# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 01:23:50 2022
#   Inital geometry file: a 105 line input string
#   Ligand name: 2-{[(2,4-dichlorophenyl)carbonyl]amino}-5-(pyrimidin-2-yloxy)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cc(Oc2ncccn2)ccc1NC(=O)c3ccc(Cl)cc3Cl
#
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
 PLB  PLB  '2-{[(2,4-dichlorophenyl)carbonyl]amino}-5-(pyrimidin-2-yloxy)benzoic acid'  ligand  37  27  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PLB
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
 PLB  CL20  CL  CL     0  -0.105   1.4475   0.4899   7.2392
 PLB  C16   C   CR6    0  -0.052   0.7863   0.3568   5.6494
 PLB  C15   C   CR16   0  -0.150  -0.4176  -0.3070   5.4766
 PLB  C14   C   CR6    0  -0.093  -0.9512  -0.4037   4.2013
 PLB  CL19  CL  CL     0  -0.103  -2.4329  -1.2741   4.0232
 PLB  C17   C   CR16   0  -0.190   1.4657   0.9060   4.5752
 PLB  C18   C   CR16   0  -0.296   0.9189   0.7811   3.3094
 PLB  C13   C   CR6    0   0.036  -0.2956   0.1336   3.0962
 PLB  C11   C   C      0   0.499  -0.8858   0.0927   1.7167
 PLB  O12   O   O      0  -0.458  -2.0418   0.4270   1.5194
 PLB  N10   N   NH1    0  -0.764  -0.0047  -0.3182   0.7877
 PLB  C2    C   CR6    0   0.352  -0.1482  -0.4118  -0.5942
 PLB  C3    C   CR16   0  -0.324  -1.3409  -0.1313  -1.2682
 PLB  C4    C   CR16   0  -0.299  -1.4160  -0.2517  -2.6447
 PLB  C5    C   CR6    0   0.366  -0.3020  -0.6517  -3.3595
 PLB  C6    C   CR16   0  -0.351   0.8831  -0.9284  -2.7107
 PLB  C1    C   CR6    0  -0.223   0.9854  -0.8215  -1.3281
 PLB  C7    C   C      0   0.479   2.3309  -1.1588  -0.6886
 PLB  O9    O   O      0  -0.600   2.4022  -1.1100   0.5694
 PLB  O8    O   OC    -1  -0.552   3.2576  -1.4607  -1.4482
 PLB  O21   O   O2     0  -0.500  -0.3852  -0.8469  -4.7247
 PLB  C22   C   CR6    0   0.579  -0.2926   0.2058  -5.5475
 PLB  N27   N   N      0  -0.441  -0.0872   1.4036  -5.0388
 PLB  C26   C   CR16   0  -0.004  -0.0101   2.4018  -5.9122
 PLB  C25   C   CR16   0  -0.364  -0.1332   2.2042  -7.2749
 PLB  C24   C   CR16   0  -0.017  -0.3414   0.8953  -7.6814
 PLB  N23   N   N      0  -0.426  -0.4238  -0.1118  -6.8245
 PLB  H15   H   HCR6   0   0.306  -0.9329  -0.7455   6.3196
 PLB  H17   H   HCR6   0   0.292   2.4028   1.4254   4.7172
 PLB  H18   H   HCR6   0   0.284   1.4457   1.2163   2.4703
 PLB  H10   H   HNH1   0   0.442   0.9548  -0.6252   1.0593
 PLB  H3    H   HCR6   0   0.285  -2.2175   0.1784  -0.7243
 PLB  H4    H   HCR6   0   0.274  -2.3492  -0.0391  -3.1510
 PLB  H6    H   HCR6   0   0.266   1.7498  -1.2437  -3.2764
 PLB  H26   H   HCR6   0   0.284   0.1581   3.3909  -5.5024
 PLB  H25   H   HCR6   0   0.285  -0.0701   3.0184  -7.9803
