# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 07:55:55 2022
#   Inital geometry file: a 150 line input string
#   Ligand name: 5-(3-{3-chloro-5-[(5-methyl-1,3-thiazol-4-yl)methoxy]phenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl)pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1scnc1COc2cc(Cl)cc(c2)C3=CC(=CN(C3=O)c4cccnc4)C5=CNC(=O)NC5=O
#
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
 06I  06I  5-(3-{3-chloro-5-[(5-methyl-1,3-thiazol-4-yl)methoxy]phenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl)pyrimidine-2,4(1H,3H)-dione  ligand  54  36  .  2022-03-08  2022-03-08
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_06I
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
 06I  C1   C   CR6   0   0.541  -14.0324  -26.6428   1.1653
 06I  C2   C   CR6   0  -0.167  -14.7894  -27.4702   0.2478
 06I  N3   N   NR16  0  -0.674  -12.1857  -32.0438  -1.9325
 06I  N4   N   NR6   0  -0.622  -12.8077  -27.1882   1.5599
 06I  C5   C   CR6   0  -0.005  -18.4334  -27.4871  -0.6018
 06I  C6   C   CR16  0  -0.322  -18.6566  -26.1980  -1.0371
 06I  C7   C   CR6   0   0.412  -17.5875  -25.2993  -1.0474
 06I  C8   C   CH2   0  -0.297  -16.8925  -23.0401  -1.3500
 06I  C9   C   CR5   0   0.309  -17.5487  -21.7372  -1.6590
 06I  C10  C   CR5   0  -0.241  -18.4081  -21.0907  -0.8181
 06I  C11  C   CH3   0  -0.718  -18.8805  -21.4942   0.5351
 06I  C12  C   CR15  0  -0.234  -17.9894  -20.0250  -2.9573
 06I  C14  C   CR16  0  -0.200  -14.2959  -28.6764  -0.1524
 06I  C15  C   CR6   0  -0.017  -13.0398  -29.1711   0.2796
 06I  C17  C   CR6   0   0.560  -11.9711  -31.4208   0.7607
 06I  C18  C   CR16  0   0.067  -12.6019  -30.8322  -1.4848
 06I  C19  C   CR6   0   0.682  -11.6475  -33.0050  -1.1178
 06I  C20  C   CR16  0   0.026  -12.3314  -28.3874   1.1360
 06I  C22  C   CR16  0  -0.138  -11.3794  -25.2880   2.1528
 06I  C23  C   CR16  0  -0.332  -10.6403  -24.6389   3.1260
 06I  C24  C   CR16  0  -0.055  -10.5939  -25.1841   4.4021
 06I  C13  C   CR16  0  -0.415  -16.3258  -25.7070  -0.6311
 06I  C16  C   CR6   0  -0.244  -12.5288  -30.4658  -0.1878
 06I  C21  C   CR6   0   0.189  -12.0394  -26.4524   2.5092
 06I  C25  C   CR16  0  -0.059  -11.9373  -26.9197   3.8101
 06I  C3   C   CR6   0   0.122  -16.1250  -27.0150  -0.1852
 06I  C4   C   CR16  0  -0.301  -17.1875  -27.9133  -0.1660
 06I  N1   N   N     0  -0.365  -17.3222  -21.1260  -2.8611
 06I  N2   N   NR16  0  -0.719  -11.5727  -32.6219   0.1976
 06I  N5   N   N     0  -0.396  -11.2243  -26.3011   4.7410
 06I  O1   O   O     0  -0.463  -14.3888  -25.5640   1.6137
 06I  O3   O   O     0  -0.436  -11.8476  -31.2347   1.9555
 06I  O4   O   O     0  -0.462  -11.2733  -34.0852  -1.5179
 06I  S1   S   S2    0   0.228  -18.9530  -19.6518  -1.5848
 06I  CL1  CL  CL    0  -0.125  -19.7598  -28.6033  -0.5746
 06I  H2   H   HCR6  0   0.284  -19.6381  -25.8758  -1.3593
