# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 21:48:28 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 4-(4-ethanoylphenyl)-~{N}-[(6-methoxypyridin-3-yl)methyl]piperazine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CNC(=O)N2CCN(CC2)c3ccc(cc3)C(C)=O)cn1
#
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
 M7W  M7W  4-(4-ethanoylphenyl)-~{N}-[(6-methoxypyridin-3-yl)methyl]piperazine-1-carboxamide  ligand  51  27  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M7W
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
 M7W  C2   C  CR16  0  -0.384  -5.8892   0.7053   1.4828
 M7W  C4   C  CR6   0  -0.037  -4.8210  -0.4994  -0.3020
 M7W  C5   C  CH2   0  -0.319  -3.8360  -1.5149  -0.8017
 M7W  C6   C  C     0   0.751  -1.4747  -2.0380  -0.4942
 M7W  O2   O  O     0  -0.416   7.9740   2.5843   0.4036
 M7W  C1   C  CR6   0   0.531  -6.6646   1.3446   0.5041
 M7W  C3   C  CR16  0  -0.163  -4.9645  -0.2204   1.0627
 M7W  O1   O  O     0  -0.539  -1.6831  -3.2156  -0.7635
 M7W  C14  C  CH3   0  -0.801   8.9182   0.4069   0.3573
 M7W  C12  C  CR6   0  -0.063   6.4005   0.8495   0.2347
 M7W  C11  C  CR16  0  -0.250   5.3097   1.7204   0.1982
 M7W  C10  C  CR16  0  -0.353   4.0140   1.2581   0.1017
 M7W  C16  C  CR16  0  -0.270   6.1257  -0.5191   0.1662
 M7W  C15  C  CR16  0  -0.330   4.8365  -0.9967   0.0741
 M7W  C9   C  CR6   0   0.402   3.7330  -0.1218   0.0480
 M7W  N2   N  NT    0  -0.524   2.4453  -0.6026   0.0023
 M7W  C8   C  CH2   0  -0.305   1.3275   0.3187   0.0426
 M7W  C7   C  CH2   0  -0.309   0.0695  -0.3742   0.5391
 M7W  C18  C  CH2   0  -0.306   2.1470  -1.8128  -0.7481
 M7W  C17  C  CH2   0  -0.296   0.8939  -2.4930  -0.2340
 M7W  N1   N  NT    0  -0.512  -0.2153  -1.5623  -0.2405
 M7W  N    N  NH1   0  -0.681  -2.4887  -1.1295  -0.4349
 M7W  C19  C  CR16  0  -0.098  -5.6351   0.2014  -1.1679
 M7W  N3   N  N     0  -0.461  -6.5400   1.1027  -0.7807
 M7W  O    O  O2    0  -0.473  -7.5622   2.2366   0.9279
 M7W  C    C  CH3   0  -0.417  -8.3586   2.8967  -0.0449
 M7W  H1   H  HCR6  0   0.273  -6.0234   0.9375   2.5307
 M7W  H2   H  HCH2  0   0.260  -4.0518  -2.4875  -0.3589
 M7W  H3   H  HCH2  0   0.244  -3.9477  -1.6295  -1.8854
 M7W  H4   H  HCR6  0   0.269  -4.3480  -0.7339   1.7904
 M7W  H5   H  HCH3  0   0.266   9.8639   0.9352   0.4544
 M7W  H6   H  HCH3  0   0.263   8.8217  -0.2949   1.1870
 M7W  H7   H  HCH3  0   0.265   8.9420  -0.1835  -0.5601
 M7W  H8   H  HCR6  0   0.259   5.4747   2.7896   0.2307
 M7W  H9   H  HCR6  0   0.273   3.2198   1.9882   0.0483
 M7W  H10  H  HCR6  0   0.260   6.9276  -1.2449   0.1930
 M7W  H11  H  HCR6  0   0.269   4.6949  -2.0677   0.0496
 M7W  H12  H  HCH2  0   0.266   1.5383   1.1267   0.7409
 M7W  H13  H  HCH2  0   0.234   1.1395   0.7654  -0.9433
 M7W  H14  H  HCH2  0   0.244   0.1996  -0.6451   1.5939
 M7W  H15  H  HCH2  0   0.263  -0.7420   0.3466   0.4937
 M7W  H16  H  HCH2  0   0.235   2.0204  -1.5737  -1.8125
 M7W  H17  H  HCH2  0   0.268   2.9642  -2.5235  -0.6712
 M7W  H18  H  HCH2  0   0.268   0.6696  -3.3408  -0.8755
 M7W  H19  H  HCH2  0   0.233   1.0709  -2.8765   0.7786
