# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 21:59:09 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 4-[5-[2-aminocarbonyl-3,6-bis(azanyl)-5-cyano-thieno[2,3-b]pyridin-4-yl]-2-methoxy-phenoxy]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1OCCCC(O)=O)c2c(C#N)c(N)nc3sc(C(N)=O)c(N)c23
#
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
 C8W  C8W  '4-[5-[2-aminocarbonyl-3,6-bis(azanyl)-5-cyano-thieno[2,3-b]pyridin-4-yl]-2-methoxy-phenoxy]butanoic acid'  ligand  49  31  .  2022-07-24  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_C8W
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
 C8W  C1   C  CH2    0  -0.173  -3.4546   0.0399   0.3826
 C8W  N6   N  NH2    0  -0.835   5.6229  -0.8126   3.2359
 C8W  C8   C  C      0   0.510   2.4103   2.7557  -1.5653
 C8W  C9   C  C      0  -0.172   1.4156   1.7452  -1.7427
 C8W  C11  C  CSP    0   0.004   0.3955   1.9429  -2.7080
 C8W  C13  C  CR5    0  -0.009   3.4218   1.4737  -0.0010
 C8W  C14  C  CR5    0   0.026   2.4971   0.4155  -0.0817
 C8W  C15  C  CR5    0   0.349   2.7992  -0.6507   0.8528
 C8W  C19  C  C1     0  -0.371  -0.3314  -2.5189  -2.2016
 C8W  C20  C  C1     0  -0.289   0.6749  -1.5804  -1.9795
 C8W  C21  C  C      0  -0.106   0.4102  -0.4508  -1.2279
 C8W  C22  C  C1     0  -0.371  -0.8654  -0.2492  -0.6929
 C8W  C27  C  CH2    0  -0.450  -4.8849  -0.1176   0.8511
 C8W  O2   O  O2     0  -0.467  -3.1166  -1.0830  -0.4232
 C8W  S3   S  S2     0   0.193   4.6565   1.1761   1.1601
 C8W  C4   C  CR5    0  -0.450   3.9409  -0.3744   1.5840
 C8W  C5   C  C      0   0.529   4.5239  -1.2515   2.5862
 C8W  N7   N  NH2    0  -0.829   2.3893   3.8863  -2.2752
 C8W  N10  N  N      0  -0.481   3.4007   2.5922  -0.6955
 C8W  N12  N  NS     0  -0.243  -0.4112   2.1493  -3.5066
 C8W  N16  N  NH2    0  -0.853   2.0286  -1.7408   1.0174
 C8W  C17  C  C      0   0.336  -1.8685  -1.1788  -0.9031
 C8W  C18  C  C      0   0.308  -1.5979  -2.3323  -1.6741
 C8W  C23  C  C      0   0.303   1.4578   0.5694  -1.0032
 C8W  O24  O  O2     0  -0.458  -2.6308  -3.1733  -1.8337
 C8W  C25  C  CH3    0  -0.440  -2.4271  -4.3473  -2.5960
 C8W  O26  O  O      0  -0.513   4.0480  -2.3671   2.8173
 C8W  C28  C  CH2    0  -0.590  -5.2949   1.0438   1.7430
 C8W  C29  C  C      0   0.416  -6.7241   0.9638   2.3133
 C8W  O30  O  OC    -1  -0.629  -7.1162   1.9718   2.9368
 C8W  O31  O  O      0  -0.607  -7.3679  -0.0861   2.1236
 C8W  H1   H  HCH2   0   0.219  -3.3362   0.9647  -0.1951
 C8W  H2   H  HCH2   0   0.219  -2.7787   0.1007   1.2438
 C8W  H3   H  HNH2   0   0.405   5.9359   0.1429   3.2091
