# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 23:26:23 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: (2R)-1-(4-{[5-bromo-4-(phenylamino)pyrimidin-2-yl]amino}phenoxy)-3-(dimethylamino)propan-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C[C@@H](O)COc1ccc(Nc2ncc(Br)c(Nc3ccccc3)n2)cc1
#
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
 BYP  BYP  (2R)-1-(4-{[5-bromo-4-(phenylamino)pyrimidin-2-yl]amino}phenoxy)-3-(dimethylamino)propan-2-ol  ligand  53  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BYP
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
 BYP  C22   C   CH2   0  -0.177   0.2878   0.3699   5.8393
 BYP  N1    N   N     0  -0.481  -1.5263  -0.2877  -1.5517
 BYP  C2    C   CR16  0   0.013  -2.1850  -0.3843  -2.7010
 BYP  C6    C   CR6   0   0.613  -0.2097  -0.1462  -1.6560
 BYP  C4    C   CR6   0   0.600  -0.1631  -0.1955  -3.9414
 BYP  C3    C   CR6   0  -0.318  -1.5730  -0.3448  -3.9305
 BYP  N5    N   N     0  -0.519   0.4843  -0.0996  -2.7946
 BYP  C11   C   CR16  0  -0.270   4.6335   0.1763  -5.9102
 BYP  C10   C   CR16  0  -0.246   3.7767  -0.5042  -6.7652
 BYP  C9    C   CR16  0  -0.344   2.4297  -0.6151  -6.4631
 BYP  C8    C   CR6   0   0.358   1.9111  -0.0387  -5.3016
 BYP  C12   C   CR16  0  -0.251   4.1172   0.7543  -4.7591
 BYP  C17   C   CR16  0  -0.344  -1.2075  -0.6388   2.6843
 BYP  C16   C   CR16  0  -0.281  -0.9704  -0.6297   1.3213
 BYP  C13   C   CR16  0  -0.290   2.7673   0.6589  -4.4492
 BYP  C15   C   CR6   0   0.338   0.1896  -0.0403   0.8118
 BYP  C18   C   CR6   0   0.374  -0.3028  -0.0747   3.5823
 BYP  C19   C   CR16  0  -0.371   0.8519   0.5179   3.0804
 BYP  C20   C   CR16  0  -0.332   1.0841   0.5320   1.7127
 BYP  O21   O   O2    0  -0.476  -0.6196  -0.1543   4.8919
 BYP  N7    N   NH1   0  -0.771   0.5293  -0.1575  -5.1020
 BYP  BR    BR  BR    0  -0.023  -2.5945  -0.4829  -5.5027
 BYP  C23   C   CH1   0  -0.029  -0.2251   0.0286   7.2290
 BYP  C24   C   CH2   0  -0.297   0.8047   0.4850   8.2597
 BYP  N25   N   NT    0  -0.401   0.4263   0.2014   9.6275
 BYP  C26   C   CH3   0  -0.531   0.4228  -1.2174   9.9134
 BYP  C27   C   CH3   0  -0.520   1.2839   0.9106  10.5530
 BYP  O28   O   OH1   0  -0.656  -1.5050   0.5588   7.4689
 BYP  H221  H   HCH2  0   0.222   0.3836   1.4578   5.7217
 BYP  H222  H   HCH2  0   0.225   1.2847  -0.0657   5.7041
 BYP  H2    H   HCR6  0   0.285  -3.2617  -0.4957  -2.6297
 BYP  H10   H   HCR6  0   0.260   4.1559  -0.9593  -7.6707
 BYP  H9    H   HCR6  0   0.269   1.7719  -1.1567  -7.1329
 BYP  H12   H   HCR6  0   0.258   4.7690   1.2985  -4.0879
 BYP  H17   H   HCR6  0   0.262  -2.1101  -1.1033   3.0620
 BYP  H16   H   HCR6  0   0.275  -1.6922  -1.0841   0.6616
