# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 10:44:15 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: N,N-diethyl-5,5-dimethyl-2-[(thiophen-2-ylcarbonyl)amino]-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(CC)C(=O)c1c(NC(=O)c2sccc2)sc3CCC(C)(C)Cc13
#
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
 K03  K03  N,N-diethyl-5,5-dimethyl-2-[(thiophen-2-ylcarbonyl)amino]-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide  ligand  52  26  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_K03
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
 K03  O12   O  O     0  -0.447  -2.0302   1.0261   0.7782
 K03  C11   C  C     0   0.568  -1.6183   0.1950  -0.0128
 K03  C13   C  CR5   0  -0.348  -2.5225  -0.6188  -0.8356
 K03  S17   S  S2    0   0.245  -2.0678  -2.1166  -1.5607
 K03  C16   C  CR15  0  -0.444  -3.6228  -2.3261  -2.2305
 K03  C15   C  CR15  0  -0.172  -4.4604  -1.2996  -1.9054
 K03  C14   C  CR15  0  -0.176  -3.8319  -0.3231  -1.0979
 K03  N10   N  NH1   0  -0.747  -0.2897  -0.0374  -0.1840
 K03  C9    C  CR5   0   0.058   0.7154   0.5663   0.5561
 K03  S18   S  S2    0   0.242   0.4394   1.9081   1.6121
 K03  C19   C  CR5   0  -0.276   2.1214   1.9960   1.9981
 K03  C26   C  CR5   0   0.225   2.8428   1.0393   1.3573
 K03  C25   C  CH2   0  -0.472   4.3271   0.9139   1.5106
 K03  C22   C  CT    0  -0.107   4.8447   1.6259   2.7691
 K03  C24   C  CH3   0  -0.642   4.5044   0.8032   4.0123
 K03  C23   C  CH3   0  -0.645   6.3606   1.7730   2.6674
 K03  C21   C  CH2   0  -0.411   4.2052   3.0195   2.8513
 K03  C20   C  CH2   0  -0.500   2.6805   2.9863   2.9654
 K03  C8    C  CR5   0  -0.085   2.0288   0.2048   0.5313
 K03  C6    C  C     0   0.463   2.5785  -0.8812  -0.3356
 K03  O7    O  O     0  -0.485   2.8157  -0.6564  -1.5179
 K03  N3    N  NT    0  -0.417   2.7936  -2.0715   0.2466
 K03  C4    C  CH2   0  -0.322   3.3807  -3.1548  -0.5307
 K03  C5    C  CH3   0  -0.653   4.8993  -3.1605  -0.4504
 K03  C2    C  CH2   0  -0.326   2.4238  -2.3834   1.6210
 K03  C1    C  CH3   0  -0.649   1.0320  -2.9867   1.7285
 K03  H10   H  HNH1  0   0.419   0.0131  -0.5601  -0.9939
 K03  H14   H  HCR5  0   0.280  -4.3217   0.5679  -0.7325
 K03  H16   H  HCR5  0   0.312  -3.8427  -3.2033  -2.8193
 K03  H15   H  HCR5  0   0.279  -5.4892  -1.2466  -2.2293
 K03  H201  H  HCH2  0   0.259   2.2779   3.9851   2.7794
 K03  H202  H  HCH2  0   0.249   2.3772   2.7259   3.9842
 K03  H251  H  HCH2  0   0.235   4.6256  -0.1400   1.5390
 K03  H252  H  HCH2  0   0.252   4.8151   1.3337   0.6233
 K03  H241  H  HCH3  0   0.226   4.8647   1.2989   4.9163
 K03  H242  H  HCH3  0   0.232   3.4307   0.6440   4.1278
 K03  H243  H  HCH3  0   0.225   4.9776  -0.1798   3.9630
 K03  H231  H  HCH3  0   0.224   6.6417   2.3904   1.8113
 K03  H232  H  HCH3  0   0.227   6.7716   2.2400   3.5647
 K03  H233  H  HCH3  0   0.225   6.8445   0.8010   2.5478
