# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 19:11:33 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: N-[3-(thiomorpholine-4-carbonyl)phenyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1cccc(c1)C(=O)N2CCSCC2
#
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
 T4J  T4J  N-[3-(thiomorpholine-4-carbonyl)phenyl]acetamide  ligand  34  18  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T4J
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
 T4J  N1   N  NT    0  -0.443  -1.8429  -0.7210   0.0657
 T4J  C4   C  CR16  0  -0.231   1.0596   2.3996  -1.1876
 T4J  C5   C  CR16  0  -0.277   0.0206   1.4798  -1.1611
 T4J  C6   C  CR6   0  -0.065   0.2760   0.1888  -0.7183
 T4J  C7   C  CR16  0  -0.338   1.5497  -0.1926  -0.3111
 T4J  C8   C  C     0   0.511  -0.7926  -0.8613  -0.7700
 T4J  C10  C  CH2   0  -0.559  -3.0836   1.2150   0.9479
 T4J  C    C  CH3   0  -0.781   5.8626  -0.5560   1.0263
 T4J  O    O  O     0  -0.471   3.7603  -1.6726   0.8514
 T4J  C1   C  C     0   0.516   4.4063  -0.6589   0.6519
 T4J  C11  C  CH2   0  -0.562  -4.2579  -0.9009  -0.3312
 T4J  C12  C  CH2   0  -0.296  -2.9693  -1.6368  -0.0042
 T4J  C2   C  CR6   0   0.386   2.5844   0.7428  -0.3126
 T4J  C3   C  CR16  0  -0.345   2.3252   2.0409  -0.7623
 T4J  C9   C  CH2   0  -0.301  -1.9190   0.2590   1.1351
 T4J  O1   O  O     0  -0.483  -0.6809  -1.7868  -1.5616
 T4J  S    S  S2    0  -0.027  -4.6736   0.3433   0.9220
 T4J  H4   H  HCR6  0   0.266   0.8812   3.4073  -1.5387
 T4J  H5   H  HCR6  0   0.262  -0.9705   1.7685  -1.4872
 T4J  H6   H  HCR6  0   0.288   1.7239  -1.2055   0.0135
 T4J  H9   H  HCH2  0   0.291  -3.1254   1.9126   1.7843
 T4J  H10  H  HCH2  0   0.268  -2.9637   1.7976   0.0320
 T4J  H2   H  HNH1  0   0.417   4.5313   1.2424  -0.0042
 T4J  H    H  HCH3  0   0.276   5.9492  -0.5420   2.1137
 T4J  H15  H  HCH3  0   0.271   6.3927  -1.4373   0.6685
 T4J  H1   H  HCH3  0   0.255   6.3565   0.3312   0.6347
 T4J  H11  H  HCH2  0   0.271  -4.1902  -0.4318  -1.3148
 T4J  H12  H  HCH2  0   0.289  -5.0895  -1.6055  -0.3540
 T4J  H13  H  HCH2  0   0.277  -2.7735  -2.3835  -0.7698
 T4J  H14  H  HCH2  0   0.253  -3.0682  -2.1561   0.9531
 T4J  H3   H  HCR6  0   0.276   3.1228   2.7741  -0.7763
 T4J  H7   H  HCH2  0   0.262  -2.0296  -0.2712   2.0856
 T4J  H8   H  HCH2  0   0.284  -0.9908   0.8228   1.1897
 T4J  N    N  NH1   0  -0.740   3.8901   0.4714   0.1004

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
 T4J  C1   C    single    1.507  0.020  1.507
 T4J  C1   O    double    1.218  0.020  1.218
 T4J  N    C1   single    1.359  0.020  1.359
 T4J  C2   N    single    1.396  0.020  1.396
 T4J  C3   C2   aromatic  1.398  0.020  1.398
 T4J  C4   C3   aromatic  1.382  0.020  1.382
 T4J  C5   C4   aromatic  1.388  0.020  1.388
 T4J  C6   C5   aromatic  1.388  0.020  1.388
