# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 10:21:20 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: 1-methyl-5-(1-methyl-3-{[4-(1-methyl-1H-benzimidazol-4-yl)phenoxy]methyl}-1H-pyrazol-4-yl)pyridin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(c(COc2ccc(cc2)c3cccc4n(C)cnc34)n1)C5=CN(C)C(=O)C=C5
#
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
 490  490  1-methyl-5-(1-methyl-3-{[4-(1-methyl-1H-benzimidazol-4-yl)phenoxy]methyl}-1H-pyrazol-4-yl)pyridin-2(1H)-one  ligand  55  32  .  2022-07-23  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_490
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
 490  C4   C  CR15  0   0.028   5.5112  -1.6947  -0.0436
 490  C7   C  CH3   0  -0.507   6.2822  -4.0697   0.0387
 490  C8   C  CR6   0  -0.078   4.0189   0.3663   0.0131
 490  C10  C  CR6   0   0.557   3.5712   3.1728  -0.1925
 490  C17  C  CR16  0  -0.329  -0.3174   0.3002  -1.0079
 490  C20  C  CR16  0  -0.298  -1.6146   0.7648  -0.9122
 490  C21  C  CR16  0  -0.363  -0.8156  -1.4014   0.6153
 490  C22  C  CR6   0   0.037  -3.9172   0.6924   0.0512
 490  C24  C  CR16  0  -0.262  -5.4695   2.5873   0.0818
 490  C26  C  CR56  0   0.359  -6.3247   0.4078   0.3065
 490  C25  C  CR16  0  -0.349  -4.1762   2.0582  -0.0117
 490  C19  C  CR16  0  -0.290  -2.1158  -0.9217   0.7006
 490  C23  C  CR16  0  -0.322  -6.5759   1.7734   0.2449
 490  C29  C  CR15  0   0.101  -6.3827  -1.7695   0.4229
 490  C18  C  CR6   0   0.067  -2.5448   0.1673  -0.0549
 490  C3   C  CR5   0  -0.181   4.2887  -1.0686   0.0963
 490  C27  C  CR56  0   0.071  -5.0349  -0.1435   0.2126
 490  C16  C  CR6   0   0.387   0.0935  -0.7929  -0.2451
 490  C2   C  CR5   0   0.277   3.3913  -2.1392   0.3057
 490  C12  C  CR16  0  -0.151   3.1185   1.0294   0.8872
 490  C11  C  CR16  0  -0.450   2.8999   2.3643   0.7876
 490  C9   C  CR16  0  -0.007   4.6418   1.1391  -0.9201
 490  C1   C  CH2   0  -0.307   1.9213  -2.0908   0.5379
 490  N28  N  N     0  -0.464  -5.1126  -1.5140   0.2855
 490  N6   N  N     0  -0.304   4.0207  -3.3001   0.2861
 490  N5   N  NR5   0  -0.270   5.2984  -3.0144   0.0766
 490  N30  N  NR5   0  -0.499  -7.1651  -0.6645   0.4458
 490  N13  N  NR6   0  -0.501   4.4396   2.4758  -1.0209
 490  O32  O  O     0  -0.522   3.4269   4.3864  -0.3286
 490  O15  O  O2    0  -0.469   1.3695  -1.1943  -0.4087
 490  H1   H  HCR5  0   0.294   6.4969  -1.2887  -0.2080
 490  H2   H  HCH3  0   0.261   6.3809  -4.5358   1.0174
 490  H3   H  HCH3  0   0.263   5.9935  -4.8245  -0.6894
 490  H4   H  HCH3  0   0.260   7.2403  -3.6486  -0.2509
 490  H5   H  HCR6  0   0.259   0.3858   0.7785  -1.6778
 490  H6   H  HCR6  0   0.254  -1.9104   1.6058  -1.5269
 490  H7   H  HCR6  0   0.280  -0.5372  -2.2548   1.2193
 490  H8   H  HCR6  0   0.256  -5.6000   3.6604   0.0343
 490  H9   H  HCR6  0   0.249  -3.3471   2.7472  -0.1140
 490  H10  H  HCR6  0   0.253  -2.8002  -1.4106   1.3794
