# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 15:00:24 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: diethyl 2-[(thiophen-2-ylacetyl)amino]-4,7-dihydrothieno[2,3-c]pyridine-3,6(5H)-dicarboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)N1CCc2c(C1)sc(NC(=O)Cc3sccc3)c2C(=O)OCC
#
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
 J25  J25  'diethyl 2-[(thiophen-2-ylacetyl)amino]-4,7-dihydrothieno[2,3-c]pyridine-3,6(5H)-dicarboxylate'  ligand  50  28  .  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_J25
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
 J25  C1    C  CR5   0   0.225   1.5854  -1.0202  -0.7803
 J25  C2    C  CR5   0  -0.127   0.2760  -1.4541  -0.3623
 J25  C3    C  CR5   0   0.108  -0.6552  -0.4351  -0.4466
 J25  S4    S  S2    0   0.270   0.0437   1.0396  -0.9887
 J25  C5    C  CR5   0  -0.306   1.5956   0.2915  -1.1244
 J25  C6    C  CH2   0  -0.336   2.7952   1.0626  -1.5912
 J25  N7    N  NT    0  -0.490   3.9854   0.2922  -1.2949
 J25  C8    C  CH2   0  -0.339   3.8792  -1.0916  -1.7206
 J25  C9    C  CH2   0  -0.495   2.8392  -1.8418  -0.8956
 J25  N10   N  NH1   0  -0.729  -1.9860  -0.5351  -0.1384
 J25  C11   C  C     0   0.573  -2.8853   0.4815  -0.2238
 J25  C12   C  CH2   0  -0.692  -4.2938   0.0802   0.1616
 J25  C13   C  CR5   0  -0.122  -5.2709   1.1980   0.0726
 J25  C14   C  CR15  0  -0.232  -6.2497   1.3773  -0.8583
 J25  C15   C  CR15  0  -0.184  -7.0051   2.5644  -0.6513
 J25  C16   C  CR15  0  -0.469  -6.5833   3.2663   0.4354
 J25  S17   S  S2    0   0.212  -5.2674   2.4891   1.2112
 J25  O18   O  O     0  -0.437  -2.5631   1.5967  -0.5794
 J25  C19   C  C     0   0.608  -0.1104  -2.7754   0.1322
 J25  O20   O  O2    0  -0.452   0.9077  -3.6004   0.2748
 J25  C21   C  CH2   0  -0.182   0.6484  -4.9304   0.7536
 J25  C22   C  CH3   0  -0.685   1.9666  -5.6622   0.8074
 J25  O23   O  O     0  -0.489  -1.2565  -3.0892   0.4033
 J25  C24   C  C     0   0.769   4.8867   0.6223  -0.3374
 J25  O25   O  O2    0  -0.479   4.7426   1.8753   0.0885
 J25  C26   C  CH2   0  -0.168   5.6565   2.3450   1.0867
 J25  C27   C  CH3   0  -0.690   5.2540   3.7548   1.4456
 J25  O28   O  O     0  -0.522   5.7534  -0.1277   0.0666
 J25  H6    H  HCH2  0   0.272   2.7409   1.2356  -2.6710
 J25  H6A   H  HCH2  0   0.286   2.8408   2.0417  -1.1217
 J25  H8    H  HCH2  0   0.259   3.5843  -1.0891  -2.7728
 J25  H8A   H  HCH2  0   0.272   4.8480  -1.5794  -1.6603
 J25  H9    H  HCH2  0   0.252   3.2389  -2.0742   0.0950
 J25  H9A   H  HCH2  0   0.257   2.6344  -2.7973  -1.3785
 J25  HN10  H  HNH1  0   0.442  -2.2839  -1.4617   0.1516
 J25  H12   H  HCH2  0   0.318  -4.6156  -0.7293  -0.4993
 J25  H12A  H  HCH2  0   0.313  -4.2675  -0.3522   1.1668
 J25  H14   H  HCR5  0   0.264  -6.4270   0.6774  -1.6636
 J25  H15   H  HCR5  0   0.266  -7.8237   2.8792  -1.2825
 J25  H16   H  HCR5  0   0.295  -6.9735   4.1952   0.8214
 J25  H21   H  HCH2  0   0.238   0.1893  -4.8781   1.7426
 J25  H21A  H  HCH2  0   0.238  -0.0511  -5.4323   0.0826
 J25  H22   H  HCH3  0   0.237   2.4275  -5.7323  -0.1776
