# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 09:28:36 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: ethenyl 6-(ethenylcarbamoyl)-2-[(phenylacetyl)amino]-4,5,6,7-tetrahydrothieno[2,3-c]pyridine-3-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C=CNC(=O)N1CCc2c(C1)sc(NC(=O)Cc3ccccc3)c2C(=O)OC=C
#
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
 JN4  JN4  'ethenyl 6-(ethenylcarbamoyl)-2-[(phenylacetyl)amino]-4,5,6,7-tetrahydrothieno[2,3-c]pyridine-3-carboxylate'  ligand  50  29  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JN4
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
 JN4  C1    C  CH2   0  -0.338   4.4200   0.6098   1.5266
 JN4  N2    N  NT    0  -0.501   4.2987  -0.7853   1.1332
 JN4  C3    C  CH2   0  -0.357   3.0178  -1.3377   1.5258
 JN4  C4    C  CR5   0  -0.295   1.9292  -0.4112   1.0704
 JN4  C5    C  CR5   0   0.229   2.1040   0.8753   0.6880
 JN4  C6    C  CH2   0  -0.492   3.4681   1.5019   0.7361
 JN4  C7    C  C     0   0.761   5.0570  -1.2255   0.0853
 JN4  O8    O  O     0  -0.525   5.9095  -0.5229  -0.4391
 JN4  N9    N  NH1   0  -0.708   4.8506  -2.5184  -0.3229
 JN4  C10   C  C1    0   0.043   5.5456  -3.0878  -1.3762
 JN4  C11   C  C2    0  -0.639   5.4002  -4.3489  -1.7776
 JN4  S12   S  S2    0   0.276   0.2833  -0.9217   0.9881
 JN4  C13   C  CR5   0   0.072  -0.2098   0.6272   0.4180
 JN4  C14   C  CR5   0  -0.104   0.8644   1.4944   0.2882
 JN4  C15   C  C     0   0.614   0.8149   2.8616  -0.2183
 JN4  O16   O  O2    0  -0.499  -0.4481   3.2857  -0.4502
 JN4  C17   C  C1    0   0.096  -0.6760   4.5401  -0.9634
 JN4  C18   C  C2    0  -0.618  -1.9128   4.9364  -1.2082
 JN4  O19   O  O     0  -0.427   1.7739   3.5601  -0.4233
 JN4  N20   N  NH1   0  -0.722  -1.5289   0.8797   0.1452
 JN4  C21   C  C     0   0.582  -2.5439  -0.0246   0.2596
 JN4  C22   C  CH2   0  -0.721  -3.9017   0.5342  -0.1030
 JN4  C23   C  CR6   0   0.152  -4.9846  -0.4993  -0.0257
 JN4  C24   C  CR16  0  -0.298  -5.6747  -0.7120   1.1636
 JN4  C25   C  CR16  0  -0.298  -5.3031  -1.2734  -1.1369
 JN4  C26   C  CR16  0  -0.242  -6.2940  -2.2432  -1.0622
 JN4  C27   C  CR16  0  -0.267  -6.9781  -2.4493   0.1288
 JN4  C28   C  CR16  0  -0.242  -6.6666  -1.6801   1.2425
 JN4  O29   O  O     0  -0.434  -2.3447  -1.1646   0.6234
 JN4  H1    H  HCH2  0   0.260   4.1780   0.6657   2.5907
 JN4  H1A   H  HCH2  0   0.272   5.4476   0.9426   1.4120
 JN4  H3    H  HCH2  0   0.269   2.8553  -2.3345   1.1214
 JN4  H3A   H  HCH2  0   0.282   2.9970  -1.4517   2.6137
 JN4  H6    H  HCH2  0   0.258   3.4272   2.4810   1.2139