 06I  H4   H   HCH2  0   0.258  -16.0661  -23.2125  -2.0456
 06I  H3   H   HCH2  0   0.250  -16.4831  -23.0340  -0.3346
 06I  H7   H   HCH3  0   0.261  -18.8736  -20.6549   1.2293
 06I  H5   H   HCH3  0   0.264  -19.8986  -21.8841   0.4984
 06I  H6   H   HCH3  0   0.259  -18.2441  -22.2743   0.9500
 06I  H8   H   HCR5  0   0.297  -17.9625  -19.3707  -3.8176
 06I  H10  H   HCR6  0   0.279  -14.8857  -29.2864  -0.8275
 06I  H12  H   HCR6  0   0.323  -12.9954  -30.1746  -2.2479
 06I  H13  H   HCR6  0   0.316  -11.3553  -28.6580   1.5108
 06I  H14  H   HCR6  0   0.287  -11.4356  -24.9054   1.1422
 06I  H15  H   HCR6  0   0.281  -10.1031  -23.7280   2.9016
 06I  H16  H   HCR6  0   0.273  -10.0207  -24.6955   5.1817
 06I  H9   H   HCR6  0   0.284  -15.4871  -25.0281  -0.6590
 06I  H17  H   HCR6  0   0.281  -12.4522  -27.8300   4.1015
 06I  H1   H   HCR6  0   0.276  -17.0527  -28.9220   0.2004
 06I  H11  H   HNR6  0   0.427  -11.1833  -33.3086   0.8325
 06I  H19  H   HNR6  0   0.439  -12.2614  -32.2613  -2.9159
 06I  O2   O   O2    0  -0.469  -17.8797  -24.0579  -1.4744

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
 06I  C12  N1   aromatic  1.291  0.020  1.291
 06I  C12  S1   aromatic  1.718  0.020  1.718
 06I  N1   C9   aromatic  1.367  0.020  1.367
 06I  S1   C10  aromatic  1.719  0.020  1.719
 06I  N3   C18  single    1.357  0.020  1.357
 06I  N3   C19  single    1.370  0.020  1.370
 06I  O4   C19  double    1.211  0.020  1.211
 06I  C18  C16  double    1.350  0.020  1.350
 06I  C9   C10  aromatic  1.365  0.020  1.365
 06I  C9   C8   single    1.491  0.020  1.491
 06I  O2   C7   single    1.345  0.020  1.345
 06I  O2   C8   single    1.423  0.020  1.423
 06I  C19  N2   single    1.372  0.020  1.372
 06I  C10  C11  single    1.489  0.020  1.489
 06I  C6   C7   aromatic  1.397  0.020  1.397
 06I  C6   C5   aromatic  1.379  0.020  1.379
 06I  C7   C13  aromatic  1.390  0.020  1.390
 06I  CL1  C5   single    1.734  0.020  1.734
 06I  C5   C4   aromatic  1.387  0.020  1.387
 06I  C13  C3   aromatic  1.396  0.020  1.396
 06I  C16  C15  single    1.468  0.020  1.468
 06I  C16  C17  single    1.457  0.020  1.457
 06I  C4   C3   aromatic  1.391  0.020  1.391
 06I  C3   C2   single    1.476  0.020  1.476
 06I  C14  C15  single    1.417  0.020  1.417
 06I  C14  C2   double    1.363  0.020  1.363
 06I  N2   C17  single    1.385  0.020  1.385
 06I  C15  C20  double    1.360  0.020  1.360
 06I  C2   C1   single    1.449  0.020  1.449
 06I  C17  O3   double    1.215  0.020  1.215
 06I  C20  N4   single    1.358  0.020  1.358
 06I  C1   N4   single    1.397  0.020  1.397
 06I  C1   O1   double    1.221  0.020  1.221
 06I  N4   C21  single    1.426  0.020  1.426
 06I  C22  C21  aromatic  1.385  0.020  1.385
 06I  C22  C23  aromatic  1.384  0.020  1.384
 06I  C21  C25  aromatic  1.386  0.020  1.386
 06I  C23  C24  aromatic  1.388  0.020  1.388
