# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 13:33:05 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 2-amino-5-(2,3-dihydrothieno[3,4-b][1,4]dioxin-5-yl)-N-[2-(dimethylamino)ethyl]pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CCNC(=O)c1cc(cnc1N)c2scc3OCCOc23
#
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
 WTJ  WTJ  2-amino-5-(2,3-dihydrothieno[3,4-b][1,4]dioxin-5-yl)-N-[2-(dimethylamino)ethyl]pyridine-3-carboxamide  ligand  44  24  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_WTJ
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
 WTJ  C01   C  CH3   0  -0.520   6.0792   2.9881  -1.1303
 WTJ  N02   N  NT    0  -0.411   5.9228   1.7079  -0.4722
 WTJ  C03   C  CH3   0  -0.527   6.5183   1.7363   0.8476
 WTJ  C04   C  CH2   0  -0.304   4.5342   1.2972  -0.4437
 WTJ  C05   C  CH2   0  -0.256   4.3846  -0.1979  -0.1933
 WTJ  N06   N  NH1   0  -0.650   2.9794  -0.5447  -0.1698
 WTJ  C07   C  C     0   0.556   2.5357  -1.7255   0.2872
 WTJ  O08   O  O     0  -0.503   3.3013  -2.5990   0.6879
 WTJ  C09   C  CR6   0  -0.178   1.0589  -1.9091   0.2984
 WTJ  C10   C  CR16  0  -0.238   0.2075  -0.8361   0.4955
 WTJ  C11   C  CR6   0   0.054  -1.1756  -1.0006   0.5333
 WTJ  C12   C  CR5   0  -0.371  -2.0812   0.1143   0.7836
 WTJ  S13   S  S2    0   0.205  -1.6668   1.3640   1.9078
 WTJ  C14   C  CR15  0  -0.572  -3.1242   2.2248   1.6213
 WTJ  C15   C  CR5   0   0.388  -3.9020   1.5755   0.7151
 WTJ  O16   O  O2    0  -0.475  -5.1091   2.0009   0.2921
 WTJ  C17   C  CH2   0  -0.232  -5.5302   1.3658  -0.9129
 WTJ  C18   C  CH2   0  -0.232  -5.2858  -0.1244  -0.8506
 WTJ  O19   O  O2    0  -0.470  -3.8962  -0.4047  -0.6994
 WTJ  C20   C  CR5   0   0.339  -3.3050   0.3694   0.2323
 WTJ  C21   C  CR16  0  -0.089  -1.6369  -2.3038   0.3520
 WTJ  N22   N  N     0  -0.448  -0.8551  -3.3490   0.1631
 WTJ  C23   C  CR6   0   0.452   0.4726  -3.1932   0.1492
 WTJ  N24   N  NH2   0  -0.829   1.2022  -4.3061  -0.0610
 WTJ  H011  H  HCH3  0   0.234   7.1370   3.2489  -1.1848
 WTJ  H012  H  HCH3  0   0.234   5.6948   2.9369  -2.1499
 WTJ  H013  H  HCH3  0   0.193   5.5600   3.8113  -0.6157
 WTJ  H031  H  HCH3  0   0.194   6.0215   2.4459   1.5283
 WTJ  H032  H  HCH3  0   0.235   6.4894   0.7524   1.3159
 WTJ  H033  H  HCH3  0   0.236   7.5668   2.0266   0.7716
 WTJ  H041  H  HCH2  0   0.204   3.9501   1.8569   0.3074
 WTJ  H042  H  HCH2  0   0.242   4.0938   1.5267  -1.4181
 WTJ  H051  H  HCH2  0   0.237   4.9136  -0.7519  -0.9744
 WTJ  H052  H  HCH2  0   0.243   4.8270  -0.4818   0.7614
 WTJ  H06   H  HNH1  0   0.408   2.3433   0.0528  -0.6733
 WTJ  H10   H  HCR6  0   0.265   0.6228   0.1553   0.6376
 WTJ  H21   H  HCR6  0   0.263  -2.7009  -2.5109   0.3781
 WTJ  H14   H  HCR5  0   0.303  -3.3335   3.1532   2.1291
