# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 11:54:07 2021
#   Inital geometry file: a 83 line input string
#   Ligand name: ~{N}-[[3-(4-methylphenyl)-1,2,4-oxadiazol-5-yl]methyl]propan-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)NCc1onc(n1)c2ccc(C)cc2
#
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
 LT7  LT7  ~{N}-[[3-(4-methylphenyl)-1,2,4-oxadiazol-5-yl]methyl]propan-2-amine  ligand  34  17  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LT7
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
 LT7  N1   N  N     0  -0.159  -6.1222  -10.7202  -15.8105
 LT7  C4   C  CR6   0  -0.014  -4.0664  -12.0114  -15.6852
 LT7  C5   C  CR16  0  -0.273  -2.7765  -12.0934  -15.1677
 LT7  C6   C  CR16  0  -0.285  -1.9947  -13.2117  -15.4132
 LT7  C7   C  CR5   0   0.319  -4.8881  -10.8342  -15.4173
 LT7  C8   C  CR5   0   0.547  -5.4633   -8.9637  -14.7186
 LT7  C10  C  CH1   0  -0.096  -6.8674   -6.3123  -12.5050
 LT7  N    N  N     0  -0.469  -4.4382   -9.7460  -14.7220
 LT7  O    O  O     0  -0.327  -6.5004   -9.4872  -15.3553
 LT7  C1   C  CR6   0   0.098  -2.4729  -14.2713  -16.1797
 LT7  C11  C  CH3   0  -0.671  -6.6995   -4.9567  -13.1907
 LT7  C12  C  CH3   0  -0.658  -8.1618   -6.3691  -11.7072
 LT7  C2   C  CR16  0  -0.280  -3.7678  -14.1797  -16.6924
 LT7  C3   C  CR16  0  -0.266  -4.5562  -13.0693  -16.4522
 LT7  C9   C  CH2   0  -0.394  -5.5878   -7.5993  -14.1366
 LT7  N2   N  NH1   0  -0.596  -6.8389   -7.4487  -13.4228
 LT7  H1   H  HCR6  0   0.259  -2.3816  -11.2851  -14.5669
 LT7  H2   H  HCR6  0   0.255  -0.9955  -13.2606  -14.9979
 LT7  H3   H  HCH1  0   0.229  -6.0311   -6.4512  -11.8112
 LT7  H4   H  HCH3  0   0.254  -1.1401  -15.3723  -17.4480
 LT7  H5   H  HCH3  0   0.247  -0.8232  -15.5794  -15.7311
 LT7  H6   H  HCH3  0   0.248  -2.2021  -16.3850  -16.4849
 LT7  H7   H  HCH3  0   0.231  -6.7236   -4.1443  -12.4633
 LT7  H8   H  HCH3  0   0.233  -5.7518   -4.8857  -13.7273
 LT7  H9   H  HCH3  0   0.218  -7.5039   -4.7860  -13.9110
 LT7  H10  H  HCH3  0   0.228  -8.2025   -5.5642  -10.9731
 LT7  H11  H  HCH3  0   0.218  -9.0306   -6.2627  -12.3617
 LT7  H12  H  HCH3  0   0.231  -8.2529   -7.3176  -11.1774
 LT7  H13  H  HCR6  0   0.255  -4.1659  -14.9918  -17.2887
 LT7  H14  H  HCR6  0   0.257  -5.5566  -13.0273  -16.8633
 LT7  H15  H  HCH2  0   0.277  -4.7579   -7.4757  -13.4396
 LT7  H16  H  HCH2  0   0.259  -5.4273   -6.8705  -14.9438
 LT7  H17  H  HNH1  0   0.349  -7.6019   -7.3503  -14.0835
 LT7  C    C  CH3   0  -0.722  -1.6158  -15.4665  -16.4694

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
 LT7  C    C1   single    1.499  0.020  1.499
 LT7  C2   C1   aromatic  1.396  0.020  1.396
 LT7  C2   C3   aromatic  1.383  0.020  1.383
 LT7  C1   C6   aromatic  1.392  0.020  1.392
 LT7  C3   C4   aromatic  1.395  0.020  1.395
 LT7  N1   O    aromatic  1.368  0.020  1.368