 K03  H211  H  HCH2  0   0.230   4.4844   3.5865   1.9575
 K03  H212  H  HCH2  0   0.235   4.6170   3.5633   3.7060
 K03  H4C1  H  HCH2  0   0.251   2.9795  -4.0932  -0.1463
 K03  H4C2  H  HCH2  0   0.254   3.0538  -3.0744  -1.5660
 K03  H2C1  H  HCH2  0   0.258   3.1668  -3.0811   2.0107
 K03  H2C2  H  HCH2  0   0.265   2.4890  -1.4906   2.2403
 K03  H5C1  H  HCH3  0   0.231   5.3172  -2.2369  -0.8510
 K03  H5C2  H  HCH3  0   0.227   5.2425  -3.2714   0.5793
 K03  H5C3  H  HCH3  0   0.236   5.3034  -3.9929  -1.0269
 K03  H1C1  H  HCH3  0   0.224   0.2705  -2.2730   1.4127
 K03  H1C2  H  HCH3  0   0.232   0.9348  -3.8822   1.1134
 K03  H1C3  H  HCH3  0   0.238   0.8226  -3.2645   2.7613

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
 K03  O12  C11   double  1.219  0.020  1.219
 K03  C11  C13   single  1.469  0.020  1.469
 K03  C13  S17   single  1.725  0.020  1.725
 K03  S17  C16   single  1.706  0.020  1.706
 K03  C16  C15   double  1.364  0.020  1.364
 K03  C13  C14   double  1.368  0.020  1.368
 K03  C15  C14   single  1.414  0.020  1.414
 K03  C11  N10   single  1.360  0.020  1.360
 K03  N10  C9    single  1.387  0.020  1.387
 K03  C9   S18   single  1.730  0.020  1.730
 K03  S18  C19   single  1.728  0.020  1.728
 K03  C19  C26   double  1.359  0.020  1.359
 K03  C26  C25   single  1.497  0.020  1.497
 K03  C25  C22   single  1.536  0.020  1.536
 K03  C22  C24   single  1.529  0.020  1.529
 K03  C22  C23   single  1.526  0.020  1.526
 K03  C22  C21   single  1.535  0.020  1.535
 K03  C19  C20   single  1.493  0.020  1.493
 K03  C21  C20   single  1.529  0.020  1.529
 K03  C9   C8    double  1.362  0.020  1.362
 K03  C26  C8    single  1.429  0.020  1.429
 K03  C8   C6    single  1.494  0.020  1.494
 K03  C6   O7    double  1.227  0.020  1.227
 K03  C6   N3    single  1.342  0.020  1.342
 K03  N3   C4    single  1.457  0.020  1.457
 K03  C4   C5    single  1.521  0.020  1.521
 K03  N3   C2    single  1.457  0.020  1.457
 K03  C2   C1    single  1.521  0.020  1.521
 K03  N10  H10   single  0.860  0.020  1.020
 K03  C14  H14   single  0.930  0.020  1.080
 K03  C16  H16   single  0.930  0.020  1.080
 K03  C15  H15   single  0.930  0.020  1.080
 K03  C20  H201  single  0.970  0.020  1.090
 K03  C20  H202  single  0.970  0.020  1.090
 K03  C25  H251  single  0.970  0.020  1.090
 K03  C25  H252  single  0.970  0.020  1.090
 K03  C24  H241  single  0.970  0.020  1.090
 K03  C24  H242  single  0.970  0.020  1.090
 K03  C24  H243  single  0.970  0.020  1.090
 K03  C23  H231  single  0.970  0.020  1.090
 K03  C23  H232  single  0.970  0.020  1.090
 K03  C23  H233  single  0.970  0.020  1.090
 K03  C21  H211  single  0.970  0.020  1.090
 K03  C21  H212  single  0.970  0.020  1.090
 K03  C4   H4C1  single  0.970  0.020  1.090
 K03  C4   H4C2  single  0.970  0.020  1.090
 K03  C2   H2C1  single  0.970  0.020  1.090
 K03  C2   H2C2  single  0.970  0.020  1.090