 BYP  H13   H   HCR6  0   0.274   2.3924   1.1270  -3.5537
 BYP  H19   H   HCR6  0   0.280   1.5853   0.9782   3.7282
 BYP  H20   H   HCR6  0   0.271   1.9909   0.9986   1.3459
 BYP  H7    H   HNH1  0   0.415   0.0097  -0.3740  -5.9390
 BYP  H23   H   HCH1  0   0.237  -0.3383  -1.0592   7.2796
 BYP  H241  H   HCH2  0   0.236   0.9350   1.5693   8.1620
 BYP  H242  H   HCH2  0   0.202   1.7801   0.0345   8.0043
 BYP  H261  H   HCH3  0   0.236   0.1629  -1.3811  10.9595
 BYP  H262  H   HCH3  0   0.237  -0.3218  -1.7377   9.3111
 BYP  H263  H   HCH3  0   0.192   1.3981  -1.6962   9.7295
 BYP  H271  H   HCH3  0   0.233   1.2126   1.9862  10.3844
 BYP  H272  H   HCH3  0   0.233   0.9689   0.7127  11.5784
 BYP  H273  H   HCH3  0   0.191   2.3457   0.6287  10.4708
 BYP  H28   H   HOH1  0   0.443  -1.4179   1.5016   7.6459
 BYP  N14   N   NH1   0  -0.763   0.5489  -0.0285  -0.5391
 BYP  H11   H   HCR6  0   0.255   5.6873   0.2587  -6.1406
 BYP  H14   H   HNH1  0   0.407   1.5231   0.1509  -0.7289

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
 BYP  C22  O21   single    1.413  0.020  1.413
 BYP  C22  C23   single    1.520  0.020  1.520
 BYP  C22  H221  single    0.970  0.020  1.090
 BYP  C22  H222  single    0.970  0.020  1.090
 BYP  N1   C2    aromatic  1.328  0.020  1.328
 BYP  N1   C6    aromatic  1.328  0.020  1.328
 BYP  C2   C3    aromatic  1.374  0.020  1.374
 BYP  C2   H2    single    0.930  0.020  1.080
 BYP  C6   N5    aromatic  1.334  0.020  1.334
 BYP  C6   N14   single    1.355  0.020  1.355
 BYP  C4   C3    aromatic  1.418  0.020  1.418
 BYP  C4   N5    aromatic  1.320  0.020  1.320
 BYP  C4   N7    single    1.352  0.020  1.352
 BYP  C3   BR    single    1.880  0.020  1.880
 BYP  C11  C10   aromatic  1.389  0.020  1.389
 BYP  C11  C12   aromatic  1.388  0.020  1.388
 BYP  C11  H11   single    0.930  0.020  1.080
 BYP  C10  C9    aromatic  1.385  0.020  1.385
 BYP  C10  H10   single    0.930  0.020  1.080
 BYP  C9   C8    aromatic  1.397  0.020  1.397
 BYP  C9   H9    single    0.930  0.020  1.080
 BYP  C8   C13   aromatic  1.395  0.020  1.395
 BYP  C8   N7    single    1.401  0.020  1.401
 BYP  C12  C13   aromatic  1.388  0.020  1.388
 BYP  C12  H12   single    0.930  0.020  1.080
 BYP  C17  C16   aromatic  1.384  0.020  1.384
 BYP  C17  C18   aromatic  1.394  0.020  1.394
 BYP  C17  H17   single    0.930  0.020  1.080
 BYP  C16  C15   aromatic  1.397  0.020  1.397
 BYP  C16  H16   single    0.930  0.020  1.080
 BYP  C13  H13   single    0.930  0.020  1.080
 BYP  C15  C20   aromatic  1.393  0.020  1.393
 BYP  C15  N14   single    1.398  0.020  1.398
 BYP  C18  C19   aromatic  1.392  0.020  1.392
