# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 22:17:33 2022
#   Inital geometry file: a 84 line input string
#   Ligand name: N-[(2H-1,3-benzodioxol-5-yl)methyl]-3-methylbutanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CC(=O)NCc1ccc2OCOc2c1
#
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
 X1G  X1G  N-[(2H-1,3-benzodioxol-5-yl)methyl]-3-methylbutanamide  ligand  34  17  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X1G
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
 X1G  C4   C  CR16  0  -0.332   3.0235  44.3972  12.4930
 X1G  C5   C  CR56  0   0.286   2.2619  43.6683  13.3693
 X1G  C6   C  CR56  0   0.308   2.6787  43.4315  14.6710
 X1G  C11  C  CH1   0  -0.237   3.9076  47.8175  18.1150
 X1G  C7   C  CH2   0   0.068   0.6304  42.6105  14.4365
 X1G  C9   C  C     0   0.542   5.3455  47.0543  16.1836
 X1G  C10  C  CH2   0  -0.542   5.3312  47.5957  17.5953
 X1G  C12  C  CH3   0  -0.660   3.1231  46.5100  18.1641
 X1G  C13  C  CH3   0  -0.650   3.9531  48.4744  19.4898
 X1G  N1   N  NH1   0  -0.628   5.9441  45.8608  16.0214
 X1G  C3   C  CR16  0  -0.323   4.2410  44.8944  12.9773
 X1G  C1   C  CR16  0  -0.372   3.8717  43.9048  15.1528
 X1G  C2   C  CR6   0   0.096   4.6681  44.6585  14.2745
 X1G  O1   O  O     0  -0.483   1.0668  43.0611  13.1629
 X1G  O2   O  O     0  -0.484   1.7509  42.6749  15.3077
 X1G  O3   O  O     0  -0.489   4.8401  47.6639  15.2509
 X1G  H3   H  HCR6  0   0.269   2.7021  44.5883  11.4779
 X1G  H11  H  HCH1  0   0.225   3.4009  48.5003  17.4262
 X1G  H4   H  HCH2  0   0.229  -0.1680  43.2622  14.8098
 X1G  H5   H  HCH2  0   0.243   0.2776  41.5814  14.3636
 X1G  H6   H  HCH2  0   0.270   6.7074  44.3616  14.8597
 X1G  H7   H  HCH2  0   0.257   6.4211  45.8517  13.9882
 X1G  H9   H  HCH2  0   0.240   5.8683  46.9346  18.2814
 X1G  H10  H  HCH2  0   0.262   5.8686  48.5485  17.5896
 X1G  H13  H  HCH3  0   0.230   2.1139  46.6760  18.5441
 X1G  H14  H  HCH3  0   0.233   3.0274  46.0463  17.1804
 X1G  H12  H  HCH3  0   0.215   3.6102  45.7889  18.8251
 X1G  H17  H  HCH3  0   0.228   2.9473  48.6671  19.8660
 X1G  H15  H  HCH3  0   0.215   4.4601  47.8318  20.2135
 X1G  H16  H  HCH3  0   0.226   4.4860  49.4262  19.4602
 X1G  H8   H  HNH1  0   0.402   6.3301  45.3940  16.8245
 X1G  H2   H  HCR6  0   0.252   4.8605  45.4871  12.3157
 X1G  H1   H  HCR6  0   0.265   4.1862  43.7084  16.1704
 X1G  C8   C  CH2   0  -0.360   6.0022  45.1863  14.7457

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
 X1G  C4   C3   aromatic  1.402  0.020  1.402
 X1G  C4   C5   aromatic  1.371  0.020  1.371
 X1G  C3   C2   aromatic  1.386  0.020  1.386
 X1G  O1   C5   single    1.356  0.020  1.356