 K03  C5   H5C1  single  0.970  0.020  1.090
 K03  C5   H5C2  single  0.970  0.020  1.090
 K03  C5   H5C3  single  0.970  0.020  1.090
 K03  C1   H1C1  single  0.970  0.020  1.090
 K03  C1   H1C2  single  0.970  0.020  1.090
 K03  C1   H1C3  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
 K03  N10   C11  C13   115.87  3.000
 K03  N10   C11  O12   121.90  3.000
 K03  C13   C11  O12   122.23  3.000
 K03  C14   C13  S17   111.07  3.000
 K03  C14   C13  C11   125.24  3.000
 K03  S17   C13  C11   123.66  3.000
 K03  C16   S17  C13    91.80  3.000
 K03  H16   C16  C15   128.07  3.000
 K03  H16   C16  S17   119.98  3.000
 K03  C15   C16  S17   111.94  3.000
 K03  H15   C15  C14   124.10  3.000
 K03  H15   C15  C16   123.39  3.000
 K03  C14   C15  C16   112.50  3.000
 K03  H14   C14  C15   124.12  3.000
 K03  H14   C14  C13   123.19  3.000
 K03  C15   C14  C13   112.68  3.000
 K03  H10   N10  C9    115.84  3.000
 K03  H10   N10  C11   118.83  3.000
 K03  C9    N10  C11   124.53  3.000
 K03  C8    C9   S18   111.76  3.000
 K03  C8    C9   N10   125.00  3.000
 K03  S18   C9   N10   123.23  3.000
 K03  C19   S18  C9     91.17  3.000
 K03  C20   C19  C26   125.01  3.000
 K03  C20   C19  S18   122.89  3.000
 K03  C26   C19  S18   112.06  3.000
 K03  C8    C26  C25   125.10  3.000
 K03  C8    C26  C19   112.42  3.000
 K03  C25   C26  C19   122.48  3.000
 K03  H252  C25  H251  105.55  3.000
 K03  H252  C25  C22   109.62  3.000
 K03  H251  C25  C22   109.45  3.000
 K03  H252  C25  C26   109.04  3.000
 K03  H251  C25  C26   110.68  3.000
 K03  C22   C25  C26   112.28  3.000
 K03  C21   C22  C23   109.25  3.000
 K03  C21   C22  C24   110.61  3.000
 K03  C23   C22  C24   109.09  3.000
 K03  C21   C22  C25   108.92  3.000
 K03  C23   C22  C25   108.95  3.000
 K03  C24   C22  C25   109.99  3.000
 K03  H243  C24  H242  107.44  3.000
 K03  H243  C24  H241  107.64  3.000
 K03  H242  C24  H241  107.65  3.000
 K03  H243  C24  C22   110.56  3.000
 K03  H242  C24  C22   112.54  3.000
 K03  H241  C24  C22   110.81  3.000
 K03  H233  C23  H232  107.69  3.000
 K03  H233  C23  H231  107.65  3.000
 K03  H232  C23  H231  107.79  3.000
 K03  H233  C23  C22   111.19  3.000
 K03  H232  C23  C22   111.12  3.000
 K03  H231  C23  C22   111.24  3.000
 K03  H212  C21  H211  106.53  3.000
 K03  H212  C21  C20   109.14  3.000
 K03  H211  C21  C20   109.05  3.000
 K03  H212  C21  C22   109.66  3.000
 K03  H211  C21  C22   108.67  3.000
 K03  C20   C21  C22   113.55  3.000
 K03  H202  C20  H201  105.89  3.000
 K03  H202  C20  C21   110.55  3.000
 K03  H201  C20  C21   109.56  3.000
 K03  H202  C20  C19   109.96  3.000
 K03  H201  C20  C19   110.98  3.000
 K03  C21   C20  C19   109.84  3.000
 K03  C6    C8   C26   123.38  3.000
 K03  C6    C8   C9    123.92  3.000
 K03  C26   C8   C9    112.57  3.000
 K03  N3    C6   O7    123.33  3.000
 K03  N3    C6   C8    116.86  3.000
