# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 17:24:12 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 1-[(6-bromanyl-1,3-benzodioxol-5-yl)methyl]-4-chloranyl-pyrazolo[3,4-d]pyrimidin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(Cl)c2cnn(Cc3cc4OCOc4cc3Br)c2n1
#
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
 8MF  8MF  1-[(6-bromanyl-1,3-benzodioxol-5-yl)methyl]-4-chloranyl-pyrazolo[3,4-d]pyrimidin-6-amine  ligand  31  22  .  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_8MF
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
 8MF  C10  C   CH2   0  -0.422   0.2990  -0.5916   1.6559
 8MF  C13  C   CR16  0  -0.308   3.4258  -0.1722  -0.5580
 8MF  C15  C   CR56  0   0.320   2.4400   1.9648  -0.0461
 8MF  C01  C   CR6   0   0.121  -3.8634   0.3700  -0.5364
 8MF  N02  N   N     0  -0.455  -4.0324   1.5414  -0.0064
 8MF  C03  C   CR6   0   0.573  -3.0896   1.9886   0.8685
 8MF  N04  N   N     0  -0.498  -1.9964   1.3331   1.2401
 8MF  C05  C   CR56  0   0.642  -1.8802   0.1378   0.6806
 8MF  C06  C   CR56  0  -0.100  -2.7740  -0.4377  -0.2355
 8MF  N07  N   NR5   0  -0.371  -0.8978  -0.7618   0.8617
 8MF  N08  N   N     0  -0.232  -1.0942  -1.8683   0.1109
 8MF  C09  C   CR15  0  -0.098  -2.2093  -1.6999  -0.5438
 8MF  C11  C   CR6   0   0.159   1.4290  -0.0011   0.8504
 8MF  C12  C   CR6   0  -0.186   2.4085  -0.7531   0.2140
 8MF  C14  C   CR56  0   0.306   3.4070   1.1927  -0.6706
 8MF  C16  C   CR16  0  -0.378   1.4536   1.4003   0.7149
 8MF  O17  O   O     0  -0.480   4.2437   1.9915  -1.3650
 8MF  C18  C   CH2   0   0.069   3.8899   3.3296  -1.0299
 8MF  O19  O   O     0  -0.481   2.6504   3.2679  -0.3353
 8MF  N21  N   NH2   0  -0.818  -3.3201   3.1960   1.3977
 8MF  BR1  BR  BR    0  -0.040   2.4460  -2.6384   0.3544
 8MF  H1   H   HCH2  0   0.297   0.0456   0.0788   2.4762
 8MF  H2   H   HCH2  0   0.296   0.5508  -1.5526   2.0979
 8MF  H3   H   HCR6  0   0.297   4.1858  -0.7668  -1.0457
 8MF  H4   H   HCR5  0   0.279  -2.5834  -2.4649  -1.2065
 8MF  H5   H   HCR6  0   0.283   0.6959   2.0054   1.1960
 8MF  H6   H   HCH2  0   0.241   4.6581   3.7648  -0.3834
 8MF  H7   H   HCH2  0   0.251   3.7755   3.9183  -1.9398
 8MF  H8   H   HNH2  0   0.407  -4.0502   3.7750   1.0223
 8MF  H9   H   HNH2  0   0.406  -2.6177   3.6303   1.9702
 8MF  CL1  CL  CL    0  -0.079  -5.0511  -0.1849  -1.6558

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
 8MF  C18  O17  single    1.424  0.020  1.424
 8MF  C18  O19  single    1.422  0.020  1.422
 8MF  O17  C14  single    1.349  0.020  1.349
 8MF  C14  C13  aromatic  1.370  0.020  1.370
 8MF  C14  C15  aromatic  1.386  0.020  1.386
 8MF  C13  C12  aromatic  1.403  0.020  1.403
 8MF  O19  C15  single    1.351  0.020  1.351
 8MF  C15  C16  aromatic  1.368  0.020  1.368
 8MF  C12  BR1  single    1.891  0.020  1.891
 8MF  C12  C11  aromatic  1.389  0.020  1.389
 8MF  C16  C11  aromatic  1.408  0.020  1.408
 8MF  C11  C10  single    1.508  0.020  1.508
 8MF  C10  N07  single    1.446  0.020  1.446
