# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 15:14:18 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 5-(4-methylpiperazin-1-yl)-2-phenylmethoxy-~{N}-pyridin-3-yl-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)c2ccc(OCc3ccccc3)c(c2)C(=O)Nc4cccnc4
#
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
 A0Q  A0Q  5-(4-methylpiperazin-1-yl)-2-phenylmethoxy-~{N}-pyridin-3-yl-benzamide  ligand  56  30  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A0Q
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
 A0Q  C1   C  CR16  0  -0.328  -1.5103   0.0471   0.2367
 A0Q  C2   C  CR6   0  -0.169  -0.1447   0.2620   0.1551
 A0Q  C3   C  CR6   0   0.366   0.3512   1.5258  -0.1900
 A0Q  C4   C  CR16  0  -0.367  -0.5553   2.5466  -0.4329
 A0Q  C5   C  CR16  0  -0.341  -1.9253   2.3183  -0.3493
 A0Q  C6   C  CR6   0   0.362  -2.4376   1.0671  -0.0118
 A0Q  O7   O  O2    0  -0.465   1.6884   1.6444  -0.2998
 A0Q  C8   C  CH2   0  -0.239   2.2493   2.9386  -0.4092
 A0Q  C9   C  CR6   0   0.080   3.7389   2.8207  -0.2672
 A0Q  N10  N  NT    0  -0.519  -3.8041   0.8080   0.1261
 A0Q  C11  C  C     0   0.518   0.7951  -0.8433   0.5194
 A0Q  N12  N  NH1   0  -0.731   0.5752  -1.9870  -0.1821
 A0Q  O13  O  O     0  -0.442   1.6491  -0.7223   1.3756
 A0Q  C14  C  CR6   0   0.287   1.2017  -3.2243  -0.0525
 A0Q  C15  C  CR16  0  -0.212   2.2339  -3.5223   0.8346
 A0Q  C16  C  CR16  0  -0.311   2.7473  -4.8106   0.8327
 A0Q  C17  C  CR16  0  -0.085   2.2307  -5.7547  -0.0377
 A0Q  N18  N  N     0  -0.388   1.2466  -5.4751  -0.8862
 A0Q  C19  C  CR16  0  -0.144   0.7522  -4.2514  -0.8898
 A0Q  C20  C  CR16  0  -0.292   4.3001   2.0249   0.7302
 A0Q  C21  C  CR16  0  -0.241   5.6775   1.9609   0.8814
 A0Q  C22  C  CR16  0  -0.265   6.5104   2.6923   0.0423
 A0Q  C23  C  CR16  0  -0.241   5.9573   3.4843  -0.9535
 A0Q  C24  C  CR16  0  -0.305   4.5776   3.5429  -1.1086
 A0Q  C25  C  CH2   0  -0.308  -4.3304  -0.3351  -0.6082
 A0Q  C26  C  CH2   0  -0.282  -5.7010  -0.7153  -0.0864
 A0Q  N27  N  NT    0  -0.413  -6.6080   0.4097  -0.1691
 A0Q  C28  C  CH2   0  -0.277  -6.0809   1.5268   0.5854
 A0Q  C29  C  CH2   0  -0.316  -4.7125   1.9348   0.0710
 A0Q  C30  C  CH3   0  -0.519  -7.9431   0.0565   0.2536
 A0Q  H1   H  HCR6  0   0.275  -1.8635  -0.9275   0.5513
 A0Q  H2   H  HCR6  0   0.286  -0.2201   3.5344  -0.7189
 A0Q  H3   H  HCR6  0   0.277  -2.5852   3.1473  -0.5643
 A0Q  H4   H  HCH2  0   0.242   1.9940   3.3968  -1.3710
 A0Q  H5   H  HCH2  0   0.244   1.8479   3.5881   0.3782
 A0Q  H6   H  HNH1  0   0.421  -0.1311  -1.9374  -0.9015
 A0Q  H7   H  HCR6  0   0.295   2.6346  -2.7833   1.5082
 A0Q  H8   H  HCR6  0   0.274   3.5498  -5.0741   1.5080
 A0Q  H9   H  HCR6  0   0.265   2.6190  -6.7662  -0.0540
 A0Q  H10  H  HCR6  0   0.273  -0.0516  -4.0533  -1.5939
