# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 22:15:37 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: (5R)-N,N-diethyl-5-methyl-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)sc3CC[C@@H](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
 K02  K02  (5R)-N,N-diethyl-5-methyl-2-[(thiophen-2-ylcarbonyl)amino]-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide  ligand  49  25  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_K02
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
 K02  O1    O  O     0  -0.450   1.4734   1.7969  -0.7316
 K02  C13   C  C     0   0.574   0.4716   1.6395  -0.0541
 K02  C14   C  CR5   0  -0.350  -0.2336   2.7696   0.5643
 K02  S2    S  S2    0   0.242  -1.8279   2.6799   1.2169
 K02  C15   C  CR15  0  -0.443  -1.7956   4.3251   1.6665
 K02  C16   C  CR15  0  -0.172  -0.6192   4.9244   1.3235
 K02  C17   C  CR15  0  -0.177   0.2756   4.0337   0.6869
 K02  N2    N  NH1   0  -0.746  -0.0509   0.4064   0.1761
 K02  C12   C  CR5   0   0.065   0.4756  -0.7721  -0.3259
 K02  S1    S  S2    0   0.244   2.0202  -0.8698  -1.0921
 K02  C6    C  CR5   0  -0.283   1.8692  -2.5832  -1.2571
 K02  C5    C  CR5   0   0.213   0.6874  -3.0442  -0.7686
 K02  C11   C  CH2   0  -0.489   0.3516  -4.5058  -0.7546
 K02  C9    C  CH1   0  -0.243   1.2328  -5.2977  -1.7216
 K02  C10   C  CH3   0  -0.659   1.0343  -6.7947  -1.5309
 K02  C8    C  CH2   0  -0.429   2.6957  -4.8961  -1.5465
 K02  C7    C  CH2   0  -0.484   2.9304  -3.4252  -1.8894
 K02  C4    C  CR5   0  -0.084  -0.1310  -1.9924  -0.2461
 K02  C3    C  C     0   0.484  -1.4659  -2.1629   0.3983
 K02  O2    O  O     0  -0.495  -1.5966  -1.9293   1.5980
 K02  N1    N  NT    0  -0.423  -2.4835  -2.5504  -0.3880
 K02  C2    C  CH2   0  -0.320  -3.7945  -2.7871   0.2044
 K02  C1    C  CH3   0  -0.654  -3.9679  -4.2311   0.6465
 K02  C18   C  CH2   0  -0.334  -2.4141  -2.5765  -1.8439
 K02  C19   C  CH3   0  -0.647  -2.7665  -1.2343  -2.4648
 K02  H2    H  HNH1  0   0.413  -0.7506   0.2890   0.8961
 K02  H17   H  HCR5  0   0.280   1.2607   4.3090   0.3393
 K02  H15   H  HCR5  0   0.312  -2.6515   4.7676   2.1524
 K02  H16   H  HCR5  0   0.279  -0.4029   5.9641   1.5190
 K02  H7C1  H  HCH2  0   0.248   2.9150  -3.2911  -2.9759
 K02  H7C2  H  HCH2  0   0.254   3.9242  -3.1161  -1.5577
 K02  H111  H  HCH2  0   0.244   0.4863  -4.8929   0.2626
 K02  H112  H  HCH2  0   0.247  -0.7017  -4.6703  -0.9971
 K02  H9    H  HCH1  0   0.227   0.9282  -5.0353  -2.7426
 K02  H101  H  HCH3  0   0.217   1.3483  -7.1077  -0.5323
 K02  H102  H  HCH3  0   0.228  -0.0139  -7.0750  -1.6503
 K02  H103  H  HCH3  0   0.230   1.6140  -7.3666  -2.2569
 K02  H8C1  H  HCH2  0   0.238   3.3352  -5.5171  -2.1776
 K02  H8C2  H  HCH2  0   0.224   2.9969  -5.0848  -0.5102
 K02  H2C1  H  HCH2  0   0.253  -3.9451  -2.1084   1.0419
 K02  H2C2  H  HCH2  0   0.249  -4.5472  -2.5329  -0.5425
 K02  H181  H  HCH2  0   0.267  -1.4231  -2.8810  -2.1719
 K02  H182  H  HCH2  0   0.259  -3.0989  -3.3512  -2.1917
 K02  H1C1  H  HCH3  0   0.227  -3.8349  -4.9189  -0.1896
 K02  H1C2  H  HCH3  0   0.231  -3.2488  -4.4945   1.4217
 K02  H1C3  H  HCH3  0   0.235  -4.9695  -4.3838   1.0490
 K02  H191  H  HCH3  0   0.232  -3.7663  -0.9044  -2.1801
 K02  H192  H  HCH3  0   0.227  -2.0545  -0.4664  -2.1594
 K02  H193  H  HCH3  0   0.238  -2.7369  -1.3054  -3.5521

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
 K02  O1   C13   double  1.220  0.020  1.220
 K02  C13  C14   single  1.469  0.020  1.469
 K02  C14  S2    single  1.725  0.020  1.725
 K02  S2   C15   single  1.706  0.020  1.706
 K02  C15  C16   double  1.364  0.020  1.364
