# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 17:37:19 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 8-bromo-2-[(4-methylpiperazin-1-yl)methyl][1]benzofuro[3,2-d]pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)CC2=Nc3c(oc4ccc(Br)cc34)C(=O)N2
#
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
 HY7  HY7  8-bromo-2-[(4-methylpiperazin-1-yl)methyl][1]benzofuro[3,2-d]pyrimidin-4(3H)-one  ligand  40  23  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HY7
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
 HY7  C5    C   CH2   0  -0.288  -4.6431  -1.0830  -0.9184
 HY7  C6    C   CH2   0  -0.285  -4.5471  -2.5965  -0.9089
 HY7  N3    N   NT    0  -0.412  -4.3985  -3.0933   0.4441
 HY7  C7    C   CH3   0  -0.517  -4.3578  -4.5366   0.4822
 HY7  C8    C   CH2   0  -0.283  -3.2280  -2.5067   1.0641
 HY7  C9    C   CH2   0  -0.291  -3.3194  -0.9936   1.0595
 HY7  N2    N   NT    0  -0.415  -3.4666  -0.5013  -0.2981
 HY7  C4    C   CH2   0  -0.371  -3.4757   0.9313  -0.3666
 HY7  C3    C   CR6   0   0.487  -2.1150   1.5371  -0.1490
 HY7  N4    N   N     0  -0.429  -1.0332   0.8496  -0.3168
 HY7  C10   C   CR56  0   0.169   0.1145   1.5396  -0.1164
 HY7  C11   C   CR56  0   0.024   1.4813   1.1024  -0.1929
 HY7  C12   C   CR16  0  -0.303   2.1056  -0.1085  -0.4802
 HY7  C13   C   CR6   0  -0.120   3.4856  -0.1245  -0.4446
 HY7  BR1   BR  BR    0  -0.037   4.3978  -1.7347  -0.8200
 HY7  C14   C   CR16  0  -0.229   4.2401   1.0161  -0.1364
 HY7  C15   C   CR16  0  -0.325   3.6221   2.2205   0.1488
 HY7  C16   C   CR56  0   0.364   2.2389   2.2349   0.1139
 HY7  O2    O   O     0  -0.456   1.4492   3.3055   0.3637
 HY7  C1    C   CR56  0   0.153   0.1789   2.8630   0.2216
 HY7  C2    C   CR6   0   0.499  -0.9946   3.6547   0.4060
 HY7  O1    O   O     0  -0.455  -1.0754   4.8315   0.7049
 HY7  N1    N   NR16  0  -0.707  -2.1135   2.8540   0.1963
 HY7  H51C  H   HCH2  0   0.242  -4.7108  -0.7382  -1.9525
 HY7  H52C  H   HCH2  0   0.197  -5.5715  -0.7760  -0.4085
 HY7  H61C  H   HCH2  0   0.237  -5.4576  -3.0124  -1.3473
 HY7  H62C  H   HCH2  0   0.190  -3.7049  -2.9082  -1.5517
 HY7  H71C  H   HCH3  0   0.191  -3.5087  -4.9614  -0.0761
 HY7  H72C  H   HCH3  0   0.232  -4.2829  -4.8817   1.5148
 HY7  H73C  H   HCH3  0   0.232  -5.2746  -4.9497   0.0584
 HY7  H81C  H   HCH2  0   0.236  -3.1563  -2.8547   2.0972
 HY7  H82C  H   HCH2  0   0.190  -2.2985  -2.8123   0.5521
 HY7  H91C  H   HCH2  0   0.198  -4.1644  -0.6762   1.6940
 HY7  H92C  H   HCH2  0   0.245  -2.4091  -0.5863   1.5022
 HY7  H41C  H   HCH2  0   0.295  -3.8033   1.2387  -1.3662
 HY7  H42C  H   HCH2  0   0.238  -4.1878   1.3950   0.3373
 HY7  H1    H   HNR6  0   0.436  -3.0093   3.3115   0.3230
 HY7  H12   H   HCR6  0   0.286   1.5246  -0.9889  -0.7187
 HY7  H14   H   HCR6  0   0.292   5.3201   0.9651  -0.1183
 HY7  H15   H   HCR6  0   0.291   4.2018   3.1014   0.3882

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
 HY7  C5   C6    single    1.517  0.020  1.517
 HY7  C5   N2    single    1.452  0.020  1.452
 HY7  C6   N3    single    1.449  0.020  1.449
 HY7  N3   C7    single    1.444  0.020  1.444
 HY7  N3   C8    single    1.449  0.020  1.449
 HY7  C8   C9    single    1.516  0.020  1.516
 HY7  C9   N2    single    1.452  0.020  1.452
 HY7  N2   C4    single    1.434  0.020  1.434
 HY7  C4   C3    single    1.505  0.020  1.505
 HY7  C3   N4    double    1.293  0.020  1.293
 HY7  C3   N1    single    1.361  0.020  1.361
 HY7  N4   C10   single    1.354  0.020  1.354