 JN4  H6A   H  HCH2  0   0.253   3.8504   1.6671  -0.2741
 JN4  HN9   H  HNH1  0   0.411   4.2209  -3.1216   0.1796
 JN4  H10   H  H     0   0.276   6.2356  -2.4190  -1.8705
 JN4  H11   H  H     0   0.245   5.9787  -4.7154  -2.6118
 JN4  H11A  H  H     0   0.243   4.7157  -5.0393  -1.3009
 JN4  H17   H  H     0   0.285   0.1981   5.1507  -1.1421
 JN4  H18   H  H     0   0.257  -2.7794   4.3156  -1.0228
 JN4  H18A  H  H     0   0.266  -2.0774   5.9237  -1.6120
 JN4  HN20  H  HNH1  0   0.435  -1.7489   1.8170  -0.1573
 JN4  H22   H  HCH2  0   0.312  -4.1170   1.3713   0.5679
 JN4  H22A  H  HCH2  0   0.308  -3.8421   0.9602  -1.1090
 JN4  H24   H  HCR6  0   0.252  -5.4392  -0.1114   2.0346
 JN4  H25   H  HCR6  0   0.252  -4.7760  -1.1152  -2.0705
 JN4  H26   H  HCR6  0   0.256  -6.5332  -2.8368  -1.9352
 JN4  H27   H  HCR6  0   0.257  -7.7531  -3.2023   0.1869
 JN4  H28   H  HCR6  0   0.256  -7.1983  -1.8312   2.1732

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
 JN4  N2   C1    single    1.455  0.020  1.455
 JN4  C1   C6    single    1.525  0.020  1.525
 JN4  C1   H1    single    0.970  0.020  1.090
 JN4  C1   H1A   single    0.970  0.020  1.090
 JN4  C7   N2    single    1.366  0.020  1.366
 JN4  C3   N2    single    1.449  0.020  1.449
 JN4  C3   C4    single    1.500  0.020  1.500
 JN4  C3   H3    single    0.970  0.020  1.090
 JN4  C3   H3A   single    0.970  0.020  1.090
 JN4  C4   S12   aromatic  1.725  0.020  1.725
 JN4  C4   C5    aromatic  1.354  0.020  1.354
 JN4  C6   C5    single    1.502  0.020  1.502
 JN4  C5   C14   aromatic  1.442  0.020  1.442
 JN4  C6   H6    single    0.970  0.020  1.090
 JN4  C6   H6A   single    0.970  0.020  1.090
 JN4  O8   C7    double    1.223  0.020  1.223
 JN4  C7   N9    single    1.371  0.020  1.371
 JN4  C10  N9    single    1.384  0.020  1.384
 JN4  N9   HN9   single    0.860  0.020  1.020
 JN4  C11  C10   double    1.331  0.020  1.331
 JN4  C10  H10   single    0.930  0.020  1.080
 JN4  C11  H11   single    0.930  0.020  1.080
 JN4  C11  H11A  single    0.930  0.020  1.080
 JN4  S12  C13   aromatic  1.723  0.020  1.723
 JN4  C13  C14   aromatic  1.387  0.020  1.387
 JN4  C13  N20   single    1.370  0.020  1.370
 JN4  C14  C15   single    1.459  0.020  1.459
 JN4  C15  O16   single    1.352  0.020  1.352
 JN4  C15  O19   double    1.204  0.020  1.204
 JN4  O16  C17   single    1.374  0.020  1.374
 JN4  C17  C18   double    1.322  0.020  1.322
 JN4  C17  H17   single    0.930  0.020  1.080
 JN4  C18  H18   single    0.930  0.020  1.080
 JN4  C18  H18A  single    0.930  0.020  1.080
 JN4  C21  N20   single    1.364  0.020  1.364