 M7W  H20  H  HNH1  0   0.398  -2.2735  -0.1542  -0.5643
 M7W  H21  H  HCR6  0   0.260  -5.5627   0.0317  -2.2378
 M7W  H22  H  HCH3  0   0.246  -9.0236   3.5526   0.5106
 M7W  H23  H  HCH3  0   0.229  -7.7525   3.4933  -0.7275
 M7W  H24  H  HCH3  0   0.229  -8.9524   2.1937  -0.6301
 M7W  C13  C  C     0   0.354   7.7716   1.3850   0.3377

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
 M7W  C2   C3   aromatic  1.374  0.020  1.374
 M7W  C2   C1   aromatic  1.403  0.020  1.403
 M7W  C3   C4   aromatic  1.400  0.020  1.400
 M7W  O    C1   single    1.335  0.020  1.335
 M7W  O    C    single    1.420  0.020  1.420
 M7W  C1   N3   aromatic  1.313  0.020  1.313
 M7W  C4   C5   single    1.500  0.020  1.500
 M7W  C4   C19  aromatic  1.380  0.020  1.380
 M7W  C5   N    single    1.449  0.020  1.449
 M7W  O1   C6   double    1.226  0.020  1.226
 M7W  N3   C19  aromatic  1.335  0.020  1.335
 M7W  C6   N    single    1.363  0.020  1.363
 M7W  C6   N1   single    1.370  0.020  1.370
 M7W  N1   C17  single    1.448  0.020  1.448
 M7W  N1   C7   single    1.449  0.020  1.449
 M7W  C17  C18  single    1.516  0.020  1.516
 M7W  C7   C8   single    1.520  0.020  1.520
 M7W  C18  N2   single    1.455  0.020  1.455
 M7W  C8   N2   single    1.449  0.020  1.449
 M7W  N2   C9   single    1.375  0.020  1.375
 M7W  C9   C15  aromatic  1.409  0.020  1.409
 M7W  C9   C10  aromatic  1.409  0.020  1.409
 M7W  C15  C16  aromatic  1.378  0.020  1.378
 M7W  C10  C11  aromatic  1.379  0.020  1.379
 M7W  C16  C12  aromatic  1.398  0.020  1.398
 M7W  C11  C12  aromatic  1.396  0.020  1.396
 M7W  C12  C13  single    1.476  0.020  1.476
 M7W  C13  O2   double    1.218  0.020  1.218
 M7W  C13  C14  single    1.507  0.020  1.507
 M7W  C2   H1   single    0.930  0.020  1.080
 M7W  C5   H2   single    0.970  0.020  1.090
 M7W  C5   H3   single    0.970  0.020  1.090
 M7W  C3   H4   single    0.930  0.020  1.080
 M7W  C14  H5   single    0.970  0.020  1.090
 M7W  C14  H6   single    0.970  0.020  1.090
 M7W  C14  H7   single    0.970  0.020  1.090
 M7W  C11  H8   single    0.930  0.020  1.080
 M7W  C10  H9   single    0.930  0.020  1.080
 M7W  C16  H10  single    0.930  0.020  1.080
 M7W  C15  H11  single    0.930  0.020  1.080
 M7W  C8   H12  single    0.970  0.020  1.090
 M7W  C8   H13  single    0.970  0.020  1.090
 M7W  C7   H14  single    0.970  0.020  1.090
 M7W  C7   H15  single    0.970  0.020  1.090
 M7W  C18  H16  single    0.970  0.020  1.090
 M7W  C18  H17  single    0.970  0.020  1.090
 M7W  C17  H18  single    0.970  0.020  1.090
 M7W  C17  H19  single    0.970  0.020  1.090
 M7W  N    H20  single    0.890  0.020  1.040
 M7W  C19  H21  single    0.930  0.020  1.080
 M7W  C    H22  single    0.970  0.020  1.090
 M7W  C    H23  single    0.970  0.020  1.090
 M7W  C    H24  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
 M7W  H1   C2   C3   121.62  3.000
 M7W  H1   C2   C1   120.63  3.000
 M7W  C3   C2   C1   117.75  3.000
 M7W  C19  C4   C3   116.74  3.000
 M7W  C19  C4   C5   121.47  3.000
 M7W  C3   C4   C5   121.79  3.000
 M7W  H3   C5   H2   106.76  3.000
