# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 22:29:28 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 2-{[(3R,5R)-5-(2,3-dihydro-1,4-benzodioxin-6-yl)-1-methylpiperidin-3-yl]amino}-3-methyl-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C[C@@H](C[C@@H](C1)c2ccc3OCCOc3c2)NC4=Nc5cc[nH]c5C(=O)N4C
#
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
 B8O  B8O  2-{[(3R,5R)-5-(2,3-dihydro-1,4-benzodioxin-6-yl)-1-methylpiperidin-3-yl]amino}-3-methyl-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one  ligand  54  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 OK
;

data_comp_B8O
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
 B8O  C7   C  CH1   0  -0.364  -1.6428  -0.8342   0.0247
 B8O  C8   C  CH2   0  -0.246  -1.4250  -2.0367   0.9434
 B8O  C6   C  CR6   0   0.335  -5.1860   0.2253  -0.8514
 B8O  C10  C  CH2   0  -0.268   0.9159  -1.5881   1.1272
 B8O  N9   N  NT    0  -0.416  -0.0885  -2.5744   0.7891
 B8O  C5   C  CR16  0  -0.454  -3.8946  -0.2804  -0.9410
 B8O  C4   C  CR6   0   0.190  -3.0401  -0.2845   0.1544
 B8O  C1   C  CR6   0   0.296  -5.6425   0.7464   0.3613
 B8O  C3   C  CR16  0  -0.329  -3.5145   0.2232   1.3639
 B8O  C2   C  CR16  0  -0.348  -4.7972   0.7362   1.4634
 B8O  C11  C  CH1   0  -0.070   0.8120  -0.3765   0.2037
 B8O  C12  C  CH2   0  -0.431  -0.5796   0.2331   0.2921
 B8O  C14  C  CH3   0  -0.518   0.0844  -3.7922   1.5487
 B8O  C15  C  CR6   0   0.744   3.0988   0.5119   0.1690
 B8O  C17  C  CR6   0   0.536   5.3284   1.5087   0.3208
 B8O  C18  C  CR56  0   0.121   5.6866   0.4369  -0.5312
 B8O  C19  C  CR56  0   0.202   4.7628  -0.5010  -0.9665
 B8O  C22  C  CR15  0  -0.017   6.7722  -0.9923  -1.8154
 B8O  C23  C  CR15  0  -0.427   5.4612  -1.4180  -1.7900
 B8O  C26  C  CH2   0  -0.225  -7.3472   0.4195  -1.7063
 B8O  C27  C  CH2   0  -0.227  -7.5234   1.5645  -0.7380
 B8O  N13  N  NH1   0  -0.713   1.7993   0.6325   0.5304
 B8O  N16  N  NR6   0  -0.591   3.9611   1.4897   0.6373
 B8O  N20  N  N     0  -0.532   3.4547  -0.4694  -0.6069
 B8O  N21  N  NR15  0  -0.647   6.9066   0.1191  -1.0592
 B8O  O24  O  O     0  -0.495   6.0809   2.3741   0.7512
 B8O  O25  O  O2    0  -0.482  -5.9683   0.1943  -1.9573
 B8O  O28  O  O2    0  -0.481  -6.8865   1.2688   0.4949
 B8O  H1   H  HCH1  0   0.248  -1.5119  -1.1846  -1.0045
 B8O  H2   H  HCH2  0   0.190  -1.6203  -1.7419   1.9909
 B8O  H3   H  HCH2  0   0.242  -2.1495  -2.8174   0.6965
 B8O  H4   H  HCH2  0   0.184   0.8206  -1.2434   2.1744
 B8O  H5   H  HCH2  0   0.245   1.9058  -2.0362   1.0218
 B8O  H7   H  HCR6  0   0.259  -3.5599  -0.6737  -1.8945
 B8O  H8   H  HCR6  0   0.246  -2.8795   0.2343   2.2413
 B8O  H9   H  HCR6  0   0.264  -5.1563   1.1378   2.4030
 B8O  H10  H  HCH1  0   0.247   0.9942  -0.7062  -0.8208
 B8O  H11  H  HCH2  0   0.255  -0.6795   1.0545  -0.4211
 B8O  H12  H  HCH2  0   0.225  -0.7271   0.6540   1.2941
 B8O  H13  H  HCH3  0   0.233  -0.6445  -4.5390   1.2298
 B8O  H14  H  HCH3  0   0.234   1.0805  -4.2021   1.3760
 B8O  H15  H  HCH3  0   0.192  -0.0370  -3.6487   2.6338
 B8O  H16  H  HCR5  0   0.285   7.6208  -1.4142  -2.3289
 B8O  H17  H  HCR5  0   0.251   5.0596  -2.2796  -2.2985