 PLB  H24   H   HCR6   0   0.285  -0.4458   0.6472  -8.7313

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
 PLB  CL20  C16   single    1.727  0.020  1.727
 PLB  C16   C15   aromatic  1.386  0.020  1.386
 PLB  C16   C17   aromatic  1.385  0.020  1.385
 PLB  C15   C14   aromatic  1.386  0.020  1.386
 PLB  C15   H15   single    0.930  0.020  1.080
 PLB  C14   CL19  single    1.728  0.020  1.728
 PLB  C14   C13   aromatic  1.393  0.020  1.393
 PLB  C17   C18   aromatic  1.384  0.020  1.384
 PLB  C17   H17   single    0.930  0.020  1.080
 PLB  C18   C13   aromatic  1.393  0.020  1.393
 PLB  C18   H18   single    0.930  0.020  1.080
 PLB  C13   C11   single    1.501  0.020  1.501
 PLB  C11   O12   double    1.219  0.020  1.219
 PLB  C11   N10   single    1.345  0.020  1.345
 PLB  N10   C2    single    1.392  0.020  1.392
 PLB  N10   H10   single    0.860  0.020  1.020
 PLB  C2    C3    aromatic  1.398  0.020  1.398
 PLB  C2    C1    aromatic  1.411  0.020  1.411
 PLB  C3    C4    aromatic  1.384  0.020  1.384
 PLB  C3    H3    single    0.930  0.020  1.080
 PLB  C4    C5    aromatic  1.383  0.020  1.383
 PLB  C4    H4    single    0.930  0.020  1.080
 PLB  C5    C6    aromatic  1.379  0.020  1.379
 PLB  C5    O21   single    1.382  0.020  1.382
 PLB  C6    C1    aromatic  1.391  0.020  1.391
 PLB  C6    H6    single    0.930  0.020  1.080
 PLB  C1    C7    single    1.527  0.020  1.527
 PLB  C7    O9    deloc     1.261  0.020  1.261
 PLB  C7    O8    deloc     1.236  0.020  1.236
 PLB  O21   C22   single    1.339  0.020  1.339
 PLB  C22   N27   aromatic  1.317  0.020  1.317
 PLB  C22   N23   aromatic  1.322  0.020  1.322
 PLB  N27   C26   aromatic  1.329  0.020  1.329
 PLB  C26   C25   aromatic  1.383  0.020  1.383
 PLB  C26   H26   single    0.930  0.020  1.080
 PLB  C25   C24   aromatic  1.386  0.020  1.386
 PLB  C25   H25   single    0.930  0.020  1.080
 PLB  C24   N23   aromatic  1.325  0.020  1.325
 PLB  C24   H24   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
 PLB  C17   C16  C15   121.30  3.000
 PLB  C17   C16  CL20  119.72  3.000
 PLB  C15   C16  CL20  118.98  3.000
 PLB  H15   C15  C14   120.38  3.000
 PLB  H15   C15  C16   120.75  3.000
 PLB  C14   C15  C16   118.87  3.000
 PLB  C13   C14  CL19  121.08  3.000
 PLB  C13   C14  C15   121.47  3.000
 PLB  CL19  C14  C15   117.41  3.000
 PLB  H17   C17  C18   120.39  3.000
 PLB  H17   C17  C16   120.94  3.000
 PLB  C18   C17  C16   118.67  3.000
 PLB  H18   C18  C13   119.52  3.000
 PLB  H18   C18  C17   118.71  3.000
 PLB  C13   C18  C17   121.76  3.000
 PLB  C11   C13  C18   119.75  3.000
 PLB  C11   C13  C14   122.25  3.000
 PLB  C18   C13  C14   117.92  3.000
 PLB  N10   C11  O12   126.37  3.000