 J25  H22A  H  HCH3  0   0.237   2.6678  -5.1781   1.4871
 J25  H22B  H  HCH3  0   0.240   1.7956  -6.6756   1.1693
 J25  H26   H  HCH2  0   0.231   5.6151   1.6966   1.9638
 J25  H26A  H  HCH2  0   0.231   6.6765   2.3201   0.6979
 J25  H27   H  HCH3  0   0.236   5.3172   4.4226   0.5866
 J25  H27A  H  HCH3  0   0.235   4.2395   3.7922   1.8427
 J25  H27B  H  HCH3  0   0.239   5.9272   4.1337   2.2140

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
 J25  C5   C1    aromatic  1.356  0.020  1.356
 J25  C9   C1    single    1.503  0.020  1.503
 J25  C1   C2    aromatic  1.441  0.020  1.441
 J25  C3   C2    aromatic  1.383  0.020  1.383
 J25  C2   C19   single    1.463  0.020  1.463
 J25  S4   C3    aromatic  1.720  0.020  1.720
 J25  C3   N10   single    1.370  0.020  1.370
 J25  C5   S4    aromatic  1.728  0.020  1.728
 J25  C6   C5    single    1.501  0.020  1.501
 J25  C6   N7    single    1.448  0.020  1.448
 J25  C6   H6    single    0.970  0.020  1.090
 J25  C6   H6A   single    0.970  0.020  1.090
 J25  C24  N7    single    1.356  0.020  1.356
 J25  N7   C8    single    1.452  0.020  1.452
 J25  C8   C9    single    1.525  0.020  1.525
 J25  C8   H8    single    0.970  0.020  1.090
 J25  C8   H8A   single    0.970  0.020  1.090
 J25  C9   H9    single    0.970  0.020  1.090
 J25  C9   H9A   single    0.970  0.020  1.090
 J25  C11  N10   single    1.360  0.020  1.360
 J25  N10  HN10  single    0.860  0.020  1.020
 J25  O18  C11   double    1.214  0.020  1.214
 J25  C11  C12   single    1.515  0.020  1.515
 J25  C12  C13   single    1.487  0.020  1.487
 J25  C12  H12   single    0.970  0.020  1.090
 J25  C12  H12A  single    0.970  0.020  1.090
 J25  C13  S17   aromatic  1.721  0.020  1.721
 J25  C13  C14   aromatic  1.363  0.020  1.363
 J25  C14  C15   aromatic  1.422  0.020  1.422
 J25  C14  H14   single    0.930  0.020  1.080
 J25  C15  C16   aromatic  1.361  0.020  1.361
 J25  C15  H15   single    0.930  0.020  1.080
 J25  S17  C16   aromatic  1.714  0.020  1.714
 J25  C16  H16   single    0.930  0.020  1.080
 J25  C19  O20   single    1.318  0.020  1.318
 J25  C19  O23   double    1.219  0.020  1.219
 J25  O20  C21   single    1.437  0.020  1.437
 J25  C22  C21   single    1.509  0.020  1.509
 J25  C21  H21   single    0.970  0.020  1.090
 J25  C21  H21A  single    0.970  0.020  1.090
 J25  C22  H22   single    0.970  0.020  1.090
 J25  C22  H22A  single    0.970  0.020  1.090
 J25  C22  H22B  single    0.970  0.020  1.090
 J25  O28  C24   double    1.215  0.020  1.215
 J25  O25  C24   single    1.331  0.020  1.331
 J25  O25  C26   single    1.433  0.020  1.433
 J25  C27  C26   single    1.509  0.020  1.509
 J25  C26  H26   single    0.970  0.020  1.090
 J25  C26  H26A  single    0.970  0.020  1.090
 J25  C27  H27   single    0.970  0.020  1.090
 J25  C27  H27A  single    0.970  0.020  1.090
 J25  C27  H27B  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
 J25  C9    C1   C5    120.19  3.000
 J25  C9    C1   C2    127.98  3.000
 J25  C5    C1   C2    111.81  3.000
 J25  C19   C2   C3    120.55  3.000
