# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 05:32:43 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 4-({6-amino-5-bromo-2-[(4-cyanophenyl)amino]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(N)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
 65B  65B  4-({6-amino-5-bromo-2-[(4-cyanophenyl)amino]pyrimidin-4-yl}oxy)-3,5-dimethylbenzonitrile  ligand  43  28  .  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_65B
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
 65B  C1    C   CR6   0   0.303  -2.9172   0.5134  -0.0035
 65B  O17   O   O2    0  -0.493  -2.4140  -0.7683   0.0301
 65B  C2    C   CR6   0   0.073  -3.1912   1.0771  -1.2460
 65B  C2'   C   CH3   0  -0.729  -2.8586   0.3540  -2.5150
 65B  C3    C   CR16  0  -0.329  -3.7788   2.3336  -1.2633
 65B  C4    C   CR6   0   0.039  -4.0674   2.9891  -0.0689
 65B  C5    C   CR16  0  -0.329  -3.7756   2.3992   1.1585
 65B  C6    C   CR6   0   0.073  -3.1882   1.1434   1.2075
 65B  C6'   C   CH3   0  -0.729  -2.8504   0.4913   2.5130
 65B  C13   C   CR6   0   0.604  -1.0887  -0.9463   0.0387
 65B  N12   N   N     0  -0.522  -0.3097   0.1106   0.0080
 65B  C11   C   CR6   0   0.629   1.0028  -0.1330   0.0202
 65B  N5    N   NH1   0  -0.769   1.7626   1.0014  -0.0150
 65B  N16   N   N     0  -0.525   1.5789  -1.3149   0.0597
 65B  C15   C   CR6   0   0.579   0.7867  -2.3965   0.0900
 65B  N18   N   NH2   0  -0.824   1.3947  -3.5811   0.1278
 65B  C14   C   CR6   0  -0.388  -0.6123  -2.2464   0.0803
 65B  C21   C   CR6   0   0.392   3.1277   1.1965  -0.0068
 65B  C22   C   CR16  0  -0.348   3.5625   2.5300  -0.0754
 65B  C23   C   CR16  0  -0.229   4.9023   2.8419  -0.0696
 65B  C24   C   CR6   0  -0.019   5.8546   1.8222   0.0057
 65B  C25   C   CR16  0  -0.231   5.4309   0.4962   0.0735
 65B  C26   C   CR16  0  -0.300   4.0861   0.1780   0.0672
 65B  C27   C   CSP   0   0.048   7.2426   2.1344   0.0137
 65B  N27   N   NS    0  -0.262   8.3679   2.3873   0.0245
 65B  C4'   C   CSP   0   0.053  -4.6735   4.2805  -0.1034
 65B  N4'   N   NS    0  -0.252  -5.1639   5.3229  -0.1332
 65B  BR    BR  BR    0  -0.011  -1.7814  -3.7085   0.1196
 65B  H2'1  H   HCH3  0   0.257  -3.2762  -0.6528  -2.5283
 65B  H2'2  H   HCH3  0   0.259  -3.2476   0.8908  -3.3777
 65B  H2'3  H   HCH3  0   0.256  -1.7785   0.2618  -2.6436
 65B  H3    H   HCR6  0   0.280  -4.0095   2.8050  -2.2097
 65B  H5    H   HCR6  0   0.279  -4.0023   2.9212   2.0789
 65B  H6'1  H   HCH3  0   0.256  -1.7699   0.4018   2.6399
 65B  H6'2  H   HCH3  0   0.259  -3.2318   1.0780   3.3462
 65B  H6'3  H   HCH3  0   0.257  -3.2718  -0.5114   2.5870
 65B  HN5   H   HNH1  0   0.418   1.2052   1.8420  -0.0566
 65B  H181  H   HNH2  0   0.411   2.3996  -3.6160   0.1327
 65B  H182  H   HNH2  0   0.414   0.8961  -4.4531   0.1556
 65B  H22   H   HCR6  0   0.285   2.8346   3.3297  -0.1333
 65B  H23   H   HCR6  0   0.282   5.2124   3.8765  -0.1241