 T4J  C6   C7   aromatic  1.391  0.020  1.391
 T4J  C7   C2   aromatic  1.395  0.020  1.395
 T4J  C8   C6   single    1.499  0.020  1.499
 T4J  O1   C8   double    1.223  0.020  1.223
 T4J  C8   N1   single    1.349  0.020  1.349
 T4J  N1   C9   single    1.453  0.020  1.453
 T4J  C10  C9   single    1.518  0.020  1.518
 T4J  S    C10  single    1.813  0.020  1.813
 T4J  C11  S    single    1.814  0.020  1.814
 T4J  C12  C11  single    1.520  0.020  1.520
 T4J  N1   C12  single    1.453  0.020  1.453
 T4J  C4   H4   single    0.930  0.020  1.080
 T4J  C5   H5   single    0.930  0.020  1.080
 T4J  C7   H6   single    0.930  0.020  1.080
 T4J  C10  H9   single    0.970  0.020  1.090
 T4J  C10  H10  single    0.970  0.020  1.090
 T4J  N    H2   single    0.860  0.020  1.020
 T4J  C    H    single    0.970  0.020  1.090
 T4J  C    H15  single    0.970  0.020  1.090
 T4J  C    H1   single    0.970  0.020  1.090
 T4J  C11  H11  single    0.970  0.020  1.090
 T4J  C11  H12  single    0.970  0.020  1.090
 T4J  C12  H13  single    0.970  0.020  1.090
 T4J  C12  H14  single    0.970  0.020  1.090
 T4J  C3   H3   single    0.930  0.020  1.080
 T4J  C9   H7   single    0.970  0.020  1.090
 T4J  C9   H8   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
 T4J  C9   N1   C12  114.83  3.000
 T4J  C12  N1   C8   120.53  3.000
 T4J  C9   N1   C8   124.53  3.000
 T4J  H4   C4   C3   119.50  3.000
 T4J  H4   C4   C5   120.00  3.000
 T4J  C3   C4   C5   120.49  3.000
 T4J  H5   C5   C6   120.82  3.000
 T4J  H5   C5   C4   120.18  3.000
 T4J  C6   C5   C4   118.99  3.000
 T4J  C8   C6   C7   118.10  3.000
 T4J  C8   C6   C5   120.61  3.000
 T4J  C7   C6   C5   121.12  3.000
 T4J  H6   C7   C2   120.71  3.000
 T4J  H6   C7   C6   119.60  3.000
 T4J  C2   C7   C6   119.68  3.000
 T4J  O1   C8   C6   119.17  3.000
 T4J  O1   C8   N1   123.41  3.000
 T4J  C6   C8   N1   117.42  3.000
 T4J  H10  C10  H9   107.84  3.000
 T4J  H10  C10  S    109.92  3.000
 T4J  H9   C10  S    106.56  3.000
 T4J  H10  C10  C9   110.80  3.000
 T4J  H9   C10  C9   109.74  3.000
 T4J  S    C10  C9   111.82  3.000
 T4J  H1   C    H15  108.70  3.000
 T4J  H1   C    H    108.19  3.000
 T4J  H15  C    H    107.41  3.000
 T4J  H1   C    C1   113.88  3.000
 T4J  H15  C    C1   109.48  3.000
 T4J  H    C    C1   108.98  3.000
 T4J  O    C1   C    121.89  3.000
 T4J  O    C1   N    123.84  3.000
 T4J  C    C1   N    114.26  3.000
 T4J  H12  C11  H11  107.83  3.000
 T4J  H12  C11  S    106.44  3.000
 T4J  H11  C11  S    109.98  3.000
 T4J  H12  C11  C12  109.78  3.000
 T4J  H11  C11  C12  110.45  3.000
 T4J  S    C11  C12  112.19  3.000
 T4J  H14  C12  H13  107.85  3.000
 T4J  H14  C12  C11  109.98  3.000
 T4J  H13  C12  C11  109.50  3.000
 T4J  H14  C12  N1   109.10  3.000
 T4J  H13  C12  N1   109.09  3.000
 T4J  C11  C12  N1   111.25  3.000
 T4J  C3   C2   N    116.68  3.000
