# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 13:02:39 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 4-({5-bromo-2-[(4-cyanophenyl)amino]-6-(hydroxymethyl)pyrimidin-4-yl}oxy)-3,5-dimethylbenzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(cc(C)c1Oc2nc(Nc3ccc(cc3)C#N)nc(CO)c2Br)C#N
#
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
 185  185  4-({5-bromo-2-[(4-cyanophenyl)amino]-6-(hydroxymethyl)pyrimidin-4-yl}oxy)-3,5-dimethylbenzonitrile  ligand  45  29  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_185
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
 185  C1    C   CR6   0   0.298   2.9182   0.6986  -0.0300
 185  O17   O   O2    0  -0.487   2.4187  -0.5879  -0.0687
 185  C2    C   CR6   0   0.075   3.1874   1.3334  -1.2377
 185  C2'   C   CH3   0  -0.728   2.8608   0.6848  -2.5478
 185  C3    C   CR16  0  -0.328   3.7661   2.5932  -1.1800
 185  C4    C   CR6   0   0.041   4.0501   3.1787   0.0510
 185  C5    C   CR16  0  -0.329   3.7639   2.5154   1.2416
 185  C6    C   CR6   0   0.077   3.1849   1.2553   1.2169
 185  C6'   C   CH3   0  -0.730   2.8579   0.5213   2.4814
 185  C13   C   CR6   0   0.621   1.1004  -0.7728  -0.0585
 185  N12   N   N     0  -0.488   0.3048   0.2622  -0.0651
 185  C11   C   CR6   0   0.633  -1.0077   0.0162  -0.0457
 185  N5    N   NH1   0  -0.772  -1.7778   1.1386  -0.0564
 185  N16   N   N     0  -0.499  -1.5632  -1.1830  -0.0220
 185  C15   C   CR6   0   0.352  -0.7549  -2.2414  -0.0187
 185  C18   C   CH2   0  -0.269  -1.4276  -3.5952  -0.0190
 185  C14   C   CR6   0  -0.330   0.6204  -2.0868  -0.0380
 185  C21   C   CR6   0   0.391  -3.1480   1.3131  -0.0472
 185  C22   C   CR16  0  -0.346  -3.6003   2.6401  -0.1135
 185  C23   C   CR16  0  -0.228  -4.9445   2.9332  -0.1043
 185  C24   C   CR6   0  -0.017  -5.8813   1.8997  -0.0285
 185  C25   C   CR16  0  -0.230  -5.4394   0.5797   0.0359
 185  C26   C   CR16  0  -0.299  -4.0900   0.2807   0.0270
 185  C27   C   CSP   0   0.049  -7.2743   2.1915  -0.0147
 185  N27   N   NS    0  -0.261  -8.4028   2.4289   0.0015
 185  C4'   C   CSP   0   0.054   4.6464   4.4747   0.0931
 185  N4'   N   NS    0  -0.251   5.1270   5.5214   0.1259
 185  O18   O   OH1   0  -0.653  -1.2838  -4.2512  -1.2541
 185  BR    BR  BR    0   0.003   1.8165  -3.5264  -0.0051
 185  H2'1  H   HCH3  0   0.259   3.3007  -0.3094  -2.6290
 185  H2'2  H   HCH3  0   0.256   1.7823   0.5774  -2.6778
 185  H2'3  H   HCH3  0   0.261   3.2327   1.2849  -3.3757
 185  H3    H   HCR6  0   0.281   3.9918   3.1213  -2.0972
 185  H5    H   HCR6  0   0.281   3.9902   2.9835   2.1906
 185  H6'1  H   HCH3  0   0.257   1.7788   0.4270   2.6167
 185  H6'2  H   HCH3  0   0.259   3.2777  -0.4847   2.4846
 185  H6'3  H   HCH3  0   0.262   3.2510   1.0516   3.3463
 185  HN5   H   HNH1  0   0.422  -1.2333   1.9886  -0.0881
 185  H181  H   HCH2  0   0.242  -1.0539  -4.1921   0.8194
 185  H182  H   HCH2  0   0.261  -2.4920  -3.4307   0.1488
 185  H22   H   HCR6  0   0.287  -2.8839   3.4501  -0.1727