 BYP  C18  O21   single    1.350  0.020  1.350
 BYP  C19  C20   aromatic  1.387  0.020  1.387
 BYP  C19  H19   single    0.930  0.020  1.080
 BYP  C20  H20   single    0.930  0.020  1.080
 BYP  N7   H7    single    0.860  0.020  1.020
 BYP  N14  H14   single    0.860  0.020  1.020
 BYP  C23  C24   single    1.527  0.020  1.527
 BYP  C23  O28   single    1.406  0.020  1.406
 BYP  C23  H23   single    0.970  0.020  1.090
 BYP  C24  N25   single    1.447  0.020  1.447
 BYP  C24  H241  single    0.970  0.020  1.090
 BYP  C24  H242  single    0.970  0.020  1.090
 BYP  N25  C26   single    1.447  0.020  1.447
 BYP  N25  C27   single    1.447  0.020  1.447
 BYP  C26  H261  single    0.970  0.020  1.090
 BYP  C26  H262  single    0.970  0.020  1.090
 BYP  C26  H263  single    0.970  0.020  1.090
 BYP  C27  H271  single    0.970  0.020  1.090
 BYP  C27  H272  single    0.970  0.020  1.090
 BYP  C27  H273  single    0.970  0.020  1.090
 BYP  O28  H28   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
 BYP  H222  C22  H221  107.52  3.000
 BYP  H222  C22  C23   109.29  3.000
 BYP  H221  C22  C23   110.47  3.000
 BYP  H222  C22  O21   110.73  3.000
 BYP  H221  C22  O21   110.59  3.000
 BYP  C23   C22  O21   108.24  3.000
 BYP  C6    N1   C2    115.55  3.000
 BYP  H2    C2   C3    120.26  3.000
 BYP  H2    C2   N1    116.28  3.000
 BYP  C3    C2   N1    123.46  3.000
 BYP  N14   C6   N5    114.15  3.000
 BYP  N14   C6   N1    119.95  3.000
 BYP  N5    C6   N1    125.90  3.000
 BYP  N7    C4   N5    119.50  3.000
 BYP  N7    C4   C3    121.25  3.000
 BYP  N5    C4   C3    119.25  3.000
 BYP  BR    C3   C4    122.79  3.000
 BYP  BR    C3   C2    120.28  3.000
 BYP  C4    C3   C2    116.93  3.000
 BYP  C4    N5   C6    118.92  3.000
 BYP  H11   C11  C12   120.49  3.000
 BYP  H11   C11  C10   120.48  3.000
 BYP  C12   C11  C10   119.03  3.000
 BYP  H10   C10  C9    119.32  3.000
 BYP  H10   C10  C11   120.34  3.000
 BYP  C9    C10  C11   120.34  3.000
 BYP  H9    C9   C8    119.66  3.000
 BYP  H9    C9   C10   119.71  3.000
 BYP  C8    C9   C10   120.63  3.000
 BYP  N7    C8   C13   124.09  3.000
 BYP  N7    C8   C9    116.72  3.000
 BYP  C13   C8   C9    119.12  3.000
 BYP  H12   C12  C13   118.79  3.000
 BYP  H12   C12  C11   119.98  3.000
 BYP  C13   C12  C11   121.22  3.000
 BYP  H17   C17  C18   119.33  3.000
 BYP  H17   C17  C16   119.29  3.000
 BYP  C18   C17  C16   121.38  3.000
 BYP  H16   C16  C15   120.69  3.000
 BYP  H16   C16  C17   119.02  3.000
 BYP  C15   C16  C17   120.28  3.000
 BYP  H13   C13  C12   119.60  3.000
 BYP  H13   C13  C8    120.75  3.000
 BYP  C12   C13  C8    119.65  3.000
 BYP  N14   C15  C20   117.17  3.000