 65B  H25   H   HCR6  0   0.281   6.1597  -0.3008   0.1318
 65B  H26   H   HCR6  0   0.301   3.7845  -0.8544   0.1201

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
 65B  C1   O17   single    1.377  0.020  1.377
 65B  C1   C2    aromatic  1.392  0.020  1.392
 65B  C1   C6    aromatic  1.392  0.020  1.392
 65B  O17  C13   single    1.337  0.020  1.337
 65B  C2   C2'   single    1.498  0.020  1.498
 65B  C2   C3    aromatic  1.387  0.020  1.387
 65B  C2'  H2'1  single    0.970  0.020  1.090
 65B  C2'  H2'2  single    0.970  0.020  1.090
 65B  C2'  H2'3  single    0.970  0.020  1.090
 65B  C3   C4    aromatic  1.393  0.020  1.393
 65B  C3   H3    single    0.930  0.020  1.080
 65B  C4   C5    aromatic  1.393  0.020  1.393
 65B  C4   C4'   single    1.427  0.020  1.427
 65B  C5   C6    aromatic  1.387  0.020  1.387
 65B  C5   H5    single    0.930  0.020  1.080
 65B  C6   C6'   single    1.498  0.020  1.498
 65B  C6'  H6'1  single    0.970  0.020  1.090
 65B  C6'  H6'2  single    0.970  0.020  1.090
 65B  C6'  H6'3  single    0.970  0.020  1.090
 65B  C13  N12   aromatic  1.313  0.020  1.313
 65B  C13  C14   aromatic  1.385  0.020  1.385
 65B  N12  C11   aromatic  1.335  0.020  1.335
 65B  C11  N5    single    1.366  0.020  1.366
 65B  C11  N16   aromatic  1.315  0.020  1.315
 65B  N5   C21   single    1.379  0.020  1.379
 65B  N5   HN5   single    0.860  0.020  1.020
 65B  N16  C15   aromatic  1.341  0.020  1.341
 65B  C15  N18   single    1.332  0.020  1.332
 65B  C15  C14   aromatic  1.407  0.020  1.407
 65B  N18  H181  single    0.860  0.020  1.020
 65B  N18  H182  single    0.860  0.020  1.020
 65B  C14  BR    single    1.872  0.020  1.872
 65B  C21  C22   aromatic  1.404  0.020  1.404
 65B  C21  C26   aromatic  1.400  0.020  1.400
 65B  C22  C23   aromatic  1.376  0.020  1.376
 65B  C22  H22   single    0.930  0.020  1.080
 65B  C23  C24   aromatic  1.397  0.020  1.397
 65B  C23  H23   single    0.930  0.020  1.080
 65B  C24  C25   aromatic  1.394  0.020  1.394
 65B  C24  C27   single    1.423  0.020  1.423
 65B  C25  C26   aromatic  1.382  0.020  1.382
 65B  C25  H25   single    0.930  0.020  1.080
 65B  C26  H26   single    0.930  0.020  1.080
 65B  C27  N27   triple    1.153  0.020  1.153
 65B  C4'  N4'   triple    1.152  0.020  1.152

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
 65B  C6    C1   C2    123.73  3.000
 65B  C6    C1   O17   118.11  3.000
 65B  C2    C1   O17   118.08  3.000
 65B  C13   O17  C1    119.09  3.000
 65B  C3    C2   C2'   121.38  3.000
 65B  C3    C2   C1    117.48  3.000
 65B  C2'   C2   C1    121.14  3.000
 65B  H2'3  C2'  H2'2  107.58  3.000
 65B  H2'3  C2'  H2'1  107.43  3.000
 65B  H2'2  C2'  H2'1  108.00  3.000
 65B  H2'3  C2'  C2    111.11  3.000
 65B  H2'2  C2'  C2    110.74  3.000
 65B  H2'1  C2'  C2    111.79  3.000
 65B  H3    C3   C4    120.05  3.000
 65B  H3    C3   C2    119.72  3.000
 65B  C4    C3   C2    120.22  3.000
 65B  C4'   C4   C5    119.58  3.000