 LT7  N1   C7   aromatic  1.300  0.020  1.300
 LT7  C6   C5   aromatic  1.386  0.020  1.386
 LT7  C4   C7   single    1.460  0.020  1.460
 LT7  C4   C5   aromatic  1.392  0.020  1.392
 LT7  O    C8   aromatic  1.325  0.020  1.325
 LT7  C7   N    aromatic  1.368  0.020  1.368
 LT7  C8   N    aromatic  1.290  0.020  1.290
 LT7  C8   C9   single    1.489  0.020  1.489
 LT7  C9   N2   single    1.448  0.020  1.448
 LT7  N2   C10  single    1.461  0.020  1.461
 LT7  C11  C10  single    1.528  0.020  1.528
 LT7  C10  C12  single    1.522  0.020  1.522
 LT7  C5   H1   single    0.930  0.020  1.080
 LT7  C6   H2   single    0.930  0.020  1.080
 LT7  C10  H3   single    0.970  0.020  1.090
 LT7  C    H4   single    0.970  0.020  1.090
 LT7  C    H5   single    0.970  0.020  1.090
 LT7  C    H6   single    0.970  0.020  1.090
 LT7  C11  H7   single    0.970  0.020  1.090
 LT7  C11  H8   single    0.970  0.020  1.090
 LT7  C11  H9   single    0.970  0.020  1.090
 LT7  C12  H10  single    0.970  0.020  1.090
 LT7  C12  H11  single    0.970  0.020  1.090
 LT7  C12  H12  single    0.970  0.020  1.090
 LT7  C2   H13  single    0.930  0.020  1.080
 LT7  C3   H14  single    0.930  0.020  1.080
 LT7  C9   H15  single    0.970  0.020  1.090
 LT7  C9   H16  single    0.970  0.020  1.090
 LT7  N2   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
 LT7  O    N1   C7   103.94  3.000
 LT7  C3   C4   C7   120.96  3.000
 LT7  C7   C4   C5   120.04  3.000
 LT7  C3   C4   C5   119.00  3.000
 LT7  H1   C5   C6   119.68  3.000
 LT7  H1   C5   C4   120.05  3.000
 LT7  C6   C5   C4   120.27  3.000
 LT7  H2   C6   C1   119.57  3.000
 LT7  H2   C6   C5   119.25  3.000
 LT7  C1   C6   C5   121.17  3.000
 LT7  N    C7   C4   123.34  3.000
 LT7  N    C7   N1   113.34  3.000
 LT7  C4   C7   N1   123.32  3.000
 LT7  C9   C8   O    118.99  3.000
 LT7  C9   C8   N    128.58  3.000
 LT7  O    C8   N    112.42  3.000
 LT7  H3   C10  N2   106.52  3.000
 LT7  H3   C10  C12  108.22  3.000
 LT7  N2   C10  C12  108.48  3.000
 LT7  H3   C10  C11  108.23  3.000
 LT7  C12  C10  C11  111.21  3.000
 LT7  N2   C10  C11  113.95  3.000
 LT7  C8   N    C7   102.86  3.000
 LT7  C8   O    N1   107.44  3.000
 LT7  C2   C1   C    120.78  3.000
 LT7  C2   C1   C6   118.09  3.000
 LT7  C    C1   C6   121.12  3.000
 LT7  H9   C11  H8   107.75  3.000
 LT7  H9   C11  H7   107.87  3.000
 LT7  H8   C11  H7   107.38  3.000
 LT7  H9   C11  C10  110.69  3.000
 LT7  H8   C11  C10  111.95  3.000
 LT7  H7   C11  C10  111.04  3.000
 LT7  H12  C12  H11  108.02  3.000
 LT7  H12  C12  H10  108.18  3.000
 LT7  H11  C12  H10  107.56  3.000
 LT7  H12  C12  C10  111.00  3.000
 LT7  H11  C12  C10  111.01  3.000
 LT7  H10  C12  C10  110.93  3.000
 LT7  H13  C2   C3   119.21  3.000
 LT7  H13  C2   C1   119.60  3.000
 LT7  C3   C2   C1   121.18  3.000
 LT7  H14  C3   C2   119.48  3.000
 LT7  H14  C3   C4   120.25  3.000
