# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 21:55:46 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 1-[(5-chloro-1H-imidazo[4,5-b]pyridin-2-yl)methyl]-4-[(2-chloro-4-methoxyphenyl)methyl]-3-ethyl-1,3-dihydro-2H-imidazol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1C(=O)N(Cc2[nH]c3ccc(Cl)nc3n2)C=C1Cc4ccc(OC)cc4Cl
#
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
 96S  96S  1-[(5-chloro-1H-imidazo[4,5-b]pyridin-2-yl)methyl]-4-[(2-chloro-4-methoxyphenyl)methyl]-3-ethyl-1,3-dihydro-2H-imidazol-2-one  ligand  48  29  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_96S
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
 96S  CL   CL  CL    0  -0.118  -1.2222  -1.1701  -1.9335
 96S  C19  C   CR5   0   0.699  -0.4381   2.7760   0.9285
 96S  N    N   NR5   0  -0.554  -1.6454   2.1331   0.8705
 96S  C1   C   CH2   0  -0.329  -2.5338   2.0508   2.0106
 96S  C    C   CH3   0  -0.663  -3.5695   3.1633   2.0358
 96S  N1   N   NR5   0  -0.500   0.0289   2.7748  -0.3588
 96S  C12  C   CH2   0  -0.440   1.3570   3.1896  -0.7301
 96S  C13  C   CR5   0   0.463   2.3060   2.0351  -0.7004
 96S  N4   N   NR15  0  -0.686   2.5619   1.2899  -1.8046
 96S  C18  C   CR56  0   0.270   3.4045   0.2863  -1.4258
 96S  C17  C   CR16  0  -0.195   4.0200  -0.7728  -2.0711
 96S  C16  C   CR16  0  -0.279   4.8254  -1.5741  -1.2821
 96S  C15  C   CR6   0   0.124   4.9607  -1.2674   0.0773
 96S  CL1  CL  CL    0  -0.117   5.9809  -2.2949   1.0421
 96S  N3   N   N     0  -0.407   4.3873  -0.2731   0.7010
 96S  C14  C   CR56  0   0.273   3.6115   0.5001  -0.0524
 96S  N2   N   N     0  -0.449   2.9162   1.5949   0.3689
 96S  C11  C   CR15  0  -0.151  -0.8748   2.1297  -1.1881
 96S  C2   C   CR5   0   0.342  -1.9193   1.7419  -0.4391
 96S  C4   C   CR6   0   0.211  -3.2845  -0.3879  -0.3461
 96S  C10  C   CR6   0  -0.091  -2.4556  -1.4379  -0.7431
 96S  C9   C   CR16  0  -0.292  -2.5895  -2.7191  -0.2441
 96S  C7   C   CR6   0   0.372  -3.5903  -3.0004   0.6868
 96S  O    O   O2    0  -0.468  -3.6456  -4.2679   1.1262
 96S  C8   C   CH3   0  -0.438  -4.6520  -4.6168   2.0579
 96S  C6   C   CR16  0  -0.365  -4.4510  -1.9829   1.0870
 96S  C5   C   CR16  0  -0.330  -4.2838  -0.7081   0.5647
 96S  H1   H   HCH2  0   0.260  -3.0152   1.0741   2.0065
 96S  H2   H   HCH2  0   0.266  -1.9172   2.0860   2.9073
 96S  H3   H   HCH3  0   0.237  -3.0926   4.1429   2.0663
 96S  H4   H   HCH3  0   0.230  -4.2180   3.1284   1.1604
 96S  H5   H   HCH3  0   0.241  -4.1991   3.0661   2.9201
 96S  H6   H   HCH2  0   0.306   1.3266   3.6370  -1.7242
 96S  H7   H   HCH2  0   0.305   1.6980   3.9557  -0.0361
 96S  H8   H   HNR5  0   0.431   2.2115   1.4615  -2.7347
 96S  H9   H   HCR6  0   0.295   3.8894  -0.9744  -3.1255
 96S  H10  H   HCR6  0   0.294   5.3422  -2.4227  -1.7052
 96S  H12  H   HCR5  0   0.298  -0.6992   2.0017  -2.2425
 96S  H13  H   HCH2  0   0.283  -4.0428   1.5815  -0.5773
 96S  H14  H   HCH2  0   0.288  -3.1533   1.0146  -1.9641
 96S  H15  H   HCR6  0   0.285  -1.9272  -3.5093  -0.5732
 96S  H16  H   HCH3  0   0.231  -4.5610  -4.0494   2.9875
 96S  H17  H   HCH3  0   0.231  -5.6545  -4.4681   1.6485
 96S  H18  H   HCH3  0   0.262  -4.5157  -5.6727   2.2772
 96S  H19  H   HCR6  0   0.286  -5.2494  -2.1566   1.7949