 65B  C4'   C4   C3    119.55  3.000
 65B  C5    C4   C3    120.86  3.000
 65B  H5    C5   C6    119.69  3.000
 65B  H5    C5   C4    120.09  3.000
 65B  C6    C5   C4    120.22  3.000
 65B  C6'   C6   C5    121.35  3.000
 65B  C6'   C6   C1    121.16  3.000
 65B  C5    C6   C1    117.48  3.000
 65B  H6'3  C6'  H6'2  107.97  3.000
 65B  H6'3  C6'  H6'1  107.42  3.000
 65B  H6'2  C6'  H6'1  107.58  3.000
 65B  H6'3  C6'  C6    111.86  3.000
 65B  H6'2  C6'  C6    110.71  3.000
 65B  H6'1  C6'  C6    111.11  3.000
 65B  C14   C13  N12   123.50  3.000
 65B  C14   C13  O17   117.78  3.000
 65B  N12   C13  O17   118.73  3.000
 65B  C11   N12  C13   115.86  3.000
 65B  N16   C11  N5    120.22  3.000
 65B  N16   C11  N12   126.50  3.000
 65B  N5    C11  N12   113.27  3.000
 65B  HN5   N5   C21   115.41  3.000
 65B  HN5   N5   C11   112.67  3.000
 65B  C21   N5   C11   131.91  3.000
 65B  C15   N16  C11   117.81  3.000
 65B  C14   C15  N18   123.29  3.000
 65B  C14   C15  N16   120.08  3.000
 65B  N18   C15  N16   116.64  3.000
 65B  H182  N18  H181  117.76  3.000
 65B  H182  N18  C15   123.10  3.000
 65B  H181  N18  C15   119.15  3.000
 65B  BR    C14  C15   122.51  3.000
 65B  BR    C14  C13   121.24  3.000
 65B  C15   C14  C13   116.25  3.000
 65B  C26   C21  C22   118.77  3.000
 65B  C26   C21  N5    125.09  3.000
 65B  C22   C21  N5    116.14  3.000
 65B  H22   C22  C23   119.17  3.000
 65B  H22   C22  C21   119.72  3.000
 65B  C23   C22  C21   121.11  3.000
 65B  H23   C23  C24   120.36  3.000
 65B  H23   C23  C22   119.74  3.000
 65B  C24   C23  C22   119.91  3.000
 65B  C27   C24  C25   120.33  3.000
 65B  C27   C24  C23   120.34  3.000
 65B  C25   C24  C23   119.32  3.000
 65B  H25   C25  C26   119.10  3.000
 65B  H25   C25  C24   119.92  3.000
 65B  C26   C25  C24   120.97  3.000
 65B  H26   C26  C25   119.54  3.000
 65B  H26   C26  C21   120.54  3.000
 65B  C25   C26  C21   119.92  3.000
 65B  N27   C27  C24   180.00  3.000
 65B  N4'   C4'  C4    180.00  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
 65B  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 65B  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 65B  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 65B  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 65B  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 65B  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 65B  CONST_07  N16   C11  N12  C13    0.00   0.0  0
 65B  CONST_08  N16   C15  C14  C13    0.00   0.0  0
 65B  CONST_09  C15   C14  C13  N12    0.00   0.0  0
 65B  CONST_10  C15   N16  C11  N12    0.00   0.0  0
 65B  CONST_11  C14   C13  N12  C11    0.00   0.0  0
 65B  CONST_12  C14   C15  N16  C11    0.00   0.0  0
 65B  CONST_13  C24   C23  C22  C21    0.00   0.0  0
 65B  CONST_14  C24   C25  C26  C21    0.00   0.0  0
 65B  CONST_15  C25   C26  C21  C22    0.00   0.0  0
 65B  CONST_16  C25   C24  C23  C22    0.00   0.0  0
