# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 22:25:27 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: 3-cyclopentyl 6-ethenyl 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: C=COC(=O)N1CCc2c(C1)sc(NC(=O)Cc3sccc3)c2C(=O)OC4CCCC4
#
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
 JN7  JN7  '3-cyclopentyl 6-ethenyl 2-[(thiophen-2-ylacetyl)amino]-4,7-dihydrothieno[2,3-c]pyridine-3,6(5H)-dicarboxylate'  ligand  55  31  .  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_JN7
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
 JN7  C1    C  CH2   0  -0.500  -2.6310   1.2376  -1.3057
 JN7  C2    C  CH2   0  -0.337  -3.6480   0.3053  -1.9531
 JN7  N3    N  NT    0  -0.498  -3.7246  -0.9604  -1.2465
 JN7  C4    C  CH2   0  -0.328  -2.5143  -1.7495  -1.3538
 JN7  C5    C  CR5   0  -0.310  -1.3421  -0.8633  -1.0550
 JN7  C6    C  CR5   0   0.231  -1.3634   0.4910  -1.0009
 JN7  S7    S  S2    0   0.273   0.2152  -1.5318  -0.7179
 JN7  C8    C  CR5   0   0.107   0.8714   0.0398  -0.4778
 JN7  C9    C  CR5   0  -0.131  -0.0752   1.0331  -0.6476
 JN7  C10   C  C     0   0.777  -4.7456  -1.2048  -0.4066
 JN7  O11   O  O     0  -0.507  -5.7030  -0.4811  -0.2402
 JN7  O12   O  O2    0  -0.475  -4.5953  -2.3858   0.2309
 JN7  C13   C  C1    0   0.090  -5.5779  -2.8165   1.0810
 JN7  C14   C  C2    0  -0.619  -5.3775  -3.8758   1.8470
 JN7  C15   C  C     0   0.619   0.2713   2.4391  -0.4335
 JN7  N16   N  NH1   0  -0.729   2.1877   0.2333  -0.1529
 JN7  C17   C  C     0   0.576   3.1036  -0.7585   0.0098
 JN7  C18   C  CH2   0  -0.692   4.4851  -0.2587   0.3771
 JN7  C19   C  CR5   0  -0.125   5.5195  -1.3280   0.3597
 JN7  S20   S  S2    0   0.212   5.6251  -2.4995   1.6155
 JN7  C21   C  CR15  0  -0.470   6.9510  -3.2839   0.8644
 JN7  C22   C  CR15  0  -0.184   7.2951  -2.6723  -0.3016
 JN7  C23   C  CR15  0  -0.228   6.4713  -1.5495  -0.5900
 JN7  O24   O  O     0  -0.438   2.8126  -1.9295  -0.1238
 JN7  O25   O  O2    0  -0.462  -0.7560   3.2506  -0.5725
 JN7  O26   O  O     0  -0.489   1.3930   2.8222  -0.1492
 JN7  C27   C  CH1   0  -0.018  -0.5908   4.6641  -0.3307
 JN7  C28   C  CH2   0  -0.459  -1.8262   5.3370  -0.9018
 JN7  C29   C  CH2   0  -0.453  -2.9320   5.0549   0.1267
 JN7  C30   C  CH2   0  -0.448  -2.2000   4.8097   1.4679
 JN7  C31   C  CH2   0  -0.472  -0.7018   4.9549   1.1591
 JN7  H1    H  HCH2  0   0.259  -2.4439   2.0640  -1.9914
 JN7  H1A   H  HCH2  0   0.254  -3.0427   1.6794  -0.3943
 JN7  H2    H  HCH2  0   0.278  -4.6282   0.7717  -1.9923
 JN7  H2A   H  HCH2  0   0.262  -3.3474   0.0917  -2.9820
 JN7  H4    H  HCH2  0   0.289  -2.5392  -2.5955  -0.6719
 JN7  H4A   H  HCH2  0   0.274  -2.4400  -2.1611  -2.3661