 WTJ  H171  H  HCH2  0   0.266  -6.5952   1.5635  -1.0221
 WTJ  H172  H  HCH2  0   0.247  -5.0062   1.8033  -1.7690
 WTJ  H181  H  HCH2  0   0.247  -5.8484  -0.5707  -0.0241
 WTJ  H182  H  HCH2  0   0.264  -5.6054  -0.5937  -1.7795
 WTJ  H241  H  HNH2  0   0.404   2.1807  -4.2975   0.1710
 WTJ  H242  H  HNH2  0   0.390   0.7227  -5.1894  -0.0150

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
 WTJ  C01  N02   single    1.448  0.020  1.448
 WTJ  N02  C03   single    1.448  0.020  1.448
 WTJ  N02  C04   single    1.448  0.020  1.448
 WTJ  C04  C05   single    1.523  0.020  1.523
 WTJ  C05  N06   single    1.448  0.020  1.448
 WTJ  N06  C07   single    1.342  0.020  1.342
 WTJ  C07  O08   double    1.229  0.020  1.229
 WTJ  C07  C09   single    1.488  0.020  1.488
 WTJ  C09  C10   aromatic  1.384  0.020  1.384
 WTJ  C09  C23   aromatic  1.419  0.020  1.419
 WTJ  C10  C11   aromatic  1.393  0.020  1.393
 WTJ  C11  C12   single    1.458  0.020  1.458
 WTJ  C11  C21   aromatic  1.394  0.020  1.394
 WTJ  C12  S13   aromatic  1.731  0.020  1.731
 WTJ  C12  C20   aromatic  1.366  0.020  1.366
 WTJ  S13  C14   aromatic  1.717  0.020  1.717
 WTJ  C14  C15   aromatic  1.359  0.020  1.359
 WTJ  C15  O16   single    1.348  0.020  1.348
 WTJ  C15  C20   aromatic  1.430  0.020  1.430
 WTJ  O16  C17   single    1.426  0.020  1.426
 WTJ  C17  C18   single    1.511  0.020  1.511
 WTJ  C18  O19   single    1.426  0.020  1.426
 WTJ  O19  C20   single    1.348  0.020  1.348
 WTJ  C21  N22   aromatic  1.319  0.020  1.319
 WTJ  N22  C23   aromatic  1.337  0.020  1.337
 WTJ  C23  N24   single    1.347  0.020  1.347
 WTJ  C01  H011  single    0.970  0.020  1.090
 WTJ  C01  H012  single    0.970  0.020  1.090
 WTJ  C01  H013  single    0.970  0.020  1.090
 WTJ  C03  H031  single    0.970  0.020  1.090
 WTJ  C03  H032  single    0.970  0.020  1.090
 WTJ  C03  H033  single    0.970  0.020  1.090
 WTJ  C04  H041  single    0.970  0.020  1.090
 WTJ  C04  H042  single    0.970  0.020  1.090
 WTJ  C05  H051  single    0.970  0.020  1.090
 WTJ  C05  H052  single    0.970  0.020  1.090
 WTJ  N06  H06   single    0.860  0.020  1.020
 WTJ  C10  H10   single    0.930  0.020  1.080
 WTJ  C21  H21   single    0.930  0.020  1.080
 WTJ  C14  H14   single    0.930  0.020  1.080
 WTJ  C17  H171  single    0.970  0.020  1.090
 WTJ  C17  H172  single    0.970  0.020  1.090
 WTJ  C18  H181  single    0.970  0.020  1.090
 WTJ  C18  H182  single    0.970  0.020  1.090
 WTJ  N24  H241  single    0.890  0.020  1.040
 WTJ  N24  H242  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
 WTJ  H013  C01  H012  107.80  3.000
 WTJ  H013  C01  H011  107.57  3.000
 WTJ  H012  C01  H011  107.83  3.000
 WTJ  H013  C01  N02   113.44  3.000
 WTJ  H012  C01  N02   110.20  3.000