 K02  C14  C17   double  1.368  0.020  1.368
 K02  C16  C17   single  1.414  0.020  1.414
 K02  C13  N2    single  1.359  0.020  1.359
 K02  N2   C12   single  1.385  0.020  1.385
 K02  C12  S1    single  1.727  0.020  1.727
 K02  S1   C6    single  1.728  0.020  1.728
 K02  C6   C5    double  1.359  0.020  1.359
 K02  C5   C11   single  1.500  0.020  1.500
 K02  C11  C9    single  1.529  0.020  1.529
 K02  C9   C10   single  1.522  0.020  1.522
 K02  C9   C8    single  1.527  0.020  1.527
 K02  C6   C7    single  1.495  0.020  1.495
 K02  C8   C7    single  1.528  0.020  1.528
 K02  C12  C4    double  1.365  0.020  1.365
 K02  C5   C4    single  1.431  0.020  1.431
 K02  C4   C3    single  1.492  0.020  1.492
 K02  C3   O2    double  1.229  0.020  1.229
 K02  C3   N1    single  1.343  0.020  1.343
 K02  N1   C2    single  1.458  0.020  1.458
 K02  C2   C1    single  1.520  0.020  1.520
 K02  N1   C18   single  1.458  0.020  1.458
 K02  C18  C19   single  1.520  0.020  1.520
 K02  N2   H2    single  0.860  0.020  1.020
 K02  C17  H17   single  0.930  0.020  1.080
 K02  C15  H15   single  0.930  0.020  1.080
 K02  C16  H16   single  0.930  0.020  1.080
 K02  C7   H7C1  single  0.970  0.020  1.090
 K02  C7   H7C2  single  0.970  0.020  1.090
 K02  C11  H111  single  0.970  0.020  1.090
 K02  C11  H112  single  0.970  0.020  1.090
 K02  C9   H9    single  0.970  0.020  1.090
 K02  C10  H101  single  0.970  0.020  1.090
 K02  C10  H102  single  0.970  0.020  1.090
 K02  C10  H103  single  0.970  0.020  1.090
 K02  C8   H8C1  single  0.970  0.020  1.090
 K02  C8   H8C2  single  0.970  0.020  1.090
 K02  C2   H2C1  single  0.970  0.020  1.090
 K02  C2   H2C2  single  0.970  0.020  1.090
 K02  C18  H181  single  0.970  0.020  1.090
 K02  C18  H182  single  0.970  0.020  1.090
 K02  C1   H1C1  single  0.970  0.020  1.090
 K02  C1   H1C2  single  0.970  0.020  1.090
 K02  C1   H1C3  single  0.970  0.020  1.090
 K02  C19  H191  single  0.970  0.020  1.090
 K02  C19  H192  single  0.970  0.020  1.090
 K02  C19  H193  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
 K02  N2    C13  C14   116.25  3.000
 K02  N2    C13  O1    121.81  3.000
 K02  C14   C13  O1    121.94  3.000
 K02  C17   C14  S2    110.99  3.000
 K02  C17   C14  C13   124.74  3.000
 K02  S2    C14  C13   124.27  3.000
 K02  C15   S2   C14    91.84  3.000
 K02  H15   C15  C16   128.10  3.000
 K02  H15   C15  S2    119.94  3.000
 K02  C16   C15  S2    111.95  3.000
 K02  H16   C16  C17   124.14  3.000
 K02  H16   C16  C15   123.38  3.000
 K02  C17   C16  C15   112.47  3.000
 K02  H17   C17  C16   124.15  3.000
 K02  H17   C17  C14   123.10  3.000
 K02  C16   C17  C14   112.75  3.000
 K02  H2    N2   C12   114.99  3.000
 K02  H2    N2   C13   119.49  3.000
 K02  C12   N2   C13   124.38  3.000
 K02  C4    C12  S1    111.89  3.000
 K02  C4    C12  N2    124.79  3.000
 K02  S1    C12  N2    123.29  3.000
 K02  C6    S1   C12    91.16  3.000
 K02  C7    C6   C5    125.32  3.000
 K02  C7    C6   S1    122.47  3.000
 K02  C5    C6   S1    112.21  3.000
 K02  C4    C5   C11   125.78  3.000
 K02  C4    C5   C6    112.27  3.000
 K02  C11   C5   C6    121.91  3.000
 K02  H112  C11  H111  105.73  3.000
 K02  H112  C11  C9    109.69  3.000
 K02  H111  C11  C9    109.45  3.000
 K02  H112  C11  C5    111.11  3.000
 K02  H111  C11  C5    108.97  3.000
 K02  C9    C11  C5    111.70  3.000
 K02  H9    C9   C8    108.04  3.000
 K02  H9    C9   C10   108.40  3.000
 K02  C8    C9   C10   111.67  3.000
 K02  H9    C9   C11   107.73  3.000
 K02  C8    C9   C11   110.08  3.000
 K02  C10   C9   C11   110.78  3.000