 JN7  H13   H  H     0   0.273  -6.5039  -2.2573   1.0692
 JN7  H14   H  H     0   0.256  -4.4467  -4.4266   1.8550
 JN7  H14A  H  H     0   0.257  -6.1725  -4.2109   2.4957
 JN7  HN16  H  HNH1  0   0.442   2.4524   1.2065  -0.0318
 JN7  H18   H  HCH2  0   0.313   4.7751   0.5321  -0.3189
 JN7  H18A  H  HCH2  0   0.317   4.4205   0.2196   1.3601
 JN7  H21   H  HCR5  0   0.295   7.4043  -4.1494   1.3223
 JN7  H22   H  HCR5  0   0.266   8.1051  -3.0074  -0.9334
 JN7  H23   H  HCR5  0   0.264   6.5797  -0.9259  -1.4671
 JN7  H27   H  HCH1  0   0.262   0.3414   5.0088  -0.7802
 JN7  H28   H  HCH2  0   0.242  -1.6202   6.4078  -0.9626
 JN7  H28A  H  HCH2  0   0.249  -2.0676   4.9983  -1.9102
 JN7  H29   H  HCH2  0   0.236  -3.6372   5.8833   0.1877
 JN7  H29A  H  HCH2  0   0.236  -3.5068   4.1746  -0.1641
 JN7  H30   H  HCH2  0   0.235  -2.5138   5.5110   2.2411
 JN7  H30A  H  HCH2  0   0.233  -2.4167   3.8103   1.8476
 JN7  H31   H  HCH2  0   0.253  -0.0640   4.3203   1.7747
 JN7  H31A  H  HCH2  0   0.244  -0.3732   5.9848   1.3183

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
 JN7  C6   C1    single    1.502  0.020  1.502
 JN7  C1   C2    single    1.524  0.020  1.524
 JN7  C1   H1    single    0.970  0.020  1.090
 JN7  C1   H1A   single    0.970  0.020  1.090
 JN7  C2   N3    single    1.452  0.020  1.452
 JN7  C2   H2    single    0.970  0.020  1.090
 JN7  C2   H2A   single    0.970  0.020  1.090
 JN7  C4   N3    single    1.449  0.020  1.449
 JN7  N3   C10   single    1.344  0.020  1.344
 JN7  C5   C4    single    1.500  0.020  1.500
 JN7  C4   H4    single    0.970  0.020  1.090
 JN7  C4   H4A   single    0.970  0.020  1.090
 JN7  C6   C5    aromatic  1.356  0.020  1.356
 JN7  S7   C5    aromatic  1.728  0.020  1.728
 JN7  C9   C6    aromatic  1.442  0.020  1.442
 JN7  C8   S7    aromatic  1.720  0.020  1.720
 JN7  N16  C8    single    1.370  0.020  1.370
 JN7  C9   C8    aromatic  1.383  0.020  1.383
 JN7  C15  C9    single    1.464  0.020  1.464
 JN7  O12  C10   single    1.350  0.020  1.350
 JN7  C10  O11   double    1.212  0.020  1.212
 JN7  O12  C13   single    1.369  0.020  1.369
 JN7  C13  C14   double    1.322  0.020  1.322
 JN7  C13  H13   single    0.930  0.020  1.080
 JN7  C14  H14   single    0.930  0.020  1.080
 JN7  C14  H14A  single    0.930  0.020  1.080
 JN7  O26  C15   double    1.219  0.020  1.219
 JN7  O25  C15   single    1.316  0.020  1.316
 JN7  N16  C17   single    1.360  0.020  1.360
 JN7  N16  HN16  single    0.860  0.020  1.020
 JN7  C18  C17   single    1.514  0.020  1.514
 JN7  C17  O24   double    1.214  0.020  1.214
 JN7  C19  C18   single    1.488  0.020  1.488
 JN7  C18  H18   single    0.970  0.020  1.090