 A0Q  H11  H  HCR6  0   0.255   3.6610   1.4471   1.3859
 A0Q  H12  H  HCR6  0   0.256   6.1041   1.3399   1.6589
 A0Q  H13  H  HCR6  0   0.257   7.5847   2.6411   0.1643
 A0Q  H14  H  HCR6  0   0.257   6.5973   4.0521  -1.6162
 A0Q  H15  H  HCR6  0   0.253   4.1518   4.1545  -1.8955
 A0Q  H16  H  HCH2  0   0.215  -4.3983  -0.1084  -1.6826
 A0Q  H17  H  HCH2  0   0.252  -3.6677  -1.1918  -0.4999
 A0Q  H18  H  HCH2  0   0.240  -6.0912  -1.5383  -0.6900
 A0Q  H19  H  HCH2  0   0.193  -5.6043  -1.0886   0.9482
 A0Q  H21  H  HCH2  0   0.241  -6.7600   2.3774   0.4904
 A0Q  H22  H  HCH2  0   0.193  -6.0025   1.2923   1.6614
 A0Q  H23  H  HCH2  0   0.251  -4.3345   2.7403   0.7026
 A0Q  H24  H  HCH2  0   0.211  -4.8109   2.3344  -0.9505
 A0Q  H25  H  HCH3  0   0.192  -7.9974  -0.2622   1.3064
 A0Q  H26  H  HCH3  0   0.234  -8.6122   0.9093   0.1296
 A0Q  H27  H  HCH3  0   0.234  -8.3243  -0.7609  -0.3603

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
 A0Q  C21  C22  aromatic  1.390  0.020  1.390
 A0Q  C21  C20  aromatic  1.387  0.020  1.387
 A0Q  C22  C23  aromatic  1.387  0.020  1.387
 A0Q  C20  C9   aromatic  1.394  0.020  1.394
 A0Q  C23  C24  aromatic  1.390  0.020  1.390
 A0Q  C9   C24  aromatic  1.390  0.020  1.390
 A0Q  C9   C8   single    1.501  0.020  1.501
 A0Q  C8   O7   single    1.415  0.020  1.415
 A0Q  O7   C3   single    1.347  0.020  1.347
 A0Q  N18  C19  aromatic  1.320  0.020  1.320
 A0Q  N18  C17  aromatic  1.329  0.020  1.329
 A0Q  C19  C14  aromatic  1.399  0.020  1.399
 A0Q  C17  C16  aromatic  1.384  0.020  1.384
 A0Q  C4   C3   aromatic  1.387  0.020  1.387
 A0Q  C4   C5   aromatic  1.391  0.020  1.391
 A0Q  C3   C2   aromatic  1.401  0.020  1.401
 A0Q  C14  N12  single    1.393  0.020  1.393
 A0Q  C14  C15  aromatic  1.393  0.020  1.393
 A0Q  N12  C11  single    1.360  0.020  1.360
 A0Q  C16  C15  aromatic  1.387  0.020  1.387
 A0Q  C5   C6   aromatic  1.394  0.020  1.394
 A0Q  C2   C11  single    1.496  0.020  1.496
 A0Q  C2   C1   aromatic  1.385  0.020  1.385
 A0Q  C11  O13  double    1.215  0.020  1.215
 A0Q  C6   C1   aromatic  1.401  0.020  1.401
 A0Q  C6   N10  single    1.398  0.020  1.398
 A0Q  N10  C29  single    1.448  0.020  1.448
 A0Q  N10  C25  single    1.457  0.020  1.457
 A0Q  C29  C28  single    1.518  0.020  1.518
 A0Q  C28  N27  single    1.447  0.020  1.447
 A0Q  C25  C26  single    1.515  0.020  1.515
 A0Q  C26  N27  single    1.447  0.020  1.447
 A0Q  N27  C30  single    1.444  0.020  1.444
 A0Q  C1   H1   single    0.930  0.020  1.080
 A0Q  C4   H2   single    0.930  0.020  1.080
 A0Q  C5   H3   single    0.930  0.020  1.080
 A0Q  C8   H4   single    0.970  0.020  1.090
 A0Q  C8   H5   single    0.970  0.020  1.090
 A0Q  N12  H6   single    0.860  0.020  1.020
 A0Q  C15  H7   single    0.930  0.020  1.080
 A0Q  C16  H8   single    0.930  0.020  1.080
