# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 14:47:55 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: N-benzyl-2-{6-[(3,5-dichloropyridin-4-yl)acetyl]-2,3-dimethoxyphenoxy}acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(C(=O)Cc2c(Cl)cncc2Cl)c(OCC(=O)NCc3ccccc3)c1OC
#
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
 3KQ  3KQ  N-benzyl-2-{6-[(3,5-dichloropyridin-4-yl)acetyl]-2,3-dimethoxyphenoxy}acetamide  ligand  55  33  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3KQ
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
 3KQ  C1   C   CR6   0   0.448  -2.4388  -2.5869   0.1659
 3KQ  C2   C   CR6   0  -0.203  -2.6360  -3.1067  -1.1096
 3KQ  C3   C   CR16  0  -0.017  -2.3307  -4.4280  -1.3983
 3KQ  C5   C   CR16  0  -0.017  -1.6035  -4.7850   0.7260
 3KQ  C6   C   CR6   0  -0.214  -1.8851  -3.4740   1.0828
 3KQ  O25  O   O     0  -0.486   2.1248   0.6747  -2.2284
 3KQ  C24  C   C     0   0.523   2.1638   0.6590  -1.0108
 3KQ  N26  N   NH1   0  -0.635   3.0074  -0.0951  -0.2877
 3KQ  C27  C   CH2   0  -0.339   4.0141  -0.9614  -0.8539
 3KQ  C28  C   CR6   0   0.095   5.3764  -0.7236  -0.2536
 3KQ  C33  C   CR16  0  -0.310   6.1640  -1.8002   0.1396
 3KQ  C32  C   CR16  0  -0.240   7.4346  -1.5970   0.6643
 3KQ  C31  C   CR16  0  -0.268   7.9290  -0.3084   0.8076
 3KQ  C30  C   CR16  0  -0.241   7.1466   0.7735   0.4207
 3KQ  C29  C   CR16  0  -0.289   5.8799   0.5674  -0.1061
 3KQ  C23  C   CH2   0  -0.276   1.2871   1.5668  -0.1705
 3KQ  C17  C   CR6   0   0.304  -0.9677   2.1787  -0.1709
 3KQ  C16  C   CR6   0   0.207  -1.2035   3.5321   0.0241
 3KQ  O20  O   O2    0  -0.477  -0.3118   4.4472  -0.4252
 3KQ  C21  C   CH3   0  -0.410  -0.5597   4.9172  -1.7459
 3KQ  C15  C   CR6   0   0.337  -2.3527   3.9615   0.7079
 3KQ  O18  O   O2    0  -0.448  -2.4944   5.2802   0.8337
 3KQ  C19  C   CH3   0  -0.443  -3.6356   5.7814   1.5100
 3KQ  C14  C   CR16  0  -0.385  -3.2423   3.0123   1.2050
 3KQ  C13  C   CR16  0  -0.298  -2.9897   1.6676   1.0097
 3KQ  C12  C   CR6   0  -0.123  -1.8570   1.2097   0.3370
 3KQ  C10  C   C     0   0.393  -1.6256  -0.2374   0.1499
 3KQ  O11  O   O     0  -0.372  -0.5839  -0.6999  -0.2602
 3KQ  C9   C   CH2   0  -0.702  -2.7762  -1.1742   0.5046
 3KQ  CL7  CL  CL    0  -0.100  -1.5173  -2.9653   2.6898
 3KQ  N4   N   N     0  -0.399  -1.8299  -5.2498  -0.4908
 3KQ  CL8  CL  CL    0  -0.098  -3.2514  -2.1063  -2.3730
 3KQ  H1   H   HCR6  0   0.294  -2.4976  -4.8219  -2.3938
 3KQ  H2   H   HCR6  0   0.294  -1.1821  -5.4692   1.4529
 3KQ  H3   H   HNH1  0   0.404   2.9122  -0.0997   0.7158
 3KQ  H4   H   HCH2  0   0.262   3.7304  -2.0083  -0.7190
 3KQ  H5   H   HCH2  0   0.270   4.0418  -0.7813  -1.9288
 3KQ  H6   H   HCR6  0   0.253   5.7811  -2.8089   0.0368
 3KQ  H7   H   HCR6  0   0.256   8.0336  -2.4468   0.9658
