# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 06:10:48 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 5-chloro-N-[2-({[4-(2-oxopyridin-1(2H)-yl)phenyl]carbonyl}amino)ethyl]thiophene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1sc(cc1)C(=O)NCCNC(=O)c2ccc(cc2)N3C=CC=CC3=O
#
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
 ME1  ME1  5-chloro-N-[2-({[4-(2-oxopyridin-1(2H)-yl)phenyl]carbonyl}amino)ethyl]thiophene-2-carboxamide  ligand  43  27  .  2021-08-14  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ME1
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
 ME1  C1    C   CR5   0  -0.247   1.5713  11.1779   3.3196
 ME1  C2    C   CR15  0  -0.124   0.9327  12.2050   3.9431
 ME1  C3    C   CR15  0  -0.186  -0.2369  12.5903   3.2444
 ME1  C9    C   CH2   0  -0.301  -2.5133  11.4653  -1.0092
 ME1  C10   C   CH2   0  -0.313  -3.4275  10.2807  -0.7058
 ME1  C12   C   C     0   0.530  -2.2481   8.5194   0.5341
 ME1  C14   C   CR6   0  -0.022  -1.5154   7.2187   0.4262
 ME1  C15   C   CR16  0  -0.277  -0.5443   6.9323   1.3842
 ME1  C16   C   CR16  0  -0.242   0.1550   5.7398   1.3452
 ME1  C19   C   CR16  0  -0.295  -1.7945   6.2784  -0.5601
 ME1  C21   C   CR16  0   0.048   1.4391   3.3876  -0.7614
 ME1  C22   C   CR16  0  -0.399   2.1406   2.2385  -0.9005
 ME1  C24   C   CR16  0  -0.453   1.1296   1.4206   1.1292
 ME1  C4    C   CR5   0  -0.307  -0.4541  11.8638   2.1101
 ME1  S5    S   S2    0   0.298   0.7693  10.6656   1.8931
 ME1  C6    C   C     0   0.561  -1.6007  12.0299   1.1893
 ME1  O7    O   O     0  -0.477  -2.6275  12.5680   1.5756
 ME1  N8    N   NH1   0  -0.650  -1.4264  11.5808  -0.0648
 ME1  N11   N   NH1   0  -0.636  -2.7069   9.0318  -0.6206
 ME1  O13   O   O     0  -0.479  -2.4063   9.0536   1.6228
 ME1  C17   C   CR6   0   0.290  -0.1333   4.8117   0.3545
 ME1  C18   C   CR16  0  -0.247  -1.1113   5.0715  -0.5914
 ME1  N20   N   NR6   0  -0.612   0.5933   3.5857   0.2888
 ME1  C23   C   CR16  0  -0.118   1.9727   1.2329   0.0815
 ME1  C25   C   CR6   0   0.553   0.3741   2.6341   1.2898
 ME1  O26   O   O     0  -0.501  -0.4121   2.8649   2.2004
 ME1  CL27  CL  CL    0  -0.065   2.9986  10.3971   3.8285
 ME1  H2    H   HCR5  0   0.294   1.2786  12.6614   4.8584
 ME1  H3    H   HCR5  0   0.282  -0.8901  13.3872   3.5697
 ME1  H91   H   HCH2  0   0.262  -2.0708  11.3535  -1.9983
 ME1  H92   H   HCH2  0   0.257  -3.1047  12.3820  -1.0238
 ME1  H101  H   HCH2  0   0.267  -4.1742  10.1992  -1.4964
 ME1  H102  H   HCH2  0   0.258  -3.9601  10.4434   0.2288
 ME1  H15   H   HCR6  0   0.264  -0.3246   7.6551   2.1583
 ME1  H16   H   HCR6  0   0.275   0.9274   5.5396   2.0754
 ME1  H19   H   HCR6  0   0.271  -2.5663   6.4540  -1.2984