 K03  O7    C6   C8    119.81  3.000
 K03  C2    N3   C4    116.51  3.000
 K03  C2    N3   C6    123.93  3.000
 K03  C4    N3   C6    119.51  3.000
 K03  H4C2  C4   H4C1  106.76  3.000
 K03  H4C2  C4   C5    110.50  3.000
 K03  H4C1  C4   C5    110.21  3.000
 K03  H4C2  C4   N3    109.36  3.000
 K03  H4C1  C4   N3    107.67  3.000
 K03  C5    C4   N3    112.15  3.000
 K03  H5C3  C5   H5C2  107.75  3.000
 K03  H5C3  C5   H5C1  108.09  3.000
 K03  H5C2  C5   H5C1  108.21  3.000
 K03  H5C3  C5   C4    110.18  3.000
 K03  H5C2  C5   C4    111.36  3.000
 K03  H5C1  C5   C4    111.12  3.000
 K03  H2C2  C2   H2C1  106.29  3.000
 K03  H2C2  C2   C1    109.88  3.000
 K03  H2C1  C2   C1    110.14  3.000
 K03  H2C2  C2   N3    110.24  3.000
 K03  H2C1  C2   N3    107.51  3.000
 K03  C1    C2   N3    112.57  3.000
 K03  H1C3  C1   H1C2  107.94  3.000
 K03  H1C3  C1   H1C1  107.89  3.000
 K03  H1C2  C1   H1C1  108.17  3.000
 K03  H1C3  C1   C2    110.12  3.000
 K03  H1C2  C1   C2    111.55  3.000
 K03  H1C1  C1   C2    111.04  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
 K03  CONST_01  C9    N10  C11  C13   180.00   0.0  0
 K03  CONST_03  C9    N10  C11  O12     0.00   0.0  0
 K03  CONST_04  C4    N3   C6   C8    180.00   0.0  0
 K03  CONST_05  C2    N3   C6   C8      0.00   0.0  0
 K03  CONST_06  H10   N10  C11  C13     0.00   0.0  0
 K03  CONST_07  C4    N3   C6   O7      0.00   0.0  0
 K03  CONST_08  C2    N3   C6   O7    180.00   0.0  0
 K03  Var_01    C21   C20  C19  S18  -167.31  30.0  1
 K03  Var_02    C22   C25  C26  C19    19.14  30.0  1
 K03  Var_03    C22   C21  C20  C19   -44.38  30.0  1
 K03  Var_04    C21   C22  C25  C26   -46.16  30.0  1
 K03  Var_05    C20   C21  C22  C25    61.45  30.0  1
 K03  Var_06    S17   C13  C11  O12  -159.19  30.0  2
 K03  Var_07    S18   C9   N10  C11   -11.23  30.0  2
 K03  Var_08    H241  C24  C22  C25  -179.87  30.0  3
 K03  Var_09    H231  C23  C22  C25    62.21  30.0  3
 K03  Var_10    C5    C4   N3   C6     90.04  30.0  3
 K03  Var_11    C1    C2   N3   C6     91.61  30.0  3
 K03  Var_12    H5C1  C5   C4   N3    -61.27  30.0  3
 K03  Var_13    H1C1  C1   C2   N3    -64.29  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
 K03  plan-1  C11  0.020
 K03  plan-1  C13  0.020
 K03  plan-1  S17  0.020
 K03  plan-1  C16  0.020
 K03  plan-1  C15  0.020
 K03  plan-1  C14  0.020
 K03  plan-1  H14  0.020
 K03  plan-1  H16  0.020
 K03  plan-1  H15  0.020
 K03  plan-2  O12  0.020
 K03  plan-2  C11  0.020
 K03  plan-2  C13  0.020
 K03  plan-2  N10  0.020
 K03  plan-2  C9   0.020
 K03  plan-2  H10  0.020
 K03  plan-3  N10  0.020
 K03  plan-3  C9   0.020
 K03  plan-3  S18  0.020
 K03  plan-3  C19  0.020
 K03  plan-3  C26  0.020
 K03  plan-3  C25  0.020
 K03  plan-3  C20  0.020
 K03  plan-3  C8   0.020
 K03  plan-3  C6   0.020
 K03  plan-3  O7   0.020
 K03  plan-3  N3   0.020
 K03  plan-3  C4   0.020
 K03  plan-3  C2   0.020