 490  H11  H  HCR6  0   0.270  -7.5755   2.1813   0.3205
 490  H12  H  HCR5  0   0.288  -6.8115  -2.7574   0.5148
 490  H13  H  HCR6  0   0.264   2.6108   0.4674   1.6613
 490  H14  H  HCR6  0   0.269   2.2169   2.8689   1.4574
 490  H15  H  HCR6  0   0.297   5.3286   0.7139  -1.6390
 490  H16  H  HCH3  0   0.260  -9.0570  -0.2506  -0.3536
 490  H17  H  HCH3  0   0.270  -8.9755  -1.6174   0.7668
 490  H18  H  HCH3  0   0.260  -8.8935   0.0336   1.3885
 490  H19  H  HCH3  0   0.260   4.4466   3.7611  -2.6834
 490  H20  H  HCH3  0   0.260   5.8088   3.9714  -1.5755
 490  H21  H  HCH3  0   0.257   5.7429   2.5598  -2.6395
 490  H22  H  HCH2  0   0.257   1.5012  -3.0968   0.4349
 490  H23  H  HCH2  0   0.248   1.6996  -1.7480   1.5558
 490  C14  C  CH3   0  -0.520   5.1488   3.2396  -2.0372
 490  C31  C  CH3   0  -0.529  -8.6020  -0.6172   0.5657

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
 490  C23  C24  aromatic  1.383  0.020  1.383
 490  C23  C26  aromatic  1.390  0.020  1.390
 490  C24  C25  aromatic  1.400  0.020  1.400
 490  C31  N30  single    1.443  0.020  1.443
 490  C26  N30  aromatic  1.369  0.020  1.369
 490  C26  C27  aromatic  1.406  0.020  1.406
 490  C25  C22  aromatic  1.392  0.020  1.392
 490  N30  C29  aromatic  1.354  0.020  1.354
 490  C27  C22  aromatic  1.405  0.020  1.405
 490  C27  N28  aromatic  1.375  0.020  1.375
 490  C22  C18  single    1.473  0.020  1.473
 490  O32  C10  double    1.230  0.020  1.230
 490  C29  N28  aromatic  1.303  0.020  1.303
 490  C14  N13  single    1.456  0.020  1.456
 490  C18  C20  aromatic  1.399  0.020  1.399
 490  C18  C19  aromatic  1.393  0.020  1.393
 490  C10  N13  single    1.388  0.020  1.388
 490  C10  C11  single    1.437  0.020  1.437
 490  C20  C17  aromatic  1.381  0.020  1.381
 490  N13  C9   single    1.356  0.020  1.356
 490  C19  C21  aromatic  1.388  0.020  1.388
 490  C11  C12  double    1.356  0.020  1.356
 490  C17  C16  aromatic  1.395  0.020  1.395
 490  C9   C8   double    1.362  0.020  1.362
 490  C21  C16  aromatic  1.392  0.020  1.392
 490  C16  O15  single    1.348  0.020  1.348
 490  C12  C8   single    1.419  0.020  1.419
 490  C8   C3   single    1.462  0.020  1.462
 490  O15  C1   single    1.416  0.020  1.416
 490  C1   C2   single    1.489  0.020  1.489
 490  C3   C2   aromatic  1.413  0.020  1.413
 490  C3   C4   aromatic  1.381  0.020  1.381
 490  C2   N6   aromatic  1.321  0.020  1.321
 490  C4   N5   aromatic  1.342  0.020  1.342
 490  N6   N5   aromatic  1.326  0.020  1.326
 490  N5   C7   single    1.443  0.020  1.443
 490  C4   H1   single    0.930  0.020  1.080
 490  C7   H2   single    0.970  0.020  1.090
 490  C7   H3   single    0.970  0.020  1.090
 490  C7   H4   single    0.970  0.020  1.090
 490  C17  H5   single    0.930  0.020  1.080
 490  C20  H6   single    0.930  0.020  1.080
 490  C21  H7   single    0.930  0.020  1.080
 490  C24  H8   single    0.930  0.020  1.080
 490  C25  H9   single    0.930  0.020  1.080
