# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 19:49:43 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 3-amino-5-chloro-N-cyclopropyl-4-methyl-6-[2-(4-methylpiperazin-1-yl)-2-oxoethoxy]thieno[2,3-b]pyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)C(=O)COc2nc3sc(C(=O)NC4CC4)c(N)c3c(C)c2Cl
#
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
 2CU  2CU  3-amino-5-chloro-N-cyclopropyl-4-methyl-6-[2-(4-methylpiperazin-1-yl)-2-oxoethoxy]thieno[2,3-b]pyridine-2-carboxamide  ligand  53  29  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_2CU
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
 2CU  C15  C   CR6   0   0.313  -1.3716  -2.6399  -0.3219
 2CU  C16  C   CH3   0  -0.781  -2.0762  -3.9256  -0.6172
 2CU  C18  C   CR5   0   0.345  -3.4955  -1.1329  -0.1797
 2CU  C20  C   CR5   0  -0.449  -3.7464   0.2146   0.0021
 2CU  C24  C   C     0   0.597  -5.0728   0.8138   0.0949
 2CU  C22  C   CR56  0  -0.026  -1.3204  -0.2681   0.0640
 2CU  C10  C   CH2   0  -0.306   2.6476  -0.1452   0.3219
 2CU  N02  N   NT    0  -0.416   6.7015   2.6757  -0.1350
 2CU  C03  C   CH2   0  -0.279   7.0771   1.2959  -0.3699
 2CU  C04  C   CH2   0  -0.311   6.4023   0.3763   0.6328
 2CU  N05  N   NT    0  -0.463   4.9624   0.5591   0.5913
 2CU  C06  C   CH2   0  -0.326   4.5620   1.9414   0.7835
 2CU  C07  C   CH2   0  -0.270   5.2648   2.8353  -0.2244
 2CU  C08  C   C     0   0.520   4.1348  -0.4781   0.3655
 2CU  O09  O   O     0  -0.481   4.5202  -1.6233   0.2037
 2CU  O11  O   O2    0  -0.442   1.9707  -1.3648   0.1060
 2CU  C12  C   CR6   0   0.600   0.6509  -1.3365   0.0221
 2CU  C13  C   CR6   0  -0.292   0.0025  -2.5720  -0.2147
 2CU  CL1  CL  CL    0  -0.094   1.0030  -3.9695  -0.3708
 2CU  C17  C   CR56  0   0.038  -2.0756  -1.4224  -0.1509
 2CU  N19  N   NH2   0  -0.857  -4.4557  -2.0648  -0.4003
 2CU  S21  S   S2    0   0.195  -2.2801   1.1554   0.1858
 2CU  N23  N   N     0  -0.492   0.0019  -0.2096   0.1466
 2CU  O25  O   O     0  -0.509  -6.0918   0.1563  -0.1229
 2CU  N26  N   NH1   0  -0.682  -5.1390   2.1235   0.4267
 2CU  C27  C   CH1   0  -0.077  -6.3882   2.7915   0.5865
 2CU  C28  C   CH2   0  -0.512  -6.4705   4.2135   0.1330
 2CU  C29  C   CH2   0  -0.482  -7.1821   3.1396  -0.6306
 2CU  H1   H   HCH3  0   0.273  -2.6143  -4.2827   0.2633
 2CU  H2   H   HCH3  0   0.273  -2.7952  -3.7934  -1.4240
 2CU  H3   H   HCH3  0   0.277  -1.3896  -4.7124  -0.9129
 2CU  H4   H   HCH2  0   0.275   2.3246   0.3177   1.2588
 2CU  H5   H   HCH2  0   0.273   2.4352   0.5634  -0.4843
 2CU  H6   H   HCH3  0   0.195   7.1652   3.4034  -2.0877
 2CU  H7   H   HCH3  0   0.235   7.1292   4.6102  -0.7924
 2CU  H8   H   HCH3  0   0.235   8.4734   3.4737  -0.8961