 HY7  C10  C11   aromatic  1.437  0.020  1.437
 HY7  C10  C1    aromatic  1.367  0.020  1.367
 HY7  C11  C12   aromatic  1.392  0.020  1.392
 HY7  C11  C16   aromatic  1.397  0.020  1.397
 HY7  C12  C13   aromatic  1.381  0.020  1.381
 HY7  C13  BR1   single    1.888  0.020  1.888
 HY7  C13  C14   aromatic  1.402  0.020  1.402
 HY7  C14  C15   aromatic  1.383  0.020  1.383
 HY7  C15  C16   aromatic  1.384  0.020  1.384
 HY7  C16  O2    aromatic  1.354  0.020  1.354
 HY7  O2   C1    aromatic  1.353  0.020  1.353
 HY7  C1   C2    single    1.428  0.020  1.428
 HY7  C2   O1    double    1.217  0.020  1.217
 HY7  C2   N1    single    1.392  0.020  1.392
 HY7  C5   H51C  single    0.970  0.020  1.090
 HY7  C5   H52C  single    0.970  0.020  1.090
 HY7  C6   H61C  single    0.970  0.020  1.090
 HY7  C6   H62C  single    0.970  0.020  1.090
 HY7  C7   H71C  single    0.970  0.020  1.090
 HY7  C7   H72C  single    0.970  0.020  1.090
 HY7  C7   H73C  single    0.970  0.020  1.090
 HY7  C8   H81C  single    0.970  0.020  1.090
 HY7  C8   H82C  single    0.970  0.020  1.090
 HY7  C9   H91C  single    0.970  0.020  1.090
 HY7  C9   H92C  single    0.970  0.020  1.090
 HY7  C4   H41C  single    0.970  0.020  1.090
 HY7  C4   H42C  single    0.970  0.020  1.090
 HY7  N1   H1    single    0.860  0.020  1.020
 HY7  C12  H12   single    0.930  0.020  1.080
 HY7  C14  H14   single    0.930  0.020  1.080
 HY7  C15  H15   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
 HY7  H52C  C5   H51C  107.33  3.000
 HY7  H52C  C5   N2    111.91  3.000
 HY7  H51C  C5   N2    109.17  3.000
 HY7  H52C  C5   C6    109.15  3.000
 HY7  H51C  C5   C6    108.96  3.000
 HY7  N2    C5   C6    110.24  3.000
 HY7  H62C  C6   H61C  107.12  3.000
 HY7  H62C  C6   N3    111.62  3.000
 HY7  H61C  C6   N3    109.24  3.000
 HY7  H62C  C6   C5    109.04  3.000
 HY7  H61C  C6   C5    108.94  3.000
 HY7  N3    C6   C5    110.77  3.000
 HY7  C8    N3   C7    111.75  3.000
 HY7  C8    N3   C6    110.10  3.000
 HY7  C7    N3   C6    111.72  3.000
 HY7  H73C  C7   H72C  107.78  3.000
 HY7  H73C  C7   H71C  107.75  3.000
 HY7  H72C  C7   H71C  107.74  3.000
 HY7  H73C  C7   N3    110.14  3.000
 HY7  H72C  C7   N3    110.06  3.000
 HY7  H71C  C7   N3    113.19  3.000
 HY7  H82C  C8   H81C  107.16  3.000
 HY7  H82C  C8   C9    109.00  3.000
 HY7  H81C  C8   C9    108.96  3.000
 HY7  H82C  C8   N3    111.69  3.000
 HY7  H81C  C8   N3    109.19  3.000
 HY7  C9    C8   N3    110.74  3.000
 HY7  H92C  C9   H91C  107.35  3.000
 HY7  H92C  C9   N2    109.72  3.000
 HY7  H91C  C9   N2    111.26  3.000
 HY7  H92C  C9   C8    108.72  3.000
 HY7  H91C  C9   C8    109.37  3.000
 HY7  N2    C9   C8    110.34  3.000
 HY7  C4    N2   C9    112.59  3.000
 HY7  C4    N2   C5    112.00  3.000
 HY7  C9    N2   C5    110.24  3.000
 HY7  H42C  C4   H41C  105.73  3.000
 HY7  H42C  C4   C3    108.79  3.000
 HY7  H41C  C4   C3    106.81  3.000
 HY7  H42C  C4   N2    113.16  3.000
 HY7  H41C  C4   N2    109.00  3.000
 HY7  C3    C4   N2    112.91  3.000
 HY7  N1    C3   N4    123.12  3.000
 HY7  N1    C3   C4    115.27  3.000
 HY7  N4    C3   C4    121.58  3.000
 HY7  C10   N4   C3    114.78  3.000
 HY7  C1    C10  C11   105.24  3.000
 HY7  C1    C10  N4    124.73  3.000
 HY7  C11   C10  N4    130.03  3.000
 HY7  C16   C11  C12   120.49  3.000
 HY7  C16   C11  C10   104.92  3.000
 HY7  C12   C11  C10   134.59  3.000
 HY7  H12   C12  C13   122.23  3.000
 HY7  H12   C12  C11   120.84  3.000
