# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 15:42:02 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 2-(4-chlorophenyl)-4-[(3S)-piperidin-3-ylamino]thieno[3,2-c]pyridine-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cnc(N[C@H]2CCCNC2)c3cc(sc13)c4ccc(Cl)cc4
#
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
 C72  C72  2-(4-chlorophenyl)-4-[(3S)-piperidin-3-ylamino]thieno[3,2-c]pyridine-7-carboxamide  ligand  45  26  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_C72
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
 C72  C01   C   CR15  0  -0.277   0.3667   0.3990   0.1284
 C72  C02   C   CR5   0  -0.211   1.5290  -0.2969   0.0275
 C72  S03   S   S2    0   0.260   1.2507  -2.0188  -0.0673
 C72  C04   C   CR56  0  -0.123  -0.4541  -1.7969   0.0271
 C72  C05   C   CR56  0   0.086  -0.7809  -0.4470   0.1273
 C72  C06   C   CR6   0  -0.206  -1.4513  -2.7889   0.0001
 C72  C07   C   CR16  0  -0.088  -2.7498  -2.3168   0.0734
 C72  N08   N   N     0  -0.481  -3.1024  -1.0390   0.1687
 C72  C09   C   CR6   0   0.513  -2.1601  -0.1011   0.2088
 C72  N10   N   NH1   0  -0.678  -2.5333   1.1812   0.3433
 C72  C11   C   CR6   0   0.152   2.8880   0.2362  -0.0251
 C72  C12   C   C     0   0.505  -1.0516  -4.2052  -0.1029
 C72  C13   C   CH1   0  -0.063  -3.9033   1.6496   0.3268
 C72  C14   C   CH2   0  -0.281  -4.3945   1.8700  -1.1042
 C72  N15   N   NH1   0  -0.600  -5.7593   2.3575  -1.0807
 C72  C16   C   CH2   0  -0.291  -5.8632   3.6462  -0.4189
 C72  C17   C   CH2   0  -0.436  -5.4308   3.5085   1.0330
 C72  C18   C   CH2   0  -0.455  -4.0170   2.9433   1.1264
 C72  C19   C   CR16  0  -0.329   3.1167   1.5371  -0.4812
 C72  C20   C   CR16  0  -0.188   4.3955   2.0631  -0.5345
 C72  C21   C   CR6   0  -0.057   5.4687   1.2792  -0.1373
 C72  C22   C   CR16  0  -0.190   5.2743  -0.0166   0.3130
 C72  C23   C   CR16  0  -0.325   3.9880  -0.5282   0.3695
 C72  CL24  CL  CL    0  -0.123   7.0725   1.9277  -0.2091
 C72  N25   N   NH2   0  -0.830  -2.0105  -5.1411  -0.1216
 C72  O26   O   O     0  -0.492   0.1432  -4.4897  -0.1634
 C72  H01   H   HCR5  0   0.268   0.3329   1.4762   0.2157
 C72  H07   H   HCR6  0   0.254  -3.5873  -3.0064   0.0511
 C72  HN10  H   HNH1  0   0.402  -1.8165   1.8872   0.2991
 C72  H13   H   HCH1  0   0.246  -4.5289   0.8856   0.7914
 C72  H14   H   HCH2  0   0.186  -3.6980   2.5641  -1.6057
 C72  H14A  H   HCH2  0   0.237  -4.3616   0.9269  -1.6536
 C72  HN15  H   HNH1  0   0.355  -6.1066   2.4301  -2.0275
 C72  H16   H   HCH2  0   0.187  -5.2442   4.4197  -0.9035
 C72  H16A  H   HCH2  0   0.233  -6.8989   3.9873  -0.4731
 C72  H17   H   HCH2  0   0.235  -5.4785   4.4787   1.5308
 C72  H17A  H   HCH2  0   0.220  -6.1273   2.8449   1.5534
 C72  H18   H   HCH2  0   0.246  -3.7387   2.7665   2.1678
 C72  H18A  H   HCH2  0   0.219  -3.3074   3.6776   0.7261
 C72  H19   H   HCR6  0   0.267   2.2894   2.1491  -0.8170
 C72  H20   H   HCR6  0   0.285   4.5533   3.0709  -0.8936
 C72  H22   H   HCR6  0   0.285   6.1133  -0.6244   0.6234
 C72  H23   H   HCR6  0   0.265   3.8525  -1.5357   0.7429
 C72  HN25  H   HNH2  0   0.413  -2.9922  -4.9329  -0.0924