 K02  H103  C10  H102  107.62  3.000
 K02  H103  C10  H101  107.77  3.000
 K02  H102  C10  H101  107.61  3.000
 K02  H103  C10  C9    111.28  3.000
 K02  H102  C10  C9    111.35  3.000
 K02  H101  C10  C9    111.03  3.000
 K02  H8C2  C8   H8C1  106.71  3.000
 K02  H8C2  C8   C7    109.62  3.000
 K02  H8C1  C8   C7    109.13  3.000
 K02  H8C2  C8   C9    109.06  3.000
 K02  H8C1  C8   C9    110.19  3.000
 K02  C7    C8   C9    111.99  3.000
 K02  H7C2  C7   H7C1  106.23  3.000
 K02  H7C2  C7   C8    110.12  3.000
 K02  H7C1  C7   C8    109.78  3.000
 K02  H7C2  C7   C6    110.98  3.000
 K02  H7C1  C7   C6    109.92  3.000
 K02  C8    C7   C6    109.76  3.000
 K02  C3    C4   C5    125.81  3.000
 K02  C3    C4   C12   121.66  3.000
 K02  C5    C4   C12   112.42  3.000
 K02  N1    C3   O2    123.07  3.000
 K02  N1    C3   C4    117.26  3.000
 K02  O2    C3   C4    119.67  3.000
 K02  C18   N1   C2    116.47  3.000
 K02  C18   N1   C3    123.62  3.000
 K02  C2    N1   C3    119.36  3.000
 K02  H2C2  C2   H2C1  106.63  3.000
 K02  H2C2  C2   C1    109.99  3.000
 K02  H2C1  C2   C1    110.66  3.000
 K02  H2C2  C2   N1    107.73  3.000
 K02  H2C1  C2   N1    109.62  3.000
 K02  C1    C2   N1    112.02  3.000
 K02  H1C3  C1   H1C2  108.05  3.000
 K02  H1C3  C1   H1C1  107.86  3.000
 K02  H1C2  C1   H1C1  108.21  3.000
 K02  H1C3  C1   C2    110.20  3.000
 K02  H1C2  C1   C2    111.17  3.000
 K02  H1C1  C1   C2    111.23  3.000
 K02  H182  C18  H181  106.09  3.000
 K02  H182  C18  C19   110.56  3.000
 K02  H181  C18  C19   109.59  3.000
 K02  H182  C18  N1    107.53  3.000
 K02  H181  C18  N1    110.47  3.000
 K02  C19   C18  N1    112.40  3.000
 K02  H193  C19  H192  107.90  3.000
 K02  H193  C19  H191  107.76  3.000
 K02  H192  C19  H191  108.20  3.000
 K02  H193  C19  C18   110.09  3.000
 K02  H192  C19  C18   110.85  3.000
 K02  H191  C19  C18   111.90  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
 K02  CONST_01  C12   N2   C13  C14  180.00   0.0  0
 K02  CONST_03  C12   N2   C13  O1     0.00   0.0  0
 K02  CONST_04  C2    N1   C3   C4   180.00   0.0  0
 K02  CONST_05  C18   N1   C3   C4     0.00   0.0  0
 K02  CONST_06  H2    N2   C13  C14    0.00   0.0  0
 K02  CONST_07  C2    N1   C3   O2     0.00   0.0  0
 K02  CONST_08  C18   N1   C3   O2   180.00   0.0  0
 K02  Var_01    C8    C7   C6   S1   164.39  30.0  1
 K02  Var_02    C9    C11  C5   C6   -18.51  30.0  1
 K02  Var_03    C9    C8   C7   C6    45.65  30.0  1
 K02  Var_04    S2    C14  C13  O1   165.24  30.0  2
 K02  Var_05    S1    C12  N2   C13   10.79  30.0  2
 K02  Var_06    C1    C2   N1   C3   -90.46  30.0  3
 K02  Var_07    C19   C18  N1   C3   -86.20  30.0  3
 K02  Var_08    H1C1  C1   C2   N1   -58.26  30.0  3
 K02  Var_09    H191  C19  C18  N1   -58.21  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 K02  chir_01  C9  C11  C10  C8  positiv

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
 K02  plan-1  C13  0.020
 K02  plan-1  C14  0.020
 K02  plan-1  S2   0.020
 K02  plan-1  C15  0.020
 K02  plan-1  C16  0.020
 K02  plan-1  C17  0.020
 K02  plan-1  H17  0.020
 K02  plan-1  H15  0.020
 K02  plan-1  H16  0.020
 K02  plan-2  O1   0.020
 K02  plan-2  C13  0.020
 K02  plan-2  C14  0.020
 K02  plan-2  N2   0.020
 K02  plan-2  C12  0.020
 K02  plan-2  H2   0.020
 K02  plan-3  N2   0.020
 K02  plan-3  C12  0.020
 K02  plan-3  S1   0.020
 K02  plan-3  C6   0.020
 K02  plan-3  C5   0.020
 K02  plan-3  C11  0.020
 K02  plan-3  C7   0.020
 K02  plan-3  C4   0.020
 K02  plan-3  C3   0.020
 K02  plan-3  O2   0.020
 K02  plan-3  N1   0.020
 K02  plan-3  C2   0.020
 K02  plan-3  C18  0.020

