3.000
 4GY  H10  C11  C10  108.11  3.000
 4GY  C16  C11  C10  112.38  3.000
 4GY  C12  C11  C10  109.72  3.000
 4GY  H12  C12  H11  106.54  3.000
 4GY  H12  C12  C11  109.98  3.000
 4GY  H11  C12  C11  109.04  3.000
 4GY  H12  C12  C13  110.20  3.000
 4GY  H11  C12  C13  109.37  3.000
 4GY  C11  C12  C13  111.57  3.000
 4GY  H14  C14  H13  106.57  3.000
 4GY  H14  C14  C15  109.14  3.000
 4GY  H13  C14  C15  110.40  3.000
 4GY  H14  C14  C13  109.29  3.000
 4GY  H13  C14  C13  110.28  3.000
 4GY  C15  C14  C13  111.04  3.000
 4GY  H16  C16  H15  106.56  3.000
 4GY  H16  C16  C11  108.90  3.000
 4GY  H15  C16  C11  110.38  3.000
 4GY  H16  C16  C15  109.33  3.000
 4GY  H15  C16  C15  109.98  3.000
 4GY  C11  C16  C15  111.55  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
 4GY  CONST_01  C6   N5   O4   N3      0.00   0.0  0
 4GY  CONST_02  N5   C6   C2   N3      0.00   0.0  0
 4GY  CONST_03  O4   N3   C2   C6      0.00   0.0  0
 4GY  CONST_04  O4   N5   C6   C2      0.00   0.0  0
 4GY  CONST_05  N5   O4   N3   C2      0.00   0.0  0
 4GY  CONST_06  N5   C6   C2   N1    180.00   0.0  0
 4GY  CONST_07  O4   N3   C2   N1    180.00   0.0  0
 4GY  CONST_08  C7   C6   C2   N3    180.00   0.0  0
 4GY  CONST_09  O4   N5   C6   C7    180.00   0.0  0
 4GY  CONST_12  C10  N9   C7   C6    180.00   0.0  0
 4GY  CONST_13  H9   N9   C7   C6      0.00   0.0  0
 4GY  CONST_14  O8   C7   N9   C10     0.00   0.0  0
 4GY  Var_01    C16  C15  C14  C13   -55.19  30.0  1
 4GY  Var_02    C12  C13  C14  C15    55.22  30.0  1
 4GY  Var_03    C14  C13  C12  C11   -55.69  30.0  1
 4GY  Var_04    C14  C15  C16  C11    55.66  30.0  1
 4GY  Var_05    N9   C7   C6   C2   -171.60  30.0  2
 4GY  Var_06    C11  C10  N9   C7    131.74  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
 4GY  chir_01  C11  C12  C16  C10  negativ

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
 4GY  plan-1  N1   0.020
 4GY  plan-1  N3   0.020
 4GY  plan-1  C6   0.020
 4GY  plan-1  C7   0.020
 4GY  plan-1  C2   0.020
 4GY  plan-1  O4   0.020
 4GY  plan-1  N5   0.020
 4GY  plan-2  C6   0.020
 4GY  plan-2  C7   0.020
 4GY  plan-2  C10  0.020
 4GY  plan-2  O8   0.020
 4GY  plan-2  N9   0.020
 4GY  plan-2  H9   0.020
 4GY  plan-3  N1   0.020
 4GY  plan-3  C2   0.020
 4GY  plan-3  H1   0.020
 4GY  plan-3  H2   0.020