 185  H23   H   HCR6  0   0.283  -5.2698   3.9631  -0.1557
 185  H25   H   HCR6  0   0.282  -6.1569  -0.2274   0.0940
 185  H26   H   HCR6  0   0.304  -3.7744  -0.7477   0.0770
 185  H18   H   HOH1  0   0.456  -0.4664  -4.7574  -1.2547

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
 185  C1   O17   single    1.381  0.020  1.381
 185  C1   C2    aromatic  1.391  0.020  1.391
 185  C1   C6    aromatic  1.391  0.020  1.391
 185  O17  C13   single    1.331  0.020  1.331
 185  C2   C2'   single    1.498  0.020  1.498
 185  C2   C3    aromatic  1.388  0.020  1.388
 185  C2'  H2'1  single    0.970  0.020  1.090
 185  C2'  H2'2  single    0.970  0.020  1.090
 185  C2'  H2'3  single    0.970  0.020  1.090
 185  C3   C4    aromatic  1.392  0.020  1.392
 185  C3   H3    single    0.930  0.020  1.080
 185  C4   C5    aromatic  1.393  0.020  1.393
 185  C4   C4'   single    1.427  0.020  1.427
 185  C5   C6    aromatic  1.387  0.020  1.387
 185  C5   H5    single    0.930  0.020  1.080
 185  C6   C6'   single    1.498  0.020  1.498
 185  C6'  H6'1  single    0.970  0.020  1.090
 185  C6'  H6'2  single    0.970  0.020  1.090
 185  C6'  H6'3  single    0.970  0.020  1.090
 185  C13  N12   aromatic  1.305  0.020  1.305
 185  C13  C14   aromatic  1.399  0.020  1.399
 185  N12  C11   aromatic  1.335  0.020  1.335
 185  C11  N5    single    1.361  0.020  1.361
 185  C11  N16   aromatic  1.322  0.020  1.322
 185  N5   C21   single    1.381  0.020  1.381
 185  N5   HN5   single    0.860  0.020  1.020
 185  N16  C15   aromatic  1.332  0.020  1.332
 185  C15  C18   single    1.512  0.020  1.512
 185  C15  C14   aromatic  1.384  0.020  1.384
 185  C18  O18   single    1.406  0.020  1.406
 185  C18  H181  single    0.970  0.020  1.090
 185  C18  H182  single    0.970  0.020  1.090
 185  C14  BR    single    1.872  0.020  1.872
 185  C21  C22   aromatic  1.403  0.020  1.403
 185  C21  C26   aromatic  1.400  0.020  1.400
 185  C22  C23   aromatic  1.376  0.020  1.376
 185  C22  H22   single    0.930  0.020  1.080
 185  C23  C24   aromatic  1.397  0.020  1.397
 185  C23  H23   single    0.930  0.020  1.080
 185  C24  C25   aromatic  1.393  0.020  1.393
 185  C24  C27   single    1.423  0.020  1.423
 185  C25  C26   aromatic  1.382  0.020  1.382
 185  C25  H25   single    0.930  0.020  1.080
 185  C26  H26   single    0.930  0.020  1.080
 185  C27  N27   triple    1.153  0.020  1.153
 185  C4'  N4'   triple    1.152  0.020  1.152
 185  O18  H18   single    0.850  0.020  0.980

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
 185  C6    C1   C2    123.96  3.000
 185  C6    C1   O17   117.86  3.000
 185  C2    C1   O17   118.10  3.000
 185  C13   O17  C1    119.18  3.000
 185  C3    C2   C2'   121.36  3.000
 185  C3    C2   C1    117.32  3.000
 185  C2'   C2   C1    121.31  3.000
 185  H2'3  C2'  H2'2  107.54  3.000
 185  H2'3  C2'  H2'1  107.95  3.000
 185  H2'2  C2'  H2'1  107.46  3.000
 185  H2'3  C2'  C2    110.62  3.000
 185  H2'2  C2'  C2    111.24  3.000
 185  H2'1  C2'  C2    111.84  3.000