 96S  H20  H   HCR6  0   0.270  -4.9675   0.0714   0.8802
 96S  C3   C   CH2   0  -0.641  -3.1518   1.0210  -0.8719
 96S  O1   O   O     0  -0.539   0.1066   3.2586   1.9145

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
 96S  C    C1   single    1.520  0.020  1.520
 96S  C3   C4   single    1.510  0.020  1.510
 96S  C3   C2   single    1.492  0.020  1.492
 96S  CL   C10  single    1.735  0.020  1.735
 96S  C10  C4   aromatic  1.395  0.020  1.395
 96S  C10  C9   aromatic  1.381  0.020  1.381
 96S  C4   C5   aromatic  1.389  0.020  1.389
 96S  C9   C7   aromatic  1.395  0.020  1.395
 96S  C5   C6   aromatic  1.388  0.020  1.388
 96S  C1   N    single    1.448  0.020  1.448
 96S  C7   C6   aromatic  1.391  0.020  1.391
 96S  C7   O    single    1.343  0.020  1.343
 96S  O    C8   single    1.415  0.020  1.415
 96S  C2   N    single    1.394  0.020  1.394
 96S  C2   C11  double    1.343  0.020  1.343
 96S  N    C19  single    1.369  0.020  1.369
 96S  C11  N1   single    1.386  0.020  1.386
 96S  C19  O1   double    1.225  0.020  1.225
 96S  C19  N1   single    1.369  0.020  1.369
 96S  N1   C12  single    1.440  0.020  1.440
 96S  C12  C13  single    1.495  0.020  1.495
 96S  C13  N4   aromatic  1.357  0.020  1.357
 96S  C13  N2   aromatic  1.307  0.020  1.307
 96S  N4   C18  aromatic  1.364  0.020  1.364
 96S  N2   C14  aromatic  1.364  0.020  1.364
 96S  C18  C14  aromatic  1.405  0.020  1.405
 96S  C18  C17  aromatic  1.384  0.020  1.384
 96S  C14  N3   aromatic  1.329  0.020  1.329
 96S  C17  C16  aromatic  1.383  0.020  1.383
 96S  N3   C15  aromatic  1.306  0.020  1.306
 96S  C16  C15  aromatic  1.400  0.020  1.400
 96S  C15  CL1  single    1.740  0.020  1.740
 96S  C1   H1   single    0.970  0.020  1.090
 96S  C1   H2   single    0.970  0.020  1.090
 96S  C    H3   single    0.970  0.020  1.090
 96S  C    H4   single    0.970  0.020  1.090
 96S  C    H5   single    0.970  0.020  1.090
 96S  C12  H6   single    0.970  0.020  1.090
 96S  C12  H7   single    0.970  0.020  1.090
 96S  N4   H8   single    0.860  0.020  1.020
 96S  C17  H9   single    0.930  0.020  1.080
 96S  C16  H10  single    0.930  0.020  1.080
 96S  C11  H12  single    0.930  0.020  1.080
 96S  C3   H13  single    0.970  0.020  1.090
 96S  C3   H14  single    0.970  0.020  1.090
 96S  C9   H15  single    0.930  0.020  1.080
 96S  C8   H16  single    0.970  0.020  1.090
 96S  C8   H17  single    0.970  0.020  1.090
 96S  C8   H18  single    0.970  0.020  1.090
 96S  C6   H19  single    0.930  0.020  1.080
 96S  C5   H20  single    0.930  0.020  1.080

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
 96S  N1   C19  N    105.10  3.000
 96S  N1   C19  O1   127.24  3.000
 96S  N    C19  O1   127.66  3.000
 96S  C2   N    C1   127.11  3.000
 96S  C2   N    C19  110.17  3.000
 96S  C1   N    C19  122.31  3.000
 96S  H2   C1   H1   106.41  3.000
 96S  H2   C1   C    110.39  3.000
 96S  H1   C1   C    110.81  3.000
 96S  H2   C1   N    107.41  3.000
 96S  H1   C1   N    108.62  3.000
 96S  C    C1   N    112.92  3.000
 96S  H5   C    H4   107.76  3.000
 96S  H5   C    H3   108.07  3.000
 96S  H4   C    H3   108.15  3.000
 96S  H5   C    C1   109.98  3.000
 96S  H4   C    C1   111.63  3.000
 96S  H3   C    C1   111.11  3.000