 490  C19  H10  single    0.930  0.020  1.080
 490  C23  H11  single    0.930  0.020  1.080
 490  C29  H12  single    0.930  0.020  1.080
 490  C12  H13  single    0.930  0.020  1.080
 490  C11  H14  single    0.930  0.020  1.080
 490  C9   H15  single    0.930  0.020  1.080
 490  C31  H16  single    0.970  0.020  1.090
 490  C31  H17  single    0.970  0.020  1.090
 490  C31  H18  single    0.970  0.020  1.090
 490  C14  H19  single    0.970  0.020  1.090
 490  C14  H20  single    0.970  0.020  1.090
 490  C14  H21  single    0.970  0.020  1.090
 490  C1   H22  single    0.970  0.020  1.090
 490  C1   H23  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
 490  H1   C4   N5   121.91  3.000
 490  H1   C4   C3   130.85  3.000
 490  N5   C4   C3   107.24  3.000
 490  H4   C7   H3   108.95  3.000
 490  H4   C7   H2   109.01  3.000
 490  H3   C7   H2   109.19  3.000
 490  H4   C7   N5   108.96  3.000
 490  H3   C7   N5   110.13  3.000
 490  H2   C7   N5   110.57  3.000
 490  C9   C8   C12  116.55  3.000
 490  C12  C8   C3   122.71  3.000
 490  C9   C8   C3   120.74  3.000
 490  O32  C10  N13  120.20  3.000
 490  N13  C10  C11  114.63  3.000
 490  O32  C10  C11  125.17  3.000
 490  H5   C17  C16  119.56  3.000
 490  H5   C17  C20  120.29  3.000
 490  C16  C17  C20  120.16  3.000
 490  H6   C20  C18  119.86  3.000
 490  H6   C20  C17  118.59  3.000
 490  C18  C20  C17  121.55  3.000
 490  H7   C21  C16  121.46  3.000
 490  H7   C21  C19  118.63  3.000
 490  C16  C21  C19  119.91  3.000
 490  C27  C22  C18  122.50  3.000
 490  C18  C22  C25  121.33  3.000
 490  C27  C22  C25  116.17  3.000
 490  H8   C24  C23  119.49  3.000
 490  H8   C24  C25  118.89  3.000
 490  C23  C24  C25  121.61  3.000
 490  N30  C26  C27  105.23  3.000
 490  C27  C26  C23  123.24  3.000
 490  N30  C26  C23  131.53  3.000
 490  H9   C25  C24  118.23  3.000
 490  H9   C25  C22  119.09  3.000
 490  C24  C25  C22  122.66  3.000
 490  H10  C19  C18  119.95  3.000
 490  H10  C19  C21  118.38  3.000
 490  C18  C19  C21  121.67  3.000
 490  H11  C23  C26  122.29  3.000
 490  H11  C23  C24  121.68  3.000
 490  C26  C23  C24  116.03  3.000
 490  H12  C29  N30  121.01  3.000
 490  H12  C29  N28  125.10  3.000
 490  N30  C29  N28  113.89  3.000
 490  C19  C18  C22  121.76  3.000
 490  C19  C18  C20  117.48  3.000
 490  C22  C18  C20  120.75  3.000
 490  C2   C3   C8   129.41  3.000
 490  C2   C3   C4   103.53  3.000
 490  C8   C3   C4   127.05  3.000
 490  N28  C27  C26  109.61  3.000
 490  N28  C27  C22  130.11  3.000
 490  C26  C27  C22  120.28  3.000
 490  O15  C16  C21  124.29  3.000
 490  O15  C16  C17  116.48  3.000
 490  C21  C16  C17  119.23  3.000
 490  N6   C2   C1   120.10  3.000
 490  N6   C2   C3   111.17  3.000
 490  C1   C2   C3   128.73  3.000
 490  H13  C12  C11  119.19  3.000
 490  H13  C12  C8   119.68  3.000
 490  C11  C12  C8   121.12  3.000
 490  H14  C11  C12  121.03  3.000
 490  H14  C11  C10  117.06  3.000