 M7W  H3   C5   N    111.91  3.000
 M7W  H2   C5   N    108.58  3.000
 M7W  H3   C5   C4   109.47  3.000
 M7W  H2   C5   C4   109.79  3.000
 M7W  N    C5   C4   110.25  3.000
 M7W  N    C6   N1   116.39  3.000
 M7W  N1   C6   O1   122.04  3.000
 M7W  N    C6   O1   121.57  3.000
 M7W  O    C1   N3   119.84  3.000
 M7W  N3   C1   C2   123.10  3.000
 M7W  O    C1   C2   117.05  3.000
 M7W  H4   C3   C4   120.13  3.000
 M7W  H4   C3   C2   119.79  3.000
 M7W  C4   C3   C2   120.08  3.000
 M7W  H7   C14  H6   107.05  3.000
 M7W  H7   C14  H5   108.60  3.000
 M7W  H6   C14  H5   108.76  3.000
 M7W  H7   C14  C13  110.90  3.000
 M7W  H6   C14  C13  111.10  3.000
 M7W  H5   C14  C13  110.33  3.000
 M7W  C16  C12  C11  117.12  3.000
 M7W  C11  C12  C13  120.09  3.000
 M7W  C16  C12  C13  122.78  3.000
 M7W  H8   C11  C10  118.45  3.000
 M7W  H8   C11  C12  119.75  3.000
 M7W  C10  C11  C12  121.79  3.000
 M7W  H9   C10  C9   120.89  3.000
 M7W  H9   C10  C11  117.89  3.000
 M7W  C9   C10  C11  121.21  3.000
 M7W  H10  C16  C15  117.55  3.000
 M7W  H10  C16  C12  120.67  3.000
 M7W  C15  C16  C12  121.78  3.000
 M7W  H11  C15  C9   120.84  3.000
 M7W  H11  C15  C16  117.89  3.000
 M7W  C9   C15  C16  121.26  3.000
 M7W  N2   C9   C15  121.13  3.000
 M7W  C15  C9   C10  116.83  3.000
 M7W  N2   C9   C10  122.03  3.000
 M7W  C18  N2   C8   112.65  3.000
 M7W  C8   N2   C9   119.94  3.000
 M7W  C18  N2   C9   120.00  3.000
 M7W  H13  C8   H12  107.88  3.000
 M7W  H13  C8   C7   109.70  3.000
 M7W  H12  C8   C7   106.82  3.000
 M7W  H13  C8   N2   111.44  3.000
 M7W  H12  C8   N2   109.90  3.000
 M7W  C7   C8   N2   110.96  3.000
 M7W  H15  C7   H14  107.02  3.000
 M7W  H15  C7   N1   112.00  3.000
 M7W  H14  C7   N1   109.76  3.000
 M7W  H15  C7   C8   107.59  3.000
 M7W  H14  C7   C8   109.19  3.000
 M7W  N1   C7   C8   111.15  3.000
 M7W  H17  C18  H16  107.34  3.000
 M7W  H17  C18  C17  107.73  3.000
 M7W  H16  C18  C17  109.34  3.000
 M7W  H17  C18  N2   110.71  3.000
 M7W  H16  C18  N2   110.02  3.000
 M7W  C17  C18  N2   111.58  3.000
 M7W  H19  C17  H18  107.79  3.000
 M7W  H19  C17  N1   110.64  3.000
 M7W  H18  C17  N1   109.92  3.000
 M7W  H19  C17  C18  109.66  3.000
 M7W  H18  C17  C18  108.70  3.000
 M7W  N1   C17  C18  110.08  3.000
 M7W  C17  N1   C7   111.96  3.000
 M7W  C7   N1   C6   124.40  3.000
 M7W  C17  N1   C6   118.81  3.000
 M7W  H20  N    C6   118.75  3.000
 M7W  H20  N    C5   115.08  3.000
 M7W  C6   N    C5   120.24  3.000
 M7W  H21  C19  N3   115.89  3.000
 M7W  H21  C19  C4   119.99  3.000
 M7W  N3   C19  C4   124.13  3.000
 M7W  C19  N3   C1   118.20  3.000
 M7W  C    O    C1   118.06  3.000
 M7W  H24  C    H23  108.63  3.000
 M7W  H24  C    H22  109.28  3.000
 M7W  H23  C    H22  109.26  3.000
 M7W  H24  C    O    111.92  3.000
 M7W  H23  C    O    111.81  3.000
 M7W  H22  C    O    105.88  3.000
 M7W  C12  C13  C14  118.18  3.000
 M7W  C14  C13  O2   120.79  3.000
 M7W  C12  C13  O2   121.03  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
 M7W  CONST_01  C19  C4   C3   C2      0.00   0.0  0
 M7W  CONST_02  C19  N3   C1   C2      0.00   0.0  0