 JN7  C18  H18A  single    0.970  0.020  1.090
 JN7  S20  C19   aromatic  1.721  0.020  1.721
 JN7  C23  C19   aromatic  1.363  0.020  1.363
 JN7  C21  S20   aromatic  1.714  0.020  1.714
 JN7  C21  C22   aromatic  1.361  0.020  1.361
 JN7  C21  H21   single    0.930  0.020  1.080
 JN7  C22  C23   aromatic  1.422  0.020  1.422
 JN7  C22  H22   single    0.930  0.020  1.080
 JN7  C23  H23   single    0.930  0.020  1.080
 JN7  C27  O25   single    1.444  0.020  1.444
 JN7  C28  C27   single    1.518  0.020  1.518
 JN7  C31  C27   single    1.522  0.020  1.522
 JN7  C27  H27   single    0.970  0.020  1.090
 JN7  C28  C29   single    1.536  0.020  1.536
 JN7  C28  H28   single    0.970  0.020  1.090
 JN7  C28  H28A  single    0.970  0.020  1.090
 JN7  C29  C30   single    1.547  0.020  1.547
 JN7  C29  H29   single    0.970  0.020  1.090
 JN7  C29  H29A  single    0.970  0.020  1.090
 JN7  C31  C30   single    1.537  0.020  1.537
 JN7  C30  H30   single    0.970  0.020  1.090
 JN7  C30  H30A  single    0.970  0.020  1.090
 JN7  C31  H31   single    0.970  0.020  1.090
 JN7  C31  H31A  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
 JN7  H1A   C1   H1   106.42  3.000
 JN7  H1A   C1   C6   110.45  3.000
 JN7  H1    C1   C6   111.07  3.000
 JN7  H1A   C1   C2   110.49  3.000
 JN7  H1    C1   C2   108.12  3.000
 JN7  C6    C1   C2   110.20  3.000
 JN7  H2A   C2   H2   107.35  3.000
 JN7  H2A   C2   N3   107.60  3.000
 JN7  H2    C2   N3   110.14  3.000
 JN7  H2A   C2   C1   109.62  3.000
 JN7  H2    C2   C1   110.79  3.000
 JN7  N3    C2   C1   111.21  3.000
 JN7  C10   N3   C4   125.56  3.000
 JN7  C10   N3   C2   120.18  3.000
 JN7  C4    N3   C2   113.25  3.000
 JN7  H4A   C4   H4   106.80  3.000
 JN7  H4A   C4   C5   110.68  3.000
 JN7  H4    C4   C5   110.66  3.000
 JN7  H4A   C4   N3   109.26  3.000
 JN7  H4    C4   N3   111.00  3.000
 JN7  C5    C4   N3   108.44  3.000
 JN7  S7    C5   C6   113.13  3.000
 JN7  S7    C5   C4   120.98  3.000
 JN7  C6    C5   C4   125.88  3.000
 JN7  C9    C6   C5   111.80  3.000
 JN7  C9    C6   C1   128.08  3.000
 JN7  C5    C6   C1   120.11  3.000
 JN7  C8    S7   C5    91.01  3.000
 JN7  N16   C8   C9   125.85  3.000
 JN7  C9    C8   S7   112.22  3.000
 JN7  N16   C8   S7   121.93  3.000
 JN7  C15   C9   C8   120.67  3.000
 JN7  C15   C9   C6   127.48  3.000
 JN7  C8    C9   C6   111.82  3.000
 JN7  O12   C10  O11  123.06  3.000
 JN7  O11   C10  N3   125.25  3.000
 JN7  O12   C10  N3   111.68  3.000
 JN7  C13   O12  C10  119.24  3.000
 JN7  H13   C13  C14  123.37  3.000
 JN7  H13   C13  O12  116.42  3.000
 JN7  C14   C13  O12  120.20  3.000
 JN7  H14A  C14  H14  118.11  3.000
 JN7  H14A  C14  C13  119.02  3.000
 JN7  H14   C14  C13  122.86  3.000