 490  C12  C11  C10  121.91  3.000
 490  H15  C9   N13  115.66  3.000
 490  H15  C9   C8   121.52  3.000
 490  N13  C9   C8   122.82  3.000
 490  H23  C1   H22  107.27  3.000
 490  H23  C1   O15  110.12  3.000
 490  H22  C1   O15  111.67  3.000
 490  H23  C1   C2   110.76  3.000
 490  H22  C1   C2   109.52  3.000
 490  O15  C1   C2   107.53  3.000
 490  C27  N28  C29  104.85  3.000
 490  N5   N6   C2   105.80  3.000
 490  N6   N5   C7   120.23  3.000
 490  C7   N5   C4   127.49  3.000
 490  N6   N5   C4   112.26  3.000
 490  C31  N30  C29  127.13  3.000
 490  C29  N30  C26  106.42  3.000
 490  C31  N30  C26  126.44  3.000
 490  C14  N13  C9   119.77  3.000
 490  C9   N13  C10  122.97  3.000
 490  C14  N13  C10  117.26  3.000
 490  C1   O15  C16  118.45  3.000
 490  H21  C14  H20  108.95  3.000
 490  H21  C14  H19  108.91  3.000
 490  H20  C14  H19  108.73  3.000
 490  H21  C14  N13  109.00  3.000
 490  H20  C14  N13  110.61  3.000
 490  H19  C14  N13  110.60  3.000
 490  H18  C31  H17  108.56  3.000
 490  H18  C31  H16  108.95  3.000
 490  H17  C31  H16  108.81  3.000
 490  H18  C31  N30  110.43  3.000
 490  H17  C31  N30  109.12  3.000
 490  H16  C31  N30  110.91  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
 490  CONST_01  N6   C2   C3   C4      0.00   0.0  0
 490  CONST_02  C2   N6   N5   C4      0.00   0.0  0
 490  CONST_03  C22  C18  C20  C17   180.00   0.0  0
 490  CONST_04  C19  C18  C20  C17     0.00   0.0  0
 490  CONST_05  C19  C21  C16  C17     0.00   0.0  0
 490  CONST_08  C21  C19  C18  C20     0.00   0.0  0
 490  CONST_09  C21  C16  C17  C20     0.00   0.0  0
 490  CONST_10  C22  C18  C19  C21   180.00   0.0  0
 490  CONST_11  C23  C24  C25  C22     0.00   0.0  0
 490  CONST_12  C23  C26  C27  C22     0.00   0.0  0
 490  CONST_13  N30  C26  C27  C22   180.00   0.0  0
 490  CONST_14  C29  N28  C27  C22   180.00   0.0  0
 490  CONST_15  N30  C26  C23  C24   180.00   0.0  0
 490  CONST_16  C27  C26  C23  C24     0.00   0.0  0
 490  CONST_17  C27  C22  C25  C24     0.00   0.0  0
 490  CONST_18  C18  C22  C25  C24   180.00   0.0  0
 490  CONST_19  C25  C24  C23  C26     0.00   0.0  0
 490  CONST_20  N28  C29  N30  C26     0.00   0.0  0
 490  CONST_21  C25  C22  C27  C26     0.00   0.0  0
 490  CONST_22  C18  C22  C27  C26   180.00   0.0  0
 490  CONST_23  C29  N28  C27  C26     0.00   0.0  0
 490  CONST_24  N28  C27  C22  C25   180.00   0.0  0
 490  CONST_27  C29  N30  C26  C23   180.00   0.0  0
 490  CONST_28  N28  C27  C26  C23   180.00   0.0  0
 490  CONST_29  C27  C26  N30  C29     0.00   0.0  0
 490  CONST_30  N28  C27  C22  C18     0.00   0.0  0
 490  CONST_31  C16  C17  C20  C18     0.00   0.0  0
 490  CONST_32  C16  C21  C19  C18     0.00   0.0  0
 490  CONST_33  N5   N6   C2   C3      0.00   0.0  0
 490  CONST_34  N6   N5   C4   C3      0.00   0.0  0
 490  CONST_35  N30  C29  N28  C27     0.00   0.0  0
 490  CONST_36  N5   C4   C3   C2      0.00   0.0  0