 06I  C25  N5   aromatic  1.326  0.020  1.326
 06I  C24  N5   aromatic  1.327  0.020  1.327
 06I  C6   H2   single    0.930  0.020  1.080
 06I  C8   H4   single    0.970  0.020  1.090
 06I  C8   H3   single    0.970  0.020  1.090
 06I  C11  H7   single    0.970  0.020  1.090
 06I  C11  H5   single    0.970  0.020  1.090
 06I  C11  H6   single    0.970  0.020  1.090
 06I  C12  H8   single    0.930  0.020  1.080
 06I  C14  H10  single    0.930  0.020  1.080
 06I  C18  H12  single    0.930  0.020  1.080
 06I  C20  H13  single    0.930  0.020  1.080
 06I  C22  H14  single    0.930  0.020  1.080
 06I  C23  H15  single    0.930  0.020  1.080
 06I  C24  H16  single    0.930  0.020  1.080
 06I  C13  H9   single    0.930  0.020  1.080
 06I  C25  H17  single    0.930  0.020  1.080
 06I  C4   H1   single    0.930  0.020  1.080
 06I  N2   H11  single    0.860  0.020  1.020
 06I  N3   H19  single    0.860  0.020  1.020

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
 06I  O1   C1   N4   119.79  3.000
 06I  O1   C1   C2   125.76  3.000
 06I  N4   C1   C2   114.44  3.000
 06I  C3   C2   C14  120.95  3.000
 06I  C14  C2   C1   120.13  3.000
 06I  C3   C2   C1   118.84  3.000
 06I  H19  N3   C19  117.20  3.000
 06I  H19  N3   C18  119.38  3.000
 06I  C19  N3   C18  123.42  3.000
 06I  C21  N4   C20  118.33  3.000
 06I  C21  N4   C1   117.31  3.000
 06I  C20  N4   C1   124.32  3.000
 06I  CL1  C5   C4   118.98  3.000
 06I  C4   C5   C6   122.13  3.000
 06I  CL1  C5   C6   118.88  3.000
 06I  H2   C6   C7   120.04  3.000
 06I  H2   C6   C5   121.28  3.000
 06I  C7   C6   C5   118.68  3.000
 06I  O2   C7   C13  124.27  3.000
 06I  C13  C7   C6   120.27  3.000
 06I  O2   C7   C6   115.46  3.000
 06I  H3   C8   H4   107.95  3.000
 06I  H3   C8   O2   110.14  3.000
 06I  H4   C8   O2   110.84  3.000
 06I  H3   C8   C9   110.60  3.000
 06I  H4   C8   C9   109.78  3.000
 06I  O2   C8   C9   107.54  3.000
 06I  N1   C9   C10  115.73  3.000
 06I  C10  C9   C8   124.28  3.000
 06I  N1   C9   C8   119.98  3.000
 06I  S1   C10  C11  122.11  3.000
 06I  C11  C10  C9   129.14  3.000
 06I  S1   C10  C9   108.74  3.000
 06I  H6   C11  H5   107.59  3.000
 06I  H6   C11  H7   107.78  3.000
 06I  H5   C11  H7   107.62  3.000
 06I  H6   C11  C10  110.80  3.000
 06I  H5   C11  C10  111.26  3.000
 06I  H7   C11  C10  111.61  3.000
 06I  H8   C12  S1   121.21  3.000
 06I  H8   C12  N1   124.23  3.000
 06I  S1   C12  N1   114.56  3.000
 06I  H10  C14  C15  118.38  3.000
 06I  H10  C14  C2   118.92  3.000
 06I  C15  C14  C2   122.69  3.000
 06I  C16  C15  C20  121.82  3.000
 06I  C20  C15  C14  116.90  3.000
 06I  C16  C15  C14  121.28  3.000
 06I  O3   C17  N2   120.22  3.000
 06I  O3   C17  C16  125.34  3.000
 06I  N2   C17  C16  114.45  3.000
 06I  H12  C18  C16  122.18  3.000
 06I  H12  C18  N3   114.95  3.000
 06I  C16  C18  N3   122.87  3.000
 06I  O4   C19  N2   123.29  3.000