 2CU  H10  H   HCH2  0   0.199   6.8196   0.9681  -1.3924
 2CU  H11  H   HCH2  0   0.244   8.1597   1.1956  -0.2626
 2CU  H12  H   HCH2  0   0.268   6.6468  -0.6592   0.4145
 2CU  H13  H   HCH2  0   0.244   6.7608   0.6047   1.6417
 2CU  H14  H   HCH2  0   0.276   3.4871   2.0637   0.6830
 2CU  H15  H   HCH2  0   0.251   4.8294   2.2510   1.7987
 2CU  H16  H   HCH2  0   0.247   5.0039   3.8742  -0.0109
 2CU  H17  H   HCH2  0   0.199   4.8852   2.6042  -1.2354
 2CU  H18  H   HNH2  0   0.404  -5.4025  -1.7379  -0.2749
 2CU  H19  H   HNH2  0   0.400  -4.2912  -3.0064  -0.0926
 2CU  H20  H   HNH1  0   0.401  -4.3237   2.5944   0.7868
 2CU  H21  H   HCH1  0   0.266  -6.9467   2.5268   1.4797
 2CU  H22  H   HCH2  0   0.258  -7.0522   4.8980   0.7355
 2CU  H23  H   HCH2  0   0.257  -5.5871   4.6498  -0.3162
 2CU  H24  H   HCH2  0   0.255  -6.7755   2.8520  -1.5911
 2CU  H25  H   HCH2  0   0.255  -8.2601   3.0786  -0.5600
 2CU  C01  C   CH3   0  -0.519   7.3953   3.5782  -1.0253

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
 2CU  C01  N02  single    1.445  0.020  1.445
 2CU  N02  C03  single    1.449  0.020  1.449
 2CU  N02  C07  single    1.448  0.020  1.448
 2CU  C03  C04  single    1.519  0.020  1.519
 2CU  C04  N05  single    1.452  0.020  1.452
 2CU  C07  C06  single    1.520  0.020  1.520
 2CU  C06  N05  single    1.452  0.020  1.452
 2CU  N05  C08  single    1.346  0.020  1.346
 2CU  C08  O09  double    1.219  0.020  1.219
 2CU  C08  C10  single    1.525  0.020  1.525
 2CU  C10  O11  single    1.411  0.020  1.411
 2CU  O11  C12  single    1.323  0.020  1.323
 2CU  N23  C12  aromatic  1.306  0.020  1.306
 2CU  N23  C22  aromatic  1.326  0.020  1.326
 2CU  C12  C13  aromatic  1.415  0.020  1.415
 2CU  S21  C22  aromatic  1.721  0.020  1.721
 2CU  S21  C20  aromatic  1.752  0.020  1.752
 2CU  C22  C17  aromatic  1.396  0.020  1.396
 2CU  C13  CL1  single    1.726  0.020  1.726
 2CU  C13  C15  aromatic  1.380  0.020  1.380
 2CU  C28  C29  single    1.498  0.020  1.498
 2CU  C28  C27  single    1.495  0.020  1.495
 2CU  C29  C27  single    1.494  0.020  1.494
 2CU  N26  C27  single    1.426  0.020  1.426
 2CU  N26  C24  single    1.353  0.020  1.353
 2CU  C17  C15  aromatic  1.417  0.020  1.417
 2CU  C17  C18  aromatic  1.449  0.020  1.449
 2CU  C20  C24  single    1.458  0.020  1.458
 2CU  C20  C18  aromatic  1.383  0.020  1.383
 2CU  C15  C16  single    1.496  0.020  1.496
 2CU  C24  O25  double    1.232  0.020  1.232
 2CU  C18  N19  single    1.356  0.020  1.356
 2CU  C16  H1   single    0.970  0.020  1.090
 2CU  C16  H2   single    0.970  0.020  1.090
 2CU  C16  H3   single    0.970  0.020  1.090
 2CU  C10  H4   single    0.970  0.020  1.090
