# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 09:46:18 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: cyclopentyl 6-(ethylcarbamoyl)-2-[(thiophen-2-ylacetyl)amino]-4,5,6,7-tetrahydrothieno[2,3-c]pyridine-3-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=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
 JN8  JN8  'cyclopentyl 6-(ethylcarbamoyl)-2-[(thiophen-2-ylacetyl)amino]-4,5,6,7-tetrahydrothieno[2,3-c]pyridine-3-carboxylate'  ligand  58  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_JN8
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
 JN8  C1    C  CR5   0   0.254   1.2051  -0.7554  -0.8181
 JN8  C2    C  CR5   0  -0.068  -0.1746  -0.9546  -0.4536
 JN8  C3    C  CR5   0   0.019  -0.9370   0.1739  -0.6882
 JN8  S4    S  S2    0   0.255   0.0024   1.4749  -1.3073
 JN8  C5    C  CR5   0  -0.358   1.4313   0.5025  -1.2708
 JN8  C6    C  CH2   0  -0.311   2.7582   1.0587  -1.7000
 JN8  N7    N  NT    0  -0.505   3.8074   0.1311  -1.3336
 JN8  C8    C  CH2   0  -0.317   3.4807  -1.2459  -1.6465
 JN8  C9    C  CH2   0  -0.488   2.3217  -1.7596  -0.8015
 JN8  N10   N  NH1   0  -0.606  -2.2815   0.2976  -0.4494
 JN8  C11   C  C     0   0.540  -3.0133   1.4165  -0.6900
 JN8  C12   C  CH2   0  -0.662  -4.4919   1.2748  -0.3962
 JN8  C13   C  CR5   0  -0.095  -5.1260   2.5686  -0.0191
 JN8  C14   C  CR15  0  -0.221  -5.9005   3.3811  -0.7896
 JN8  C15   C  CR15  0  -0.162  -6.3228   4.5576  -0.1101
 JN8  C16   C  CR15  0  -0.444  -5.8563   4.6184   1.1662
 JN8  S17   S  S2    0   0.136  -4.9061   3.2439   1.5508
 JN8  O18   O  O     0  -0.491  -2.5103   2.4313  -1.1293
 JN8  C19   C  C     0   0.471  -0.7720  -2.1506   0.1436
 JN8  O20   O  O2    0  -0.517   0.1155  -3.0689   0.4631
 JN8  C24   C  C     0   0.756   4.7462   0.3817  -0.3635
 JN8  C27   C  CR15  0  -0.004  -0.3334  -4.2988   1.0748
 JN8  C28   C  CH2   0  -0.476   0.9098  -4.9695   1.6383
 JN8  N28   N  NH1   0  -0.625   5.0171   1.6921  -0.1180
 JN8  C29   C  CH2   0  -0.416   1.5052  -5.7102   0.4448
 JN8  O29   O  O     0  -0.625   5.3094  -0.5284   0.2345
 JN8  C30   C  CH2   0  -0.477   0.2719  -6.2804  -0.2634
 JN8  C31   C  CH2   0  -0.462  -0.8697  -5.2791   0.0197
 JN8  O31   O  O     0  -0.311  -1.9673  -2.2778   0.3471
 JN8  C32   C  CH3   0  -0.739   5.7654   3.4908   1.3474
 JN8  C33   C  CH2   0  -0.275   6.0341   2.0863   0.8374
 JN8  H6    H  HCH2  0   0.254   2.7706   1.2436  -2.7794
 JN8  H6A   H  HCH2  0   0.234   2.9174   2.0241  -1.2220
 JN8  H8    H  HCH2  0   0.243   3.2083  -1.2895  -2.7053
 JN8  H8A   H  HCH2  0   0.273   4.3578  -1.8738  -1.5172
 JN8  H9    H  HCH2  0   0.276   2.6580  -1.9542   0.2202
 JN8  H9A   H  HCH2  0   0.263   1.9883  -2.7167  -1.2037
 JN8  HN10  H  HNH1  0   0.426  -2.7223  -0.5418  -0.0858
 JN8  H12   H  HCH2  0   0.305  -4.9707   0.9026  -1.3079
 JN8  H12A  H  HCH2  0   0.308  -4.6592   0.5099   0.3652