 65B  CONST_17  C26   C21  C22  C23    0.00   0.0  0
 65B  CONST_18  C26   C25  C24  C23    0.00   0.0  0
 65B  CONST_19  C3    C2   C1   O17  180.00   0.0  0
 65B  CONST_20  C5    C6   C1   O17  180.00   0.0  0
 65B  CONST_21  C11   N12  C13  O17  180.00   0.0  0
 65B  CONST_22  C15   C14  C13  O17  180.00   0.0  0
 65B  CONST_23  C6'   C6   C1   C2   180.00   0.0  0
 65B  CONST_24  C4'   C4   C3   C2   180.00   0.0  0
 65B  CONST_25  C6    C1   C2   C2'  180.00   0.0  0
 65B  CONST_26  C4    C3   C2   C2'  180.00   0.0  0
 65B  CONST_27  C6'   C6   C5   C4   180.00   0.0  0
 65B  CONST_28  C4'   C4   C5   C6   180.00   0.0  0
 65B  CONST_29  N5    C11  N12  C13  180.00   0.0  0
 65B  CONST_30  N18   C15  C14  C13  180.00   0.0  0
 65B  CONST_31  BR    C14  C13  N12  180.00   0.0  0
 65B  CONST_32  N18   C15  N16  C11  180.00   0.0  0
 65B  CONST_33  C15   N16  C11  N5   180.00   0.0  0
 65B  CONST_34  C23   C22  C21  N5   180.00   0.0  0
 65B  CONST_35  C25   C26  C21  N5   180.00   0.0  0
 65B  CONST_36  BR    C14  C15  N16  180.00   0.0  0
 65B  CONST_37  C27   C24  C23  C22  180.00   0.0  0
 65B  CONST_38  C27   C24  C25  C26  180.00   0.0  0
 65B  CONST_39  H3    C3   C2   C1   180.00   0.0  0
 65B  CONST_40  H5    C5   C6   C1   180.00   0.0  0
 65B  CONST_41  H23   C23  C22  C21  180.00   0.0  0
 65B  CONST_42  H25   C25  C26  C21  180.00   0.0  0
 65B  CONST_43  H26   C26  C21  C22  180.00   0.0  0
 65B  CONST_44  H22   C22  C23  C24  180.00   0.0  0
 65B  CONST_45  H181  N18  C15  N16    0.00   0.0  0
 65B  CONST_46  H182  N18  C15  N16  180.00   0.0  0
 65B  Var_01    N12   C13  O17  C1    -0.33  30.0  2
 65B  Var_02    C21   N5   C11  N12  179.42  30.0  2
 65B  Var_03    C22   C21  N5   C11  179.01  30.0  2
 65B  Var_04    H2'1  C2'  C2   C1    52.87  30.0  2
 65B  Var_05    H6'1  C6'  C6   C1    66.75  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
 65B  plan-1  C1    0.020
 65B  plan-1  O17   0.020
 65B  plan-1  C2    0.020
 65B  plan-1  C2'   0.020
 65B  plan-1  C3    0.020
 65B  plan-1  C4    0.020
 65B  plan-1  C5    0.020
 65B  plan-1  C6    0.020
 65B  plan-1  C6'   0.020
 65B  plan-1  C4'   0.020
 65B  plan-1  N4'   0.020
 65B  plan-1  H3    0.020
 65B  plan-1  H5    0.020
 65B  plan-2  O17   0.020
 65B  plan-2  C13   0.020
 65B  plan-2  N12   0.020
 65B  plan-2  C11   0.020
 65B  plan-2  N5    0.020
 65B  plan-2  N16   0.020
 65B  plan-2  C15   0.020
 65B  plan-2  N18   0.020
 65B  plan-2  C14   0.020
 65B  plan-2  BR    0.020
 65B  plan-3  N5    0.020
 65B  plan-3  C21   0.020
 65B  plan-3  C22   0.020
 65B  plan-3  C23   0.020
 65B  plan-3  C24   0.020
 65B  plan-3  C25   0.020
 65B  plan-3  C26   0.020
 65B  plan-3  C27   0.020
 65B  plan-3  N27   0.020
 65B  plan-3  H22   0.020
 65B  plan-3  H23   0.020
 65B  plan-3  H25   0.020
 65B  plan-3  H26   0.020
 65B  plan-4  C15   0.020
 65B  plan-4  N18   0.020
 65B  plan-4  H181  0.020
 65B  plan-4  H182  0.020