 C72  HN2A  H   HNH2  0   0.407  -1.7537  -6.1115  -0.1946

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
 C72  C02   C01   aromatic  1.359  0.020  1.359
 C72  C01   C05   aromatic  1.426  0.020  1.426
 C72  C01   H01   single    0.930  0.020  1.080
 C72  C11   C02   single    1.461  0.020  1.461
 C72  S03   C02   aromatic  1.747  0.020  1.747
 C72  S03   C04   aromatic  1.722  0.020  1.722
 C72  C04   C06   aromatic  1.407  0.020  1.407
 C72  C04   C05   aromatic  1.392  0.020  1.392
 C72  C05   C09   aromatic  1.424  0.020  1.424
 C72  C12   C06   single    1.475  0.020  1.475
 C72  C06   C07   aromatic  1.384  0.020  1.384
 C72  C07   N08   aromatic  1.329  0.020  1.329
 C72  C07   H07   single    0.930  0.020  1.080
 C72  C09   N08   aromatic  1.330  0.020  1.330
 C72  C09   N10   single    1.342  0.020  1.342
 C72  N10   C13   single    1.448  0.020  1.448
 C72  N10   HN10  single    0.860  0.020  1.020
 C72  C19   C11   aromatic  1.397  0.020  1.397
 C72  C11   C23   aromatic  1.396  0.020  1.396
 C72  O26   C12   double    1.230  0.020  1.230
 C72  C12   N25   single    1.340  0.020  1.340
 C72  C13   C18   single    1.525  0.020  1.525
 C72  C13   C14   single    1.529  0.020  1.529
 C72  C13   H13   single    0.970  0.020  1.090
 C72  C14   N15   single    1.449  0.020  1.449
 C72  C14   H14   single    0.970  0.020  1.090
 C72  C14   H14A  single    0.970  0.020  1.090
 C72  N15   C16   single    1.452  0.020  1.452
 C72  N15   HN15  single    0.890  0.020  1.040
 C72  C17   C16   single    1.521  0.020  1.521
 C72  C16   H16   single    0.970  0.020  1.090
 C72  C16   H16A  single    0.970  0.020  1.090
 C72  C18   C17   single    1.525  0.020  1.525
 C72  C17   H17   single    0.970  0.020  1.090
 C72  C17   H17A  single    0.970  0.020  1.090
 C72  C18   H18   single    0.970  0.020  1.090
 C72  C18   H18A  single    0.970  0.020  1.090
 C72  C20   C19   aromatic  1.384  0.020  1.384
 C72  C19   H19   single    0.930  0.020  1.080
 C72  C20   C21   aromatic  1.387  0.020  1.387
 C72  C20   H20   single    0.930  0.020  1.080
 C72  CL24  C21   single    1.731  0.020  1.731
 C72  C21   C22   aromatic  1.386  0.020  1.386
 C72  C22   C23   aromatic  1.385  0.020  1.385
 C72  C22   H22   single    0.930  0.020  1.080
 C72  C23   H23   single    0.930  0.020  1.080
 C72  N25   HN25  single    0.860  0.020  1.020
 C72  N25   HN2A  single    0.860  0.020  1.020

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
 C72  H01   C01  C05   124.48  3.000
 C72  H01   C01  C02   122.89  3.000
 C72  C05   C01  C02   112.62  3.000
 C72  C11   C02  S03   120.40  3.000
 C72  S03   C02  C01   111.88  3.000
 C72  C11   C02  C01   127.71  3.000
 C72  C04   S03  C02    91.59  3.000
 C72  C06   C04  C05   121.24  3.000
 C72  C05   C04  S03   111.18  3.000
 C72  C06   C04  S03   127.58  3.000
 C72  C09   C05  C04   117.83  3.000
 C72  C09   C05  C01   129.44  3.000
 C72  C04   C05  C01   112.73  3.000
 C72  C12   C06  C07   125.85  3.000
 C72  C07   C06  C04   115.06  3.000
 C72  C12   C06  C04   119.09  3.000
 C72  H07   C07  N08   114.07  3.000