 96S  C11  N1   C12  125.53  3.000
 96S  C12  N1   C19  123.82  3.000
 96S  C11  N1   C19  109.91  3.000
 96S  H7   C12  H6   107.53  3.000
 96S  H7   C12  C13  109.39  3.000
 96S  H6   C12  C13  110.65  3.000
 96S  H7   C12  N1   109.10  3.000
 96S  H6   C12  N1   109.12  3.000
 96S  C13  C12  N1   110.97  3.000
 96S  N2   C13  N4   113.12  3.000
 96S  N2   C13  C12  124.93  3.000
 96S  N4   C13  C12  121.86  3.000
 96S  H8   N4   C18  126.57  3.000
 96S  H8   N4   C13  126.28  3.000
 96S  C18  N4   C13  107.14  3.000
 96S  C14  C18  C17  120.43  3.000
 96S  C17  C18  N4   135.07  3.000
 96S  C14  C18  N4   104.50  3.000
 96S  H9   C17  C16  121.23  3.000
 96S  H9   C17  C18  122.91  3.000
 96S  C16  C17  C18  115.86  3.000
 96S  H10  C16  C15  120.42  3.000
 96S  H10  C16  C17  120.69  3.000
 96S  C15  C16  C17  118.89  3.000
 96S  N3   C15  CL1  116.24  3.000
 96S  CL1  C15  C16  117.75  3.000
 96S  N3   C15  C16  126.01  3.000
 96S  C14  N3   C15  115.35  3.000
 96S  N2   C14  N3   126.11  3.000
 96S  N3   C14  C18  123.46  3.000
 96S  N2   C14  C18  110.42  3.000
 96S  C14  N2   C13  104.81  3.000
 96S  H12  C11  C2   129.71  3.000
 96S  H12  C11  N1   122.35  3.000
 96S  C2   C11  N1   107.94  3.000
 96S  C3   C2   C11  128.35  3.000
 96S  C11  C2   N    106.87  3.000
 96S  C3   C2   N    124.78  3.000
 96S  C5   C4   C10  116.12  3.000
 96S  C5   C4   C3   120.44  3.000
 96S  C10  C4   C3   123.43  3.000
 96S  C9   C10  C4   122.52  3.000
 96S  C9   C10  CL   117.38  3.000
 96S  C4   C10  CL   120.09  3.000
 96S  H15  C9   C7   119.64  3.000
 96S  H15  C9   C10  120.53  3.000
 96S  C7   C9   C10  119.83  3.000
 96S  C6   C7   O    124.80  3.000
 96S  O    C7   C9   115.99  3.000
 96S  C6   C7   C9   119.21  3.000
 96S  C8   O    C7   118.53  3.000
 96S  H18  C8   H17  108.83  3.000
 96S  H18  C8   H16  108.80  3.000
 96S  H17  C8   H16  108.92  3.000
 96S  H18  C8   O    106.46  3.000
 96S  H17  C8   O    111.84  3.000
 96S  H16  C8   O    111.89  3.000
 96S  H19  C6   C5   118.89  3.000
 96S  H19  C6   C7   121.84  3.000
 96S  C5   C6   C7   119.27  3.000
 96S  H20  C5   C6   118.37  3.000
 96S  H20  C5   C4   118.61  3.000
 96S  C6   C5   C4   123.03  3.000
 96S  H14  C3   H13  105.75  3.000
 96S  H14  C3   C4   110.04  3.000
 96S  H13  C3   C4   108.24  3.000
 96S  H14  C3   C2   107.10  3.000
 96S  H13  C3   C2   110.33  3.000
 96S  C4   C3   C2   114.99  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
 96S  CONST_01  C14  C18  N4   C13    0.00   0.0  0
 96S  CONST_02  C17  C18  N4   C13  180.00   0.0  0
 96S  CONST_03  C18  C14  N2   C13    0.00   0.0  0
 96S  CONST_04  N3   C14  N2   C13  180.00   0.0  0
 96S  CONST_05  C14  N2   C13  N4     0.00   0.0  0
 96S  CONST_06  N2   C14  C18  N4     0.00   0.0  0
 96S  CONST_07  N3   C14  C18  N4   180.00   0.0  0
 96S  CONST_08  C16  C17  C18  N4   180.00   0.0  0
 96S  CONST_09  N2   C13  N4   C18    0.00   0.0  0
 96S  CONST_10  C15  N3   C14  C18    0.00   0.0  0
 96S  CONST_11  C15  C16  C17  C18    0.00   0.0  0
 96S  CONST_12  N2   C14  C18  C17  180.00   0.0  0
 96S  CONST_13  N3   C14  C18  C17    0.00   0.0  0
 96S  CONST_14  N3   C15  C16  C17    0.00   0.0  0
 96S  CONST_15  C14  C18  C17  C16    0.00   0.0  0