 M7W  CONST_03  C1   C2   C3   C4      0.00   0.0  0
 M7W  CONST_04  C1   N3   C19  C4      0.00   0.0  0
 M7W  CONST_05  N3   C1   C2   C3      0.00   0.0  0
 M7W  CONST_06  N3   C19  C4   C3      0.00   0.0  0
 M7W  CONST_07  C9   C15  C16  C12     0.00   0.0  0
 M7W  CONST_08  C9   C10  C11  C12     0.00   0.0  0
 M7W  CONST_09  C15  C9   C10  C11     0.00   0.0  0
 M7W  CONST_10  C15  C16  C12  C11     0.00   0.0  0
 M7W  CONST_11  C16  C15  C9   C10     0.00   0.0  0
 M7W  CONST_12  C16  C12  C11  C10     0.00   0.0  0
 M7W  CONST_13  N2   C9   C10  C11   180.00   0.0  0
 M7W  CONST_14  N2   C9   C15  C16   180.00   0.0  0
 M7W  CONST_15  C5   C4   C3   C2    180.00   0.0  0
 M7W  CONST_16  N3   C19  C4   C5    180.00   0.0  0
 M7W  CONST_17  O    C1   C2   C3    180.00   0.0  0
 M7W  CONST_18  C15  C16  C12  C13   180.00   0.0  0
 M7W  CONST_19  C10  C11  C12  C13   180.00   0.0  0
 M7W  CONST_20  O    C1   N3   C19   180.00   0.0  0
 M7W  CONST_21  H1   C2   C3   C4    180.00   0.0  0
 M7W  CONST_22  H4   C3   C2   C1    180.00   0.0  0
 M7W  CONST_23  H21  C19  N3   C1    180.00   0.0  0
 M7W  CONST_24  H11  C15  C16  C12   180.00   0.0  0
 M7W  CONST_25  H9   C10  C11  C12   180.00   0.0  0
 M7W  CONST_26  H10  C16  C12  C11   180.00   0.0  0
 M7W  CONST_27  H8   C11  C12  C16   180.00   0.0  0
 M7W  CONST_28  C17  N1   C6   O1      0.00   0.0  0
 M7W  CONST_31  N    C6   N1   C17   180.00   0.0  0
 M7W  CONST_32  N1   C6   N    C5    180.00   0.0  0
 M7W  CONST_34  O1   C6   N    C5      0.00   0.0  0
 M7W  Var_01    C18  N2   C9   C10   146.16  30.0  3
 M7W  Var_02    C17  C18  N2   C9    156.02  30.0  1
 M7W  Var_03    C7   C8   N2   C9   -157.05  30.0  1
 M7W  Var_04    N1   C17  C18  N2     54.95  30.0  1
 M7W  Var_05    N1   C7   C8   N2    -53.86  30.0  1
 M7W  Var_06    C17  N1   C7   C8     56.73  30.0  1
 M7W  Var_07    C18  C17  N1   C7    -56.85  30.0  1
 M7W  Var_08    C16  C12  C13  O2   -179.55  30.0  2
 M7W  Var_09    N    C5   C4   C3    -60.98  30.0  2
 M7W  Var_10    C6   N    C5   C4    164.20  30.0  3
 M7W  Var_11    H22  C    O    C1    178.87  30.0  3
 M7W  Var_12    H5   C14  C13  C12  -178.95  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
 M7W  plan-1  C2   0.020
 M7W  plan-1  C4   0.020
 M7W  plan-1  C5   0.020
 M7W  plan-1  C1   0.020
 M7W  plan-1  C3   0.020
 M7W  plan-1  C19  0.020
 M7W  plan-1  N3   0.020
 M7W  plan-1  O    0.020
 M7W  plan-1  H1   0.020
 M7W  plan-1  H4   0.020
 M7W  plan-1  H21  0.020
 M7W  plan-2  C12  0.020
 M7W  plan-2  C11  0.020
 M7W  plan-2  C10  0.020
 M7W  plan-2  C16  0.020
 M7W  plan-2  C15  0.020
 M7W  plan-2  C9   0.020
 M7W  plan-2  N2   0.020
 M7W  plan-2  H8   0.020
 M7W  plan-2  H9   0.020
 M7W  plan-2  H10  0.020
 M7W  plan-2  H11  0.020
 M7W  plan-2  C13  0.020
 M7W  plan-3  C5   0.020
 M7W  plan-3  C6   0.020
 M7W  plan-3  O1   0.020
 M7W  plan-3  C7   0.020
 M7W  plan-3  C17  0.020
 M7W  plan-3  N1   0.020
 M7W  plan-3  N    0.020
 M7W  plan-3  H20  0.020
 M7W  plan-4  O2   0.020
 M7W  plan-4  C14  0.020
 M7W  plan-4  C12  0.020
 M7W  plan-4  C13  0.020