 C72  H07   C07  C06   120.42  3.000
 C72  N08   C07  C06   125.51  3.000
 C72  C09   N08  C07   119.49  3.000
 C72  N10   C09  N08   118.67  3.000
 C72  N10   C09  C05   120.46  3.000
 C72  N08   C09  C05   120.86  3.000
 C72  HN10  N10  C13   116.50  3.000
 C72  HN10  N10  C09   117.87  3.000
 C72  C13   N10  C09   124.82  3.000
 C72  C23   C11  C19   118.22  3.000
 C72  C23   C11  C02   121.53  3.000
 C72  C19   C11  C02   120.25  3.000
 C72  O26   C12  N25   122.21  3.000
 C72  N25   C12  C06   118.52  3.000
 C72  O26   C12  C06   119.27  3.000
 C72  H13   C13  C18   109.14  3.000
 C72  H13   C13  C14   108.38  3.000
 C72  C18   C13  C14   110.15  3.000
 C72  H13   C13  N10   108.12  3.000
 C72  C14   C13  N10   111.18  3.000
 C72  C18   C13  N10   109.81  3.000
 C72  H14A  C14  H14   107.19  3.000
 C72  H14A  C14  N15   109.09  3.000
 C72  H14   C14  N15   112.96  3.000
 C72  H14A  C14  C13   109.67  3.000
 C72  H14   C14  C13   108.25  3.000
 C72  N15   C14  C13   109.62  3.000
 C72  HN15  N15  C16   109.78  3.000
 C72  HN15  N15  C14   109.41  3.000
 C72  C16   N15  C14   111.91  3.000
 C72  H16A  C16  H16   106.95  3.000
 C72  H16A  C16  C17   110.21  3.000
 C72  H16   C16  C17   108.87  3.000
 C72  H16A  C16  N15   108.80  3.000
 C72  H16   C16  N15   112.45  3.000
 C72  C17   C16  N15   109.53  3.000
 C72  H17A  C17  H17   107.12  3.000
 C72  H17A  C17  C18   109.65  3.000
 C72  H17   C17  C18   109.99  3.000
 C72  H17A  C17  C16   109.15  3.000
 C72  H17   C17  C16   110.02  3.000
 C72  C18   C17  C16   110.82  3.000
 C72  H18A  C18  H18   106.95  3.000
 C72  H18A  C18  C17   109.22  3.000
 C72  H18   C18  C17   110.76  3.000
 C72  H18A  C18  C13   109.16  3.000
 C72  H18   C18  C13   110.09  3.000
 C72  C17   C18  C13   110.56  3.000
 C72  H19   C19  C20   118.65  3.000
 C72  H19   C19  C11   120.17  3.000
 C72  C20   C19  C11   121.17  3.000
 C72  H20   C20  C21   120.58  3.000
 C72  H20   C20  C19   120.12  3.000
 C72  C21   C20  C19   119.29  3.000
 C72  CL24  C21  C22   119.58  3.000
 C72  C22   C21  C20   120.87  3.000
 C72  CL24  C21  C20   119.55  3.000
 C72  H22   C22  C23   120.07  3.000
 C72  H22   C22  C21   120.67  3.000
 C72  C23   C22  C21   119.27  3.000
 C72  H23   C23  C22   118.28  3.000
 C72  H23   C23  C11   120.54  3.000
 C72  C22   C23  C11   121.18  3.000
 C72  HN2A  N25  HN25  116.84  3.000
 C72  HN2A  N25  C12   119.46  3.000
 C72  HN25  N25  C12   123.68  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
 C72  CONST_03  C04   S03  C02  C01    0.00   0.0  0
 C72  CONST_04  S03   C04  C05  C01    0.00   0.0  0
 C72  CONST_05  C06   C04  C05  C01  180.00   0.0  0
 C72  CONST_06  N08   C09  C05  C01  180.00   0.0  0
 C72  CONST_07  C04   C05  C01  C02    0.00   0.0  0
 C72  CONST_08  C09   C05  C01  C02  180.00   0.0  0
 C72  CONST_09  C20   C19  C11  C02  180.00   0.0  0
 C72  CONST_10  C22   C23  C11  C02  180.00   0.0  0
 C72  CONST_11  C06   C04  S03  C02  180.00   0.0  0
 C72  CONST_12  C05   C04  S03  C02    0.00   0.0  0
 C72  CONST_13  C05   C01  C02  S03    0.00   0.0  0
 C72  CONST_16  C07   C06  C04  S03  180.00   0.0  0