 J25  C19   C2   C1    127.58  3.000
 J25  C3    C2   C1    111.85  3.000
 J25  N10   C3   S4    121.90  3.000
 J25  N10   C3   C2    125.92  3.000
 J25  S4    C3   C2    112.17  3.000
 J25  C5    S4   C3     91.06  3.000
 J25  C6    C5   S4    121.32  3.000
 J25  C6    C5   C1    125.59  3.000
 J25  S4    C5   C1    113.08  3.000
 J25  H6A   C6   H6    106.61  3.000
 J25  H6A   C6   N7    110.88  3.000
 J25  H6    C6   N7    109.06  3.000
 J25  H6A   C6   C5    111.23  3.000
 J25  H6    C6   C5    110.38  3.000
 J25  N7    C6   C5    108.66  3.000
 J25  C24   N7   C8    119.20  3.000
 J25  C8    N7   C6    112.76  3.000
 J25  C24   N7   C6    124.14  3.000
 J25  H8A   C8   H8    107.16  3.000
 J25  H8A   C8   C9    110.93  3.000
 J25  H8    C8   C9    109.75  3.000
 J25  H8A   C8   N7    110.28  3.000
 J25  H8    C8   N7    107.45  3.000
 J25  C9    C8   N7    111.12  3.000
 J25  H9A   C9   H9    106.49  3.000
 J25  H9A   C9   C8    108.65  3.000
 J25  H9    C9   C8    110.21  3.000
 J25  H9A   C9   C1    110.88  3.000
 J25  H9    C9   C1    110.59  3.000
 J25  C8    C9   C1    109.96  3.000
 J25  HN10  N10  C11   120.40  3.000
 J25  HN10  N10  C3    114.58  3.000
 J25  C11   N10  C3    125.01  3.000
 J25  O18   C11  C12   124.39  3.000
 J25  C12   C11  N10   113.64  3.000
 J25  O18   C11  N10   121.98  3.000
 J25  H12A  C12  H12   105.65  3.000
 J25  H12A  C12  C13   111.58  3.000
 J25  H12   C12  C13   109.08  3.000
 J25  H12A  C12  C11   108.42  3.000
 J25  H12   C12  C11   108.42  3.000
 J25  C13   C12  C11   113.37  3.000
 J25  S17   C13  C14   110.77  3.000
 J25  C14   C13  C12   127.71  3.000
 J25  S17   C13  C12   121.51  3.000
 J25  H14   C14  C15   124.15  3.000
 J25  H14   C14  C13   122.77  3.000
 J25  C15   C14  C13   113.07  3.000
 J25  H15   C15  C16   123.44  3.000
 J25  H15   C15  C14   124.09  3.000
 J25  C16   C15  C14   112.47  3.000
 J25  H16   C16  S17   120.41  3.000
 J25  H16   C16  C15   128.15  3.000
 J25  S17   C16  C15   111.44  3.000
 J25  C16   S17  C13    92.24  3.000
 J25  O23   C19  O20   122.76  3.000
 J25  O23   C19  C2    123.79  3.000
 J25  O20   C19  C2    113.45  3.000
 J25  C21   O20  C19   118.42  3.000
 J25  H21A  C21  H21   108.02  3.000
 J25  H21A  C21  C22   111.03  3.000
 J25  H21   C21  C22   111.00  3.000
 J25  H21A  C21  O20   109.65  3.000
 J25  H21   C21  O20   109.48  3.000
 J25  C22   C21  O20   107.65  3.000
 J25  H22B  C22  H22A  107.87  3.000
 J25  H22B  C22  H22   107.86  3.000
 J25  H22A  C22  H22   108.67  3.000
 J25  H22B  C22  C21   109.01  3.000
 J25  H22A  C22  C21   111.65  3.000
 J25  H22   C22  C21   111.63  3.000
 J25  O28   C24  O25   123.49  3.000
 J25  O25   C24  N7    112.53  3.000
 J25  O28   C24  N7    123.96  3.000
 J25  C26   O25  C24   117.55  3.000
 J25  H26A  C26  H26   107.94  3.000
 J25  H26A  C26  C27   110.80  3.000
 J25  H26   C26  C27   110.71  3.000
 J25  H26A  C26  O25   109.90  3.000
 J25  H26   C26  O25   109.93  3.000
 J25  C27   C26  O25   107.56  3.000
 J25  H27B  C27  H27A  107.83  3.000
 J25  H27B  C27  H27   107.87  3.000
 J25  H27A  C27  H27   108.67  3.000