 C8W  H4   H  HNH2   0   0.403   5.9908  -1.3726   3.9874
 C8W  H5   H  H      0   0.290  -0.1020  -3.3919  -2.7967
 C8W  H6   H  H      0   0.269   1.6584  -1.7430  -2.4009
 C8W  H7   H  H      0   0.289  -1.0529   0.6404  -0.1071
 C8W  H8   H  HCH2   0   0.223  -5.5491  -0.1780  -0.0145
 C8W  H9   H  HCH2   0   0.223  -4.9841  -1.0585   1.3964
 C8W  H10  H  HNH2   0   0.418   1.6391   4.1211  -2.9016
 C8W  H11  H  HNH2   0   0.412   3.0712   4.6002  -2.0824
 C8W  H12  H  HNH2   0   0.411   1.3516  -1.9902   0.3187
 C8W  H13  H  HNH2   0   0.405   2.3965  -2.4775   1.5981
 C8W  H14  H  HCH3   0   0.262  -3.3802  -4.8698  -2.6171
 C8W  H15  H  HCH3   0   0.231  -2.1263  -4.1202  -3.6219
 C8W  H16  H  HCH3   0   0.231  -1.6762  -5.0008  -2.1444
 C8W  H17  H  HCH2   0   0.227  -4.5997   1.1223   2.5874
 C8W  H18  H  HCH2   0   0.222  -5.1926   1.9894   1.2000

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
 C8W  N6   C5   single    1.350  0.020  1.350
 C8W  O26  C5   double    1.235  0.020  1.235
 C8W  C5   C4   single    1.454  0.020  1.454
 C8W  C4   S3   aromatic  1.759  0.020  1.759
 C8W  C4   C15  aromatic  1.384  0.020  1.384
 C8W  S3   C13  aromatic  1.721  0.020  1.721
 C8W  C15  N16  single    1.345  0.020  1.345
 C8W  C15  C14  aromatic  1.450  0.020  1.450
 C8W  C13  C14  aromatic  1.408  0.020  1.408
 C8W  C13  N10  aromatic  1.317  0.020  1.317
 C8W  C14  C23  aromatic  1.398  0.020  1.398
 C8W  N10  C8   aromatic  1.328  0.020  1.328
 C8W  C23  C21  single    1.479  0.020  1.479
 C8W  C23  C9   aromatic  1.390  0.020  1.390
 C8W  C8   C9   aromatic  1.429  0.020  1.429
 C8W  C8   N7   single    1.335  0.020  1.335
 C8W  O31  C29  deloc     1.246  0.020  1.246
 C8W  C20  C21  aromatic  1.382  0.020  1.382
 C8W  C20  C19  aromatic  1.394  0.020  1.394
 C8W  C21  C22  aromatic  1.398  0.020  1.398
 C8W  C9   C11  single    1.418  0.020  1.418
 C8W  C19  C18  aromatic  1.385  0.020  1.385
 C8W  C22  C17  aromatic  1.384  0.020  1.384
 C8W  C18  C17  aromatic  1.414  0.020  1.414
 C8W  C18  O24  single    1.342  0.020  1.342
 C8W  C17  O2   single    1.341  0.020  1.341
 C8W  C29  O30  deloc     1.248  0.020  1.248
 C8W  C29  C28  single    1.541  0.020  1.541
 C8W  C11  N12  triple    1.154  0.020  1.154
 C8W  C25  O24  single    1.414  0.020  1.414
 C8W  O2   C1   single    1.423  0.020  1.423
 C8W  C1   C27  single    1.513  0.020  1.513
 C8W  C28  C27  single    1.521  0.020  1.521
 C8W  C1   H1   single    0.970  0.020  1.090
 C8W  C1   H2   single    0.970  0.020  1.090
 C8W  N6   H3   single    0.860  0.020  1.020
 C8W  N6   H4   single    0.860  0.020  1.020