 3KQ  H8   H   HCR6  0   0.256   8.9155  -0.1449   1.2217
 3KQ  H9   H   HCR6  0   0.256   7.5247   1.7818   0.5306
 3KQ  H10  H   HCR6  0   0.250   5.2795   1.4201  -0.4009
 3KQ  H11  H   HCH2  0   0.247   1.0646   1.1089   0.7966
 3KQ  H12  H   HCH2  0   0.270   1.8351   2.4958   0.0282
 3KQ  H13  H   HCH3  0   0.225  -1.5444   5.3822  -1.8316
 3KQ  H14  H   HCH3  0   0.241   0.1993   5.6654  -1.9656
 3KQ  H15  H   HCH3  0   0.226  -0.4821   4.1117  -2.4790
 3KQ  H16  H   HCH3  0   0.237  -3.6665   5.4498   2.5502
 3KQ  H17  H   HCH3  0   0.267  -3.5524   6.8644   1.4862
 3KQ  H18  H   HCH3  0   0.237  -4.5619   5.4863   1.0123
 3KQ  H19  H   HCR6  0   0.294  -4.1365   3.3054   1.7366
 3KQ  H20  H   HCR6  0   0.282  -3.7065   0.9662   1.4128
 3KQ  H21  H   HCH2  0   0.314  -3.6813  -0.8619  -0.0199
 3KQ  H22  H   HCH2  0   0.314  -2.9988  -1.0808   1.5691
 3KQ  O22  O   O2    0  -0.466   0.1127   1.8369  -0.9059

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
 3KQ  C19  O18  single    1.418  0.020  1.418
 3KQ  O18  C15  single    1.332  0.020  1.332
 3KQ  C21  O20  single    1.424  0.020  1.424
 3KQ  C15  C14  aromatic  1.393  0.020  1.393
 3KQ  C15  C16  aromatic  1.404  0.020  1.404
 3KQ  O20  C16  single    1.354  0.020  1.354
 3KQ  C14  C13  aromatic  1.382  0.020  1.382
 3KQ  C16  C17  aromatic  1.388  0.020  1.388
 3KQ  C13  C12  aromatic  1.395  0.020  1.395
 3KQ  C17  C12  aromatic  1.410  0.020  1.410
 3KQ  C17  O22  single    1.351  0.020  1.351
 3KQ  C12  C10  single    1.477  0.020  1.477
 3KQ  C23  O22  single    1.412  0.020  1.412
 3KQ  C23  C24  single    1.516  0.020  1.516
 3KQ  O25  C24  double    1.218  0.020  1.218
 3KQ  C24  N26  single    1.343  0.020  1.343
 3KQ  C10  C9   single    1.526  0.020  1.526
 3KQ  C10  O11  double    1.211  0.020  1.211
 3KQ  C9   C1   single    1.491  0.020  1.491
 3KQ  N26  C27  single    1.444  0.020  1.444
 3KQ  CL7  C6   single    1.725  0.020  1.725
 3KQ  C1   C6   aromatic  1.391  0.020  1.391
 3KQ  C1   C2   aromatic  1.391  0.020  1.391
 3KQ  C27  C28  single    1.508  0.020  1.508
 3KQ  C6   C5   aromatic  1.387  0.020  1.387
 3KQ  CL8  C2   single    1.725  0.020  1.725
 3KQ  C29  C28  aromatic  1.393  0.020  1.393
 3KQ  C29  C30  aromatic  1.387  0.020  1.387
 3KQ  C2   C3   aromatic  1.386  0.020  1.386
 3KQ  C28  C33  aromatic  1.391  0.020  1.391
 3KQ  C30  C31  aromatic  1.390  0.020  1.390
 3KQ  C5   N4   aromatic  1.322  0.020  1.322
 3KQ  C3   N4   aromatic  1.323  0.020  1.323
 3KQ  C33  C32  aromatic  1.390  0.020  1.390
 3KQ  C31  C32  aromatic  1.388  0.020  1.388
 3KQ  C3   H1   single    0.930  0.020  1.080
 3KQ  C5   H2   single    0.930  0.020  1.080
 3KQ  N26  H3   single    0.860  0.020  1.020
 3KQ  C27  H4   single    0.970  0.020  1.090