 JN8  H14   H  HCR5  0   0.254  -6.1626   3.1448  -1.8117
 JN8  H15   H  HCR5  0   0.262  -6.9476   5.3200  -0.5529
 JN8  H16   H  HCR5  0   0.302  -6.0275   5.3866   1.9044
 JN8  H27   H  HCR5  0   0.284  -1.0702  -4.0609   1.8427
 JN8  H28   H  HCH2  0   0.275   1.5866  -4.2618   2.1195
 JN8  H28A  H  HCH2  0   0.203   0.5942  -5.6860   2.4014
 JN8  HN28  H  HNH1  0   0.393   4.8485   2.3576  -0.8557
 JN8  H29   H  HCH2  0   0.235   2.0396  -5.0134  -0.2058
 JN8  H29A  H  HCH2  0   0.265   2.2154  -6.4832   0.7398
 JN8  H30   H  HCH2  0   0.213   0.4359  -6.4269  -1.3310
 JN8  H30A  H  HCH2  0   0.230   0.0254  -7.2569   0.1573
 JN8  H31   H  HCH2  0   0.244  -1.7538  -5.7857   0.4076
 JN8  H31A  H  HCH2  0   0.232  -1.1865  -4.7568  -0.8834
 JN8  H32   H  HCH3  0   0.243   6.5282   3.7810   2.0695
 JN8  H32A  H  HCH3  0   0.232   5.7817   4.2209   0.5367
 JN8  H32B  H  HCH3  0   0.254   4.7935   3.5488   1.8382
 JN8  H33   H  HCH2  0   0.262   6.0211   1.3812   1.6661
 JN8  H33A  H  HCH2  0   0.255   7.0334   2.0361   0.3922

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
 JN8  C5   C1    aromatic  1.356  0.020  1.356
 JN8  C9   C1    single    1.502  0.020  1.502
 JN8  C1   C2    aromatic  1.441  0.020  1.441
 JN8  C3   C2    aromatic  1.382  0.020  1.382
 JN8  C2   C19   single    1.464  0.020  1.464
 JN8  S4   C3    aromatic  1.720  0.020  1.720
 JN8  C3   N10   single    1.371  0.020  1.371
 JN8  C5   S4    aromatic  1.729  0.020  1.729
 JN8  C6   C5    single    1.501  0.020  1.501
 JN8  N7   C6    single    1.448  0.020  1.448
 JN8  C6   H6    single    0.970  0.020  1.090
 JN8  C6   H6A   single    0.970  0.020  1.090
 JN8  C24  N7    single    1.373  0.020  1.373
 JN8  N7   C8    single    1.449  0.020  1.449
 JN8  C8   C9    single    1.524  0.020  1.524
 JN8  C8   H8    single    0.970  0.020  1.090
 JN8  C8   H8A   single    0.970  0.020  1.090
 JN8  C9   H9    single    0.970  0.020  1.090
 JN8  C9   H9A   single    0.970  0.020  1.090
 JN8  C11  N10   single    1.358  0.020  1.358
 JN8  N10  HN10  single    0.860  0.020  1.020
 JN8  O18  C11   double    1.215  0.020  1.215
 JN8  C11  C12   single    1.514  0.020  1.514
 JN8  C12  C13   single    1.489  0.020  1.489
 JN8  C12  H12   single    0.970  0.020  1.090
 JN8  C12  H12A  single    0.970  0.020  1.090
 JN8  C13  C14   aromatic  1.361  0.020  1.361
 JN8  C13  S17   aromatic  1.723  0.020  1.723
 JN8  C14  C15   aromatic  1.423  0.020  1.423
 JN8  C14  H14   single    0.930  0.020  1.080
 JN8  C15  C16   aromatic  1.360  0.020  1.360
 JN8  C15  H15   single    0.930  0.020  1.080
 JN8  S17  C16   aromatic  1.715  0.020  1.715
 JN8  C16  H16   single    0.930  0.020  1.080
 JN8  C19  O20   single    1.316  0.020  1.316
 JN8  C19  O31   double    1.219  0.020  1.219
 JN8  O20  C27   single    1.445  0.020  1.445