 X1G  O1   C7   single    1.420  0.020  1.420
 X1G  C5   C6   aromatic  1.387  0.020  1.387
 X1G  C2   C8   single    1.510  0.020  1.510
 X1G  C2   C1   aromatic  1.405  0.020  1.405
 X1G  C7   O2   single    1.421  0.020  1.421
 X1G  C6   C1   aromatic  1.371  0.020  1.371
 X1G  C6   O2   single    1.356  0.020  1.356
 X1G  C8   N1   single    1.444  0.020  1.444
 X1G  O3   C9   double    1.224  0.020  1.224
 X1G  N1   C9   single    1.345  0.020  1.345
 X1G  C9   C10  single    1.512  0.020  1.512
 X1G  C10  C11  single    1.532  0.020  1.532
 X1G  C11  C12  single    1.526  0.020  1.526
 X1G  C11  C13  single    1.524  0.020  1.524
 X1G  C4   H3   single    0.930  0.020  1.080
 X1G  C11  H11  single    0.970  0.020  1.090
 X1G  C7   H4   single    0.970  0.020  1.090
 X1G  C7   H5   single    0.970  0.020  1.090
 X1G  C8   H6   single    0.970  0.020  1.090
 X1G  C8   H7   single    0.970  0.020  1.090
 X1G  C10  H9   single    0.970  0.020  1.090
 X1G  C10  H10  single    0.970  0.020  1.090
 X1G  C12  H13  single    0.970  0.020  1.090
 X1G  C12  H14  single    0.970  0.020  1.090
 X1G  C12  H12  single    0.970  0.020  1.090
 X1G  C13  H17  single    0.970  0.020  1.090
 X1G  C13  H15  single    0.970  0.020  1.090
 X1G  C13  H16  single    0.970  0.020  1.090
 X1G  N1   H8   single    0.860  0.020  1.020
 X1G  C3   H2   single    0.930  0.020  1.080
 X1G  C1   H1   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
 X1G  H3   C4   C3   121.31  3.000
 X1G  H3   C4   C5   121.92  3.000
 X1G  C3   C4   C5   116.77  3.000
 X1G  O1   C5   C6   109.34  3.000
 X1G  C6   C5   C4   121.58  3.000
 X1G  O1   C5   C4   129.07  3.000
 X1G  O2   C6   C1   128.54  3.000
 X1G  O2   C6   C5   109.29  3.000
 X1G  C1   C6   C5   122.16  3.000
 X1G  H11  C11  C13  108.22  3.000
 X1G  H11  C11  C12  108.48  3.000
 X1G  C13  C11  C12  110.83  3.000
 X1G  H11  C11  C10  107.89  3.000
 X1G  C13  C11  C10  109.92  3.000
 X1G  C12  C11  C10  111.39  3.000
 X1G  H5   C7   H4   110.39  3.000
 X1G  H5   C7   O2   109.82  3.000
 X1G  H4   C7   O2   109.79  3.000
 X1G  H5   C7   O1   109.82  3.000
 X1G  H4   C7   O1   109.92  3.000
 X1G  O2   C7   O1   107.05  3.000
 X1G  O3   C9   N1   122.28  3.000
 X1G  N1   C9   C10  115.75  3.000
 X1G  O3   C9   C10  121.97  3.000
 X1G  H10  C10  H9   106.77  3.000
 X1G  H10  C10  C9   107.60  3.000
 X1G  H9   C10  C9   111.39  3.000
 X1G  H10  C10  C11  109.40  3.000
 X1G  H9   C10  C11  109.34  3.000
 X1G  C9   C10  C11  112.17  3.000
 X1G  H12  C12  H14  107.69  3.000
 X1G  H12  C12  H13  107.58  3.000
 X1G  H14  C12  H13  107.29  3.000
 X1G  H12  C12  C11  110.84  3.000
 X1G  H14  C12  C11  112.34  3.000