 185  H3    C3   C4    120.10  3.000
 185  H3    C3   C2    119.66  3.000
 185  C4    C3   C2    120.24  3.000
 185  C4'   C4   C5    119.54  3.000
 185  C4'   C4   C3    119.55  3.000
 185  C5    C4   C3    120.91  3.000
 185  H5    C5   C6    119.73  3.000
 185  H5    C5   C4    120.05  3.000
 185  C6    C5   C4    120.22  3.000
 185  C6'   C6   C5    121.41  3.000
 185  C6'   C6   C1    121.24  3.000
 185  C5    C6   C1    117.35  3.000
 185  H6'3  C6'  H6'2  107.96  3.000
 185  H6'3  C6'  H6'1  107.50  3.000
 185  H6'2  C6'  H6'1  107.49  3.000
 185  H6'3  C6'  C6    110.69  3.000
 185  H6'2  C6'  C6    111.75  3.000
 185  H6'1  C6'  C6    111.26  3.000
 185  C14   C13  N12   122.39  3.000
 185  C14   C13  O17   118.05  3.000
 185  N12   C13  O17   119.56  3.000
 185  C11   N12  C13   116.93  3.000
 185  N16   C11  N5    120.69  3.000
 185  N16   C11  N12   125.48  3.000
 185  N5    C11  N12   113.83  3.000
 185  HN5   N5   C21   115.39  3.000
 185  HN5   N5   C11   112.90  3.000
 185  C21   N5   C11   131.71  3.000
 185  C15   N16  C11   117.77  3.000
 185  C14   C15  C18   122.83  3.000
 185  C14   C15  N16   120.95  3.000
 185  C18   C15  N16   116.21  3.000
 185  H182  C18  H181  107.32  3.000
 185  H182  C18  O18   107.79  3.000
 185  H181  C18  O18   112.55  3.000
 185  H182  C18  C15   107.42  3.000
 185  H181  C18  C15   109.65  3.000
 185  O18   C18  C15   111.87  3.000
 185  BR    C14  C15   123.28  3.000
 185  BR    C14  C13   120.22  3.000
 185  C15   C14  C13   116.49  3.000
 185  C26   C21  C22   118.89  3.000
 185  C26   C21  N5    125.09  3.000
 185  C22   C21  N5    116.03  3.000
 185  H22   C22  C23   119.16  3.000
 185  H22   C22  C21   119.78  3.000
 185  C23   C22  C21   121.06  3.000
 185  H23   C23  C24   120.37  3.000
 185  H23   C23  C22   119.77  3.000
 185  C24   C23  C22   119.86  3.000
 185  C27   C24  C25   120.28  3.000
 185  C27   C24  C23   120.34  3.000
 185  C25   C24  C23   119.38  3.000
 185  H25   C25  C26   119.12  3.000
 185  H25   C25  C24   119.93  3.000
 185  C26   C25  C24   120.95  3.000
 185  H26   C26  C25   119.51  3.000
 185  H26   C26  C21   120.64  3.000
 185  C25   C26  C21   119.86  3.000
 185  N27   C27  C24   180.00  3.000
 185  N4'   C4'  C4    180.00  3.000
 185  H18   O18  C18   109.46  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
 185  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 185  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 185  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 185  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 185  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 185  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 185  CONST_07  N16   C11  N12  C13     0.00   0.0  0
 185  CONST_08  N16   C15  C14  C13     0.00   0.0  0
 185  CONST_09  C15   C14  C13  N12     0.00   0.0  0
 185  CONST_10  C15   N16  C11  N12     0.00   0.0  0
 185  CONST_11  C14   C13  N12  C11     0.00   0.0  0
 185  CONST_12  C14   C15  N16  C11     0.00   0.0  0