 JN8  O29  C24   double    1.226  0.020  1.226
 JN8  C24  N28   single    1.360  0.020  1.360
 JN8  C31  C27   single    1.537  0.020  1.537
 JN8  C27  C28   single    1.521  0.020  1.521
 JN8  C27  H27   single    0.970  0.020  1.090
 JN8  C29  C28   single    1.526  0.020  1.526
 JN8  C28  H28   single    0.970  0.020  1.090
 JN8  C28  H28A  single    0.970  0.020  1.090
 JN8  C33  N28   single    1.450  0.020  1.450
 JN8  N28  HN28  single    0.890  0.020  1.040
 JN8  C30  C29   single    1.532  0.020  1.532
 JN8  C29  H29   single    0.970  0.020  1.090
 JN8  C29  H29A  single    0.970  0.020  1.090
 JN8  C30  C31   single    1.545  0.020  1.545
 JN8  C30  H30   single    0.970  0.020  1.090
 JN8  C30  H30A  single    0.970  0.020  1.090
 JN8  C31  H31   single    0.970  0.020  1.090
 JN8  C31  H31A  single    0.970  0.020  1.090
 JN8  C33  C32   single    1.518  0.020  1.518
 JN8  C32  H32   single    0.970  0.020  1.090
 JN8  C32  H32A  single    0.970  0.020  1.090
 JN8  C32  H32B  single    0.970  0.020  1.090
 JN8  C33  H33   single    0.970  0.020  1.090
 JN8  C33  H33A  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
 JN8  C9    C1   C5    120.00  3.000
 JN8  C9    C1   C2    128.08  3.000
 JN8  C5    C1   C2    111.87  3.000
 JN8  C19   C2   C3    120.74  3.000
 JN8  C19   C2   C1    127.36  3.000
 JN8  C3    C2   C1    111.86  3.000
 JN8  N10   C3   S4    122.00  3.000
 JN8  N10   C3   C2    125.81  3.000
 JN8  S4    C3   C2    112.18  3.000
 JN8  C5    S4   C3     91.05  3.000
 JN8  C6    C5   S4    121.07  3.000
 JN8  C6    C5   C1    125.91  3.000
 JN8  S4    C5   C1    113.02  3.000
 JN8  H6A   C6   H6    106.33  3.000
 JN8  H6A   C6   N7    110.55  3.000
 JN8  H6    C6   N7    110.45  3.000
 JN8  H6A   C6   C5    109.40  3.000
 JN8  H6    C6   C5    110.75  3.000
 JN8  N7    C6   C5    109.32  3.000
 JN8  C24   N7   C8    118.69  3.000
 JN8  C8    N7   C6    113.00  3.000
 JN8  C24   N7   C6    123.88  3.000
 JN8  H8A   C8   H8    107.05  3.000
 JN8  H8A   C8   C9    110.69  3.000
 JN8  H8    C8   C9    109.51  3.000
 JN8  H8A   C8   N7    109.96  3.000
 JN8  H8    C8   N7    107.63  3.000
 JN8  C9    C8   N7    111.84  3.000
 JN8  H9A   C9   H9    106.41  3.000
 JN8  H9A   C9   C8    108.90  3.000
 JN8  H9    C9   C8    110.15  3.000
 JN8  H9A   C9   C1    110.82  3.000
 JN8  H9    C9   C1    110.99  3.000
 JN8  C8    C9   C1    109.51  3.000
 JN8  HN10  N10  C11   120.69  3.000
 JN8  HN10  N10  C3    114.42  3.000
 JN8  C11   N10  C3    124.87  3.000
 JN8  O18   C11  C12   123.55  3.000
 JN8  C12   C11  N10   114.50  3.000
 JN8  O18   C11  N10   121.94  3.000
 JN8  H12A  C12  H12   105.99  3.000
 JN8  H12A  C12  C13   111.51  3.000
 JN8  H12   C12  C13   108.66  3.000
 JN8  H12A  C12  C11   110.51  3.000
 JN8  H12   C12  C11   107.30  3.000
 JN8  C13   C12  C11   112.56  3.000
 JN8  S17   C13  C14   110.75  3.000