 ME1  H22   H   HCR6  0   0.281   2.8084   2.1108  -1.7384
 ME1  H24   H   HCR6  0   0.277   0.9906   0.6558   1.8811
 ME1  HN8   H   HNH1  0   0.403  -0.5282  11.2314  -0.3549
 ME1  HN11  H   HNH1  0   0.408  -2.4304   8.6020  -1.4886
 ME1  H18   H   HCR6  0   0.280  -1.3452   4.3332  -1.3475
 ME1  H23   H   HCR6  0   0.281   2.5223   0.3043  -0.0050
 ME1  H21   H   HCR6  0   0.315   1.5183   4.2058  -1.4630

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
 ME1  C1   C2    double    1.361  0.020  1.361
 ME1  C1   CL27  single    1.705  0.020  1.705
 ME1  C1   S5    single    1.715  0.020  1.715
 ME1  C2   C3    single    1.416  0.020  1.416
 ME1  C2   H2    single    0.930  0.020  1.080
 ME1  C3   C4    double    1.364  0.020  1.364
 ME1  C3   H3    single    0.930  0.020  1.080
 ME1  C9   C10   single    1.527  0.020  1.527
 ME1  C9   N8    single    1.445  0.020  1.445
 ME1  C9   H91   single    0.970  0.020  1.090
 ME1  C9   H92   single    0.970  0.020  1.090
 ME1  C10  N11   single    1.444  0.020  1.444
 ME1  C10  H101  single    0.970  0.020  1.090
 ME1  C10  H102  single    0.970  0.020  1.090
 ME1  C12  C14   single    1.497  0.020  1.497
 ME1  C12  O13   double    1.223  0.020  1.223
 ME1  C12  N11   single    1.344  0.020  1.344
 ME1  C14  C15   aromatic  1.394  0.020  1.394
 ME1  C14  C19   aromatic  1.391  0.020  1.391
 ME1  C15  C16   aromatic  1.383  0.020  1.383
 ME1  C15  H15   single    0.930  0.020  1.080
 ME1  C16  C17   aromatic  1.388  0.020  1.388
 ME1  C16  H16   single    0.930  0.020  1.080
 ME1  C19  C18   aromatic  1.387  0.020  1.387
 ME1  C19  H19   single    0.930  0.020  1.080
 ME1  C21  C22   double    1.354  0.020  1.354
 ME1  C21  N20   single    1.363  0.020  1.363
 ME1  C21  H21   single    0.930  0.020  1.080
 ME1  C22  C23   single    1.416  0.020  1.416
 ME1  C22  H22   single    0.930  0.020  1.080
 ME1  C24  C23   double    1.358  0.020  1.358
 ME1  C24  C25   single    1.439  0.020  1.439
 ME1  C24  H24   single    0.930  0.020  1.080
 ME1  C4   C6    single    1.480  0.020  1.480
 ME1  C4   S5    single    1.726  0.020  1.726
 ME1  C6   O7    double    1.222  0.020  1.222
 ME1  C6   N8    single    1.343  0.020  1.343
 ME1  N8   HN8   single    0.860  0.020  1.020
 ME1  N11  HN11  single    0.860  0.020  1.020
 ME1  C17  N20   single    1.427  0.020  1.427
 ME1  C17  C18   aromatic  1.385  0.020  1.385
 ME1  C18  H18   single    0.930  0.020  1.080
 ME1  N20  C25   single    1.398  0.020  1.398
 ME1  C23  H23   single    0.930  0.020  1.080
 ME1  C25  O26   double    1.225  0.020  1.225

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
 ME1  CL27  C1   S5    120.21  3.000
 ME1  S5    C1   C2    112.78  3.000
 ME1  CL27  C1   C2    127.01  3.000