 HY7  C13   C12  C11   116.93  3.000
 HY7  C14   C13  BR1   118.52  3.000
 HY7  C14   C13  C12   122.29  3.000
 HY7  BR1   C13  C12   119.18  3.000
 HY7  H14   C14  C15   118.94  3.000
 HY7  H14   C14  C13   120.18  3.000
 HY7  C15   C14  C13   120.88  3.000
 HY7  H15   C15  C16   122.21  3.000
 HY7  H15   C15  C14   121.02  3.000
 HY7  C16   C15  C14   116.77  3.000
 HY7  O2    C16  C15   125.92  3.000
 HY7  O2    C16  C11   111.44  3.000
 HY7  C15   C16  C11   122.64  3.000
 HY7  C1    O2   C16   105.65  3.000
 HY7  C2    C1   O2    125.24  3.000
 HY7  C2    C1   C10   122.00  3.000
 HY7  O2    C1   C10   112.76  3.000
 HY7  N1    C2   O1    122.69  3.000
 HY7  N1    C2   C1    108.80  3.000
 HY7  O1    C2   C1    128.51  3.000
 HY7  H1    N1   C2    115.58  3.000
 HY7  H1    N1   C3    117.86  3.000
 HY7  C2    N1   C3    126.56  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
 HY7  CONST_01  C13   C12  C11  C10   180.00   0.0  0
 HY7  CONST_02  C15   C16  C11  C10   180.00   0.0  0
 HY7  CONST_03  O2    C16  C11  C10     0.00   0.0  0
 HY7  CONST_04  C16   O2   C1   C10     0.00   0.0  0
 HY7  CONST_05  O2    C1   C10  C11     0.00   0.0  0
 HY7  CONST_06  C14   C13  C12  C11     0.00   0.0  0
 HY7  CONST_07  C14   C15  C16  C11     0.00   0.0  0
 HY7  CONST_08  C1    O2   C16  C11     0.00   0.0  0
 HY7  CONST_09  C1    C10  C11  C12   180.00   0.0  0
 HY7  CONST_10  C15   C16  C11  C12     0.00   0.0  0
 HY7  CONST_11  O2    C16  C11  C12   180.00   0.0  0
 HY7  CONST_12  C15   C14  C13  C12     0.00   0.0  0
 HY7  CONST_13  C16   C11  C12  C13     0.00   0.0  0
 HY7  CONST_14  C16   C15  C14  C13     0.00   0.0  0
 HY7  CONST_15  O2    C16  C15  C14   180.00   0.0  0
 HY7  CONST_16  C1    O2   C16  C15   180.00   0.0  0
 HY7  CONST_17  C1    C10  C11  C16     0.00   0.0  0
 HY7  CONST_18  C1    C2   N1   C3      0.00   0.0  0
 HY7  CONST_19  C2    N1   C3   N4      0.00   0.0  0
 HY7  CONST_20  N1    C3   N4   C10     0.00   0.0  0
 HY7  CONST_21  BR1   C13  C12  C11   180.00   0.0  0
 HY7  CONST_22  C15   C14  C13  BR1   180.00   0.0  0
 HY7  CONST_23  C10   N4   C3   C4    180.00   0.0  0
 HY7  CONST_24  C2    N1   C3   C4    180.00   0.0  0
 HY7  CONST_25  O1    C2   N1   C3    180.00   0.0  0
 HY7  CONST_26  H12   C12  C11  C10     0.00   0.0  0
 HY7  CONST_27  H15   C15  C16  C11   180.00   0.0  0
 HY7  CONST_28  H14   C14  C13  C12   180.00   0.0  0
 HY7  CONST_29  H1    N1   C3   N4    180.00   0.0  0
 HY7  Var_01    C8    N3   C6   C5    -57.47  30.0  1
 HY7  Var_02    C8    C9   N2   C5     57.71  30.0  1
 HY7  Var_03    C9    N2   C5   C6    -57.70  30.0  1
 HY7  Var_04    C9    C8   N3   C6     57.41  30.0  1
 HY7  Var_05    N2    C5   C6   N3     57.81  30.0  1
 HY7  Var_06    N2    C9   C8   N3    -57.75  30.0  1
 HY7  Var_07    C3    C4   N2   C5   -161.48  30.0  3
 HY7  Var_08    N4    C3   C4   N2     20.66  30.0  3
 HY7  Var_09    H71C  C7   N3   C6     61.48  30.0  3

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
 HY7  plan-1  C4   0.020
 HY7  plan-1  C3   0.020
 HY7  plan-1  N4   0.020
 HY7  plan-1  C10  0.020
 HY7  plan-1  C11  0.020
 HY7  plan-1  C12  0.020
 HY7  plan-1  C13  0.020
 HY7  plan-1  BR1  0.020
 HY7  plan-1  C14  0.020
 HY7  plan-1  C15  0.020
 HY7  plan-1  C16  0.020
 HY7  plan-1  O2   0.020
 HY7  plan-1  C1   0.020
 HY7  plan-1  C2   0.020
 HY7  plan-1  O1   0.020
 HY7  plan-1  N1   0.020
 HY7  plan-1  H1   0.020
 HY7  plan-1  H12  0.020
 HY7  plan-1  H14  0.020
 HY7  plan-1  H15  0.020

