# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 16:43:25 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: ~{N}-[(2,6-dimethoxyphenyl)methyl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(OC)c1CNC(C)=O
#
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
 5QB  5QB  ~{N}-[(2,6-dimethoxyphenyl)methyl]ethanamide  ligand  30  15  .  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_5QB
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
 5QB  C4   C  CR6   0   0.395  -1.2459  -1.2397  -0.0669
 5QB  C5   C  CR16  0  -0.408  -2.5600  -1.2228   0.4017
 5QB  C6   C  CR16  0  -0.232  -3.1706  -0.0035   0.6424
 5QB  C7   C  CR16  0  -0.408  -2.5096   1.1957   0.4334
 5QB  C8   C  CR6   0   0.395  -1.1963   1.1692  -0.0351
 5QB  C10  C  CH3   0  -0.435  -1.2178  -3.6160  -0.1452
 5QB  O2   O  O     0  -0.516   3.6174   0.2664  -1.0098
 5QB  C1   C  C     0   0.522   3.1170   0.1367   0.1018
 5QB  C    C  CH3   0  -0.774   3.9533   0.1388   1.3577
 5QB  N    N  NH1   0  -0.619   1.7987  -0.0195   0.2816
 5QB  C3   C  CR6   0  -0.192  -0.5559  -0.0458  -0.3093
 5QB  O    O  O2    0  -0.467  -0.4660   2.2771  -0.2537
 5QB  C9   C  CH3   0  -0.436  -1.0650   3.5427  -0.0564
 5QB  O1   O  O2    0  -0.469  -0.5638  -2.3733  -0.3117
 5QB  H1   H  HCR6  0   0.276  -3.1060  -2.1367   0.5874
 5QB  H2   H  HCR6  0   0.263  -4.1893   0.0130   1.0076
 5QB  H3   H  HCR6  0   0.276  -3.0176   2.1262   0.6426
 5QB  H4   H  HCH3  0   0.230  -1.5261  -3.7805   0.8901
 5QB  H5   H  HCH3  0   0.230  -2.0930  -3.7071  -0.7932
 5QB  H6   H  HCH3  0   0.260  -0.4960  -4.3806  -0.4213
 5QB  H7   H  HCH3  0   0.263   4.5665   1.0392   1.3825
 5QB  H8   H  HCH3  0   0.247   3.3675   0.0940   2.2741
 5QB  H9   H  HCH3  0   0.265   4.6306  -0.7153   1.3412
 5QB  H10  H  HNH1  0   0.402   1.4419  -0.1539   1.2131
 5QB  H11  H  HCH2  0   0.252   1.0288   0.7938  -1.4765
 5QB  H12  H  HCH2  0   0.251   1.0285  -0.9518  -1.4306
 5QB  H13  H  HCH3  0   0.260  -0.3099   4.2816  -0.3128
 5QB  H14  H  HCH3  0   0.229  -1.9341   3.6894  -0.7023
 5QB  H15  H  HCH3  0   0.230  -1.3671   3.6951   0.9826
 5QB  C2   C  CH2   0  -0.290   0.8559  -0.0619  -0.8231

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
 5QB  O2   C1   double    1.226  0.020  1.226
 5QB  C1   C    single    1.509  0.020  1.509
 5QB  C1   N    single    1.340  0.020  1.340
 5QB  C2   N    single    1.453  0.020  1.453
 5QB  C2   C3   single    1.503  0.020  1.503
 5QB  O    C9   single    1.414  0.020  1.414
 5QB  O    C8   single    1.345  0.020  1.345
 5QB  C3   C8   aromatic  1.401  0.020  1.401
 5QB  C3   C4   aromatic  1.400  0.020  1.400
 5QB  O1   C4   single    1.345  0.020  1.345
 5QB  O1   C10  single    1.414  0.020  1.414
 5QB  C8   C7   aromatic  1.395  0.020  1.395
 5QB  C4   C5   aromatic  1.395  0.020  1.395
 5QB  C7   C6   aromatic  1.385  0.020  1.385
 5QB  C5   C6   aromatic  1.385  0.020  1.385
 5QB  C5   H1   single    0.930  0.020  1.080
 5QB  C6   H2   single    0.930  0.020  1.080
 5QB  C7   H3   single    0.930  0.020  1.080
 5QB  C10  H4   single    0.970  0.020  1.090
 5QB  C10  H5   single    0.970  0.020  1.090
 5QB  C10  H6   single    0.970  0.020  1.090
 5QB  C    H7   single    0.970  0.020  1.090
 5QB  C    H8   single    0.970  0.020  1.090
 5QB  C    H9   single    0.970  0.020  1.090
 5QB  N    H10  single    0.860  0.020  1.020
 5QB  C2   H11  single    0.970  0.020  1.090
 5QB  C2   H12  single    0.970  0.020  1.090
 5QB  C9   H13  single    0.970  0.020  1.090
 5QB  C9   H14  single    0.970  0.020  1.090