 BYP  N14   C15  C16   124.70  3.000
 BYP  C20   C15  C16   118.08  3.000
 BYP  O21   C18  C19   124.74  3.000
 BYP  O21   C18  C17   116.67  3.000
 BYP  C19   C18  C17   118.59  3.000
 BYP  H19   C19  C20   118.21  3.000
 BYP  H19   C19  C18   121.87  3.000
 BYP  C20   C19  C18   119.92  3.000
 BYP  H20   C20  C19   118.56  3.000
 BYP  H20   C20  C15   119.70  3.000
 BYP  C19   C20  C15   121.74  3.000
 BYP  C18   O21  C22   118.56  3.000
 BYP  H7    N7   C8    114.08  3.000
 BYP  H7    N7   C4    116.27  3.000
 BYP  C8    N7   C4    129.03  3.000
 BYP  H23   C23  O28   105.82  3.000
 BYP  H23   C23  C24   109.61  3.000
 BYP  O28   C23  C24   112.71  3.000
 BYP  H23   C23  C22   107.47  3.000
 BYP  O28   C23  C22   112.24  3.000
 BYP  C24   C23  C22   108.81  3.000
 BYP  H242  C24  H241  106.13  3.000
 BYP  H242  C24  N25   111.69  3.000
 BYP  H241  C24  N25   108.00  3.000
 BYP  H242  C24  C23   108.52  3.000
 BYP  H241  C24  C23   108.40  3.000
 BYP  N25   C24  C23   113.78  3.000
 BYP  C27   N25  C26   110.82  3.000
 BYP  C27   N25  C24   110.70  3.000
 BYP  C26   N25  C24   112.29  3.000
 BYP  H263  C26  H262  107.76  3.000
 BYP  H263  C26  H261  107.81  3.000
 BYP  H262  C26  H261  107.19  3.000
 BYP  H263  C26  N25   113.01  3.000
 BYP  H262  C26  N25   111.13  3.000
 BYP  H261  C26  N25   109.71  3.000
 BYP  H273  C27  H272  107.58  3.000
 BYP  H273  C27  H271  107.68  3.000
 BYP  H272  C27  H271  107.77  3.000
 BYP  H273  C27  N25   113.45  3.000
 BYP  H272  C27  N25   109.94  3.000
 BYP  H271  C27  N25   110.21  3.000
 BYP  H28   O28  C23   108.55  3.000
 BYP  H14   N14  C15   115.57  3.000
 BYP  H14   N14  C6    113.64  3.000
 BYP  C15   N14  C6    130.68  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
 BYP  CONST_01  C4    C3   C2   N1      0.00   0.0  0
 BYP  CONST_02  C4    N5   C6   N1      0.00   0.0  0
 BYP  CONST_03  N5    C6   N1   C2      0.00   0.0  0
 BYP  CONST_04  N5    C4   C3   C2      0.00   0.0  0
 BYP  CONST_05  C3    C2   N1   C6      0.00   0.0  0
 BYP  CONST_06  C3    C4   N5   C6      0.00   0.0  0
 BYP  CONST_07  C8    C9   C10  C11     0.00   0.0  0
 BYP  CONST_08  C8    C13  C12  C11     0.00   0.0  0
 BYP  CONST_09  C13   C12  C11  C10     0.00   0.0  0
 BYP  CONST_10  C13   C8   C9   C10     0.00   0.0  0
 BYP  CONST_11  C12   C11  C10  C9      0.00   0.0  0
 BYP  CONST_12  C12   C13  C8   C9      0.00   0.0  0
 BYP  CONST_13  C20   C15  C16  C17     0.00   0.0  0
 BYP  CONST_14  C20   C19  C18  C17     0.00   0.0  0
 BYP  CONST_15  C19   C18  C17  C16     0.00   0.0  0
 BYP  CONST_16  C19   C20  C15  C16     0.00   0.0  0
 BYP  CONST_17  C18   C17  C16  C15     0.00   0.0  0
 BYP  CONST_18  C18   C19  C20  C15     0.00   0.0  0