 C8W  C19  H5   single    0.930  0.020  1.080
 C8W  C20  H6   single    0.930  0.020  1.080
 C8W  C22  H7   single    0.930  0.020  1.080
 C8W  C27  H8   single    0.970  0.020  1.090
 C8W  C27  H9   single    0.970  0.020  1.090
 C8W  N7   H10  single    0.860  0.020  1.020
 C8W  N7   H11  single    0.860  0.020  1.020
 C8W  N16  H12  single    0.890  0.020  1.040
 C8W  N16  H13  single    0.890  0.020  1.040
 C8W  C25  H14  single    0.970  0.020  1.090
 C8W  C25  H15  single    0.970  0.020  1.090
 C8W  C25  H16  single    0.970  0.020  1.090
 C8W  C28  H17  single    0.970  0.020  1.090
 C8W  C28  H18  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
 C8W  H2   C1   H1   107.49  3.000
 C8W  H2   C1   O2   110.00  3.000
 C8W  H1   C1   O2   109.97  3.000
 C8W  H2   C1   C27  110.20  3.000
 C8W  H1   C1   C27  110.66  3.000
 C8W  O2   C1   C27  108.52  3.000
 C8W  H4   N6   H3   115.76  3.000
 C8W  H4   N6   C5   118.42  3.000
 C8W  H3   N6   C5   123.32  3.000
 C8W  N10  C8   N7   117.66  3.000
 C8W  N7   C8   C9   121.46  3.000
 C8W  N10  C8   C9   120.88  3.000
 C8W  C23  C9   C11  120.13  3.000
 C8W  C11  C9   C8   119.11  3.000
 C8W  C23  C9   C8   120.74  3.000
 C8W  N12  C11  C9   180.00  3.000
 C8W  N10  C13  S3   120.95  3.000
 C8W  N10  C13  C14  126.72  3.000
 C8W  S3   C13  C14  112.33  3.000
 C8W  C23  C14  C15  131.38  3.000
 C8W  C23  C14  C13  116.33  3.000
 C8W  C15  C14  C13  112.28  3.000
 C8W  N16  C15  C4   124.74  3.000
 C8W  N16  C15  C14  123.75  3.000
 C8W  C4   C15  C14  111.45  3.000
 C8W  H5   C19  C18  120.83  3.000
 C8W  H5   C19  C20  118.57  3.000
 C8W  C18  C19  C20  120.60  3.000
 C8W  H6   C20  C21  120.56  3.000
 C8W  H6   C20  C19  119.53  3.000
 C8W  C21  C20  C19  119.91  3.000
 C8W  C23  C21  C22  119.25  3.000
 C8W  C22  C21  C20  120.04  3.000
 C8W  C23  C21  C20  120.70  3.000
 C8W  H7   C22  C17  120.61  3.000
 C8W  H7   C22  C21  118.95  3.000
 C8W  C17  C22  C21  120.44  3.000
 C8W  H9   C27  H8   107.02  3.000
 C8W  H9   C27  C28  109.92  3.000
 C8W  H8   C27  C28  110.06  3.000
 C8W  H9   C27  C1   109.28  3.000
 C8W  H8   C27  C1   109.57  3.000
 C8W  C28  C27  C1   110.91  3.000
 C8W  C17  O2   C1   118.70  3.000
 C8W  C4   S3   C13   91.33  3.000
 C8W  C5   C4   S3   122.32  3.000
 C8W  S3   C4   C15  112.60  3.000
 C8W  C5   C4   C15  125.08  3.000
 C8W  O26  C5   C4   121.30  3.000
 C8W  C4   C5   N6   117.52  3.000
 C8W  O26  C5   N6   121.16  3.000
 C8W  H11  N7   H10  117.36  3.000
 C8W  H11  N7   C8   119.23  3.000
 C8W  H10  N7   C8   122.75  3.000
 C8W  C13  N10  C8   117.51  3.000