 A0Q  C17  H9   single    0.930  0.020  1.080
 A0Q  C19  H10  single    0.930  0.020  1.080
 A0Q  C20  H11  single    0.930  0.020  1.080
 A0Q  C21  H12  single    0.930  0.020  1.080
 A0Q  C22  H13  single    0.930  0.020  1.080
 A0Q  C23  H14  single    0.930  0.020  1.080
 A0Q  C24  H15  single    0.930  0.020  1.080
 A0Q  C25  H16  single    0.970  0.020  1.090
 A0Q  C25  H17  single    0.970  0.020  1.090
 A0Q  C26  H18  single    0.970  0.020  1.090
 A0Q  C26  H19  single    0.970  0.020  1.090
 A0Q  C28  H21  single    0.970  0.020  1.090
 A0Q  C28  H22  single    0.970  0.020  1.090
 A0Q  C29  H23  single    0.970  0.020  1.090
 A0Q  C29  H24  single    0.970  0.020  1.090
 A0Q  C30  H25  single    0.970  0.020  1.090
 A0Q  C30  H26  single    0.970  0.020  1.090
 A0Q  C30  H27  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
 A0Q  H1   C1   C6   119.39  3.000
 A0Q  H1   C1   C2   118.58  3.000
 A0Q  C6   C1   C2   121.96  3.000
 A0Q  C11  C2   C3   120.28  3.000
 A0Q  C11  C2   C1   119.37  3.000
 A0Q  C3   C2   C1   120.24  3.000
 A0Q  O7   C3   C4   124.75  3.000
 A0Q  C4   C3   C2   118.42  3.000
 A0Q  O7   C3   C2   116.81  3.000
 A0Q  H2   C4   C5   118.10  3.000
 A0Q  H2   C4   C3   121.06  3.000
 A0Q  C5   C4   C3   120.82  3.000
 A0Q  H3   C5   C6   120.81  3.000
 A0Q  H3   C5   C4   117.59  3.000
 A0Q  C6   C5   C4   121.59  3.000
 A0Q  N10  C6   C5   123.35  3.000
 A0Q  N10  C6   C1   119.66  3.000
 A0Q  C5   C6   C1   116.96  3.000
 A0Q  C8   O7   C3   118.72  3.000
 A0Q  H5   C8   H4   107.29  3.000
 A0Q  H5   C8   C9   109.99  3.000
 A0Q  H4   C8   C9   110.32  3.000
 A0Q  H5   C8   O7   109.94  3.000
 A0Q  H4   C8   O7   110.99  3.000
 A0Q  C9   C8   O7   108.32  3.000
 A0Q  C24  C9   C20  119.12  3.000
 A0Q  C24  C9   C8   120.04  3.000
 A0Q  C20  C9   C8   120.81  3.000
 A0Q  C29  N10  C25  111.38  3.000
 A0Q  C25  N10  C6   116.67  3.000
 A0Q  C29  N10  C6   117.73  3.000
 A0Q  O13  C11  N12  124.12  3.000
 A0Q  O13  C11  C2   122.65  3.000
 A0Q  N12  C11  C2   113.23  3.000
 A0Q  H6   N12  C14  115.13  3.000
 A0Q  H6   N12  C11  116.07  3.000
 A0Q  C14  N12  C11  128.79  3.000
 A0Q  C19  C14  C15  117.52  3.000
 A0Q  C15  C14  N12  125.62  3.000
 A0Q  C19  C14  N12  116.86  3.000
 A0Q  H7   C15  C16  120.03  3.000
 A0Q  H7   C15  C14  121.81  3.000
 A0Q  C16  C15  C14  118.16  3.000
 A0Q  H8   C16  C17  120.22  3.000
 A0Q  H8   C16  C15  120.01  3.000
 A0Q  C17  C16  C15  119.76  3.000
 A0Q  H9   C17  N18  116.88  3.000
 A0Q  H9   C17  C16  120.83  3.000
 A0Q  N18  C17  C16  122.29  3.000
 A0Q  C19  N18  C17  118.30  3.000
 A0Q  H10  C19  N18  116.60  3.000
 A0Q  H10  C19  C14  119.44  3.000
 A0Q  N18  C19  C14  123.96  3.000
 A0Q  H11  C20  C21  119.70  3.000
 A0Q  H11  C20  C9   120.02  3.000
 A0Q  C21  C20  C9   120.27  3.000
 A0Q  H12  C21  C22  119.94  3.000