 ME1  H2    C2   C3    124.61  3.000
 ME1  H2    C2   C1    123.86  3.000
 ME1  C3    C2   C1    111.53  3.000
 ME1  H3    C3   C4    123.14  3.000
 ME1  H3    C3   C2    123.47  3.000
 ME1  C4    C3   C2    113.39  3.000
 ME1  H92   C9   H91   107.12  3.000
 ME1  H92   C9   N8    110.45  3.000
 ME1  H91   C9   N8    107.23  3.000
 ME1  H92   C9   C10   109.27  3.000
 ME1  H91   C9   C10   110.12  3.000
 ME1  N8    C9   C10   112.49  3.000
 ME1  H102  C10  H101  107.39  3.000
 ME1  H102  C10  N11   108.84  3.000
 ME1  H101  C10  N11   108.65  3.000
 ME1  H102  C10  C9    110.35  3.000
 ME1  H101  C10  C9    108.89  3.000
 ME1  N11   C10  C9    112.57  3.000
 ME1  O13   C12  N11   123.65  3.000
 ME1  N11   C12  C14   115.88  3.000
 ME1  O13   C12  C14   120.47  3.000
 ME1  C19   C14  C15   119.23  3.000
 ME1  C19   C14  C12   122.71  3.000
 ME1  C15   C14  C12   118.03  3.000
 ME1  H15   C15  C16   119.58  3.000
 ME1  H15   C15  C14   119.75  3.000
 ME1  C16   C15  C14   120.66  3.000
 ME1  H16   C16  C17   120.43  3.000
 ME1  H16   C16  C15   120.11  3.000
 ME1  C17   C16  C15   119.46  3.000
 ME1  H19   C19  C18   118.48  3.000
 ME1  H19   C19  C14   121.14  3.000
 ME1  C18   C19  C14   120.35  3.000
 ME1  H21   C21  N20   115.83  3.000
 ME1  H21   C21  C22   122.55  3.000
 ME1  N20   C21  C22   121.62  3.000
 ME1  H22   C22  C23   121.87  3.000
 ME1  H22   C22  C21   120.07  3.000
 ME1  C23   C22  C21   118.05  3.000
 ME1  H24   C24  C25   116.84  3.000
 ME1  H24   C24  C23   121.23  3.000
 ME1  C25   C24  C23   121.93  3.000
 ME1  C6    C4   S5    123.29  3.000
 ME1  S5    C4   C3    111.18  3.000
 ME1  C6    C4   C3    125.51  3.000
 ME1  C4    S5   C1     91.12  3.000
 ME1  N8    C6   O7    123.46  3.000
 ME1  N8    C6   C4    116.28  3.000
 ME1  O7    C6   C4    120.25  3.000
 ME1  HN8   N8   C6    120.06  3.000
 ME1  HN8   N8   C9    117.08  3.000
 ME1  C6    N8   C9    122.64  3.000
 ME1  HN11  N11  C12   118.95  3.000
 ME1  HN11  N11  C10   117.07  3.000
 ME1  C12   N11  C10   123.41  3.000
 ME1  N20   C17  C18   119.29  3.000
 ME1  C18   C17  C16   120.58  3.000
 ME1  N20   C17  C16   120.12  3.000
 ME1  H18   C18  C17   120.11  3.000
 ME1  H18   C18  C19   120.19  3.000
 ME1  C17   C18  C19   119.70  3.000
 ME1  C25   N20  C17   118.16  3.000
 ME1  C25   N20  C21   123.36  3.000
 ME1  C17   N20  C21   118.46  3.000
 ME1  H23   C23  C24   119.70  3.000
 ME1  H23   C23  C22   119.58  3.000
 ME1  C24   C23  C22   120.72  3.000
 ME1  O26   C25  N20   120.30  3.000
 ME1  O26   C25  C24   125.38  3.000
 ME1  N20   C25  C24   114.32  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
 ME1  CONST_01  C17   C16  C15  C14     0.00   0.0  0
 ME1  CONST_02  C17   C18  C19  C14     0.00   0.0  0