 06I  N2   C19  N3   113.30  3.000
 06I  O4   C19  N3   123.41  3.000
 06I  H13  C20  C15  123.01  3.000
 06I  H13  C20  N4   115.46  3.000
 06I  C15  C20  N4   121.51  3.000
 06I  H14  C22  C21  120.85  3.000
 06I  H14  C22  C23  121.25  3.000
 06I  C21  C22  C23  117.90  3.000
 06I  H15  C23  C24  120.33  3.000
 06I  H15  C23  C22  120.98  3.000
 06I  C24  C23  C22  118.69  3.000
 06I  H16  C24  N5   116.55  3.000
 06I  H16  C24  C23  120.11  3.000
 06I  N5   C24  C23  123.33  3.000
 06I  H9   C13  C3   119.06  3.000
 06I  H9   C13  C7   120.87  3.000
 06I  C3   C13  C7   120.06  3.000
 06I  C18  C16  C17  117.92  3.000
 06I  C17  C16  C15  120.27  3.000
 06I  C18  C16  C15  121.76  3.000
 06I  C25  C21  C22  119.33  3.000
 06I  C25  C21  N4   119.38  3.000
 06I  C22  C21  N4   121.29  3.000
 06I  H17  C25  N5   117.24  3.000
 06I  H17  C25  C21  119.98  3.000
 06I  N5   C25  C21  122.78  3.000
 06I  C4   C3   C13  119.96  3.000
 06I  C4   C3   C2   119.20  3.000
 06I  C13  C3   C2   120.84  3.000
 06I  H1   C4   C3   120.77  3.000
 06I  H1   C4   C5   120.33  3.000
 06I  C3   C4   C5   118.89  3.000
 06I  C12  N1   C9   111.17  3.000
 06I  H11  N2   C19  115.63  3.000
 06I  H11  N2   C17  116.33  3.000
 06I  C19  N2   C17  128.04  3.000
 06I  C25  N5   C24  117.97  3.000
 06I  C12  S1   C10   89.81  3.000
 06I  C8   O2   C7   118.79  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
 06I  CONST_01  C13  C7   C6   C5      0.00   0.0  0
 06I  CONST_02  C13  C3   C4   C5      0.00   0.0  0
 06I  CONST_03  C3   C13  C7   C6      0.00   0.0  0
 06I  CONST_04  C3   C4   C5   C6      0.00   0.0  0
 06I  CONST_05  C4   C5   C6   C7      0.00   0.0  0
 06I  CONST_06  C4   C3   C13  C7      0.00   0.0  0
 06I  CONST_07  S1   C12  N1   C9      0.00   0.0  0
 06I  CONST_08  C12  S1   C10  C9      0.00   0.0  0
 06I  CONST_09  N1   C12  S1   C10     0.00   0.0  0
 06I  CONST_10  C12  N1   C9   C10     0.00   0.0  0
 06I  CONST_11  N5   C25  C21  C22     0.00   0.0  0
 06I  CONST_12  N5   C24  C23  C22     0.00   0.0  0
 06I  CONST_13  C25  C21  C22  C23     0.00   0.0  0
 06I  CONST_14  C25  N5   C24  C23     0.00   0.0  0
 06I  CONST_15  C21  C22  C23  C24     0.00   0.0  0
 06I  CONST_16  C21  C25  N5   C24     0.00   0.0  0
 06I  CONST_17  S1   C10  C9   N1      0.00   0.0  0
 06I  CONST_18  C7   C13  C3   C2    180.00   0.0  0
 06I  CONST_19  C5   C4   C3   C2    180.00   0.0  0
 06I  CONST_20  C23  C22  C21  N4    180.00   0.0  0
 06I  CONST_21  N5   C25  C21  N4    180.00   0.0  0
 06I  CONST_22  C20  N4   C1   C2      0.00   0.0  0
 06I  CONST_23  C21  N4   C1   C2    180.00   0.0  0
 06I  CONST_24  C17  N2   C19  N3      0.00   0.0  0
 06I  CONST_25  N2   C19  N3   C18     0.00   0.0  0
 06I  CONST_26  C16  C17  N2   C19     0.00   0.0  0
 06I  CONST_27  O2   C7   C6   C5    180.00   0.0  0
 06I  CONST_28  CL1  C5   C6   C7    180.00   0.0  0