 C72  CONST_17  C09   C05  C04  S03  180.00   0.0  0
 C72  CONST_18  C11   C02  S03  C04  180.00   0.0  0
 C72  CONST_19  N08   C07  C06  C04    0.00   0.0  0
 C72  CONST_20  N08   C09  C05  C04    0.00   0.0  0
 C72  CONST_21  C11   C02  C01  C05  180.00   0.0  0
 C72  CONST_22  C07   C06  C04  C05    0.00   0.0  0
 C72  CONST_23  C07   N08  C09  C05    0.00   0.0  0
 C72  CONST_24  C09   C05  C04  C06    0.00   0.0  0
 C72  CONST_25  C09   N08  C07  C06    0.00   0.0  0
 C72  CONST_26  C21   C20  C19  C11    0.00   0.0  0
 C72  CONST_27  C21   C22  C23  C11    0.00   0.0  0
 C72  CONST_28  C22   C23  C11  C19    0.00   0.0  0
 C72  CONST_29  C22   C21  C20  C19    0.00   0.0  0
 C72  CONST_30  C23   C11  C19  C20    0.00   0.0  0
 C72  CONST_31  C23   C22  C21  C20    0.00   0.0  0
 C72  CONST_32  N10   C09  C05  C01    0.00   0.0  0
 C72  CONST_33  C12   C06  C04  S03    0.00   0.0  0
 C72  CONST_34  N10   C09  C05  C04  180.00   0.0  0
 C72  CONST_35  C12   C06  C04  C05  180.00   0.0  0
 C72  CONST_36  N10   C09  N08  C07  180.00   0.0  0
 C72  CONST_37  C12   C06  C07  N08  180.00   0.0  0
 C72  CONST_38  CL24  C21  C20  C19  180.00   0.0  0
 C72  CONST_39  CL24  C21  C22  C23  180.00   0.0  0
 C72  CONST_40  C13   N10  C09  C05  180.00   0.0  0
 C72  CONST_41  C13   N10  C09  N08    0.00   0.0  0
 C72  CONST_42  H19   C19  C11  C02    0.00   0.0  0
 C72  CONST_43  H23   C23  C11  C02    0.00   0.0  0
 C72  CONST_44  H01   C01  C02  S03  180.00   0.0  0
 C72  CONST_45  H07   C07  C06  C04  180.00   0.0  0
 C72  CONST_46  H20   C20  C19  C11  180.00   0.0  0
 C72  CONST_47  H22   C22  C23  C11  180.00   0.0  0
 C72  CONST_48  HN10  N10  C09  C05    0.00   0.0  0
 C72  CONST_49  HN25  N25  C12  C06    0.00   0.0  0
 C72  CONST_50  HN2A  N25  C12  C06  180.00   0.0  0
 C72  Var_01    C16   C17  C18  C13  -52.95  30.0  1
 C72  Var_02    C16   N15  C14  C13   62.70  30.0  1
 C72  Var_03    C17   C16  N15  C14  -62.24  30.0  1
 C72  Var_04    C18   C17  C16  N15   56.53  30.0  1
 C72  Var_05    O26   C12  C06  C04   -0.02  30.0  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
 C72  chir_01  C13  N10  C18  C14  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
 C72  plan-1  C02   0.020
 C72  plan-1  C11   0.020
 C72  plan-1  C19   0.020
 C72  plan-1  C20   0.020
 C72  plan-1  C21   0.020
 C72  plan-1  C22   0.020
 C72  plan-1  C23   0.020
 C72  plan-1  CL24  0.020
 C72  plan-1  H19   0.020
 C72  plan-1  H20   0.020
 C72  plan-1  H22   0.020
 C72  plan-1  H23   0.020
 C72  plan-2  C01   0.020
 C72  plan-2  C02   0.020
 C72  plan-2  S03   0.020
 C72  plan-2  C04   0.020
 C72  plan-2  C05   0.020
 C72  plan-2  C06   0.020
 C72  plan-2  C07   0.020
 C72  plan-2  N08   0.020
 C72  plan-2  C09   0.020
 C72  plan-2  N10   0.020
 C72  plan-2  C11   0.020
 C72  plan-2  C12   0.020
 C72  plan-2  H01   0.020
 C72  plan-2  H07   0.020
 C72  plan-3  C09   0.020
 C72  plan-3  N10   0.020
 C72  plan-3  C13   0.020
 C72  plan-3  HN10  0.020
 C72  plan-4  C06   0.020
 C72  plan-4  C12   0.020
 C72  plan-4  N25   0.020
 C72  plan-4  O26   0.020
 C72  plan-4  HN25  0.020
 C72  plan-4  HN2A  0.020