 PLB  N10   C11  C13   112.69  3.000
 PLB  O12   C11  C13   120.93  3.000
 PLB  H10   N10  C2    109.47  3.000
 PLB  H10   N10  C11   120.84  3.000
 PLB  C2    N10  C11   129.69  3.000
 PLB  C1    C2   C3    119.52  3.000
 PLB  C1    C2   N10   116.93  3.000
 PLB  C3    C2   N10   123.55  3.000
 PLB  H3    C3   C4    118.89  3.000
 PLB  H3    C3   C2    120.56  3.000
 PLB  C4    C3   C2    120.55  3.000
 PLB  H4    C4   C5    120.63  3.000
 PLB  H4    C4   C3    119.66  3.000
 PLB  C5    C4   C3    119.72  3.000
 PLB  O21   C5   C6    119.23  3.000
 PLB  O21   C5   C4    120.21  3.000
 PLB  C6    C5   C4    120.47  3.000
 PLB  H6    C6   C1    118.90  3.000
 PLB  H6    C6   C5    120.06  3.000
 PLB  C1    C6   C5    121.04  3.000
 PLB  C7    C1   C6    117.66  3.000
 PLB  C7    C1   C2    123.64  3.000
 PLB  C6    C1   C2    118.71  3.000
 PLB  O8    C7   O9    125.47  3.000
 PLB  O8    C7   C1    117.21  3.000
 PLB  O9    C7   C1    117.32  3.000
 PLB  C22   O21  C5    119.46  3.000
 PLB  N23   C22  N27   127.35  3.000
 PLB  N23   C22  O21   113.43  3.000
 PLB  N27   C22  O21   119.22  3.000
 PLB  C26   N27  C22   116.00  3.000
 PLB  H26   C26  C25   121.13  3.000
 PLB  H26   C26  N27   116.50  3.000
 PLB  C25   C26  N27   122.37  3.000
 PLB  H25   C25  C24   121.97  3.000
 PLB  H25   C25  C26   122.09  3.000
 PLB  C24   C25  C26   115.94  3.000
 PLB  H24   C24  N23   116.52  3.000
 PLB  H24   C24  C25   120.97  3.000
 PLB  N23   C24  C25   122.51  3.000
 PLB  C24   N23  C22   115.84  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
 PLB  CONST_01  C13   C14  C15  C16     0.00   0.0  0
 PLB  CONST_02  C13   C18  C17  C16     0.00   0.0  0
 PLB  CONST_03  C18   C17  C16  C15     0.00   0.0  0
 PLB  CONST_04  C18   C13  C14  C15     0.00   0.0  0
 PLB  CONST_05  C17   C16  C15  C14     0.00   0.0  0
 PLB  CONST_06  C17   C18  C13  C14     0.00   0.0  0
 PLB  CONST_07  C5    C4   C3   C2      0.00   0.0  0
 PLB  CONST_08  C5    C6   C1   C2      0.00   0.0  0
 PLB  CONST_09  C6    C1   C2   C3      0.00   0.0  0
 PLB  CONST_10  C6    C5   C4   C3      0.00   0.0  0
 PLB  CONST_11  C1    C2   C3   C4      0.00   0.0  0
 PLB  CONST_12  C1    C6   C5   C4      0.00   0.0  0
 PLB  CONST_13  C25   C26  N27  C22     0.00   0.0  0
 PLB  CONST_14  C25   C24  N23  C22     0.00   0.0  0
 PLB  CONST_15  C24   N23  C22  N27     0.00   0.0  0
 PLB  CONST_16  C24   C25  C26  N27     0.00   0.0  0
 PLB  CONST_17  N23   C22  N27  C26     0.00   0.0  0
 PLB  CONST_18  N23   C24  C25  C26     0.00   0.0  0
 PLB  CONST_19  C14   C15  C16  CL20  180.00   0.0  0
 PLB  CONST_20  C18   C17  C16  CL20  180.00   0.0  0
 PLB  CONST_21  CL19  C14  C15  C16   180.00   0.0  0