 2CU  C10  H5   single    0.970  0.020  1.090
 2CU  C01  H6   single    0.970  0.020  1.090
 2CU  C01  H7   single    0.970  0.020  1.090
 2CU  C01  H8   single    0.970  0.020  1.090
 2CU  C03  H10  single    0.970  0.020  1.090
 2CU  C03  H11  single    0.970  0.020  1.090
 2CU  C04  H12  single    0.970  0.020  1.090
 2CU  C04  H13  single    0.970  0.020  1.090
 2CU  C06  H14  single    0.970  0.020  1.090
 2CU  C06  H15  single    0.970  0.020  1.090
 2CU  C07  H16  single    0.970  0.020  1.090
 2CU  C07  H17  single    0.970  0.020  1.090
 2CU  N19  H18  single    0.890  0.020  1.040
 2CU  N19  H19  single    0.890  0.020  1.040
 2CU  N26  H20  single    0.860  0.020  1.020
 2CU  C27  H21  single    0.970  0.020  1.090
 2CU  C28  H22  single    0.970  0.020  1.090
 2CU  C28  H23  single    0.970  0.020  1.090
 2CU  C29  H24  single    0.970  0.020  1.090
 2CU  C29  H25  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
 2CU  C17  C15  C13  116.30  3.000
 2CU  C17  C15  C16  121.90  3.000
 2CU  C13  C15  C16  121.79  3.000
 2CU  H3   C16  H2   107.69  3.000
 2CU  H3   C16  H1   107.12  3.000
 2CU  H2   C16  H1   108.17  3.000
 2CU  H3   C16  C15  112.27  3.000
 2CU  H2   C16  C15  110.68  3.000
 2CU  H1   C16  C15  110.74  3.000
 2CU  N19  C18  C17  124.03  3.000
 2CU  N19  C18  C20  124.24  3.000
 2CU  C17  C18  C20  111.70  3.000
 2CU  S21  C20  C24  122.27  3.000
 2CU  C24  C20  C18  125.02  3.000
 2CU  S21  C20  C18  112.66  3.000
 2CU  N26  C24  O25  121.30  3.000
 2CU  O25  C24  C20  121.44  3.000
 2CU  N26  C24  C20  117.25  3.000
 2CU  N23  C22  S21  121.00  3.000
 2CU  S21  C22  C17  113.15  3.000
 2CU  N23  C22  C17  125.83  3.000
 2CU  H5   C10  H4   107.44  3.000
 2CU  H5   C10  O11  110.72  3.000
 2CU  H4   C10  O11  110.80  3.000
 2CU  H5   C10  C08  110.60  3.000
 2CU  H4   C10  C08  110.85  3.000
 2CU  O11  C10  C08  106.47  3.000
 2CU  C07  N02  C03  110.61  3.000
 2CU  C07  N02  C01  111.68  3.000
 2CU  C03  N02  C01  111.73  3.000
 2CU  H11  C03  H10  107.15  3.000
 2CU  H11  C03  C04  108.65  3.000
 2CU  H10  C03  C04  109.14  3.000
 2CU  H11  C03  N02  109.17  3.000
 2CU  H10  C03  N02  111.86  3.000
 2CU  C04  C03  N02  110.75  3.000
 2CU  H13  C04  H12  108.09  3.000
 2CU  H13  C04  N05  108.96  3.000
 2CU  H12  C04  N05  109.72  3.000
 2CU  H13  C04  C03  109.67  3.000
 2CU  H12  C04  C03  110.15  3.000
 2CU  N05  C04  C03  110.21  3.000
 2CU  C08  N05  C06  125.90  3.000
 2CU  C08  N05  C04  121.16  3.000
 2CU  C06  N05  C04  112.92  3.000
 2CU  H15  C06  H14  107.20  3.000
 2CU  H15  C06  C07  109.62  3.000
 2CU  H14  C06  C07  109.27  3.000
 2CU  H15  C06  N05  108.95  3.000
 2CU  H14  C06  N05  111.57  3.000
 2CU  C07  C06  N05  110.17  3.000