 JN4  N20  HN20  single    0.860  0.020  1.020
 JN4  O29  C21   double    1.213  0.020  1.213
 JN4  C21  C22   single    1.512  0.020  1.512
 JN4  C22  C23   single    1.499  0.020  1.499
 JN4  C22  H22   single    0.970  0.020  1.090
 JN4  C22  H22A  single    0.970  0.020  1.090
 JN4  C23  C24   aromatic  1.391  0.020  1.391
 JN4  C23  C25   aromatic  1.391  0.020  1.391
 JN4  C24  C28   aromatic  1.388  0.020  1.388
 JN4  C24  H24   single    0.930  0.020  1.080
 JN4  C25  C26   aromatic  1.388  0.020  1.388
 JN4  C25  H25   single    0.930  0.020  1.080
 JN4  C26  C27   aromatic  1.389  0.020  1.389
 JN4  C26  H26   single    0.930  0.020  1.080
 JN4  C28  C27   aromatic  1.389  0.020  1.389
 JN4  C27  H27   single    0.930  0.020  1.080
 JN4  C28  H28   single    0.930  0.020  1.080

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
 JN4  H1A   C1   H1   107.25  3.000
 JN4  H1A   C1   C6   110.89  3.000
 JN4  H1    C1   C6   109.67  3.000
 JN4  H1A   C1   N2   110.13  3.000
 JN4  H1    C1   N2   107.09  3.000
 JN4  C6    C1   N2   111.64  3.000
 JN4  C7    N2   C3   125.13  3.000
 JN4  C3    N2   C1   111.47  3.000
 JN4  C7    N2   C1   118.04  3.000
 JN4  H3A   C3   H3   105.74  3.000
 JN4  H3A   C3   C4   110.63  3.000
 JN4  H3    C3   C4   110.16  3.000
 JN4  H3A   C3   N2   109.02  3.000
 JN4  H3    C3   N2   112.38  3.000
 JN4  C4    C3   N2   108.89  3.000
 JN4  S12   C4   C5   113.02  3.000
 JN4  C5    C4   C3   125.38  3.000
 JN4  S12   C4   C3   121.60  3.000
 JN4  C14   C5   C6   127.62  3.000
 JN4  C14   C5   C4   112.05  3.000
 JN4  C6    C5   C4   120.32  3.000
 JN4  H6A   C6   H6   106.41  3.000
 JN4  H6A   C6   C5   110.56  3.000
 JN4  H6    C6   C5   110.78  3.000
 JN4  H6A   C6   C1   110.43  3.000
 JN4  H6    C6   C1   108.75  3.000
 JN4  C5    C6   C1   109.84  3.000
 JN4  N9    C7   O8   121.26  3.000
 JN4  N9    C7   N2   116.64  3.000
 JN4  O8    C7   N2   122.05  3.000
 JN4  HN9   N9   C10  116.58  3.000
 JN4  HN9   N9   C7   120.71  3.000
 JN4  C10   N9   C7   122.59  3.000
 JN4  H10   C10  C11  121.20  3.000
 JN4  H10   C10  N9   114.46  3.000
 JN4  C11   C10  N9   124.34  3.000
 JN4  H11A  C11  H11  117.55  3.000
 JN4  H11A  C11  C10  122.70  3.000
 JN4  H11   C11  C10  119.75  3.000
 JN4  C13   S12  C4    91.31  3.000
 JN4  N20   C13  C14  127.72  3.000
 JN4  N20   C13  S12  120.47  3.000
 JN4  C14   C13  S12  111.81  3.000
 JN4  C15   C14  C13  126.32  3.000
 JN4  C15   C14  C5   121.85  3.000
 JN4  C13   C14  C5   111.81  3.000
 JN4  O19   C15  O16  122.20  3.000
 JN4  O19   C15  C14  125.15  3.000