 96S  CONST_16  C14  N3   C15  C16    0.00   0.0  0
 96S  CONST_17  N2   C14  N3   C15  180.00   0.0  0
 96S  CONST_18  C7   C9   C10  C4     0.00   0.0  0
 96S  CONST_19  C7   C6   C5   C4     0.00   0.0  0
 96S  CONST_20  C6   C5   C4   C10    0.00   0.0  0
 96S  CONST_21  C6   C7   C9   C10    0.00   0.0  0
 96S  CONST_22  C5   C4   C10  C9     0.00   0.0  0
 96S  CONST_23  C5   C6   C7   C9     0.00   0.0  0
 96S  CONST_24  C11  C2   N    C19    0.00   0.0  0
 96S  CONST_25  C2   C11  N1   C19    0.00   0.0  0
 96S  CONST_26  N1   C11  C2   N      0.00   0.0  0
 96S  CONST_27  C11  N1   C19  N      0.00   0.0  0
 96S  CONST_28  C2   N    C19  N1     0.00   0.0  0
 96S  CONST_29  C5   C4   C10  CL   180.00   0.0  0
 96S  CONST_30  C7   C9   C10  CL   180.00   0.0  0
 96S  CONST_31  C18  N4   C13  C12  180.00   0.0  0
 96S  CONST_32  C14  N2   C13  C12  180.00   0.0  0
 96S  CONST_33  CL1  C15  C16  C17  180.00   0.0  0
 96S  CONST_34  C14  N3   C15  CL1  180.00   0.0  0
 96S  CONST_35  C9   C10  C4   C3   180.00   0.0  0
 96S  CONST_36  C6   C5   C4   C3   180.00   0.0  0
 96S  CONST_37  O    C7   C9   C10  180.00   0.0  0
 96S  CONST_38  C5   C6   C7   O    180.00   0.0  0
 96S  CONST_39  C2   N    C19  O1   180.00   0.0  0
 96S  CONST_40  C11  N1   C19  O1   180.00   0.0  0
 96S  CONST_41  C12  N1   C19  N    180.00   0.0  0
 96S  CONST_42  C11  C2   N    C1   180.00   0.0  0
 96S  CONST_43  N1   C19  N    C1   180.00   0.0  0
 96S  CONST_44  C2   C11  N1   C12  180.00   0.0  0
 96S  CONST_45  H9   C17  C18  N4     0.00   0.0  0
 96S  CONST_46  H10  C16  C17  C18  180.00   0.0  0
 96S  CONST_47  H8   N4   C18  C17    0.00   0.0  0
 96S  CONST_48  H15  C9   C10  C4   180.00   0.0  0
 96S  CONST_49  H19  C6   C5   C4   180.00   0.0  0
 96S  CONST_50  H20  C5   C4   C10  180.00   0.0  0
 96S  CONST_51  C1   N    C19  O1     0.00   0.0  0
 96S  CONST_52  C12  N1   C19  O1     0.00   0.0  0
 96S  Var_01    C13  C12  N1   C19   89.95  30.0  3
 96S  Var_02    C4   C3   C2   N    -67.15  30.0  1
 96S  Var_03    N4   C13  C12  N1    92.65  30.0  2
 96S  Var_04    C10  C4   C3   C2   -68.49  30.0  2
 96S  Var_05    C    C1   N    C19   93.55  30.0  1
 96S  Var_06    C6   C7   O    C8     0.47  30.0  3
 96S  Var_07    H3   C    C1   N    -59.37  30.0  3
 96S  Var_08    H16  C8   O    C7   -61.16  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
 96S  plan-1  C19  0.020
 96S  plan-1  N    0.020
 96S  plan-1  C1   0.020
 96S  plan-1  N1   0.020
 96S  plan-1  C12  0.020
 96S  plan-1  C11  0.020
 96S  plan-1  C2   0.020
 96S  plan-1  H12  0.020
 96S  plan-1  C3   0.020
 96S  plan-1  O1   0.020
 96S  plan-2  CL   0.020
 96S  plan-2  C4   0.020
 96S  plan-2  C10  0.020
 96S  plan-2  C9   0.020
 96S  plan-2  C7   0.020
 96S  plan-2  O    0.020
 96S  plan-2  C6   0.020
 96S  plan-2  C5   0.020
 96S  plan-2  H15  0.020
 96S  plan-2  H19  0.020
 96S  plan-2  H20  0.020
 96S  plan-2  C3   0.020
 96S  plan-3  C12  0.020
 96S  plan-3  C13  0.020
 96S  plan-3  N4   0.020
 96S  plan-3  C18  0.020
 96S  plan-3  C17  0.020
 96S  plan-3  C16  0.020
 96S  plan-3  C15  0.020
 96S  plan-3  CL1  0.020
 96S  plan-3  N3   0.020
 96S  plan-3  C14  0.020
 96S  plan-3  N2   0.020
 96S  plan-3  H8   0.020
 96S  plan-3  H9   0.020
 96S  plan-3  H10  0.020