 JN8  S17   C13  C12   121.12  3.000
 JN8  C14   C13  C12   128.12  3.000
 JN8  H14   C14  C15   124.07  3.000
 JN8  H14   C14  C13   122.84  3.000
 JN8  C15   C14  C13   113.08  3.000
 JN8  H15   C15  C16   123.46  3.000
 JN8  H15   C15  C14   124.01  3.000
 JN8  C16   C15  C14   112.53  3.000
 JN8  H16   C16  S17   120.34  3.000
 JN8  H16   C16  C15   128.26  3.000
 JN8  S17   C16  C15   111.39  3.000
 JN8  C16   S17  C13    92.24  3.000
 JN8  O31   C19  O20   123.21  3.000
 JN8  O31   C19  C2    123.59  3.000
 JN8  O20   C19  C2    113.19  3.000
 JN8  C27   O20  C19   119.14  3.000
 JN8  O29   C24  N28   122.39  3.000
 JN8  N28   C24  N7    116.07  3.000
 JN8  O29   C24  N7    121.54  3.000
 JN8  H27   C27  C31   112.76  3.000
 JN8  H27   C27  C28   112.81  3.000
 JN8  C31   C27  C28   104.98  3.000
 JN8  H27   C27  O20   108.80  3.000
 JN8  C28   C27  O20   106.16  3.000
 JN8  C31   C27  O20   111.14  3.000
 JN8  H28A  C28  H28   107.24  3.000
 JN8  H28A  C28  C29   109.90  3.000
 JN8  H28   C28  C29   114.70  3.000
 JN8  H28A  C28  C27   108.16  3.000
 JN8  H28   C28  C27   112.61  3.000
 JN8  C29   C28  C27   104.08  3.000
 JN8  HN28  N28  C33   114.85  3.000
 JN8  HN28  N28  C24   118.08  3.000
 JN8  C33   N28  C24   121.36  3.000
 JN8  H29A  C29  H29   107.13  3.000
 JN8  H29A  C29  C30   112.68  3.000
 JN8  H29   C29  C30   110.83  3.000
 JN8  H29A  C29  C28   112.76  3.000
 JN8  H29   C29  C28   110.30  3.000
 JN8  C30   C29  C28   103.19  3.000
 JN8  H30A  C30  H30   106.93  3.000
 JN8  H30A  C30  C31   110.02  3.000
 JN8  H30   C30  C31   112.20  3.000
 JN8  H30A  C30  C29   109.66  3.000
 JN8  H30   C30  C29   112.44  3.000
 JN8  C31   C30  C29   105.60  3.000
 JN8  H31A  C31  H31   106.36  3.000
 JN8  H31A  C31  C30   111.93  3.000
 JN8  H31   C31  C30   111.30  3.000
 JN8  H31A  C31  C27   111.38  3.000
 JN8  H31   C31  C27   109.58  3.000
 JN8  C30   C31  C27   106.34  3.000
 JN8  H32B  C32  H32A  108.19  3.000
 JN8  H32B  C32  H32   108.14  3.000
 JN8  H32A  C32  H32   107.68  3.000
 JN8  H32B  C32  C33   110.99  3.000
 JN8  H32A  C32  C33   111.52  3.000
 JN8  H32   C32  C33   110.19  3.000
 JN8  H33A  C33  H33   106.91  3.000
 JN8  H33A  C33  C32   109.90  3.000
 JN8  H33   C33  C32   109.97  3.000
 JN8  H33A  C33  N28   111.08  3.000
 JN8  H33   C33  N28   108.50  3.000
 JN8  C32   C33  N28   110.41  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
 JN8  CONST_01  C3    S4   C5   C1      0.00   0.0  0
 JN8  CONST_02  S4    C3   C2   C1      0.00   0.0  0
 JN8  CONST_03  S4    C5   C1   C2      0.00   0.0  0
 JN8  CONST_04  C5    S4   C3   C2      0.00   0.0  0
 JN8  CONST_05  C5    C1   C2   C3      0.00   0.0  0
 JN8  CONST_06  C16   C15  C14  C13     0.00   0.0  0
 JN8  CONST_07  C15   C16  S17  C13     0.00   0.0  0
 JN8  CONST_08  C16   S17  C13  C14     0.00   0.0  0
 JN8  CONST_09  S17   C16  C15  C14     0.00   0.0  0