 JN7  O26   C15  O25  123.30  3.000
 JN7  O25   C15  C9   113.07  3.000
 JN7  O26   C15  C9   123.62  3.000
 JN7  HN16  N16  C17  120.59  3.000
 JN7  HN16  N16  C8   114.46  3.000
 JN7  C17   N16  C8   124.94  3.000
 JN7  O24   C17  C18  124.31  3.000
 JN7  O24   C17  N16  121.93  3.000
 JN7  C18   C17  N16  113.76  3.000
 JN7  H18A  C18  H18  105.74  3.000
 JN7  H18A  C18  C19  111.44  3.000
 JN7  H18   C18  C19  109.16  3.000
 JN7  H18A  C18  C17  107.94  3.000
 JN7  H18   C18  C17  109.05  3.000
 JN7  C19   C18  C17  113.22  3.000
 JN7  C23   C19  S20  110.80  3.000
 JN7  C23   C19  C18  127.63  3.000
 JN7  S20   C19  C18  121.56  3.000
 JN7  C21   S20  C19   92.25  3.000
 JN7  H21   C21  C22  128.16  3.000
 JN7  H21   C21  S20  120.41  3.000
 JN7  C22   C21  S20  111.43  3.000
 JN7  H22   C22  C23  124.08  3.000
 JN7  H22   C22  C21  123.45  3.000
 JN7  C23   C22  C21  112.47  3.000
 JN7  H23   C23  C22  124.17  3.000
 JN7  H23   C23  C19  122.78  3.000
 JN7  C22   C23  C19  113.05  3.000
 JN7  C27   O25  C15  119.77  3.000
 JN7  H27   C27  C31  113.92  3.000
 JN7  H27   C27  C28  113.59  3.000
 JN7  C31   C27  C28  102.95  3.000
 JN7  H27   C27  O25  109.77  3.000
 JN7  C31   C27  O25  110.05  3.000
 JN7  C28   C27  O25  106.13  3.000
 JN7  H28A  C28  H28  107.14  3.000
 JN7  H28A  C28  C29  113.74  3.000
 JN7  H28   C28  C29  110.68  3.000
 JN7  H28A  C28  C27  112.97  3.000
 JN7  H28   C28  C27  107.58  3.000
 JN7  C29   C28  C27  104.62  3.000
 JN7  H29A  C29  H29  106.71  3.000
 JN7  H29A  C29  C30  110.64  3.000
 JN7  H29   C29  C30  112.22  3.000
 JN7  H29A  C29  C28  110.42  3.000
 JN7  H29   C29  C28  111.32  3.000
 JN7  C30   C29  C28  105.60  3.000
 JN7  H30A  C30  H30  106.58  3.000
 JN7  H30A  C30  C31  110.50  3.000
 JN7  H30   C30  C31  111.25  3.000
 JN7  H30A  C30  C29  110.67  3.000
 JN7  H30   C30  C29  112.13  3.000
 JN7  C31   C30  C29  105.79  3.000
 JN7  H31A  C31  H31  106.89  3.000
 JN7  H31A  C31  C30  110.67  3.000
 JN7  H31   C31  C30  113.70  3.000
 JN7  H31A  C31  C27  107.50  3.000
 JN7  H31   C31  C27  113.50  3.000
 JN7  C30   C31  C27  104.46  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
 JN7  CONST_01  C8    C9   C6   C5      0.00   0.0  0
 JN7  CONST_02  C9    C8   S7   C5      0.00   0.0  0
 JN7  CONST_03  C8    S7   C5   C6      0.00   0.0  0
 JN7  CONST_04  S7    C8   C9   C6      0.00   0.0  0
 JN7  CONST_05  C9    C6   C5   S7      0.00   0.0  0
 JN7  CONST_06  C22   C21  S20  C19     0.00   0.0  0
 JN7  CONST_07  C21   C22  C23  C19     0.00   0.0  0
 JN7  CONST_08  C22   C23  C19  S20     0.00   0.0  0
 JN7  CONST_09  C23   C22  C21  S20     0.00   0.0  0
 JN7  CONST_10  C23   C19  S20  C21     0.00   0.0  0