 JN4  O16   C15  C14  112.65  3.000
 JN4  C17   O16  C15  120.33  3.000
 JN4  H17   C17  C18  123.82  3.000
 JN4  H17   C17  O16  116.31  3.000
 JN4  C18   C17  O16  119.87  3.000
 JN4  H18A  C18  H18  117.83  3.000
 JN4  H18A  C18  C17  119.10  3.000
 JN4  H18   C18  C17  123.07  3.000
 JN4  HN20  N20  C21  118.59  3.000
 JN4  HN20  N20  C13  116.14  3.000
 JN4  C21   N20  C13  125.26  3.000
 JN4  O29   C21  C22  124.51  3.000
 JN4  C22   C21  N20  113.76  3.000
 JN4  O29   C21  N20  121.73  3.000
 JN4  H22A  C22  H22  106.06  3.000
 JN4  H22A  C22  C23  110.81  3.000
 JN4  H22   C22  C23  110.72  3.000
 JN4  H22A  C22  C21  108.39  3.000
 JN4  H22   C22  C21  108.20  3.000
 JN4  C23   C22  C21  112.42  3.000
 JN4  C25   C23  C24  118.95  3.000
 JN4  C25   C23  C22  120.53  3.000
 JN4  C24   C23  C22  120.52  3.000
 JN4  H24   C24  C28  119.74  3.000
 JN4  H24   C24  C23  119.63  3.000
 JN4  C28   C24  C23  120.63  3.000
 JN4  H25   C25  C26  119.69  3.000
 JN4  H25   C25  C23  119.70  3.000
 JN4  C26   C25  C23  120.60  3.000
 JN4  H26   C26  C27  120.09  3.000
 JN4  H26   C26  C25  119.83  3.000
 JN4  C27   C26  C25  120.09  3.000
 JN4  H27   C27  C28  120.19  3.000
 JN4  H27   C27  C26  120.14  3.000
 JN4  C28   C27  C26  119.67  3.000
 JN4  H28   C28  C27  120.13  3.000
 JN4  H28   C28  C24  119.81  3.000
 JN4  C27   C28  C24  120.06  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
 JN4  CONST_01  C14   C13  S12  C4      0.00   0.0  0
 JN4  CONST_02  C13   C14  C5   C4      0.00   0.0  0
 JN4  CONST_03  C13   S12  C4   C5      0.00   0.0  0
 JN4  CONST_04  S12   C13  C14  C5      0.00   0.0  0
 JN4  CONST_05  C14   C5   C4   S12     0.00   0.0  0
 JN4  CONST_06  C27   C28  C24  C23     0.00   0.0  0
 JN4  CONST_07  C27   C26  C25  C23     0.00   0.0  0
 JN4  CONST_08  C26   C25  C23  C24     0.00   0.0  0
 JN4  CONST_09  C26   C27  C28  C24     0.00   0.0  0
 JN4  CONST_10  C28   C24  C23  C25     0.00   0.0  0
 JN4  CONST_11  C28   C27  C26  C25     0.00   0.0  0
 JN4  CONST_12  N20   C13  S12  C4    180.00   0.0  0
 JN4  CONST_13  C15   C14  C5   C4    180.00   0.0  0
 JN4  CONST_14  N20   C13  C14  C5    180.00   0.0  0
 JN4  CONST_15  C15   C14  C5   C6      0.00   0.0  0
 JN4  CONST_16  C15   C14  C13  S12   180.00   0.0  0
 JN4  CONST_17  C28   C24  C23  C22   180.00   0.0  0
 JN4  CONST_18  C26   C25  C23  C22   180.00   0.0  0
 JN4  CONST_19  H28   C28  C24  C23   180.00   0.0  0
 JN4  CONST_20  H26   C26  C25  C23   180.00   0.0  0
 JN4  CONST_21  H25   C25  C23  C24   180.00   0.0  0
 JN4  CONST_22  H27   C27  C28  C24   180.00   0.0  0