 5QB  C9   H15  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
 5QB  O1   C4   C3   115.92  3.000
 5QB  O1   C4   C5   123.28  3.000
 5QB  C3   C4   C5   120.80  3.000
 5QB  H1   C5   C6   119.48  3.000
 5QB  H1   C5   C4   121.56  3.000
 5QB  C6   C5   C4   118.96  3.000
 5QB  H2   C6   C7   119.14  3.000
 5QB  H2   C6   C5   119.14  3.000
 5QB  C7   C6   C5   121.72  3.000
 5QB  H3   C7   C8   121.61  3.000
 5QB  H3   C7   C6   119.47  3.000
 5QB  C8   C7   C6   118.92  3.000
 5QB  O    C8   C3   115.76  3.000
 5QB  C3   C8   C7   120.86  3.000
 5QB  O    C8   C7   123.39  3.000
 5QB  H6   C10  H5   108.82  3.000
 5QB  H6   C10  H4   108.79  3.000
 5QB  H5   C10  H4   108.86  3.000
 5QB  H6   C10  O1   106.33  3.000
 5QB  H5   C10  O1   111.95  3.000
 5QB  H4   C10  O1   111.98  3.000
 5QB  N    C1   C    115.72  3.000
 5QB  N    C1   O2   122.40  3.000
 5QB  C    C1   O2   121.89  3.000
 5QB  H9   C    H8   108.35  3.000
 5QB  H9   C    H7   107.34  3.000
 5QB  H8   C    H7   108.52  3.000
 5QB  H9   C    C1   109.31  3.000
 5QB  H8   C    C1   113.72  3.000
 5QB  H7   C    C1   109.39  3.000
 5QB  H10  N    C2   118.02  3.000
 5QB  H10  N    C1   119.25  3.000
 5QB  C2   N    C1   122.67  3.000
 5QB  C2   C3   C8   120.39  3.000
 5QB  C8   C3   C4   118.72  3.000
 5QB  C2   C3   C4   120.88  3.000
 5QB  C9   O    C8   118.99  3.000
 5QB  H15  C9   H14  108.86  3.000
 5QB  H15  C9   H13  108.75  3.000
 5QB  H14  C9   H13  108.77  3.000
 5QB  H15  C9   O    112.01  3.000
 5QB  H14  C9   O    112.00  3.000
 5QB  H13  C9   O    106.33  3.000
 5QB  C10  O1   C4   118.98  3.000
 5QB  H12  C2   H11  106.34  3.000
 5QB  H12  C2   C3   110.35  3.000
 5QB  H11  C2   C3   110.21  3.000
 5QB  H12  C2   N    110.15  3.000
 5QB  H11  C2   N    109.26  3.000
 5QB  C3   C2   N    110.45  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
 5QB  CONST_01  C7   C8   C3  C4      0.00   0.0  0
 5QB  CONST_02  C7   C6   C5  C4      0.00   0.0  0
 5QB  CONST_03  C8   C3   C4  C5      0.00   0.0  0
 5QB  CONST_04  C8   C7   C6  C5      0.00   0.0  0
 5QB  CONST_05  C3   C8   C7  C6      0.00   0.0  0
 5QB  CONST_06  C3   C4   C5  C6      0.00   0.0  0
 5QB  CONST_07  O    C8   C3  C4    180.00   0.0  0
 5QB  CONST_08  C2   C3   C4  C5    180.00   0.0  0
 5QB  CONST_09  O    C8   C7  C6    180.00   0.0  0
 5QB  CONST_10  O1   C4   C5  C6    180.00   0.0  0
 5QB  CONST_11  C2   C3   C8  C7    180.00   0.0  0
 5QB  CONST_12  O1   C4   C3  C8    180.00   0.0  0
 5QB  CONST_13  H2   C6   C5  C4    180.00   0.0  0
 5QB  CONST_14  H3   C7   C6  C5    180.00   0.0  0
 5QB  CONST_15  H1   C5   C6  C7    180.00   0.0  0
 5QB  CONST_16  C2   N    C1  O2      0.00   0.0  0
 5QB  CONST_17  C2   N    C1  C     180.00   0.0  0
 5QB  CONST_18  H10  N    C1  O2    180.00   0.0  0
 5QB  Var_01    N    C2   C3  C4    -92.40  30.0  2
 5QB  Var_02    C3   C4   O1  C10  -177.25  30.0  2
 5QB  Var_03    C3   C2   N   C1   -171.84  30.0  1
 5QB  Var_04    H4   C10  O1  C4    -62.86  30.0  3
 5QB  Var_05    H13  C9   O   C8   -178.59  30.0  3
 5QB  Var_06    H7   C    C1  O2     53.90  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
 5QB  plan-1  C4   0.020
 5QB  plan-1  C5   0.020
 5QB  plan-1  C6   0.020
 5QB  plan-1  C7   0.020
 5QB  plan-1  C8   0.020
 5QB  plan-1  C3   0.020
 5QB  plan-1  O    0.020
 5QB  plan-1  O1   0.020
 5QB  plan-1  H1   0.020
 5QB  plan-1  H2   0.020
 5QB  plan-1  H3   0.020
 5QB  plan-1  C2   0.020
 5QB  plan-2  O2   0.020
 5QB  plan-2  C1   0.020
 5QB  plan-2  C    0.020
 5QB  plan-2  N    0.020
 5QB  plan-2  H10  0.020
 5QB  plan-2  C2   0.020