 A0Q  H12  C21  C20  119.74  3.000
 A0Q  C22  C21  C20  120.32  3.000
 A0Q  H13  C22  C23  120.24  3.000
 A0Q  H13  C22  C21  120.12  3.000
 A0Q  C23  C22  C21  119.65  3.000
 A0Q  H14  C23  C24  119.78  3.000
 A0Q  H14  C23  C22  120.22  3.000
 A0Q  C24  C23  C22  120.00  3.000
 A0Q  H15  C24  C23  119.67  3.000
 A0Q  H15  C24  C9   119.70  3.000
 A0Q  C23  C24  C9   120.63  3.000
 A0Q  H17  C25  H16  107.27  3.000
 A0Q  H17  C25  C26  108.61  3.000
 A0Q  H16  C25  C26  109.40  3.000
 A0Q  H17  C25  N10  110.33  3.000
 A0Q  H16  C25  N10  110.66  3.000
 A0Q  C26  C25  N10  110.49  3.000
 A0Q  H19  C26  H18  107.11  3.000
 A0Q  H19  C26  N27  111.79  3.000
 A0Q  H18  C26  N27  109.28  3.000
 A0Q  H19  C26  C25  109.17  3.000
 A0Q  H18  C26  C25  108.77  3.000
 A0Q  N27  C26  C25  110.62  3.000
 A0Q  C30  N27  C28  111.89  3.000
 A0Q  C30  N27  C26  111.87  3.000
 A0Q  C28  N27  C26  110.00  3.000
 A0Q  H22  C28  H21  107.11  3.000
 A0Q  H22  C28  C29  108.87  3.000
 A0Q  H21  C28  C29  108.76  3.000
 A0Q  H22  C28  N27  111.71  3.000
 A0Q  H21  C28  N27  109.22  3.000
 A0Q  C29  C28  N27  111.05  3.000
 A0Q  H24  C29  H23  107.45  3.000
 A0Q  H24  C29  C28  109.35  3.000
 A0Q  H23  C29  C28  108.33  3.000
 A0Q  H24  C29  N10  111.94  3.000
 A0Q  H23  C29  N10  109.57  3.000
 A0Q  C28  C29  N10  110.09  3.000
 A0Q  H27  C30  H26  107.91  3.000
 A0Q  H27  C30  H25  107.69  3.000
 A0Q  H26  C30  H25  107.74  3.000
 A0Q  H27  C30  N27  109.97  3.000
 A0Q  H26  C30  N27  110.03  3.000
 A0Q  H25  C30  N27  113.33  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
 A0Q  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 A0Q  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 A0Q  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 A0Q  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 A0Q  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 A0Q  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 A0Q  CONST_07  C22  C21  C20  C9      0.00   0.0  0
 A0Q  CONST_08  C22  C23  C24  C9      0.00   0.0  0
 A0Q  CONST_09  C17  N18  C19  C14     0.00   0.0  0
 A0Q  CONST_10  C17  C16  C15  C14     0.00   0.0  0
 A0Q  CONST_11  N18  C19  C14  C15     0.00   0.0  0
 A0Q  CONST_12  N18  C17  C16  C15     0.00   0.0  0
 A0Q  CONST_13  C19  N18  C17  C16     0.00   0.0  0
 A0Q  CONST_14  C19  C14  C15  C16     0.00   0.0  0
 A0Q  CONST_15  C23  C22  C21  C20     0.00   0.0  0
 A0Q  CONST_16  C23  C24  C9   C20     0.00   0.0  0
 A0Q  CONST_17  C24  C23  C22  C21     0.00   0.0  0
 A0Q  CONST_18  C24  C9   C20  C21     0.00   0.0  0
 A0Q  CONST_19  N10  C6   C1   C2    180.00   0.0  0
 A0Q  CONST_20  N10  C6   C5   C4    180.00   0.0  0
 A0Q  CONST_21  O7   C3   C2   C1    180.00   0.0  0
 A0Q  CONST_22  C11  C2   C3   C4    180.00   0.0  0
 A0Q  CONST_23  O7   C3   C4   C5    180.00   0.0  0