 JN4  CONST_23  H24   C24  C23  C25   180.00   0.0  0
 JN4  CONST_24  O8    C7   N2   C1      0.00   0.0  0
 JN4  CONST_26  C21   N20  C13  S12     0.00   0.0  0
 JN4  CONST_27  C21   N20  C13  C14   180.00   0.0  0
 JN4  CONST_28  N9    C7   N2   C1    180.00   0.0  0
 JN4  CONST_30  HN20  N20  C13  S12   180.00   0.0  0
 JN4  CONST_31  O29   C21  N20  C13     0.00   0.0  0
 JN4  CONST_32  C22   C21  N20  C13   180.00   0.0  0
 JN4  CONST_33  C10   N9   C7   N2    180.00   0.0  0
 JN4  CONST_34  HN9   N9   C7   N2      0.00   0.0  0
 JN4  CONST_35  C10   N9   C7   O8      0.00   0.0  0
 JN4  Var_01    C4    C3   N2   C1     49.81  30.0  1
 JN4  Var_02    C4    C5   C6   C1    -12.40  30.0  1
 JN4  Var_03    C5    C6   C1   N2     45.79  30.0  1
 JN4  Var_04    S12   C4   C3   N2    163.72  30.0  1
 JN4  Var_05    C6    C1   N2   C3    -68.05  30.0  1
 JN4  Var_06    O16   C15  C14  C5   -175.73  30.0  2
 JN4  Var_07    C24   C23  C22  C21    89.29  30.0  2
 JN4  Var_08    C23   C22  C21  N20   177.45  30.0  3
 JN4  Var_09    C11   C10  N9   C7    178.05  30.0  1
 JN4  Var_10    C18   C17  O16  C15   178.83  30.0  3
 JN4  Var_11    H11   C11  C10  N9    179.77   0.0  2
 JN4  Var_12    H18   C18  C17  O16     0.05   0.0  2

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
 JN4  plan-1  C22   0.020
 JN4  plan-1  C23   0.020
 JN4  plan-1  C24   0.020
 JN4  plan-1  C25   0.020
 JN4  plan-1  C26   0.020
 JN4  plan-1  C27   0.020
 JN4  plan-1  C28   0.020
 JN4  plan-1  H24   0.020
 JN4  plan-1  H25   0.020
 JN4  plan-1  H26   0.020
 JN4  plan-1  H27   0.020
 JN4  plan-1  H28   0.020
 JN4  plan-2  N9    0.020
 JN4  plan-2  C10   0.020
 JN4  plan-2  C11   0.020
 JN4  plan-2  H10   0.020
 JN4  plan-2  H11   0.020
 JN4  plan-2  H11A  0.020
 JN4  plan-3  C14   0.020
 JN4  plan-3  C15   0.020
 JN4  plan-3  O16   0.020
 JN4  plan-3  O19   0.020
 JN4  plan-4  O16   0.020
 JN4  plan-4  C17   0.020
 JN4  plan-4  C18   0.020
 JN4  plan-4  H17   0.020
 JN4  plan-4  H18   0.020
 JN4  plan-4  H18A  0.020
 JN4  plan-5  C3    0.020
 JN4  plan-5  C4    0.020
 JN4  plan-5  C5    0.020
 JN4  plan-5  C6    0.020
 JN4  plan-5  S12   0.020
 JN4  plan-5  C13   0.020
 JN4  plan-5  C14   0.020
 JN4  plan-5  C15   0.020
 JN4  plan-5  N20   0.020
 JN4  plan-6  C1    0.020
 JN4  plan-6  N2    0.020
 JN4  plan-6  C3    0.020
 JN4  plan-6  C7    0.020
 JN4  plan-6  O8    0.020
 JN4  plan-6  N9    0.020
 JN4  plan-6  C10   0.020
 JN4  plan-6  HN9   0.020
 JN4  plan-7  C13   0.020
 JN4  plan-7  N20   0.020
 JN4  plan-7  C21   0.020
 JN4  plan-7  C22   0.020
 JN4  plan-7  O29   0.020
 JN4  plan-7  HN20  0.020