 185  CONST_13  C24   C23  C22  C21     0.00   0.0  0
 185  CONST_14  C24   C25  C26  C21     0.00   0.0  0
 185  CONST_15  C25   C26  C21  C22     0.00   0.0  0
 185  CONST_16  C25   C24  C23  C22     0.00   0.0  0
 185  CONST_17  C26   C21  C22  C23     0.00   0.0  0
 185  CONST_18  C26   C25  C24  C23     0.00   0.0  0
 185  CONST_19  C3    C2   C1   O17   180.00   0.0  0
 185  CONST_20  C5    C6   C1   O17   180.00   0.0  0
 185  CONST_21  C11   N12  C13  O17   180.00   0.0  0
 185  CONST_22  C15   C14  C13  O17   180.00   0.0  0
 185  CONST_23  C6'   C6   C1   C2    180.00   0.0  0
 185  CONST_24  C4'   C4   C3   C2    180.00   0.0  0
 185  CONST_25  C6    C1   C2   C2'   180.00   0.0  0
 185  CONST_26  C4    C3   C2   C2'   180.00   0.0  0
 185  CONST_27  C6'   C6   C5   C4    180.00   0.0  0
 185  CONST_28  C4'   C4   C5   C6    180.00   0.0  0
 185  CONST_29  N5    C11  N12  C13   180.00   0.0  0
 185  CONST_30  C18   C15  C14  C13   180.00   0.0  0
 185  CONST_31  BR    C14  C13  N12   180.00   0.0  0
 185  CONST_32  C18   C15  N16  C11   180.00   0.0  0
 185  CONST_33  C15   N16  C11  N5    180.00   0.0  0
 185  CONST_34  C23   C22  C21  N5    180.00   0.0  0
 185  CONST_35  C25   C26  C21  N5    180.00   0.0  0
 185  CONST_36  BR    C14  C15  N16   180.00   0.0  0
 185  CONST_37  C27   C24  C23  C22   180.00   0.0  0
 185  CONST_38  C27   C24  C25  C26   180.00   0.0  0
 185  CONST_39  H3    C3   C2   C1    180.00   0.0  0
 185  CONST_40  H5    C5   C6   C1    180.00   0.0  0
 185  CONST_41  H23   C23  C22  C21   180.00   0.0  0
 185  CONST_42  H25   C25  C26  C21   180.00   0.0  0
 185  CONST_43  H26   C26  C21  C22   180.00   0.0  0
 185  CONST_44  H22   C22  C23  C24   180.00   0.0  0
 185  Var_01    N12   C13  O17  C1      2.68  30.0  2
 185  Var_02    C21   N5   C11  N12   179.80  30.0  2
 185  Var_03    C22   C21  N5   C11  -177.74  30.0  2
 185  Var_04    O18   C18  C15  N16   108.64  30.0  2
 185  Var_05    H2'1  C2'  C2   C1    -53.95  30.0  2
 185  Var_06    H6'1  C6'  C6   C1    -67.80  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
 185  plan-1  C1   0.020
 185  plan-1  O17  0.020
 185  plan-1  C2   0.020
 185  plan-1  C2'  0.020
 185  plan-1  C3   0.020
 185  plan-1  C4   0.020
 185  plan-1  C5   0.020
 185  plan-1  C6   0.020
 185  plan-1  C6'  0.020
 185  plan-1  C4'  0.020
 185  plan-1  N4'  0.020
 185  plan-1  H3   0.020
 185  plan-1  H5   0.020
 185  plan-2  O17  0.020
 185  plan-2  C13  0.020
 185  plan-2  N12  0.020
 185  plan-2  C11  0.020
 185  plan-2  N5   0.020
 185  plan-2  N16  0.020
 185  plan-2  C15  0.020
 185  plan-2  C18  0.020
 185  plan-2  C14  0.020
 185  plan-2  BR   0.020
 185  plan-3  N5   0.020
 185  plan-3  C21  0.020
 185  plan-3  C22  0.020
 185  plan-3  C23  0.020
 185  plan-3  C24  0.020
 185  plan-3  C25  0.020
 185  plan-3  C26  0.020
 185  plan-3  C27  0.020
 185  plan-3  N27  0.020
 185  plan-3  H22  0.020
 185  plan-3  H23  0.020
 185  plan-3  H25  0.020
 185  plan-3  H26  0.020