 BYP  CONST_19  BR    C3   C2   N1    180.00   0.0  0
 BYP  CONST_20  N14   C6   N1   C2    180.00   0.0  0
 BYP  CONST_21  N7    C4   C3   C2    180.00   0.0  0
 BYP  CONST_22  N7    C4   N5   C6    180.00   0.0  0
 BYP  CONST_23  N14   C6   N5   C4    180.00   0.0  0
 BYP  CONST_24  BR    C3   C4   N5    180.00   0.0  0
 BYP  CONST_25  N7    C8   C9   C10   180.00   0.0  0
 BYP  CONST_26  N7    C8   C13  C12   180.00   0.0  0
 BYP  CONST_27  N14   C15  C16  C17   180.00   0.0  0
 BYP  CONST_28  O21   C18  C17  C16   180.00   0.0  0
 BYP  CONST_29  N14   C15  C20  C19   180.00   0.0  0
 BYP  CONST_30  O21   C18  C19  C20   180.00   0.0  0
 BYP  CONST_31  H2    C2   N1   C6    180.00   0.0  0
 BYP  CONST_32  H9    C9   C10  C11   180.00   0.0  0
 BYP  CONST_33  H13   C13  C12  C11   180.00   0.0  0
 BYP  CONST_34  H12   C12  C11  C10   180.00   0.0  0
 BYP  CONST_35  H11   C11  C10  C9    180.00   0.0  0
 BYP  CONST_36  H10   C10  C9   C8    180.00   0.0  0
 BYP  CONST_37  H19   C19  C18  C17   180.00   0.0  0
 BYP  CONST_38  H20   C20  C15  C16   180.00   0.0  0
 BYP  CONST_39  H17   C17  C16  C15   180.00   0.0  0
 BYP  CONST_40  H16   C16  C17  C18   180.00   0.0  0
 BYP  Var_01    C15   N14  C6   N1      0.74  30.0  2
 BYP  Var_02    C16   C15  N14  C6     23.48  30.0  2
 BYP  Var_03    C9    C8   N7   C4    151.44  30.0  2
 BYP  Var_04    C8    N7   C4   C3   -178.86  30.0  2
 BYP  Var_05    C17   C18  O21  C22   178.18  30.0  3
 BYP  Var_06    C23   C22  O21  C18  -174.12  30.0  1
 BYP  Var_07    C26   N25  C24  C23    68.22  30.0  3
 BYP  Var_08    H261  C26  N25  C24   178.27  30.0  3
 BYP  Var_09    H271  C27  N25  C24    59.60  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 BYP  chir_01  C23  C22  C24  O28  negativ

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
 BYP  plan-1  N1   0.020
 BYP  plan-1  C2   0.020
 BYP  plan-1  C6   0.020
 BYP  plan-1  C4   0.020
 BYP  plan-1  C3   0.020
 BYP  plan-1  N5   0.020
 BYP  plan-1  N7   0.020
 BYP  plan-1  BR   0.020
 BYP  plan-1  H2   0.020
 BYP  plan-1  N14  0.020
 BYP  plan-2  C11  0.020
 BYP  plan-2  C10  0.020
 BYP  plan-2  C9   0.020
 BYP  plan-2  C8   0.020
 BYP  plan-2  C12  0.020
 BYP  plan-2  C13  0.020
 BYP  plan-2  N7   0.020
 BYP  plan-2  H10  0.020
 BYP  plan-2  H9   0.020
 BYP  plan-2  H12  0.020
 BYP  plan-2  H13  0.020
 BYP  plan-2  H11  0.020
 BYP  plan-3  C17  0.020
 BYP  plan-3  C16  0.020
 BYP  plan-3  C15  0.020
 BYP  plan-3  C18  0.020
 BYP  plan-3  C19  0.020
 BYP  plan-3  C20  0.020
 BYP  plan-3  O21  0.020
 BYP  plan-3  H17  0.020
 BYP  plan-3  H16  0.020
 BYP  plan-3  H19  0.020
 BYP  plan-3  H20  0.020
 BYP  plan-3  N14  0.020