 WTJ  H011  C01  N02   109.81  3.000
 WTJ  C04   N02  C03   112.45  3.000
 WTJ  C04   N02  C01   111.30  3.000
 WTJ  C03   N02  C01   110.64  3.000
 WTJ  H033  C03  H032  107.20  3.000
 WTJ  H033  C03  H031  107.76  3.000
 WTJ  H032  C03  H031  107.69  3.000
 WTJ  H033  C03  N02   109.70  3.000
 WTJ  H032  C03  N02   111.28  3.000
 WTJ  H031  C03  N02   112.97  3.000
 WTJ  H042  C04  H041  106.67  3.000
 WTJ  H042  C04  C05   108.23  3.000
 WTJ  H041  C04  C05   109.50  3.000
 WTJ  H042  C04  N02   108.00  3.000
 WTJ  H041  C04  N02   112.14  3.000
 WTJ  C05   C04  N02   112.06  3.000
 WTJ  H052  C05  H051  107.29  3.000
 WTJ  H052  C05  N06   108.51  3.000
 WTJ  H051  C05  N06   111.08  3.000
 WTJ  H052  C05  C04   111.09  3.000
 WTJ  H051  C05  C04   109.40  3.000
 WTJ  N06   C05  C04   109.45  3.000
 WTJ  H06   N06  C07   118.91  3.000
 WTJ  H06   N06  C05   117.56  3.000
 WTJ  C07   N06  C05   122.50  3.000
 WTJ  C09   C07  O08   121.88  3.000
 WTJ  C09   C07  N06   116.06  3.000
 WTJ  O08   C07  N06   122.05  3.000
 WTJ  C23   C09  C10   117.54  3.000
 WTJ  C23   C09  C07   121.38  3.000
 WTJ  C10   C09  C07   121.06  3.000
 WTJ  H10   C10  C11   118.99  3.000
 WTJ  H10   C10  C09   119.48  3.000
 WTJ  C11   C10  C09   121.53  3.000
 WTJ  C21   C11  C12   122.11  3.000
 WTJ  C21   C11  C10   115.80  3.000
 WTJ  C12   C11  C10   122.06  3.000
 WTJ  C20   C12  S13   109.98  3.000
 WTJ  C20   C12  C11   129.04  3.000
 WTJ  S13   C12  C11   120.98  3.000
 WTJ  C14   S13  C12    92.89  3.000
 WTJ  H14   C14  C15   127.87  3.000
 WTJ  H14   C14  S13   121.18  3.000
 WTJ  C15   C14  S13   110.95  3.000
 WTJ  C20   C15  O16   122.29  3.000
 WTJ  C20   C15  C14   112.90  3.000
 WTJ  O16   C15  C14   124.81  3.000
 WTJ  C17   O16  C15   112.90  3.000
 WTJ  H172  C17  H171  108.49  3.000
 WTJ  H172  C17  C18   110.42  3.000
 WTJ  H171  C17  C18   109.96  3.000
 WTJ  H172  C17  O16   109.97  3.000
 WTJ  H171  C17  O16   107.03  3.000
 WTJ  C18   C17  O16   110.89  3.000
 WTJ  H182  C18  H181  108.52  3.000
 WTJ  H182  C18  O19   106.97  3.000
 WTJ  H181  C18  O19   109.92  3.000
 WTJ  H182  C18  C17   110.02  3.000
 WTJ  H181  C18  C17   110.48  3.000
 WTJ  O19   C18  C17   110.85  3.000
 WTJ  C20   O19  C18   112.82  3.000
 WTJ  O19   C20  C15   122.32  3.000
 WTJ  O19   C20  C12   124.38  3.000
 WTJ  C15   C20  C12   113.28  3.000
 WTJ  H21   C21  N22   115.70  3.000
 WTJ  H21   C21  C11   120.01  3.000
 WTJ  N22   C21  C11   124.29  3.000
 WTJ  C23   N22  C21   119.85  3.000
 WTJ  N24   C23  N22   116.30  3.000
 WTJ  N24   C23  C09   122.68  3.000
 WTJ  N22   C23  C09   120.97  3.000
 WTJ  H242  N24  H241  117.43  3.000
 WTJ  H242  N24  C23   117.39  3.000
 WTJ  H241  N24  C23   118.94  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