 490  CONST_37  N30  C26  C27  N28     0.00   0.0  0
 490  CONST_38  N6   C2   C3   C8    180.00   0.0  0
 490  CONST_39  N5   C4   C3   C8    180.00   0.0  0
 490  CONST_40  C9   N13  C10  C11     0.00   0.0  0
 490  CONST_41  C1   C2   C3   C4    180.00   0.0  0
 490  CONST_42  C3   C4   N5   C7    180.00   0.0  0
 490  CONST_43  C2   N6   N5   C7    180.00   0.0  0
 490  CONST_44  C1   C2   C3   C8      0.00   0.0  0
 490  CONST_45  O15  C16  C17  C20   180.00   0.0  0
 490  CONST_46  O15  C16  C21  C19   180.00   0.0  0
 490  CONST_47  C31  N30  C26  C23     0.00   0.0  0
 490  CONST_48  C31  N30  C26  C27   180.00   0.0  0
 490  CONST_49  N28  C29  N30  C31   180.00   0.0  0
 490  CONST_50  N5   N6   C2   C1    180.00   0.0  0
 490  CONST_51  C14  N13  C10  C11   180.00   0.0  0
 490  CONST_52  O32  C10  N13  C9    180.00   0.0  0
 490  CONST_53  H1   C4   C3   C8      0.00   0.0  0
 490  CONST_54  H7   C21  C16  C17   180.00   0.0  0
 490  CONST_55  H10  C19  C18  C20   180.00   0.0  0
 490  CONST_56  H5   C17  C16  C21   180.00   0.0  0
 490  CONST_57  H8   C24  C25  C22   180.00   0.0  0
 490  CONST_58  H6   C20  C18  C22     0.00   0.0  0
 490  CONST_59  H12  C29  N30  C26   180.00   0.0  0
 490  CONST_60  H11  C23  C24  C25   180.00   0.0  0
 490  CONST_61  H9   C25  C24  C23   180.00   0.0  0
 490  CONST_62  O32  C10  N13  C14     0.00   0.0  0
 490  Var_01    C9   C8   C3   C4     40.05  30.0  2
 490  Var_02    O15  C1   C2   C3     45.67  30.0  1
 490  Var_03    C2   C1   O15  C16  -167.95  30.0  3
 490  Var_04    H2   C7   N5   C4    111.59  30.0  2
 490  Var_05    H19  C14  N13  C10   -57.14  30.0  3
 490  Var_06    H16  C31  N30  C26    66.05  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
 490  plan-1  C4   0.020
 490  plan-1  C7   0.020
 490  plan-1  C8   0.020
 490  plan-1  C3   0.020
 490  plan-1  C2   0.020
 490  plan-1  C1   0.020
 490  plan-1  N6   0.020
 490  plan-1  N5   0.020
 490  plan-1  H1   0.020
 490  plan-2  C8   0.020
 490  plan-2  C10  0.020
 490  plan-2  C3   0.020
 490  plan-2  C12  0.020
 490  plan-2  C11  0.020
 490  plan-2  C9   0.020
 490  plan-2  N13  0.020
 490  plan-2  O32  0.020
 490  plan-2  H13  0.020
 490  plan-2  H14  0.020
 490  plan-2  H15  0.020
 490  plan-2  C14  0.020
 490  plan-3  C17  0.020
 490  plan-3  C20  0.020
 490  plan-3  C21  0.020
 490  plan-3  C22  0.020
 490  plan-3  C19  0.020
 490  plan-3  C18  0.020
 490  plan-3  C16  0.020
 490  plan-3  O15  0.020
 490  plan-3  H5   0.020
 490  plan-3  H6   0.020
 490  plan-3  H7   0.020
 490  plan-3  H10  0.020
 490  plan-4  C22  0.020
 490  plan-4  C24  0.020
 490  plan-4  C26  0.020
 490  plan-4  C25  0.020
 490  plan-4  C23  0.020
 490  plan-4  C29  0.020
 490  plan-4  C18  0.020
 490  plan-4  C27  0.020
 490  plan-4  N28  0.020
 490  plan-4  N30  0.020
 490  plan-4  H8   0.020
 490  plan-4  H9   0.020
 490  plan-4  H11  0.020
 490  plan-4  H12  0.020
 490  plan-4  C31  0.020

