# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 16:47:44 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: N-[(2H-1,3-benzodioxol-5-yl)methyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: 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
 T2Y  T2Y  N-[(2H-1,3-benzodioxol-5-yl)methyl]acetamide  ligand  25  14  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T2Y
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
 T2Y  C4   C  CR16  0  -0.323   0.4637  -1.8682  -0.4191
 T2Y  C5   C  CR16  0  -0.331   1.8404  -1.8520  -0.1533
 T2Y  C6   C  CR56  0   0.290   2.4180  -0.6231   0.0335
 T2Y  C7   C  CH2   0   0.069   3.8143   1.0913   0.2299
 T2Y  C8   C  CR56  0   0.313   1.6779   0.5489  -0.0401
 T2Y  N    N  NH1   0  -0.621  -2.5209  -0.1565   0.2838
 T2Y  C    C  CH3   0  -0.777  -4.3321   1.0127   1.3624
 T2Y  O    O  O     0  -0.509  -4.1848   0.6687  -1.0002
 T2Y  C1   C  C     0   0.523  -3.6795   0.5009   0.1022
 T2Y  C3   C  CR6   0   0.057  -0.2828  -0.7028  -0.4961
 T2Y  C9   C  CR16  0  -0.368   0.3329   0.5463  -0.3011
 T2Y  O1   O  O     0  -0.485   3.7062  -0.3225   0.3285
 T2Y  O2   O  O     0  -0.486   2.4896   1.6066   0.2041
 T2Y  H5   H  HCR6  0   0.257  -0.0257  -2.8223  -0.5698
 T2Y  H6   H  HCR6  0   0.273   2.4112  -2.7683  -0.0888
 T2Y  H7   H  HCH2  0   0.246   4.3459   1.4821   1.0971
 T2Y  H8   H  HCH2  0   0.233   4.3363   1.3609  -0.6948
 T2Y  H2   H  HNH1  0   0.400  -2.1973  -0.3120   1.2247
 T2Y  H    H  HCH3  0   0.268  -5.2219   0.4181   1.5739
 T2Y  H1   H  HCH3  0   0.248  -3.6838   0.9742   2.2358
 T2Y  H10  H  HCH3  0   0.263  -4.6574   2.0413   1.2135
 T2Y  H4   H  HCH2  0   0.256  -2.0598  -1.8015  -0.9413
 T2Y  H3   H  HCH2  0   0.262  -1.9892  -0.2266  -1.7091
 T2Y  H9   H  HCR6  0   0.269  -0.2356   1.4665  -0.3534
 T2Y  C2   C  CH2   0  -0.329  -1.7585  -0.7614  -0.7868

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
 T2Y  C1  C    single    1.509  0.020  1.509
 T2Y  O   C1   double    1.224  0.020  1.224
 T2Y  C1  N    single    1.344  0.020  1.344
 T2Y  N   C2   single    1.447  0.020  1.447
 T2Y  C2  C3   single    1.505  0.020  1.505
 T2Y  C3  C4   aromatic  1.386  0.020  1.386
 T2Y  C5  C4   aromatic  1.402  0.020  1.402
 T2Y  C6  C5   aromatic  1.371  0.020  1.371
 T2Y  O1  C6   single    1.355  0.020  1.355
 T2Y  C7  O1   single    1.421  0.020  1.421
 T2Y  O2  C7   single    1.422  0.020  1.422
 T2Y  C8  O2   single    1.355  0.020  1.355
 T2Y  C8  C6   aromatic  1.388  0.020  1.388
 T2Y  C9  C8   aromatic  1.370  0.020  1.370
 T2Y  C3  C9   aromatic  1.406  0.020  1.406
 T2Y  C4  H5   single    0.930  0.020  1.080
 T2Y  C5  H6   single    0.930  0.020  1.080
 T2Y  C7  H7   single    0.970  0.020  1.090
 T2Y  C7  H8   single    0.970  0.020  1.090
 T2Y  N   H2   single    0.860  0.020  1.020
 T2Y  C   H    single    0.970  0.020  1.090
 T2Y  C   H1   single    0.970  0.020  1.090
 T2Y  C   H10  single    0.970  0.020  1.090
 T2Y  C2  H4   single    0.970  0.020  1.090
 T2Y  C2  H3   single    0.970  0.020  1.090