 2CU  H17  C07  H16  107.21  3.000
 2CU  H17  C07  C06  108.97  3.000
 2CU  H16  C07  C06  108.63  3.000
 2CU  H17  C07  N02  111.99  3.000
 2CU  H16  C07  N02  109.25  3.000
 2CU  C06  C07  N02  110.67  3.000
 2CU  O09  C08  N05  123.50  3.000
 2CU  O09  C08  C10  120.64  3.000
 2CU  N05  C08  C10  115.87  3.000
 2CU  C12  O11  C10  118.01  3.000
 2CU  N23  C12  C13  122.78  3.000
 2CU  C13  C12  O11  116.68  3.000
 2CU  N23  C12  O11  120.54  3.000
 2CU  CL1  C13  C12  117.16  3.000
 2CU  CL1  C13  C15  122.03  3.000
 2CU  C12  C13  C15  120.81  3.000
 2CU  C22  C17  C18  111.58  3.000
 2CU  C18  C17  C15  131.00  3.000
 2CU  C22  C17  C15  117.41  3.000
 2CU  H19  N19  H18  114.78  3.000
 2CU  H19  N19  C18  118.59  3.000
 2CU  H18  N19  C18  114.92  3.000
 2CU  C22  S21  C20   90.87  3.000
 2CU  C12  N23  C22  116.83  3.000
 2CU  H20  N26  C27  116.73  3.000
 2CU  H20  N26  C24  120.03  3.000
 2CU  C27  N26  C24  121.60  3.000
 2CU  H21  C27  C29  116.96  3.000
 2CU  H21  C27  C28  116.93  3.000
 2CU  C29  C27  C28   60.13  3.000
 2CU  H21  C27  N26  115.38  3.000
 2CU  C29  C27  N26  118.91  3.000
 2CU  C28  C27  N26  117.39  3.000
 2CU  H23  C28  H22  114.51  3.000
 2CU  H23  C28  C29  117.72  3.000
 2CU  H22  C28  C29  118.83  3.000
 2CU  H23  C28  C27  117.66  3.000
 2CU  H22  C28  C27  117.56  3.000
 2CU  C29  C28  C27   59.91  3.000
 2CU  H25  C29  H24  114.67  3.000
 2CU  H25  C29  C28  118.73  3.000
 2CU  H24  C29  C28  117.69  3.000
 2CU  H25  C29  C27  117.59  3.000
 2CU  H24  C29  C27  117.48  3.000
 2CU  C28  C29  C27   59.95  3.000
 2CU  H8   C01  H7   107.84  3.000
 2CU  H8   C01  H6   107.79  3.000
 2CU  H7   C01  H6   107.77  3.000
 2CU  H8   C01  N02  109.98  3.000
 2CU  H7   C01  N02  110.01  3.000
 2CU  H6   C01  N02  113.27  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
 2CU  CONST_01  N23  C12  C13  C15     0.00   0.0  0
 2CU  CONST_02  N23  C22  C17  C15     0.00   0.0  0
 2CU  CONST_03  S21  C22  C17  C15   180.00   0.0  0
 2CU  CONST_04  C20  C18  C17  C15   180.00   0.0  0
 2CU  CONST_05  N23  C22  C17  C18   180.00   0.0  0
 2CU  CONST_06  S21  C22  C17  C18     0.00   0.0  0
 2CU  CONST_07  C13  C15  C17  C18   180.00   0.0  0
 2CU  CONST_08  C22  S21  C20  C18     0.00   0.0  0
 2CU  CONST_09  N23  C22  S21  C20   180.00   0.0  0
 2CU  CONST_10  C17  C22  S21  C20     0.00   0.0  0
 2CU  CONST_11  C22  C17  C18  C20     0.00   0.0  0
 2CU  CONST_12  C13  C12  N23  C22     0.00   0.0  0
 2CU  CONST_13  C13  C15  C17  C22     0.00   0.0  0
 2CU  CONST_14  S21  C22  N23  C12   180.00   0.0  0
 2CU  CONST_15  C17  C22  N23  C12     0.00   0.0  0
 2CU  CONST_16  C17  C15  C13  C12     0.00   0.0  0
 2CU  CONST_17  S21  C20  C18  C17     0.00   0.0  0