 C8W  H13  N16  H12  117.74  3.000
 C8W  H13  N16  C15  117.00  3.000
 C8W  H12  N16  C15  120.16  3.000
 C8W  C18  C17  O2   115.58  3.000
 C8W  O2   C17  C22  124.93  3.000
 C8W  C18  C17  C22  119.49  3.000
 C8W  O24  C18  C17  115.41  3.000
 C8W  O24  C18  C19  125.07  3.000
 C8W  C17  C18  C19  119.53  3.000
 C8W  C21  C23  C14  123.42  3.000
 C8W  C21  C23  C9   118.76  3.000
 C8W  C14  C23  C9   117.81  3.000
 C8W  C25  O24  C18  118.27  3.000
 C8W  H16  C25  H15  108.84  3.000
 C8W  H16  C25  H14  108.84  3.000
 C8W  H15  C25  H14  108.84  3.000
 C8W  H16  C25  O24  111.87  3.000
 C8W  H15  C25  O24  111.90  3.000
 C8W  H14  C25  O24  106.45  3.000
 C8W  H18  C28  H17  105.12  3.000
 C8W  H18  C28  C29  108.36  3.000
 C8W  H17  C28  C29  107.87  3.000
 C8W  H18  C28  C27  110.09  3.000
 C8W  H17  C28  C27  109.60  3.000
 C8W  C29  C28  C27  115.31  3.000
 C8W  O31  C29  O30  126.44  3.000
 C8W  O30  C29  C28  115.74  3.000
 C8W  O31  C29  C28  117.81  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
 C8W  CONST_01  S3   C13  N10  C8    180.00   0.0  0
 C8W  CONST_02  C14  C13  N10  C8      0.00   0.0  0
 C8W  CONST_03  C14  C23  C9   C8      0.00   0.0  0
 C8W  CONST_04  C21  C23  C9   C8    180.00   0.0  0
 C8W  CONST_05  C15  C14  C23  C9    180.00   0.0  0
 C8W  CONST_06  C13  C14  C23  C9      0.00   0.0  0
 C8W  CONST_09  C13  N10  C8   C9      0.00   0.0  0
 C8W  CONST_10  C15  C4   S3   C13     0.00   0.0  0
 C8W  CONST_11  C4   C15  C14  C13     0.00   0.0  0
 C8W  CONST_12  C21  C23  C14  C13   180.00   0.0  0
 C8W  CONST_13  S3   C4   C15  C14     0.00   0.0  0
 C8W  CONST_14  C4   S3   C13  C14     0.00   0.0  0
 C8W  CONST_17  S3   C13  C14  C15     0.00   0.0  0
 C8W  CONST_18  N10  C13  C14  C15   180.00   0.0  0
 C8W  CONST_19  C21  C23  C14  C15     0.00   0.0  0
 C8W  CONST_20  C23  C21  C20  C19   180.00   0.0  0
 C8W  CONST_21  C22  C21  C20  C19     0.00   0.0  0
 C8W  CONST_22  C22  C17  C18  C19     0.00   0.0  0
 C8W  CONST_23  C17  C22  C21  C20     0.00   0.0  0
 C8W  CONST_24  C17  C18  C19  C20     0.00   0.0  0
 C8W  CONST_25  C18  C19  C20  C21     0.00   0.0  0
 C8W  CONST_26  C18  C17  C22  C21     0.00   0.0  0
 C8W  CONST_27  C23  C14  C13  S3    180.00   0.0  0
 C8W  CONST_28  N10  C13  S3   C4    180.00   0.0  0
 C8W  CONST_29  C23  C14  C15  C4    180.00   0.0  0
 C8W  CONST_30  C23  C14  C13  N10     0.00   0.0  0
 C8W  CONST_31  C23  C9   C8   N10     0.00   0.0  0
 C8W  CONST_32  C23  C21  C22  C17   180.00   0.0  0
 C8W  CONST_33  C14  C23  C9   C11   180.00   0.0  0
 C8W  CONST_34  C21  C23  C9   C11     0.00   0.0  0