 JN7  CONST_11  C15   C9   C6   C1      0.00   0.0  0
 JN7  CONST_12  C15   C9   C6   C5    180.00   0.0  0
 JN7  CONST_13  N16   C8   S7   C5    180.00   0.0  0
 JN7  CONST_14  N16   C8   C9   C6    180.00   0.0  0
 JN7  CONST_15  C15   C9   C8   S7    180.00   0.0  0
 JN7  CONST_16  C21   S20  C19  C18   180.00   0.0  0
 JN7  CONST_17  C22   C23  C19  C18   180.00   0.0  0
 JN7  CONST_18  H21   C21  S20  C19   180.00   0.0  0
 JN7  CONST_19  H22   C22  C23  C19   180.00   0.0  0
 JN7  CONST_20  H23   C23  C19  S20   180.00   0.0  0
 JN7  CONST_21  C17   N16  C8   S7      0.00   0.0  0
 JN7  CONST_22  C17   N16  C8   C9    180.00   0.0  0
 JN7  CONST_23  HN16  N16  C8   S7    180.00   0.0  0
 JN7  CONST_24  C18   C17  N16  C8    180.00   0.0  0
 JN7  CONST_25  O24   C17  N16  C8      0.00   0.0  0
 JN7  Var_01    C4    N3   C2   C1    -66.93  30.0  1
 JN7  Var_02    C5    C6   C1   C2    -13.07  30.0  1
 JN7  Var_03    C5    C4   N3   C2     47.89  30.0  1
 JN7  Var_04    C6    C1   C2   N3     45.57  30.0  1
 JN7  Var_05    C6    C5   C4   N3    -14.04  30.0  1
 JN7  Var_06    C30   C29  C28  C27    24.36  30.0  1
 JN7  Var_07    C29   C30  C31  C27   -23.95  30.0  1
 JN7  Var_08    C31   C30  C29  C28    -0.20  30.0  1
 JN7  Var_09    O12   C10  N3   C2   -175.41  30.0  2
 JN7  Var_10    O26   C15  C9   C6   -179.19  30.0  2
 JN7  Var_11    S20   C19  C18  C17   -75.35  30.0  2
 JN7  Var_12    C19   C18  C17  N16  -171.66  30.0  2
 JN7  Var_13    C14   C13  O12  C10  -171.08  30.0  3
 JN7  Var_14    H14   C14  C13  O12     1.28   0.0  2

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
 JN7  chir_01  C27  O25  C28  C31  negativ

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
 JN7  plan-1  C18   0.020
 JN7  plan-1  C19   0.020
 JN7  plan-1  S20   0.020
 JN7  plan-1  C21   0.020
 JN7  plan-1  C22   0.020
 JN7  plan-1  C23   0.020
 JN7  plan-1  H21   0.020
 JN7  plan-1  H22   0.020
 JN7  plan-1  H23   0.020
 JN7  plan-2  C1    0.020
 JN7  plan-2  C4    0.020
 JN7  plan-2  C5    0.020
 JN7  plan-2  C6    0.020
 JN7  plan-2  S7    0.020
 JN7  plan-2  C8    0.020
 JN7  plan-2  C9    0.020
 JN7  plan-2  C15   0.020
 JN7  plan-2  N16   0.020
 JN7  plan-3  C8    0.020
 JN7  plan-3  N16   0.020
 JN7  plan-3  C17   0.020
 JN7  plan-3  C18   0.020
 JN7  plan-3  O24   0.020
 JN7  plan-3  HN16  0.020
 JN7  plan-4  N3    0.020
 JN7  plan-4  C10   0.020
 JN7  plan-4  O11   0.020
 JN7  plan-4  O12   0.020
 JN7  plan-5  O12   0.020
 JN7  plan-5  C13   0.020
 JN7  plan-5  C14   0.020
 JN7  plan-5  H13   0.020
 JN7  plan-5  H14   0.020
 JN7  plan-5  H14A  0.020
 JN7  plan-6  C9    0.020
 JN7  plan-6  C15   0.020
 JN7  plan-6  O25   0.020
 JN7  plan-6  O26   0.020

