# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 30 22:44:03 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: N-methyl-2,3-dihydrothieno[3,4-b][1,4]dioxine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1scc2OCCOc12
#
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
 2LY  2LY  N-methyl-2,3-dihydrothieno[3,4-b][1,4]dioxine-5-carboxamide  ligand  22  13  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2LY
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
 2LY  C01  C  CH3   0  -0.511   4.2414   0.6891  -0.0150
 2LY  N02  N  NH1   0  -0.648   2.9640   0.0183  -0.0710
 2LY  C03  C  C     0   0.561   1.8228   0.6374   0.2813
 2LY  C04  C  CR5   0  -0.458   0.5969  -0.1745   0.1994
 2LY  C05  C  CR5   0   0.391  -0.6864   0.2946   0.0956
 2LY  C06  C  CR5   0   0.382  -1.6550  -0.7570   0.0394
 2LY  C07  C  CR15  0  -0.552  -1.0944  -1.9934   0.1105
 2LY  S08  S  S2    0   0.226   0.6087  -1.9046   0.2437
 2LY  O09  O  O2    0  -0.471  -2.9754  -0.5190  -0.0704
 2LY  C10  C  CH2   0  -0.236  -3.3206   0.8259   0.2530
 2LY  C11  C  CH2   0  -0.233  -2.3730   1.7932  -0.4147
 2LY  O12  O  O2    0  -0.454  -1.0319   1.5855   0.0324
 2LY  O13  O  O     0  -0.486   1.7935   1.7997   0.6644
 2LY  H1   H  HCH3  0   0.237   4.3188   1.4964  -0.7457
 2LY  H2   H  HCH3  0   0.242   4.4209   1.1049   0.9754
 2LY  H3   H  HCH3  0   0.251   5.0189  -0.0400  -0.2248
 2LY  H4   H  HNH1  0   0.404   2.9249  -0.8584  -0.5646
 2LY  H5   H  HCR5  0   0.312  -1.6004  -2.9465   0.1079
 2LY  H6   H  HCH2  0   0.270  -4.3346   0.9906  -0.1070
 2LY  H7   H  HCH2  0   0.251  -3.3106   0.9643   1.3390
 2LY  H8   H  HCH2  0   0.253  -2.4192   1.6878  -1.5031
 2LY  H9   H  HCH2  0   0.269  -2.6356   2.8167  -0.1544

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
 2LY  C10  O09  single    1.426  0.020  1.426
 2LY  C10  C11  single    1.510  0.020  1.510
 2LY  O09  C06  single    1.346  0.020  1.346
 2LY  C06  C05  aromatic  1.431  0.020  1.431
 2LY  C06  C07  aromatic  1.359  0.020  1.359
 2LY  O12  C05  single    1.338  0.020  1.338
 2LY  O12  C11  single    1.429  0.020  1.429
 2LY  C05  C04  aromatic  1.370  0.020  1.370
 2LY  C07  S08  aromatic  1.711  0.020  1.711
 2LY  N02  C01  single    1.444  0.020  1.444
 2LY  N02  C03  single    1.345  0.020  1.345
 2LY  C04  S08  aromatic  1.731  0.020  1.731
 2LY  C04  C03  single    1.473  0.020  1.473
 2LY  C03  O13  double    1.224  0.020  1.224
 2LY  C01  H1   single    0.970  0.020  1.090
 2LY  C01  H2   single    0.970  0.020  1.090
 2LY  C01  H3   single    0.970  0.020  1.090
 2LY  N02  H4   single    0.860  0.020  1.020
 2LY  C07  H5   single    0.930  0.020  1.080
 2LY  C10  H6   single    0.970  0.020  1.090
 2LY  C10  H7   single    0.970  0.020  1.090
 2LY  C11  H8   single    0.970  0.020  1.090