 8MF  N07  C05  aromatic  1.344  0.020  1.344
 8MF  N07  N08  aromatic  1.352  0.020  1.352
 8MF  N04  C05  aromatic  1.325  0.020  1.325
 8MF  N04  C03  aromatic  1.328  0.020  1.328
 8MF  C05  C06  aromatic  1.403  0.020  1.403
 8MF  N08  C09  aromatic  1.304  0.020  1.304
 8MF  N21  C03  single    1.338  0.020  1.338
 8MF  C03  N02  aromatic  1.362  0.020  1.362
 8MF  C09  C06  aromatic  1.417  0.020  1.417
 8MF  C06  C01  aromatic  1.389  0.020  1.389
 8MF  N02  C01  aromatic  1.297  0.020  1.297
 8MF  C01  CL1  single    1.724  0.020  1.724
 8MF  C10  H1   single    0.970  0.020  1.090
 8MF  C10  H2   single    0.970  0.020  1.090
 8MF  C13  H3   single    0.930  0.020  1.080
 8MF  C09  H4   single    0.930  0.020  1.080
 8MF  C16  H5   single    0.930  0.020  1.080
 8MF  C18  H6   single    0.970  0.020  1.090
 8MF  C18  H7   single    0.970  0.020  1.090
 8MF  N21  H8   single    0.860  0.020  1.020
 8MF  N21  H9   single    0.860  0.020  1.020

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
 8MF  H2   C10  H1   106.96  3.000
 8MF  H2   C10  C11  112.93  3.000
 8MF  H1   C10  C11  109.61  3.000
 8MF  H2   C10  N07  108.11  3.000
 8MF  H1   C10  N07  107.06  3.000
 8MF  C11  C10  N07  111.89  3.000
 8MF  H3   C13  C14  121.37  3.000
 8MF  H3   C13  C12  122.02  3.000
 8MF  C14  C13  C12  116.61  3.000
 8MF  O19  C15  C16  129.00  3.000
 8MF  C16  C15  C14  121.59  3.000
 8MF  O19  C15  C14  109.40  3.000
 8MF  CL1  C01  C06  119.60  3.000
 8MF  CL1  C01  N02  117.80  3.000
 8MF  C06  C01  N02  122.61  3.000
 8MF  C03  N02  C01  117.97  3.000
 8MF  N21  C03  N04  118.46  3.000
 8MF  N21  C03  N02  115.54  3.000
 8MF  N04  C03  N02  126.00  3.000
 8MF  C05  N04  C03  113.54  3.000
 8MF  N07  C05  C06  106.20  3.000
 8MF  C06  C05  N04  126.15  3.000
 8MF  N07  C05  N04  127.65  3.000
 8MF  C09  C06  C05  104.69  3.000
 8MF  C09  C06  C01  141.58  3.000
 8MF  C05  C06  C01  113.73  3.000
 8MF  N08  N07  C05  111.52  3.000
 8MF  N08  N07  C10  121.44  3.000
 8MF  C05  N07  C10  126.86  3.000
 8MF  C09  N08  N07  107.31  3.000
 8MF  H4   C09  N08  120.89  3.000
 8MF  H4   C09  C06  128.84  3.000
 8MF  N08  C09  C06  110.28  3.000
 8MF  C16  C11  C12  118.84  3.000
 8MF  C16  C11  C10  117.01  3.000
 8MF  C12  C11  C10  124.13  3.000
 8MF  BR1  C12  C11  121.31  3.000
 8MF  C11  C12  C13  122.63  3.000
 8MF  BR1  C12  C13  116.06  3.000
 8MF  O17  C14  C15  109.55  3.000
 8MF  C15  C14  C13  121.85  3.000
 8MF  O17  C14  C13  128.60  3.000
 8MF  H5   C16  C11  120.09  3.000
 8MF  H5   C16  C15  121.42  3.000
 8MF  C11  C16  C15  118.48  3.000
 8MF  C18  O17  C14  106.33  3.000
 8MF  H7   C18  H6   110.62  3.000
 8MF  H7   C18  O19  109.86  3.000
 8MF  H6   C18  O19  109.91  3.000
 8MF  H7   C18  O17  109.71  3.000
 8MF  H6   C18  O17  109.78  3.000
 8MF  O19  C18  O17  106.90  3.000
 8MF  C18  O19  C15  106.38  3.000
 8MF  H9   N21  H8   118.15  3.000
 8MF  H9   N21  C03  119.65  3.000
 8MF  H8   N21  C03  119.83  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