 3KQ  C27  H5   single    0.970  0.020  1.090
 3KQ  C33  H6   single    0.930  0.020  1.080
 3KQ  C32  H7   single    0.930  0.020  1.080
 3KQ  C31  H8   single    0.930  0.020  1.080
 3KQ  C30  H9   single    0.930  0.020  1.080
 3KQ  C29  H10  single    0.930  0.020  1.080
 3KQ  C23  H11  single    0.970  0.020  1.090
 3KQ  C23  H12  single    0.970  0.020  1.090
 3KQ  C21  H13  single    0.970  0.020  1.090
 3KQ  C21  H14  single    0.970  0.020  1.090
 3KQ  C21  H15  single    0.970  0.020  1.090
 3KQ  C19  H16  single    0.970  0.020  1.090
 3KQ  C19  H17  single    0.970  0.020  1.090
 3KQ  C19  H18  single    0.970  0.020  1.090
 3KQ  C14  H19  single    0.930  0.020  1.080
 3KQ  C13  H20  single    0.930  0.020  1.080
 3KQ  C9   H21  single    0.970  0.020  1.090
 3KQ  C9   H22  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
 3KQ  C9   C1   C6   122.99  3.000
 3KQ  C6   C1   C2   114.99  3.000
 3KQ  C9   C1   C2   122.01  3.000
 3KQ  CL8  C2   C3   118.60  3.000
 3KQ  C3   C2   C1   121.05  3.000
 3KQ  CL8  C2   C1   120.35  3.000
 3KQ  H1   C3   N4   117.56  3.000
 3KQ  H1   C3   C2   120.26  3.000
 3KQ  N4   C3   C2   122.18  3.000
 3KQ  H2   C5   N4   117.51  3.000
 3KQ  H2   C5   C6   120.20  3.000
 3KQ  N4   C5   C6   122.28  3.000
 3KQ  CL7  C6   C5   118.35  3.000
 3KQ  C5   C6   C1   120.93  3.000
 3KQ  CL7  C6   C1   120.72  3.000
 3KQ  C23  C24  N26  113.64  3.000
 3KQ  N26  C24  O25  124.44  3.000
 3KQ  C23  C24  O25  121.85  3.000
 3KQ  H3   N26  C27  116.97  3.000
 3KQ  H3   N26  C24  118.64  3.000
 3KQ  C27  N26  C24  124.32  3.000
 3KQ  H5   C27  H4   106.64  3.000
 3KQ  H5   C27  C28  110.09  3.000
 3KQ  H4   C27  C28  109.66  3.000
 3KQ  H5   C27  N26  107.78  3.000
 3KQ  H4   C27  N26  110.20  3.000
 3KQ  C28  C27  N26  112.29  3.000
 3KQ  C29  C28  C33  118.86  3.000
 3KQ  C33  C28  C27  120.15  3.000
 3KQ  C29  C28  C27  120.98  3.000
 3KQ  H6   C33  C32  119.66  3.000
 3KQ  H6   C33  C28  119.58  3.000
 3KQ  C32  C33  C28  120.76  3.000
 3KQ  H7   C32  C31  120.21  3.000
 3KQ  H7   C32  C33  119.76  3.000
 3KQ  C31  C32  C33  120.04  3.000
 3KQ  H8   C31  C30  120.12  3.000
 3KQ  H8   C31  C32  120.30  3.000
 3KQ  C30  C31  C32  119.57  3.000
 3KQ  H9   C30  C29  119.73  3.000
 3KQ  H9   C30  C31  120.01  3.000
 3KQ  C29  C30  C31  120.26  3.000
 3KQ  H10  C29  C30  119.49  3.000
 3KQ  H10  C29  C28  120.00  3.000
 3KQ  C30  C29  C28  120.52  3.000
 3KQ  H12  C23  H11  107.24  3.000
 3KQ  H12  C23  O22  110.36  3.000
 3KQ  H11  C23  O22  111.83  3.000
 3KQ  H12  C23  C24  108.58  3.000
 3KQ  H11  C23  C24  110.93  3.000
 3KQ  O22  C23  C24  107.87  3.000
 3KQ  C12  C17  C16  120.83  3.000
 3KQ  C12  C17  O22  121.78  3.000
 3KQ  C16  C17  O22  117.34  3.000
 3KQ  C15  C16  O20  119.58  3.000
 3KQ  O20  C16  C17  120.03  3.000
 3KQ  C15  C16  C17  120.38  3.000