 2CU  CONST_18  O11  C12  C13  C15   180.00   0.0  0
 2CU  CONST_19  N19  C18  C17  C15     0.00   0.0  0
 2CU  CONST_20  C12  C13  C15  C16   180.00   0.0  0
 2CU  CONST_21  C22  C17  C15  C16   180.00   0.0  0
 2CU  CONST_22  C18  C17  C15  C16     0.00   0.0  0
 2CU  CONST_23  C22  S21  C20  C24   180.00   0.0  0
 2CU  CONST_24  C17  C18  C20  C24   180.00   0.0  0
 2CU  CONST_25  O11  C12  N23  C22   180.00   0.0  0
 2CU  CONST_26  N19  C18  C17  C22   180.00   0.0  0
 2CU  CONST_27  N23  C12  C13  CL1   180.00   0.0  0
 2CU  CONST_28  C17  C15  C13  CL1   180.00   0.0  0
 2CU  CONST_29  S21  C20  C18  N19   180.00   0.0  0
 2CU  CONST_30  C27  N26  C24  C20   180.00   0.0  0
 2CU  CONST_31  C04  N05  C08  C10   180.00   0.0  0
 2CU  CONST_32  C06  N05  C08  C10     0.00   0.0  0
 2CU  CONST_33  O09  C08  N05  C04     0.00   0.0  0
 2CU  CONST_34  O09  C08  N05  C06   180.00   0.0  0
 2CU  CONST_35  H18  N19  C18  C20     0.00   0.0  0
 2CU  CONST_37  C27  N26  C24  O25     0.00   0.0  0
 2CU  CONST_38  H20  N26  C24  C20     0.00   0.0  0
 2CU  Var_01    N05  C04  C03  N02    55.69  30.0  1
 2CU  Var_02    N05  C06  C07  N02   -55.93  30.0  1
 2CU  Var_03    C06  C07  N02  C03    58.54  30.0  1
 2CU  Var_04    C06  N05  C04  C03   -54.56  30.0  1
 2CU  Var_05    C07  N02  C03  C04   -58.45  30.0  1
 2CU  Var_06    C07  C06  N05  C04    54.67  30.0  1
 2CU  Var_07    C29  C28  C27  N26   109.29  30.0  1
 2CU  Var_08    H24  C29  C28  C27  -107.36  30.0  1
 2CU  Var_09    N26  C24  C20  C18   172.57  30.0  2
 2CU  Var_10    C28  C27  N26  C24  -143.54  30.0  3
 2CU  Var_11    N23  C12  O11  C10    -0.49  30.0  2
 2CU  Var_12    H6   C01  N02  C03    62.07  30.0  3
 2CU  Var_13    H1   C16  C15  C13   108.91  30.0  2
 2CU  Var_14    O11  C10  C08  N05  -178.75  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
 2CU  chir_01  C27  C28  C29  N26  both

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
 2CU  plan-1  C20  0.020
 2CU  plan-1  C24  0.020
 2CU  plan-1  O25  0.020
 2CU  plan-1  N26  0.020
 2CU  plan-1  C27  0.020
 2CU  plan-1  H20  0.020
 2CU  plan-2  C15  0.020
 2CU  plan-2  C16  0.020
 2CU  plan-2  C18  0.020
 2CU  plan-2  C20  0.020
 2CU  plan-2  C24  0.020
 2CU  plan-2  C22  0.020
 2CU  plan-2  O11  0.020
 2CU  plan-2  C12  0.020
 2CU  plan-2  C13  0.020
 2CU  plan-2  CL1  0.020
 2CU  plan-2  C17  0.020
 2CU  plan-2  N19  0.020
 2CU  plan-2  S21  0.020
 2CU  plan-2  N23  0.020
 2CU  plan-3  C18  0.020
 2CU  plan-3  N19  0.020
 2CU  plan-3  H18  0.020
 2CU  plan-3  H19  0.020
 2CU  plan-4  C10  0.020
 2CU  plan-4  C04  0.020
 2CU  plan-4  N05  0.020
 2CU  plan-4  C06  0.020
 2CU  plan-4  C08  0.020
 2CU  plan-4  O09  0.020