 X1G  H13  C12  C11  110.89  3.000
 X1G  H16  C13  H15  107.72  3.000
 X1G  H16  C13  H17  107.79  3.000
 X1G  H15  C13  H17  107.65  3.000
 X1G  H16  C13  C11  111.47  3.000
 X1G  H15  C13  C11  110.97  3.000
 X1G  H17  C13  C11  111.07  3.000
 X1G  H8   N1   C9   119.10  3.000
 X1G  H8   N1   C8   118.23  3.000
 X1G  C9   N1   C8   122.61  3.000
 X1G  H2   C3   C2   119.25  3.000
 X1G  H2   C3   C4   118.69  3.000
 X1G  C2   C3   C4   122.06  3.000
 X1G  H1   C1   C2   121.34  3.000
 X1G  H1   C1   C6   121.35  3.000
 X1G  C2   C1   C6   117.31  3.000
 X1G  C1   C2   C3   120.12  3.000
 X1G  C1   C2   C8   119.56  3.000
 X1G  C3   C2   C8   120.32  3.000
 X1G  C7   O1   C5   106.05  3.000
 X1G  C7   O2   C6   106.09  3.000
 X1G  H7   C8   H6   106.57  3.000
 X1G  H7   C8   C2   109.60  3.000
 X1G  H6   C8   C2   109.85  3.000
 X1G  H7   C8   N1   110.10  3.000
 X1G  H6   C8   N1   106.66  3.000
 X1G  C2   C8   N1   113.78  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
 X1G  CONST_01  C1   C2   C3   C4     0.00   0.0  0
 X1G  CONST_02  C1   C6   C5   C4     0.00   0.0  0
 X1G  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 X1G  CONST_04  C2   C1   C6   C5     0.00   0.0  0
 X1G  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 X1G  CONST_06  C3   C2   C1   C6     0.00   0.0  0
 X1G  CONST_07  C8   C2   C3   C4   180.00   0.0  0
 X1G  CONST_08  C8   C2   C1   C6   180.00   0.0  0
 X1G  CONST_09  H2   C3   C4   C5   180.00   0.0  0
 X1G  CONST_10  H1   C1   C6   C5   180.00   0.0  0
 X1G  CONST_11  H3   C4   C5   C6   180.00   0.0  0
 X1G  CONST_12  O3   C9   N1   C8     0.00   0.0  0
 X1G  CONST_13  C10  C9   N1   C8   180.00   0.0  0
 X1G  CONST_14  H8   N1   C9   C10    0.00   0.0  0
 X1G  Var_01    O2   C7   O1   C5   -14.48  30.0  1
 X1G  Var_02    O1   C7   O2   C6    14.37  30.0  1
 X1G  Var_03    C1   C6   O2   C7   172.34  30.0  1
 X1G  Var_04    C3   C2   C8   N1   132.27  30.0  2
 X1G  Var_05    C2   C8   N1   C9   -70.07  30.0  2
 X1G  Var_06    O3   C9   C10  C11   59.62  30.0  1
 X1G  Var_07    C12  C11  C10  C9    61.64  30.0  3
 X1G  Var_08    H13  C12  C11  C10  179.47  30.0  3
 X1G  Var_09    H17  C13  C11  C10  178.39  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
 X1G  plan-1  C9   0.020
 X1G  plan-1  C10  0.020
 X1G  plan-1  N1   0.020
 X1G  plan-1  O3   0.020
 X1G  plan-1  H8   0.020
 X1G  plan-1  C8   0.020
 X1G  plan-2  C4   0.020
 X1G  plan-2  C5   0.020
 X1G  plan-2  C6   0.020
 X1G  plan-2  C3   0.020
 X1G  plan-2  C1   0.020
 X1G  plan-2  C2   0.020
 X1G  plan-2  O1   0.020
 X1G  plan-2  O2   0.020
 X1G  plan-2  H3   0.020
 X1G  plan-2  H2   0.020
 X1G  plan-2  H1   0.020
 X1G  plan-2  C8   0.020

