# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 11:38:42 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: 5-[(4-chlorophenyl)methyl]-1,3,4-oxadiazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1oc(Cc2ccc(Cl)cc2)nn1
#
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
 6AX  6AX  5-[(4-chlorophenyl)methyl]-1,3,4-oxadiazol-2-amine  ligand  22  14  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6AX
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
 6AX  C10  C   CR6   0  -0.052  -2.7092  -0.3205   0.0062
 6AX  C02  C   CR5   0   0.631   3.4280  -0.5902  -0.3488
 6AX  N03  N   N     0  -0.378   3.8219   0.5077  -0.9084
 6AX  N04  N   N     0  -0.309   2.9711   1.4892  -0.4433
 6AX  C05  C   CR5   0   0.484   2.1358   0.9308   0.3453
 6AX  C06  C   CH2   0  -0.635   1.0030   1.5219   1.0953
 6AX  C07  C   CR6   0   0.126  -0.3108   0.8807   0.7224
 6AX  C08  C   CR16  0  -0.314  -0.9404  -0.0092   1.5836
 6AX  C09  C   CR16  0  -0.196  -2.1400  -0.6139   1.2341
 6AX  CL   CL  CL    0  -0.129  -4.2083  -1.0688  -0.4393
 6AX  C12  C   CR16  0  -0.197  -2.1011   0.5644  -0.8719
 6AX  C13  C   CR16  0  -0.285  -0.9039   1.1587  -0.5058
 6AX  O14  O   O     0  -0.422   2.3707  -0.4011   0.4531
 6AX  H1   H   HNH2  0   0.410   4.6238  -1.9603  -1.1719
 6AX  H2   H   HNH2  0   0.412   3.3535  -2.6052  -0.2636
 6AX  H3   H   HCH2  0   0.298   1.1801   1.4190   2.1687
 6AX  H4   H   HCH2  0   0.303   0.9903   2.5896   0.8745
 6AX  H5   H   HCR6  0   0.267  -0.4972  -0.2389   2.5447
 6AX  H6   H   HCR6  0   0.282  -2.6211  -1.3035   1.9141
 6AX  H7   H   HCR6  0   0.282  -2.5537   0.7915  -1.8277
 6AX  H8   H   HCR6  0   0.266  -0.4291   1.8505  -1.1911
 6AX  N01  N   NH2   0  -0.845   3.9663  -1.8206  -0.4215

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
 6AX  N01  C02  single    1.345  0.020  1.345
 6AX  O14  C02  aromatic  1.340  0.020  1.340
 6AX  O14  C05  aromatic  1.357  0.020  1.357
 6AX  C13  C12  aromatic  1.386  0.020  1.386
 6AX  C13  C07  aromatic  1.392  0.020  1.392
 6AX  C02  N03  aromatic  1.294  0.020  1.294
 6AX  C06  C05  single    1.482  0.020  1.482
 6AX  C06  C07  single    1.509  0.020  1.509
 6AX  C05  N04  aromatic  1.277  0.020  1.277
 6AX  N03  N04  aromatic  1.380  0.020  1.380
 6AX  C12  C10  aromatic  1.387  0.020  1.387
 6AX  C07  C08  aromatic  1.389  0.020  1.389
 6AX  C10  CL   single    1.734  0.020  1.734
 6AX  C10  C09  aromatic  1.385  0.020  1.385
 6AX  C08  C09  aromatic  1.388  0.020  1.388
 6AX  N01  H1   single    0.890  0.020  1.040
 6AX  N01  H2   single    0.890  0.020  1.040
 6AX  C06  H3   single    0.970  0.020  1.090
 6AX  C06  H4   single    0.970  0.020  1.090
 6AX  C08  H5   single    0.930  0.020  1.080
 6AX  C09  H6   single    0.930  0.020  1.080
 6AX  C12  H7   single    0.930  0.020  1.080
 6AX  C13  H8   single    0.930  0.020  1.080

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
 6AX  C12  C10  CL   119.46  3.000
 6AX  CL   C10  C09  119.46  3.000
 6AX  C12  C10  C09  121.08  3.000
 6AX  O14  C02  N03  112.29  3.000