 PLB  CONST_22  C11   C13  C14  C15   180.00   0.0  0
 PLB  CONST_23  C18   C13  C14  CL19  180.00   0.0  0
 PLB  CONST_24  C11   C13  C18  C17   180.00   0.0  0
 PLB  CONST_25  C4    C3   C2   N10   180.00   0.0  0
 PLB  CONST_26  C6    C1   C2   N10   180.00   0.0  0
 PLB  CONST_27  C7    C1   C2   C3    180.00   0.0  0
 PLB  CONST_28  O21   C5   C4   C3    180.00   0.0  0
 PLB  CONST_29  C7    C1   C6   C5    180.00   0.0  0
 PLB  CONST_30  O21   C5   C6   C1    180.00   0.0  0
 PLB  CONST_31  C26   N27  C22  O21   180.00   0.0  0
 PLB  CONST_32  C24   N23  C22  O21   180.00   0.0  0
 PLB  CONST_33  H18   C18  C17  C16   180.00   0.0  0
 PLB  CONST_34  H17   C17  C16  C15   180.00   0.0  0
 PLB  CONST_35  H15   C15  C16  C17   180.00   0.0  0
 PLB  CONST_36  H4    C4   C3   C2    180.00   0.0  0
 PLB  CONST_37  H6    C6   C1   C2    180.00   0.0  0
 PLB  CONST_38  H3    C3   C4   C5    180.00   0.0  0
 PLB  CONST_39  H26   C26  N27  C22   180.00   0.0  0
 PLB  CONST_40  H24   C24  N23  C22   180.00   0.0  0
 PLB  CONST_41  H25   C25  C26  N27   180.00   0.0  0
 PLB  CONST_42  C2    N10  C11  C13   180.00   0.0  0
 PLB  CONST_43  C3    C2   N10  C11     0.00   0.0  0
 PLB  CONST_44  C1    C2   N10  C11   180.00   0.0  0
 PLB  CONST_45  H10   N10  C2   C3    180.00   0.0  0
 PLB  CONST_46  C2    N10  C11  O12     0.00   0.0  0
 PLB  Var_01    N27   C22  O21  C5      1.84  30.0  2
 PLB  Var_02    O12   C11  C13  C14    47.90  30.0  2
 PLB  Var_03    O9    C7   C1   C2      2.64  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
 PLB  plan-1  CL20  0.020
 PLB  plan-1  C16   0.020
 PLB  plan-1  C15   0.020
 PLB  plan-1  C14   0.020
 PLB  plan-1  CL19  0.020
 PLB  plan-1  C17   0.020
 PLB  plan-1  C18   0.020
 PLB  plan-1  C13   0.020
 PLB  plan-1  C11   0.020
 PLB  plan-1  H15   0.020
 PLB  plan-1  H17   0.020
 PLB  plan-1  H18   0.020
 PLB  plan-2  N10   0.020
 PLB  plan-2  C2    0.020
 PLB  plan-2  C3    0.020
 PLB  plan-2  C4    0.020
 PLB  plan-2  C5    0.020
 PLB  plan-2  C6    0.020
 PLB  plan-2  C1    0.020
 PLB  plan-2  C7    0.020
 PLB  plan-2  O21   0.020
 PLB  plan-2  H3    0.020
 PLB  plan-2  H4    0.020
 PLB  plan-2  H6    0.020
 PLB  plan-3  O21   0.020
 PLB  plan-3  C22   0.020
 PLB  plan-3  N27   0.020
 PLB  plan-3  C26   0.020
 PLB  plan-3  C25   0.020
 PLB  plan-3  C24   0.020
 PLB  plan-3  N23   0.020
 PLB  plan-3  H26   0.020
 PLB  plan-3  H25   0.020
 PLB  plan-3  H24   0.020
 PLB  plan-4  C13   0.020
 PLB  plan-4  C11   0.020
 PLB  plan-4  O12   0.020
 PLB  plan-4  N10   0.020
 PLB  plan-4  C2    0.020
 PLB  plan-4  H10   0.020
 PLB  plan-5  C1    0.020
 PLB  plan-5  C7    0.020
 PLB  plan-5  O9    0.020
 PLB  plan-5  O8    0.020