 JN8  CONST_10  S17   C13  C14  C15     0.00   0.0  0
 JN8  CONST_11  N10   C3   C2   C1    180.00   0.0  0
 JN8  CONST_12  C19   C2   C3   S4    180.00   0.0  0
 JN8  CONST_13  C19   C2   C1   C5    180.00   0.0  0
 JN8  CONST_14  N10   C3   S4   C5    180.00   0.0  0
 JN8  CONST_15  C19   C2   C1   C9      0.00   0.0  0
 JN8  CONST_16  C15   C14  C13  C12   180.00   0.0  0
 JN8  CONST_17  C16   S17  C13  C12   180.00   0.0  0
 JN8  CONST_18  H15   C15  C14  C13   180.00   0.0  0
 JN8  CONST_19  H16   C16  S17  C13   180.00   0.0  0
 JN8  CONST_20  H14   C14  C15  C16   180.00   0.0  0
 JN8  CONST_22  O29   C24  N7   C8      0.00   0.0  0
 JN8  CONST_23  C11   N10  C3   C2    180.00   0.0  0
 JN8  CONST_24  C11   N10  C3   S4      0.00   0.0  0
 JN8  CONST_26  N28   C24  N7   C8    180.00   0.0  0
 JN8  CONST_27  HN10  N10  C3   C2      0.00   0.0  0
 JN8  CONST_28  O18   C11  N10  C3      0.00   0.0  0
 JN8  CONST_29  C12   C11  N10  C3    180.00   0.0  0
 JN8  CONST_30  C33   N28  C24  N7    180.00   0.0  0
 JN8  CONST_32  C33   N28  C24  O29     0.00   0.0  0
 JN8  Var_01    N7    C6   C5   C1    -10.24  30.0  1
 JN8  Var_02    N7    C8   C9   C1     47.64  30.0  1
 JN8  Var_03    C8    C9   C1   C2    162.94  30.0  1
 JN8  Var_04    C8    N7   C6   C5     44.58  30.0  1
 JN8  Var_05    C9    C8   N7   C6    -66.53  30.0  1
 JN8  Var_06    C29   C30  C31  C27    -9.61  30.0  1
 JN8  Var_07    C30   C29  C28  C27   -40.26  30.0  1
 JN8  Var_08    C31   C30  C29  C28    30.51  30.0  1
 JN8  Var_09    O20   C19  C2   C1      6.05  30.0  2
 JN8  Var_10    C14   C13  C12  C11   102.16  30.0  2
 JN8  Var_11    C13   C12  C11  N10   151.85  30.0  3
 JN8  Var_12    C32   C33  N28  C24  -156.69  30.0  2
 JN8  Var_13    H32   C32  C33  N28   179.65  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
 JN8  chir_01  C27  O20  C31  C28  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
 JN8  plan-1  C12   0.020
 JN8  plan-1  C13   0.020
 JN8  plan-1  C14   0.020
 JN8  plan-1  C15   0.020
 JN8  plan-1  C16   0.020
 JN8  plan-1  S17   0.020
 JN8  plan-1  H14   0.020
 JN8  plan-1  H15   0.020
 JN8  plan-1  H16   0.020
 JN8  plan-2  C2    0.020
 JN8  plan-2  C19   0.020
 JN8  plan-2  O20   0.020
 JN8  plan-2  O31   0.020
 JN8  plan-3  C1    0.020
 JN8  plan-3  C2    0.020
 JN8  plan-3  C3    0.020
 JN8  plan-3  S4    0.020
 JN8  plan-3  C5    0.020
 JN8  plan-3  C6    0.020
 JN8  plan-3  C9    0.020
 JN8  plan-3  N10   0.020
 JN8  plan-3  C19   0.020
 JN8  plan-4  C3    0.020
 JN8  plan-4  N10   0.020
 JN8  plan-4  C11   0.020
 JN8  plan-4  C12   0.020
 JN8  plan-4  O18   0.020
 JN8  plan-4  HN10  0.020
 JN8  plan-5  C6    0.020
 JN8  plan-5  N7    0.020
 JN8  plan-5  C8    0.020
 JN8  plan-5  C24   0.020
 JN8  plan-5  N28   0.020
 JN8  plan-5  O29   0.020
 JN8  plan-5  C33   0.020
 JN8  plan-5  HN28  0.020