 T2Y  C9  H9   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
 T2Y  H5   C4  C3  119.32  3.000
 T2Y  H5   C4  C5  118.71  3.000
 T2Y  C3   C4  C5  121.97  3.000
 T2Y  H6   C5  C6  121.94  3.000
 T2Y  H6   C5  C4  121.31  3.000
 T2Y  C6   C5  C4  116.74  3.000
 T2Y  O1   C6  C8  109.33  3.000
 T2Y  C8   C6  C5  121.68  3.000
 T2Y  O1   C6  C5  128.98  3.000
 T2Y  H8   C7  H7  110.55  3.000
 T2Y  H8   C7  O2  109.85  3.000
 T2Y  H7   C7  O2  109.82  3.000
 T2Y  H8   C7  O1  109.85  3.000
 T2Y  H7   C7  O1  109.79  3.000
 T2Y  O2   C7  O1  106.91  3.000
 T2Y  O2   C8  C9  128.59  3.000
 T2Y  C9   C8  C6  122.13  3.000
 T2Y  O2   C8  C6  109.27  3.000
 T2Y  H2   N   C2  117.22  3.000
 T2Y  H2   N   C1  118.60  3.000
 T2Y  C2   N   C1  123.96  3.000
 T2Y  H10  C   H1  108.73  3.000
 T2Y  H10  C   H   107.32  3.000
 T2Y  H1   C   H   108.12  3.000
 T2Y  H10  C   C1  109.60  3.000
 T2Y  H1   C   C1  113.62  3.000
 T2Y  H    C   C1  109.26  3.000
 T2Y  O    C1  C   121.82  3.000
 T2Y  O    C1  N   122.98  3.000
 T2Y  C    C1  N   115.20  3.000
 T2Y  C9   C3  C2  119.38  3.000
 T2Y  C9   C3  C4  120.22  3.000
 T2Y  C2   C3  C4  120.40  3.000
 T2Y  H9   C9  C3  121.21  3.000
 T2Y  H9   C9  C8  121.53  3.000
 T2Y  C3   C9  C8  117.26  3.000
 T2Y  C7   O1  C6  106.13  3.000
 T2Y  C8   O2  C7  106.17  3.000
 T2Y  H3   C2  H4  106.77  3.000
 T2Y  H3   C2  C3  110.59  3.000
 T2Y  H4   C2  C3  109.53  3.000
 T2Y  H3   C2  N   108.01  3.000
 T2Y  H4   C2  N   110.91  3.000
 T2Y  C3   C2  N   110.94  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
 T2Y  CONST_01  C8  C9  C3  C4     0.00   0.0  0
 T2Y  CONST_02  C8  C6  C5  C4     0.00   0.0  0
 T2Y  CONST_03  C9  C3  C4  C5     0.00   0.0  0
 T2Y  CONST_04  C9  C8  C6  C5     0.00   0.0  0
 T2Y  CONST_05  C3  C4  C5  C6     0.00   0.0  0
 T2Y  CONST_06  C3  C9  C8  C6     0.00   0.0  0
 T2Y  CONST_07  C2  C3  C4  C5   180.00   0.0  0
 T2Y  CONST_08  C2  C3  C9  C8   180.00   0.0  0
 T2Y  CONST_09  H9  C9  C3  C4   180.00   0.0  0
 T2Y  CONST_10  H5  C4  C5  C6   180.00   0.0  0
 T2Y  CONST_11  H6  C5  C6  C8   180.00   0.0  0
 T2Y  CONST_12  C2  N   C1  C    180.00   0.0  0
 T2Y  CONST_13  C2  N   C1  O      0.00   0.0  0
 T2Y  CONST_14  H2  N   C1  C      0.00   0.0  0
 T2Y  Var_01    O2  C7  O1  C6    14.44  30.0  1
 T2Y  Var_02    C8  C6  O1  C7    -9.14  30.0  1
 T2Y  Var_03    C9  C8  O2  C7  -172.22  30.0  1
 T2Y  Var_04    O1  C7  O2  C8   -14.35  30.0  1
 T2Y  Var_05    N   C2  C3  C4   120.87  30.0  2
 T2Y  Var_06    C3  C2  N   C1   147.36  30.0  3
 T2Y  Var_07    H   C   C1  N   -108.41  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
 T2Y  plan-1  N   0.020
 T2Y  plan-1  C   0.020
 T2Y  plan-1  O   0.020
 T2Y  plan-1  C1  0.020
 T2Y  plan-1  H2  0.020
 T2Y  plan-1  C2  0.020
 T2Y  plan-2  C4  0.020
 T2Y  plan-2  C5  0.020
 T2Y  plan-2  C6  0.020
 T2Y  plan-2  C8  0.020
 T2Y  plan-2  C3  0.020
 T2Y  plan-2  C9  0.020
 T2Y  plan-2  O1  0.020
 T2Y  plan-2  O2  0.020
 T2Y  plan-2  H5  0.020
 T2Y  plan-2  H6  0.020
 T2Y  plan-2  H9  0.020
 T2Y  plan-2  C2  0.020