 C8W  CONST_35  N10  C8   C9   C11   180.00   0.0  0
 C8W  CONST_36  C5   C4   S3   C13   180.00   0.0  0
 C8W  CONST_37  N16  C15  C14  C13   180.00   0.0  0
 C8W  CONST_38  N7   C8   N10  C13   180.00   0.0  0
 C8W  CONST_39  C5   C4   C15  C14   180.00   0.0  0
 C8W  CONST_40  O2   C17  C18  C19   180.00   0.0  0
 C8W  CONST_41  O24  C18  C19  C20   180.00   0.0  0
 C8W  CONST_42  O2   C17  C22  C21   180.00   0.0  0
 C8W  CONST_43  O24  C18  C17  C22   180.00   0.0  0
 C8W  CONST_44  N16  C15  C4   S3    180.00   0.0  0
 C8W  CONST_45  C23  C9   C8   N7    180.00   0.0  0
 C8W  CONST_46  C23  C14  C15  N16     0.00   0.0  0
 C8W  CONST_47  H7   C22  C21  C20   180.00   0.0  0
 C8W  CONST_48  H5   C19  C20  C21   180.00   0.0  0
 C8W  CONST_49  H6   C20  C21  C22   180.00   0.0  0
 C8W  CONST_50  H10  N7   C8   C9      0.00   0.0  0
 C8W  CONST_51  H11  N7   C8   C9    180.00   0.0  0
 C8W  CONST_53  H13  N16  C15  C14   180.00   0.0  0
 C8W  CONST_54  H3   N6   C5   C4      0.00   0.0  0
 C8W  CONST_55  H4   N6   C5   C4    180.00   0.0  0
 C8W  Var_01    C22  C17  O2   C1     -1.00  30.0  2
 C8W  Var_02    S3   C4   C5   N6      2.64  30.0  2
 C8W  Var_03    H1   C1   O2   C17    61.54  30.0  3
 C8W  Var_04    H14  C25  O24  C18  -178.91  30.0  3
 C8W  Var_05    C29  C28  C27  C1   -178.23  30.0  1
 C8W  Var_06    O31  C29  C28  C27     7.38  30.0  2
 C8W  Var_07    C28  C27  C1   O2    178.86  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
 C8W  plan-1  C19  0.020
 C8W  plan-1  C20  0.020
 C8W  plan-1  C21  0.020
 C8W  plan-1  C22  0.020
 C8W  plan-1  O2   0.020
 C8W  plan-1  C17  0.020
 C8W  plan-1  C18  0.020
 C8W  plan-1  C23  0.020
 C8W  plan-1  O24  0.020
 C8W  plan-1  H5   0.020
 C8W  plan-1  H6   0.020
 C8W  plan-1  H7   0.020
 C8W  plan-2  C8   0.020
 C8W  plan-2  C9   0.020
 C8W  plan-2  C11  0.020
 C8W  plan-2  C13  0.020
 C8W  plan-2  C14  0.020
 C8W  plan-2  C15  0.020
 C8W  plan-2  C21  0.020
 C8W  plan-2  S3   0.020
 C8W  plan-2  C4   0.020
 C8W  plan-2  C5   0.020
 C8W  plan-2  N7   0.020
 C8W  plan-2  N10  0.020
 C8W  plan-2  N12  0.020
 C8W  plan-2  N16  0.020
 C8W  plan-2  C23  0.020
 C8W  plan-3  N6   0.020
 C8W  plan-3  C4   0.020
 C8W  plan-3  C5   0.020
 C8W  plan-3  O26  0.020
 C8W  plan-3  H3   0.020
 C8W  plan-3  H4   0.020
 C8W  plan-4  C8   0.020
 C8W  plan-4  N7   0.020
 C8W  plan-4  H10  0.020
 C8W  plan-4  H11  0.020
 C8W  plan-5  C15  0.020
 C8W  plan-5  N16  0.020
 C8W  plan-5  H12  0.020
 C8W  plan-5  H13  0.020
 C8W  plan-6  C28  0.020
 C8W  plan-6  C29  0.020
 C8W  plan-6  O30  0.020
 C8W  plan-6  O31  0.020