 T4J  C3   C2   C7   119.05  3.000
 T4J  N    C2   C7   124.27  3.000
 T4J  H3   C3   C2   119.74  3.000
 T4J  H3   C3   C4   119.63  3.000
 T4J  C2   C3   C4   120.64  3.000
 T4J  H8   C9   H7   107.10  3.000
 T4J  H8   C9   C10  109.54  3.000
 T4J  H7   C9   C10  109.56  3.000
 T4J  H8   C9   N1   110.00  3.000
 T4J  H7   C9   N1   108.54  3.000
 T4J  C10  C9   N1   111.97  3.000
 T4J  C11  S    C10   97.97  3.000
 T4J  H2   N    C2   114.55  3.000
 T4J  H2   N    C1   115.88  3.000
 T4J  C2   N    C1   129.55  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
 T4J  CONST_01  C7   C2   C3   C4     0.00   0.0  0
 T4J  CONST_02  C7   C6   C5   C4     0.00   0.0  0
 T4J  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 T4J  CONST_04  C2   C7   C6   C5     0.00   0.0  0
 T4J  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 T4J  CONST_06  C3   C2   C7   C6     0.00   0.0  0
 T4J  CONST_07  N    C2   C3   C4   180.00   0.0  0
 T4J  CONST_08  C8   C6   C5   C4   180.00   0.0  0
 T4J  CONST_09  N    C2   C7   C6   180.00   0.0  0
 T4J  CONST_10  C2   C7   C6   C8   180.00   0.0  0
 T4J  CONST_11  C9   N1   C8   C6     0.00   0.0  0
 T4J  CONST_12  C12  N1   C8   C6   180.00   0.0  0
 T4J  CONST_13  H3   C3   C4   C5   180.00   0.0  0
 T4J  CONST_14  H6   C7   C6   C5   180.00   0.0  0
 T4J  CONST_15  H4   C4   C5   C6   180.00   0.0  0
 T4J  CONST_16  H5   C5   C6   C7   180.00   0.0  0
 T4J  CONST_17  O1   C8   N1   C12    0.00   0.0  0
 T4J  CONST_18  O1   C8   N1   C9   180.00   0.0  0
 T4J  CONST_19  C1   N    C2   C7     0.00   0.0  0
 T4J  CONST_20  C3   C2   N    C1   180.00   0.0  0
 T4J  CONST_21  H2   N    C2   C7   180.00   0.0  0
 T4J  CONST_22  C2   N    C1   C    180.00   0.0  0
 T4J  CONST_23  C2   N    C1   O      0.00   0.0  0
 T4J  Var_01    S    C10  C9   N1    60.19  30.0  1
 T4J  Var_02    S    C11  C12  N1   -60.52  30.0  1
 T4J  Var_03    C12  N1   C9   C10  -64.62  30.0  1
 T4J  Var_04    C12  C11  S    C10   51.87  30.0  1
 T4J  Var_05    C9   C10  S    C11  -51.38  30.0  1
 T4J  Var_06    C9   N1   C12  C11   64.45  30.0  1
 T4J  Var_07    C5   C6   C8   N1   -68.76  30.0  2
 T4J  Var_08    H    C    C1   N    109.67  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
 T4J  plan-1  C4   0.020
 T4J  plan-1  C5   0.020
 T4J  plan-1  C6   0.020
 T4J  plan-1  C7   0.020
 T4J  plan-1  C8   0.020
 T4J  plan-1  C2   0.020
 T4J  plan-1  C3   0.020
 T4J  plan-1  H4   0.020
 T4J  plan-1  H5   0.020
 T4J  plan-1  H6   0.020
 T4J  plan-1  H3   0.020
 T4J  plan-1  N    0.020
 T4J  plan-2  C    0.020
 T4J  plan-2  O    0.020
 T4J  plan-2  C1   0.020
 T4J  plan-2  C2   0.020
 T4J  plan-2  H2   0.020
 T4J  plan-2  N    0.020
 T4J  plan-3  N1   0.020
 T4J  plan-3  C6   0.020
 T4J  plan-3  C8   0.020
 T4J  plan-3  C12  0.020
 T4J  plan-3  C9   0.020
 T4J  plan-3  O1   0.020