 J25  H27B  C27  C26   109.13  3.000
 J25  H27A  C27  C26   111.52  3.000
 J25  H27   C27  C26   111.68  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
 J25  CONST_01  C3    S4   C5   C1      0.00   0.0  0
 J25  CONST_02  S4    C3   C2   C1      0.00   0.0  0
 J25  CONST_03  S4    C5   C1   C2      0.00   0.0  0
 J25  CONST_04  C5    S4   C3   C2      0.00   0.0  0
 J25  CONST_05  C5    C1   C2   C3      0.00   0.0  0
 J25  CONST_06  C15   C16  S17  C13     0.00   0.0  0
 J25  CONST_07  C16   C15  C14  C13     0.00   0.0  0
 J25  CONST_08  C16   S17  C13  C14     0.00   0.0  0
 J25  CONST_09  S17   C16  C15  C14     0.00   0.0  0
 J25  CONST_10  S17   C13  C14  C15     0.00   0.0  0
 J25  CONST_11  N10   C3   C2   C1    180.00   0.0  0
 J25  CONST_12  C19   C2   C3   S4    180.00   0.0  0
 J25  CONST_13  C19   C2   C1   C5    180.00   0.0  0
 J25  CONST_14  N10   C3   S4   C5    180.00   0.0  0
 J25  CONST_15  C19   C2   C1   C9      0.00   0.0  0
 J25  CONST_16  C16   S17  C13  C12   180.00   0.0  0
 J25  CONST_17  C15   C14  C13  C12   180.00   0.0  0
 J25  CONST_18  H16   C16  S17  C13   180.00   0.0  0
 J25  CONST_19  H15   C15  C14  C13   180.00   0.0  0
 J25  CONST_20  H14   C14  C15  C16   180.00   0.0  0
 J25  CONST_21  C11   N10  C3   C2    180.00   0.0  0
 J25  CONST_22  C11   N10  C3   S4      0.00   0.0  0
 J25  CONST_23  HN10  N10  C3   C2      0.00   0.0  0
 J25  CONST_24  O18   C11  N10  C3      0.00   0.0  0
 J25  CONST_25  C12   C11  N10  C3    180.00   0.0  0
 J25  Var_01    N7    C6   C5   C1    -14.34  30.0  1
 J25  Var_02    N7    C8   C9   C1     46.33  30.0  1
 J25  Var_03    C8    C9   C1   C2    164.67  30.0  1
 J25  Var_04    C8    N7   C6   C5     48.32  30.0  1
 J25  Var_05    C9    C8   N7   C6    -67.62  30.0  1
 J25  Var_06    O20   C19  C2   C1      4.70  30.0  2
 J25  Var_07    O28   C24  N7   C6    166.97  30.0  2
 J25  Var_08    S17   C13  C12  C11   -72.17  30.0  2
 J25  Var_09    C13   C12  C11  N10   179.71  30.0  3
 J25  Var_10    C22   C21  O20  C19   179.31  30.0  3
 J25  Var_11    C27   C26  O25  C24  -177.48  30.0  3
 J25  Var_12    H22   C22  C21  O20   -60.99  30.0  3
 J25  Var_13    H27   C27  C26  O25   -61.51  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
 J25  plan-1  C12   0.020
 J25  plan-1  C13   0.020
 J25  plan-1  C14   0.020
 J25  plan-1  C15   0.020
 J25  plan-1  C16   0.020
 J25  plan-1  S17   0.020
 J25  plan-1  H14   0.020
 J25  plan-1  H15   0.020
 J25  plan-1  H16   0.020
 J25  plan-2  C1    0.020
 J25  plan-2  C2    0.020
 J25  plan-2  C3    0.020
 J25  plan-2  S4    0.020
 J25  plan-2  C5    0.020
 J25  plan-2  C6    0.020
 J25  plan-2  C9    0.020
 J25  plan-2  N10   0.020
 J25  plan-2  C19   0.020
 J25  plan-3  C3    0.020
 J25  plan-3  N10   0.020
 J25  plan-3  C11   0.020
 J25  plan-3  C12   0.020
 J25  plan-3  O18   0.020
 J25  plan-3  HN10  0.020
 J25  plan-4  C2    0.020
 J25  plan-4  C19   0.020
 J25  plan-4  O20   0.020
 J25  plan-4  O23   0.020
 J25  plan-5  N7    0.020
 J25  plan-5  C24   0.020
 J25  plan-5  O25   0.020
 J25  plan-5  O28   0.020