 06I  CONST_29  C12  N1   C9   C8    180.00   0.0  0
 06I  CONST_30  S1   C10  C9   C8    180.00   0.0  0
 06I  CONST_31  C12  S1   C10  C11   180.00   0.0  0
 06I  CONST_32  N1   C9   C10  C11   180.00   0.0  0
 06I  CONST_33  O2   C7   C13  C3    180.00   0.0  0
 06I  CONST_34  CL1  C5   C4   C3    180.00   0.0  0
 06I  CONST_35  O4   C19  N2   C17   180.00   0.0  0
 06I  CONST_36  O4   C19  N3   C18   180.00   0.0  0
 06I  CONST_37  O3   C17  N2   C19   180.00   0.0  0
 06I  CONST_38  O1   C1   N4   C20   180.00   0.0  0
 06I  CONST_39  O1   C1   N4   C21     0.00   0.0  0
 06I  CONST_40  H9   C13  C3   C2      0.00   0.0  0
 06I  CONST_41  H1   C4   C3   C2      0.00   0.0  0
 06I  CONST_42  H14  C22  C21  N4      0.00   0.0  0
 06I  CONST_43  H17  C25  C21  N4      0.00   0.0  0
 06I  CONST_44  H8   C12  N1   C9    180.00   0.0  0
 06I  CONST_45  H16  C24  C23  C22   180.00   0.0  0
 06I  CONST_46  H2   C6   C7   C13   180.00   0.0  0
 06I  CONST_47  H15  C23  C22  C21   180.00   0.0  0
 06I  CONST_48  H11  N2   C19  N3    180.00   0.0  0
 06I  CONST_49  H19  N3   C19  N2    180.00   0.0  0
 06I  Var_01    C13  C3   C2   C1     47.84  30.0  3
 06I  Var_02    C22  C21  N4   C1    -73.04  30.0  2
 06I  Var_03    C18  C16  C15  C14    44.37  30.0  3
 06I  Var_04    C9   C8   O2   C7   -169.91  30.0  3
 06I  Var_05    C13  C7   O2   C8     -7.94  30.0  2
 06I  Var_06    O2   C8   C9   C10    74.25  30.0  2
 06I  Var_07    H7   C11  C10  C9    136.26  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
 06I  plan-1  C8   0.020
 06I  plan-1  C9   0.020
 06I  plan-1  C10  0.020
 06I  plan-1  C11  0.020
 06I  plan-1  C12  0.020
 06I  plan-1  N1   0.020
 06I  plan-1  S1   0.020
 06I  plan-1  H8   0.020
 06I  plan-2  N3   0.020
 06I  plan-2  C15  0.020
 06I  plan-2  C17  0.020
 06I  plan-2  C18  0.020
 06I  plan-2  C19  0.020
 06I  plan-2  C16  0.020
 06I  plan-2  N2   0.020
 06I  plan-2  O3   0.020
 06I  plan-2  O4   0.020
 06I  plan-2  H12  0.020
 06I  plan-2  H11  0.020
 06I  plan-2  H19  0.020
 06I  plan-3  C2   0.020
 06I  plan-3  C5   0.020
 06I  plan-3  C6   0.020
 06I  plan-3  C7   0.020
 06I  plan-3  C13  0.020
 06I  plan-3  C3   0.020
 06I  plan-3  C4   0.020
 06I  plan-3  CL1  0.020
 06I  plan-3  H2   0.020
 06I  plan-3  H9   0.020
 06I  plan-3  H1   0.020
 06I  plan-3  O2   0.020
 06I  plan-4  C1   0.020
 06I  plan-4  C2   0.020
 06I  plan-4  N4   0.020
 06I  plan-4  C14  0.020
 06I  plan-4  C15  0.020
 06I  plan-4  C20  0.020
 06I  plan-4  C16  0.020
 06I  plan-4  C21  0.020
 06I  plan-4  C3   0.020
 06I  plan-4  O1   0.020
 06I  plan-4  H10  0.020
 06I  plan-4  H13  0.020
 06I  plan-5  N4   0.020
 06I  plan-5  C22  0.020
 06I  plan-5  C23  0.020
 06I  plan-5  C24  0.020
 06I  plan-5  C21  0.020
 06I  plan-5  C25  0.020
 06I  plan-5  N5   0.020
 06I  plan-5  H14  0.020
 06I  plan-5  H15  0.020
 06I  plan-5  H16  0.020
 06I  plan-5  H17  0.020