 3KQ  C21  O20  C16  114.59  3.000
 3KQ  H15  C21  H14  108.79  3.000
 3KQ  H15  C21  H13  109.00  3.000
 3KQ  H14  C21  H13  108.68  3.000
 3KQ  H15  C21  O20  111.53  3.000
 3KQ  H14  C21  O20  107.02  3.000
 3KQ  H13  C21  O20  111.73  3.000
 3KQ  C14  C15  O18  124.96  3.000
 3KQ  C14  C15  C16  119.22  3.000
 3KQ  O18  C15  C16  115.82  3.000
 3KQ  C19  O18  C15  118.72  3.000
 3KQ  H18  C19  H17  108.93  3.000
 3KQ  H18  C19  H16  109.14  3.000
 3KQ  H17  C19  H16  109.00  3.000
 3KQ  H18  C19  O18  111.70  3.000
 3KQ  H17  C19  O18  106.28  3.000
 3KQ  H16  C19  O18  111.69  3.000
 3KQ  H19  C14  C13  118.98  3.000
 3KQ  H19  C14  C15  121.29  3.000
 3KQ  C13  C14  C15  119.73  3.000
 3KQ  H20  C13  C12  120.36  3.000
 3KQ  H20  C13  C14  117.23  3.000
 3KQ  C12  C13  C14  122.41  3.000
 3KQ  C10  C12  C13  120.66  3.000
 3KQ  C10  C12  C17  121.92  3.000
 3KQ  C13  C12  C17  117.41  3.000
 3KQ  C9   C10  O11  119.53  3.000
 3KQ  O11  C10  C12  123.48  3.000
 3KQ  C9   C10  C12  116.99  3.000
 3KQ  H22  C9   H21  105.97  3.000
 3KQ  H22  C9   C10  109.15  3.000
 3KQ  H21  C9   C10  109.75  3.000
 3KQ  H22  C9   C1   110.40  3.000
 3KQ  H21  C9   C1   110.45  3.000
 3KQ  C10  C9   C1   110.99  3.000
 3KQ  C5   N4   C3   118.54  3.000
 3KQ  C17  O22  C23  115.49  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
 3KQ  CONST_01  N4   C5   C6   C1      0.00   0.0  0
 3KQ  CONST_02  N4   C3   C2   C1      0.00   0.0  0
 3KQ  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 3KQ  CONST_04  C5   N4   C3   C2      0.00   0.0  0
 3KQ  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 3KQ  CONST_06  C6   C5   N4   C3      0.00   0.0  0
 3KQ  CONST_07  C31  C30  C29  C28     0.00   0.0  0
 3KQ  CONST_08  C31  C32  C33  C28     0.00   0.0  0
 3KQ  CONST_09  C30  C29  C28  C33     0.00   0.0  0
 3KQ  CONST_10  C30  C31  C32  C33     0.00   0.0  0
 3KQ  CONST_11  C29  C28  C33  C32     0.00   0.0  0
 3KQ  CONST_12  C29  C30  C31  C32     0.00   0.0  0
 3KQ  CONST_13  C14  C15  C16  C17     0.00   0.0  0
 3KQ  CONST_14  C14  C13  C12  C17     0.00   0.0  0
 3KQ  CONST_15  C13  C14  C15  C16     0.00   0.0  0
 3KQ  CONST_16  C13  C12  C17  C16     0.00   0.0  0
 3KQ  CONST_17  C12  C13  C14  C15     0.00   0.0  0
 3KQ  CONST_18  C12  C17  C16  C15     0.00   0.0  0
 3KQ  CONST_19  CL7  C6   C1   C2    180.00   0.0  0
 3KQ  CONST_20  C9   C1   C2   C3    180.00   0.0  0
 3KQ  CONST_21  C9   C1   C6   C5    180.00   0.0  0
 3KQ  CONST_22  CL8  C2   C1   C6    180.00   0.0  0
 3KQ  CONST_23  C30  C29  C28  C27   180.00   0.0  0
 3KQ  CONST_24  C32  C33  C28  C27   180.00   0.0  0
 3KQ  CONST_25  C15  C16  C17  O22   180.00   0.0  0
 3KQ  CONST_26  C13  C12  C17  O22   180.00   0.0  0
 3KQ  CONST_27  O18  C15  C16  C17   180.00   0.0  0