 A0Q  CONST_24  C11  C2   C1   C6    180.00   0.0  0
 A0Q  CONST_25  C21  C20  C9   C8    180.00   0.0  0
 A0Q  CONST_26  C23  C24  C9   C8    180.00   0.0  0
 A0Q  CONST_27  N18  C19  C14  N12   180.00   0.0  0
 A0Q  CONST_28  C16  C15  C14  N12   180.00   0.0  0
 A0Q  CONST_29  H3   C5   C6   C1    180.00   0.0  0
 A0Q  CONST_30  H2   C4   C3   C2    180.00   0.0  0
 A0Q  CONST_31  H1   C1   C2   C3    180.00   0.0  0
 A0Q  CONST_32  H12  C21  C20  C9    180.00   0.0  0
 A0Q  CONST_33  H14  C23  C24  C9    180.00   0.0  0
 A0Q  CONST_34  H8   C16  C15  C14   180.00   0.0  0
 A0Q  CONST_35  H10  C19  C14  C15   180.00   0.0  0
 A0Q  CONST_36  H9   C17  C16  C15   180.00   0.0  0
 A0Q  CONST_37  H7   C15  C16  C17   180.00   0.0  0
 A0Q  CONST_38  H13  C22  C21  C20   180.00   0.0  0
 A0Q  CONST_39  H15  C24  C9   C20   180.00   0.0  0
 A0Q  CONST_40  H11  C20  C21  C22   180.00   0.0  0
 A0Q  CONST_41  C14  N12  C11  C2    180.00   0.0  0
 A0Q  CONST_42  C19  C14  N12  C11   180.00   0.0  0
 A0Q  CONST_43  C15  C14  N12  C11     0.00   0.0  0
 A0Q  CONST_44  H6   N12  C14  C15   180.00   0.0  0
 A0Q  CONST_45  C14  N12  C11  O13     0.00   0.0  0
 A0Q  Var_01    C29  N10  C6   C1    170.31  30.0  2
 A0Q  Var_02    C28  C29  N10  C6   -165.53  30.0  1
 A0Q  Var_03    C26  C25  N10  C6    164.82  30.0  1
 A0Q  Var_04    N27  C28  C29  N10   -57.15  30.0  1
 A0Q  Var_05    N27  C26  C25  N10    56.96  30.0  1
 A0Q  Var_06    C28  N27  C26  C25   -58.16  30.0  1
 A0Q  Var_07    C29  C28  N27  C26    58.41  30.0  1
 A0Q  Var_08    N12  C11  C2   C1     55.54  30.0  2
 A0Q  Var_09    C9   C8   O7   C3    169.87  30.0  1
 A0Q  Var_10    C20  C9   C8   O7    -44.77  30.0  1
 A0Q  Var_11    H25  C30  N27  C26    62.30  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
 A0Q  plan-1  C1   0.020
 A0Q  plan-1  C2   0.020
 A0Q  plan-1  C3   0.020
 A0Q  plan-1  C4   0.020
 A0Q  plan-1  C5   0.020
 A0Q  plan-1  C6   0.020
 A0Q  plan-1  O7   0.020
 A0Q  plan-1  N10  0.020
 A0Q  plan-1  C11  0.020
 A0Q  plan-1  H1   0.020
 A0Q  plan-1  H2   0.020
 A0Q  plan-1  H3   0.020
 A0Q  plan-2  N12  0.020
 A0Q  plan-2  C14  0.020
 A0Q  plan-2  C15  0.020
 A0Q  plan-2  C16  0.020
 A0Q  plan-2  C17  0.020
 A0Q  plan-2  N18  0.020
 A0Q  plan-2  C19  0.020
 A0Q  plan-2  H7   0.020
 A0Q  plan-2  H8   0.020
 A0Q  plan-2  H9   0.020
 A0Q  plan-2  H10  0.020
 A0Q  plan-3  C8   0.020
 A0Q  plan-3  C9   0.020
 A0Q  plan-3  C20  0.020
 A0Q  plan-3  C21  0.020
 A0Q  plan-3  C22  0.020
 A0Q  plan-3  C23  0.020
 A0Q  plan-3  C24  0.020
 A0Q  plan-3  H11  0.020
 A0Q  plan-3  H12  0.020
 A0Q  plan-3  H13  0.020
 A0Q  plan-3  H14  0.020
 A0Q  plan-3  H15  0.020
 A0Q  plan-4  C2   0.020
 A0Q  plan-4  C11  0.020
 A0Q  plan-4  N12  0.020
 A0Q  plan-4  O13  0.020
 A0Q  plan-4  C14  0.020
 A0Q  plan-4  H6   0.020