 WTJ  CONST_01  C12   C11  C10  C09   180.00   0.0  0
 WTJ  CONST_02  C21   C11  C10  C09     0.00   0.0  0
 WTJ  CONST_03  C21   N22  C23  C09     0.00   0.0  0
 WTJ  CONST_04  N22   C23  C09  C10     0.00   0.0  0
 WTJ  CONST_07  N22   C21  C11  C10     0.00   0.0  0
 WTJ  CONST_08  C23   C09  C10  C11     0.00   0.0  0
 WTJ  CONST_09  C14   S13  C12  C11   180.00   0.0  0
 WTJ  CONST_10  C15   C20  C12  C11   180.00   0.0  0
 WTJ  CONST_11  C23   N22  C21  C11     0.00   0.0  0
 WTJ  CONST_12  N22   C21  C11  C12   180.00   0.0  0
 WTJ  CONST_13  C15   C14  S13  C12     0.00   0.0  0
 WTJ  CONST_14  C14   C15  C20  C12     0.00   0.0  0
 WTJ  CONST_16  C15   C20  C12  S13     0.00   0.0  0
 WTJ  CONST_17  C20   C15  C14  S13     0.00   0.0  0
 WTJ  CONST_18  C20   C12  S13  C14     0.00   0.0  0
 WTJ  CONST_20  O19   C20  C12  C11     0.00   0.0  0
 WTJ  CONST_21  C11   C10  C09  C07   180.00   0.0  0
 WTJ  CONST_22  N22   C23  C09  C07   180.00   0.0  0
 WTJ  CONST_23  N24   C23  C09  C10   180.00   0.0  0
 WTJ  CONST_24  N24   C23  N22  C21   180.00   0.0  0
 WTJ  CONST_25  H21   C21  C11  C10   180.00   0.0  0
 WTJ  CONST_26  H10   C10  C11  C12     0.00   0.0  0
 WTJ  CONST_27  H14   C14  S13  C12   180.00   0.0  0
 WTJ  CONST_29  H242  N24  C23  C09   180.00   0.0  0
 WTJ  CONST_30  C09   C07  N06  C05   180.00   0.0  0
 WTJ  CONST_31  H06   N06  C07  C09     0.00   0.0  0
 WTJ  CONST_32  O08   C07  N06  C05     0.00   0.0  0
 WTJ  Var_01    C18   C17  O16  C15    45.08  30.0  1
 WTJ  Var_02    O19   C18  C17  O16   -61.48  30.0  1
 WTJ  Var_03    C20   C15  O16  C17   -16.75  30.0  1
 WTJ  Var_04    C10   C09  C07  N06   -31.36  30.0  2
 WTJ  Var_05    C05   C04  N02  C01   161.05  30.0  3
 WTJ  Var_06    N06   C05  C04  N02   179.73  30.0  3
 WTJ  Var_07    C07   N06  C05  C04  -166.53  30.0  3
 WTJ  Var_08    H031  C03  N02  C01    64.02  30.0  3
 WTJ  Var_09    H011  C01  N02  C03    57.17  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
 WTJ  plan-1  C07   0.020
 WTJ  plan-1  C09   0.020
 WTJ  plan-1  C10   0.020
 WTJ  plan-1  C11   0.020
 WTJ  plan-1  C12   0.020
 WTJ  plan-1  C21   0.020
 WTJ  plan-1  N22   0.020
 WTJ  plan-1  C23   0.020
 WTJ  plan-1  N24   0.020
 WTJ  plan-1  H10   0.020
 WTJ  plan-1  H21   0.020
 WTJ  plan-2  C11   0.020
 WTJ  plan-2  C12   0.020
 WTJ  plan-2  S13   0.020
 WTJ  plan-2  C14   0.020
 WTJ  plan-2  C15   0.020
 WTJ  plan-2  O16   0.020
 WTJ  plan-2  O19   0.020
 WTJ  plan-2  C20   0.020
 WTJ  plan-2  H14   0.020
 WTJ  plan-3  C05   0.020
 WTJ  plan-3  N06   0.020
 WTJ  plan-3  C07   0.020
 WTJ  plan-3  O08   0.020
 WTJ  plan-3  C09   0.020
 WTJ  plan-3  H06   0.020
 WTJ  plan-4  C23   0.020
 WTJ  plan-4  N24   0.020
 WTJ  plan-4  H241  0.020
 WTJ  plan-4  H242  0.020