 2LY  C11  H9   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
 2LY  H3   C01  H2   108.30  3.000
 2LY  H3   C01  H1   108.44  3.000
 2LY  H2   C01  H1   108.34  3.000
 2LY  H3   C01  N02  108.29  3.000
 2LY  H2   C01  N02  111.01  3.000
 2LY  H1   C01  N02  112.35  3.000
 2LY  H4   N02  C03  119.75  3.000
 2LY  H4   N02  C01  117.25  3.000
 2LY  C03  N02  C01  121.77  3.000
 2LY  O13  C03  C04  121.39  3.000
 2LY  O13  C03  N02  122.63  3.000
 2LY  C04  C03  N02  115.97  3.000
 2LY  S08  C04  C05  110.52  3.000
 2LY  S08  C04  C03  122.96  3.000
 2LY  C05  C04  C03  126.52  3.000
 2LY  O12  C05  C06  122.17  3.000
 2LY  O12  C05  C04  125.15  3.000
 2LY  C06  C05  C04  112.67  3.000
 2LY  O09  C06  C07  124.72  3.000
 2LY  C07  C06  C05  112.78  3.000
 2LY  O09  C06  C05  122.50  3.000
 2LY  H5   C07  S08  120.86  3.000
 2LY  H5   C07  C06  127.58  3.000
 2LY  S08  C07  C06  111.56  3.000
 2LY  C07  S08  C04   92.47  3.000
 2LY  C10  O09  C06  112.69  3.000
 2LY  H7   C10  H6   108.51  3.000
 2LY  H7   C10  C11  110.61  3.000
 2LY  H6   C10  C11  109.97  3.000
 2LY  H7   C10  O09  110.00  3.000
 2LY  H6   C10  O09  107.05  3.000
 2LY  C11  C10  O09  110.61  3.000
 2LY  H9   C11  H8   108.56  3.000
 2LY  H9   C11  O12  106.76  3.000
 2LY  H8   C11  O12  109.68  3.000
 2LY  H9   C11  C10  110.20  3.000
 2LY  H8   C11  C10  110.59  3.000
 2LY  O12  C11  C10  110.95  3.000
 2LY  C11  O12  C05  113.42  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
 2LY  CONST_01  C07  C06  C05  C04     0.00   0.0  0
 2LY  CONST_02  C06  C07  S08  C04     0.00   0.0  0
 2LY  CONST_03  S08  C07  C06  C05     0.00   0.0  0
 2LY  CONST_04  C07  S08  C04  C05     0.00   0.0  0
 2LY  CONST_05  S08  C04  C05  C06     0.00   0.0  0
 2LY  CONST_06  C06  C05  C04  C03   180.00   0.0  0
 2LY  CONST_07  O12  C05  C04  C03     0.00   0.0  0
 2LY  CONST_08  C07  S08  C04  C03   180.00   0.0  0
 2LY  CONST_09  H5   C07  S08  C04   180.00   0.0  0
 2LY  CONST_10  C04  C03  N02  C01   180.00   0.0  0
 2LY  CONST_11  H4   N02  C03  C04     0.00   0.0  0
 2LY  CONST_12  O13  C03  N02  C01     0.00   0.0  0
 2LY  Var_01    C10  C11  O12  C05    43.74  30.0  1
 2LY  Var_02    C11  C10  O09  C06    45.80  30.0  1
 2LY  Var_03    O12  C11  C10  O09   -61.33  30.0  1
 2LY  Var_04    C05  C04  C03  N02  -158.36  30.0  1
 2LY  Var_05    H1   C01  N02  C03   -67.17  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
 2LY  plan-1  C01  0.020
 2LY  plan-1  N02  0.020
 2LY  plan-1  C03  0.020
 2LY  plan-1  C04  0.020
 2LY  plan-1  O13  0.020
 2LY  plan-1  H4   0.020
 2LY  plan-2  C03  0.020
 2LY  plan-2  C04  0.020
 2LY  plan-2  C05  0.020
 2LY  plan-2  C06  0.020
 2LY  plan-2  C07  0.020
 2LY  plan-2  S08  0.020
 2LY  plan-2  O09  0.020
 2LY  plan-2  O12  0.020
 2LY  plan-2  H5   0.020