 8MF  CONST_01  C16  C15  C14  C13    0.00   0.0  0
 8MF  CONST_02  C16  C11  C12  C13    0.00   0.0  0
 8MF  CONST_03  C12  C13  C14  C15    0.00   0.0  0
 8MF  CONST_04  C12  C11  C16  C15    0.00   0.0  0
 8MF  CONST_05  N07  C05  C06  C01  180.00   0.0  0
 8MF  CONST_06  N04  C05  C06  C01    0.00   0.0  0
 8MF  CONST_07  N08  C09  C06  C01  180.00   0.0  0
 8MF  CONST_08  N04  C03  N02  C01    0.00   0.0  0
 8MF  CONST_09  C05  N04  C03  N02    0.00   0.0  0
 8MF  CONST_10  C05  C06  C01  N02    0.00   0.0  0
 8MF  CONST_11  C09  C06  C01  N02  180.00   0.0  0
 8MF  CONST_12  N07  C05  N04  C03  180.00   0.0  0
 8MF  CONST_13  C06  C05  N04  C03    0.00   0.0  0
 8MF  CONST_14  C06  C01  N02  C03    0.00   0.0  0
 8MF  CONST_15  N08  N07  C05  N04  180.00   0.0  0
 8MF  CONST_16  C09  C06  C05  N04  180.00   0.0  0
 8MF  CONST_17  C09  N08  N07  C05    0.00   0.0  0
 8MF  CONST_18  N08  C09  C06  C05    0.00   0.0  0
 8MF  CONST_19  N08  N07  C05  C06    0.00   0.0  0
 8MF  CONST_20  N07  N08  C09  C06    0.00   0.0  0
 8MF  CONST_21  C09  C06  C05  N07    0.00   0.0  0
 8MF  CONST_22  C14  C13  C12  C11    0.00   0.0  0
 8MF  CONST_23  C14  C15  C16  C11    0.00   0.0  0
 8MF  CONST_24  C13  C12  C11  C10  180.00   0.0  0
 8MF  CONST_25  C15  C16  C11  C10  180.00   0.0  0
 8MF  CONST_26  N04  C05  N07  C10    0.00   0.0  0
 8MF  CONST_27  C06  C05  N07  C10  180.00   0.0  0
 8MF  CONST_28  C09  N08  N07  C10  180.00   0.0  0
 8MF  CONST_29  N21  C03  N02  C01  180.00   0.0  0
 8MF  CONST_30  CL1  C01  N02  C03  180.00   0.0  0
 8MF  CONST_31  N21  C03  N04  C05  180.00   0.0  0
 8MF  CONST_32  CL1  C01  C06  C05  180.00   0.0  0
 8MF  CONST_33  CL1  C01  C06  C09    0.00   0.0  0
 8MF  CONST_34  BR1  C12  C13  C14  180.00   0.0  0
 8MF  CONST_35  BR1  C12  C11  C16  180.00   0.0  0
 8MF  CONST_36  H3   C13  C14  C15  180.00   0.0  0
 8MF  CONST_37  H4   C09  C06  C01    0.00   0.0  0
 8MF  CONST_38  H5   C16  C11  C12  180.00   0.0  0
 8MF  CONST_39  H8   N21  C03  N02    0.00   0.0  0
 8MF  CONST_40  H9   N21  C03  N02  180.00   0.0  0
 8MF  Var_01    O17  C18  O19  C15   11.65  30.0  1
 8MF  Var_02    O19  C18  O17  C14  -11.67  30.0  1
 8MF  Var_03    C11  C10  N07  C05  -89.22  30.0  2
 8MF  Var_04    C12  C11  C10  N07  -94.40  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
 8MF  plan-1  C10  0.020
 8MF  plan-1  C01  0.020
 8MF  plan-1  N02  0.020
 8MF  plan-1  C03  0.020
 8MF  plan-1  N04  0.020
 8MF  plan-1  C05  0.020
 8MF  plan-1  C06  0.020
 8MF  plan-1  N07  0.020
 8MF  plan-1  N08  0.020
 8MF  plan-1  C09  0.020
 8MF  plan-1  N21  0.020
 8MF  plan-1  H4   0.020
 8MF  plan-1  CL1  0.020
 8MF  plan-2  C10  0.020
 8MF  plan-2  C13  0.020
 8MF  plan-2  C15  0.020
 8MF  plan-2  C11  0.020
 8MF  plan-2  C12  0.020
 8MF  plan-2  C14  0.020
 8MF  plan-2  C16  0.020
 8MF  plan-2  O17  0.020
 8MF  plan-2  O19  0.020
 8MF  plan-2  BR1  0.020
 8MF  plan-2  H3   0.020
 8MF  plan-2  H5   0.020
 8MF  plan-3  C03  0.020
 8MF  plan-3  N21  0.020
 8MF  plan-3  H8   0.020
 8MF  plan-3  H9   0.020