 6AX  N03  C02  N01  129.13  3.000
 6AX  O14  C02  N01  118.49  3.000
 6AX  N04  N03  C02  105.67  3.000
 6AX  C05  N04  N03  107.48  3.000
 6AX  O14  C05  C06  118.94  3.000
 6AX  C06  C05  N04  129.65  3.000
 6AX  O14  C05  N04  111.41  3.000
 6AX  H4   C06  H3   107.04  3.000
 6AX  H4   C06  C07  110.85  3.000
 6AX  H3   C06  C07  110.11  3.000
 6AX  H4   C06  C05  107.28  3.000
 6AX  H3   C06  C05  109.62  3.000
 6AX  C07  C06  C05  111.79  3.000
 6AX  C13  C07  C08  118.80  3.000
 6AX  C08  C07  C06  120.91  3.000
 6AX  C13  C07  C06  120.28  3.000
 6AX  H5   C08  C09  118.99  3.000
 6AX  H5   C08  C07  120.03  3.000
 6AX  C09  C08  C07  120.98  3.000
 6AX  H6   C09  C08  120.26  3.000
 6AX  H6   C09  C10  120.65  3.000
 6AX  C08  C09  C10  119.09  3.000
 6AX  H7   C12  C13  120.32  3.000
 6AX  H7   C12  C10  120.66  3.000
 6AX  C13  C12  C10  119.02  3.000
 6AX  H8   C13  C12  119.03  3.000
 6AX  H8   C13  C07  119.93  3.000
 6AX  C12  C13  C07  121.04  3.000
 6AX  C05  O14  C02  103.15  3.000
 6AX  H2   N01  H1   113.93  3.000
 6AX  H2   N01  C02  117.41  3.000
 6AX  H1   N01  C02  115.36  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
 6AX  CONST_01  C07  C13  C12  C10    0.00   0.0  0
 6AX  CONST_02  C07  C08  C09  C10    0.00   0.0  0
 6AX  CONST_03  N04  C05  O14  C02    0.00   0.0  0
 6AX  CONST_04  C05  N04  N03  C02    0.00   0.0  0
 6AX  CONST_05  C05  O14  C02  N03    0.00   0.0  0
 6AX  CONST_06  O14  C05  N04  N03    0.00   0.0  0
 6AX  CONST_07  O14  C02  N03  N04    0.00   0.0  0
 6AX  CONST_08  C12  C13  C07  C08    0.00   0.0  0
 6AX  CONST_09  C12  C10  C09  C08    0.00   0.0  0
 6AX  CONST_10  C13  C12  C10  C09    0.00   0.0  0
 6AX  CONST_11  C13  C07  C08  C09    0.00   0.0  0
 6AX  CONST_12  C05  O14  C02  N01  180.00   0.0  0
 6AX  CONST_13  N04  N03  C02  N01  180.00   0.0  0
 6AX  CONST_14  C06  C05  O14  C02  180.00   0.0  0
 6AX  CONST_15  C06  C05  N04  N03  180.00   0.0  0
 6AX  CONST_16  C12  C13  C07  C06  180.00   0.0  0
 6AX  CONST_17  C09  C08  C07  C06  180.00   0.0  0
 6AX  CONST_18  CL   C10  C09  C08  180.00   0.0  0
 6AX  CONST_19  C13  C12  C10  CL   180.00   0.0  0
 6AX  CONST_20  H8   C13  C12  C10  180.00   0.0  0
 6AX  CONST_21  H5   C08  C09  C10  180.00   0.0  0
 6AX  CONST_22  H7   C12  C13  C07  180.00   0.0  0
 6AX  CONST_23  H6   C09  C08  C07  180.00   0.0  0
 6AX  Var_01    C07  C06  C05  N04  120.78  30.0  2
 6AX  Var_02    C13  C07  C06  C05  -73.45  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
 6AX  plan-1  C02  0.020
 6AX  plan-1  N03  0.020
 6AX  plan-1  N04  0.020
 6AX  plan-1  C05  0.020
 6AX  plan-1  C06  0.020
 6AX  plan-1  O14  0.020
 6AX  plan-1  N01  0.020
 6AX  plan-2  C10  0.020
 6AX  plan-2  C06  0.020
 6AX  plan-2  C07  0.020
 6AX  plan-2  C08  0.020
 6AX  plan-2  C09  0.020
 6AX  plan-2  CL   0.020
 6AX  plan-2  C12  0.020
 6AX  plan-2  C13  0.020
 6AX  plan-2  H5   0.020
 6AX  plan-2  H6   0.020
 6AX  plan-2  H7   0.020
 6AX  plan-2  H8   0.020
 6AX  plan-3  C02  0.020
 6AX  plan-3  H1   0.020
 6AX  plan-3  H2   0.020
 6AX  plan-3  N01  0.020