 ME1  CONST_03  C18   C19  C14  C15     0.00   0.0  0
 ME1  CONST_04  C18   C17  C16  C15     0.00   0.0  0
 ME1  CONST_05  C19   C14  C15  C16     0.00   0.0  0
 ME1  CONST_06  C19   C18  C17  C16     0.00   0.0  0
 ME1  CONST_07  N20   C17  C16  C15   180.00   0.0  0
 ME1  CONST_08  N20   C17  C18  C19   180.00   0.0  0
 ME1  CONST_09  C24   C25  N20  C21     0.00   0.0  0
 ME1  CONST_10  C17   N20  C25  C24   180.00   0.0  0
 ME1  CONST_11  C16   C15  C14  C12   180.00   0.0  0
 ME1  CONST_12  C18   C19  C14  C12   180.00   0.0  0
 ME1  CONST_13  O26   C25  N20  C21   180.00   0.0  0
 ME1  CONST_14  O26   C25  N20  C17     0.00   0.0  0
 ME1  CONST_15  H16   C16  C15  C14   180.00   0.0  0
 ME1  CONST_16  H18   C18  C19  C14   180.00   0.0  0
 ME1  CONST_17  H19   C19  C14  C15   180.00   0.0  0
 ME1  CONST_18  H15   C15  C14  C19   180.00   0.0  0
 ME1  CONST_19  C4    C6   N8   C9    180.00   0.0  0
 ME1  CONST_20  C14   C12  N11  C10   180.00   0.0  0
 ME1  CONST_21  HN11  N11  C12  C14     0.00   0.0  0
 ME1  CONST_22  HN8   N8   C6   C4      0.00   0.0  0
 ME1  CONST_23  O7    C6   N8   C9      0.00   0.0  0
 ME1  CONST_24  O13   C12  N11  C10     0.00   0.0  0
 ME1  Var_01    C21   N20  C17  C16  -111.54  30.0  2
 ME1  Var_02    O7    C6   C4   C3    -21.07  30.0  2
 ME1  Var_03    O13   C12  C14  C15   -28.21  30.0  2
 ME1  Var_04    C12   N11  C10  C9     93.78  30.0  3
 ME1  Var_05    C6    N8   C9   C10   -74.32  30.0  3
 ME1  Var_06    N11   C10  C9   N8    -54.81  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
 ME1  plan-1  C1    0.020
 ME1  plan-1  C2    0.020
 ME1  plan-1  C3    0.020
 ME1  plan-1  C4    0.020
 ME1  plan-1  S5    0.020
 ME1  plan-1  C6    0.020
 ME1  plan-1  CL27  0.020
 ME1  plan-1  H2    0.020
 ME1  plan-1  H3    0.020
 ME1  plan-2  C12   0.020
 ME1  plan-2  C14   0.020
 ME1  plan-2  C15   0.020
 ME1  plan-2  C16   0.020
 ME1  plan-2  C19   0.020
 ME1  plan-2  C17   0.020
 ME1  plan-2  C18   0.020
 ME1  plan-2  N20   0.020
 ME1  plan-2  H15   0.020
 ME1  plan-2  H16   0.020
 ME1  plan-2  H19   0.020
 ME1  plan-2  H18   0.020
 ME1  plan-3  C21   0.020
 ME1  plan-3  C22   0.020
 ME1  plan-3  C24   0.020
 ME1  plan-3  C17   0.020
 ME1  plan-3  N20   0.020
 ME1  plan-3  C23   0.020
 ME1  plan-3  C25   0.020
 ME1  plan-3  O26   0.020
 ME1  plan-3  H22   0.020
 ME1  plan-3  H24   0.020
 ME1  plan-3  H23   0.020
 ME1  plan-3  H21   0.020
 ME1  plan-4  C10   0.020
 ME1  plan-4  C12   0.020
 ME1  plan-4  C14   0.020
 ME1  plan-4  N11   0.020
 ME1  plan-4  O13   0.020
 ME1  plan-4  HN11  0.020
 ME1  plan-5  C9    0.020
 ME1  plan-5  C4    0.020
 ME1  plan-5  C6    0.020
 ME1  plan-5  O7    0.020
 ME1  plan-5  N8    0.020
 ME1  plan-5  HN8   0.020