 LT7  C2   C3   C4   120.27  3.000
 LT7  H16  C9   H15  106.43  3.000
 LT7  H16  C9   N2   114.78  3.000
 LT7  H15  C9   N2   109.30  3.000
 LT7  H16  C9   C8   107.96  3.000
 LT7  H15  C9   C8   106.86  3.000
 LT7  N2   C9   C8   111.12  3.000
 LT7  H17  N2   C9   109.81  3.000
 LT7  H17  N2   C10  108.61  3.000
 LT7  C9   N2   C10  114.04  3.000
 LT7  H6   C    H5   108.29  3.000
 LT7  H6   C    H4   107.11  3.000
 LT7  H5   C    H4   107.42  3.000
 LT7  H6   C    C1   111.54  3.000
 LT7  H5   C    C1   111.57  3.000
 LT7  H4   C    C1   110.70  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
 LT7  CONST_01  N    C8   O    N1      0.00   0.0  0
 LT7  CONST_02  C3   C4   C7   N1      0.00   0.0  0
 LT7  CONST_03  C5   C4   C7   N1    180.00   0.0  0
 LT7  CONST_04  C8   N    C7   N1      0.00   0.0  0
 LT7  CONST_05  C1   C2   C3   C4      0.00   0.0  0
 LT7  CONST_06  O    N1   C7   C4    180.00   0.0  0
 LT7  CONST_07  C8   N    C7   C4    180.00   0.0  0
 LT7  CONST_08  C1   C6   C5   C4      0.00   0.0  0
 LT7  CONST_09  C2   C1   C6   C5      0.00   0.0  0
 LT7  CONST_10  C2   C3   C4   C5      0.00   0.0  0
 LT7  CONST_11  N    C7   C4   C5      0.00   0.0  0
 LT7  CONST_12  C3   C2   C1   C6      0.00   0.0  0
 LT7  CONST_13  C3   C4   C5   C6      0.00   0.0  0
 LT7  CONST_14  C7   C4   C5   C6    180.00   0.0  0
 LT7  CONST_15  C8   O    N1   C7      0.00   0.0  0
 LT7  CONST_16  C2   C3   C4   C7    180.00   0.0  0
 LT7  CONST_17  O    C8   N    C7      0.00   0.0  0
 LT7  CONST_18  O    N1   C7   N       0.00   0.0  0
 LT7  CONST_19  C3   C4   C7   N     180.00   0.0  0
 LT7  CONST_20  C9   C8   O    N1    180.00   0.0  0
 LT7  CONST_21  C    C1   C6   C5    180.00   0.0  0
 LT7  CONST_22  C9   C8   N    C7    180.00   0.0  0
 LT7  CONST_23  C3   C2   C1   C     180.00   0.0  0
 LT7  CONST_24  H13  C2   C3   C4    180.00   0.0  0
 LT7  CONST_25  H2   C6   C5   C4    180.00   0.0  0
 LT7  CONST_26  H14  C3   C4   C5    180.00   0.0  0
 LT7  CONST_27  H1   C5   C4   C7      0.00   0.0  0
 LT7  Var_01    N2   C9   C8   N    -136.21  30.0  2
 LT7  Var_02    H4   C    C1   C6    -96.84  30.0  2
 LT7  Var_03    C10  N2   C9   C8    162.70  30.0  3
 LT7  Var_04    C9   N2   C10  C11    62.21  30.0  3
 LT7  Var_05    H10  C12  C10  C11   -56.71  30.0  3
 LT7  Var_06    H7   C11  C10  C12    57.26  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
 LT7  plan-1  N1   0.020
 LT7  plan-1  C4   0.020
 LT7  plan-1  C7   0.020
 LT7  plan-1  C8   0.020
 LT7  plan-1  N    0.020
 LT7  plan-1  O    0.020
 LT7  plan-1  C9   0.020
 LT7  plan-2  C4   0.020
 LT7  plan-2  C5   0.020
 LT7  plan-2  C6   0.020
 LT7  plan-2  C7   0.020
 LT7  plan-2  C1   0.020
 LT7  plan-2  C2   0.020
 LT7  plan-2  C3   0.020
 LT7  plan-2  H1   0.020
 LT7  plan-2  H2   0.020
 LT7  plan-2  H13  0.020
 LT7  plan-2  H14  0.020
 LT7  plan-2  C    0.020