 3KQ  CONST_28  C10  C12  C17  C16   180.00   0.0  0
 3KQ  CONST_29  C14  C15  C16  O20   180.00   0.0  0
 3KQ  CONST_30  C12  C17  C16  O20   180.00   0.0  0
 3KQ  CONST_31  C13  C14  C15  O18   180.00   0.0  0
 3KQ  CONST_32  C10  C12  C13  C14   180.00   0.0  0
 3KQ  CONST_33  N4   C5   C6   CL7   180.00   0.0  0
 3KQ  CONST_34  CL8  C2   C3   N4    180.00   0.0  0
 3KQ  CONST_35  H2   C5   C6   C1    180.00   0.0  0
 3KQ  CONST_36  H1   C3   C2   C1    180.00   0.0  0
 3KQ  CONST_37  H9   C30  C29  C28   180.00   0.0  0
 3KQ  CONST_38  H7   C32  C33  C28   180.00   0.0  0
 3KQ  CONST_39  H10  C29  C28  C33   180.00   0.0  0
 3KQ  CONST_40  H8   C31  C32  C33   180.00   0.0  0
 3KQ  CONST_41  H6   C33  C32  C31   180.00   0.0  0
 3KQ  CONST_42  H20  C13  C12  C17   180.00   0.0  0
 3KQ  CONST_43  H19  C14  C15  C16   180.00   0.0  0
 3KQ  CONST_44  C27  N26  C24  O25     0.00   0.0  0
 3KQ  CONST_45  C23  C24  N26  C27   180.00   0.0  0
 3KQ  CONST_46  H3   N26  C24  O25   180.00   0.0  0
 3KQ  Var_01    C12  C10  C9   C1    175.55  30.0  2
 3KQ  Var_02    C10  C9   C1   C2    -85.17  30.0  2
 3KQ  Var_03    C29  C28  C27  N26   -47.03  30.0  2
 3KQ  Var_04    C16  C17  O22  C23    94.09  30.0  2
 3KQ  Var_05    C9   C10  C12  C17  -168.66  30.0  2
 3KQ  Var_06    C15  C16  O20  C21   -90.21  30.0  2
 3KQ  Var_07    C14  C15  O18  C19    -0.62  30.0  2
 3KQ  Var_08    C28  C27  N26  C24   128.88  30.0  3
 3KQ  Var_09    H11  C23  O22  C17    33.55  30.0  2
 3KQ  Var_10    H13  C21  O20  C16    59.09  30.0  3
 3KQ  Var_11    H16  C19  O18  C15    61.79  30.0  3
 3KQ  Var_12    O22  C23  C24  O25    28.33  30.0  2

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
 3KQ  plan-1  C1   0.020
 3KQ  plan-1  C2   0.020
 3KQ  plan-1  C3   0.020
 3KQ  plan-1  C5   0.020
 3KQ  plan-1  C6   0.020
 3KQ  plan-1  C9   0.020
 3KQ  plan-1  CL7  0.020
 3KQ  plan-1  N4   0.020
 3KQ  plan-1  CL8  0.020
 3KQ  plan-1  H1   0.020
 3KQ  plan-1  H2   0.020
 3KQ  plan-2  C27  0.020
 3KQ  plan-2  C28  0.020
 3KQ  plan-2  C33  0.020
 3KQ  plan-2  C32  0.020
 3KQ  plan-2  C31  0.020
 3KQ  plan-2  C30  0.020
 3KQ  plan-2  C29  0.020
 3KQ  plan-2  H6   0.020
 3KQ  plan-2  H7   0.020
 3KQ  plan-2  H8   0.020
 3KQ  plan-2  H9   0.020
 3KQ  plan-2  H10  0.020
 3KQ  plan-3  C17  0.020
 3KQ  plan-3  C16  0.020
 3KQ  plan-3  O20  0.020
 3KQ  plan-3  C15  0.020
 3KQ  plan-3  O18  0.020
 3KQ  plan-3  C14  0.020
 3KQ  plan-3  C13  0.020
 3KQ  plan-3  C12  0.020
 3KQ  plan-3  C10  0.020
 3KQ  plan-3  H19  0.020
 3KQ  plan-3  H20  0.020
 3KQ  plan-3  O22  0.020
 3KQ  plan-4  O25  0.020
 3KQ  plan-4  C24  0.020
 3KQ  plan-4  N26  0.020
 3KQ  plan-4  C27  0.020
 3KQ  plan-4  C23  0.020
 3KQ  plan-4  H3   0.020
 3KQ  plan-5  C12  0.020
 3KQ  plan-5  C10  0.020
 3KQ  plan-5  O11  0.020
 3KQ  plan-5  C9   0.020