 B8O  H18  H  HCH2  0   0.242  -7.8117  -0.4905  -1.3112
 B8O  H19  H  HCH2  0   0.259  -7.8143   0.6563  -2.6615
 B8O  H20  H  HCH2  0   0.242  -7.1135   2.4878  -1.1618
 B8O  H21  H  HCH2  0   0.260  -8.5797   1.7237  -0.5266
 B8O  H22  H  HCH3  0   0.289   4.2531   3.2469   1.7043
 B8O  H23  H  HCH3  0   0.264   2.6533   3.1037   0.9799
 B8O  H24  H  HCH3  0   0.262   3.0748   2.1620   2.4307
 B8O  H25  H  HNH1  0   0.412   1.5638   1.2381   1.2989
 B8O  H26  H  HNR5  0   0.415   7.7628   0.6282  -0.9145
 B8O  C29  C  CH3   0  -0.587   3.4482   2.5560   1.4851

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
 B8O  O24  C17  double    1.225  0.020  1.225
 B8O  C29  N16  single    1.456  0.020  1.456
 B8O  C17  N16  single    1.404  0.020  1.404
 B8O  C17  C18  single    1.415  0.020  1.415
 B8O  N16  C15  single    1.385  0.020  1.385
 B8O  C18  N21  aromatic  1.367  0.020  1.367
 B8O  C18  C19  aromatic  1.387  0.020  1.387
 B8O  N21  C22  aromatic  1.351  0.020  1.351
 B8O  C15  N13  single    1.354  0.020  1.354
 B8O  C15  N20  double    1.301  0.020  1.301
 B8O  N13  C11  single    1.449  0.020  1.449
 B8O  C19  N20  single    1.357  0.020  1.357
 B8O  C19  C23  aromatic  1.417  0.020  1.417
 B8O  C22  C23  aromatic  1.379  0.020  1.379
 B8O  C26  O25  single    1.420  0.020  1.420
 B8O  C26  C27  single    1.510  0.020  1.510
 B8O  O25  C6   single    1.355  0.020  1.355
 B8O  C12  C11  single    1.522  0.020  1.522
 B8O  C12  C7   single    1.530  0.020  1.530
 B8O  C11  C10  single    1.527  0.020  1.527
 B8O  C10  N9   single    1.448  0.020  1.448
 B8O  C6   C5   aromatic  1.390  0.020  1.390
 B8O  C6   C1   aromatic  1.397  0.020  1.397
 B8O  C27  O28  single    1.419  0.020  1.419
 B8O  C5   C4   aromatic  1.389  0.020  1.389
 B8O  O28  C1   single    1.356  0.020  1.356
 B8O  C1   C2   aromatic  1.389  0.020  1.389
 B8O  C4   C7   single    1.507  0.020  1.507
 B8O  C4   C3   aromatic  1.395  0.020  1.395
 B8O  C7   C8   single    1.529  0.020  1.529
 B8O  C8   N9   single    1.449  0.020  1.449
 B8O  N9   C14  single    1.446  0.020  1.446
 B8O  C3   C2   aromatic  1.385  0.020  1.385
 B8O  C7   H1   single    0.970  0.020  1.090
 B8O  C8   H2   single    0.970  0.020  1.090
 B8O  C8   H3   single    0.970  0.020  1.090
 B8O  C10  H4   single    0.970  0.020  1.090
 B8O  C10  H5   single    0.970  0.020  1.090
 B8O  C5   H7   single    0.930  0.020  1.080
 B8O  C3   H8   single    0.930  0.020  1.080
 B8O  C2   H9   single    0.930  0.020  1.080
 B8O  C11  H10  single    0.970  0.020  1.090
 B8O  C12  H11  single    0.970  0.020  1.090
 B8O  C12  H12  single    0.970  0.020  1.090
 B8O  C14  H13  single    0.970  0.020  1.090
 B8O  C14  H14  single    0.970  0.020  1.090
 B8O  C14  H15  single    0.970  0.020  1.090
 B8O  C22  H16  single    0.930  0.020  1.080
 B8O  C23  H17  single    0.930  0.020  1.080
 B8O  C26  H18  single    0.970  0.020  1.090
 B8O  C26  H19  single    0.970  0.020  1.090
 B8O  C27  H20  single    0.970  0.020  1.090
 B8O  C27  H21  single    0.970  0.020  1.090
 B8O  C29  H22  single    0.970  0.020  1.090
 B8O  C29  H23  single    0.970  0.020  1.090
 B8O  C29  H24  single    0.970  0.020  1.090
 B8O  N13  H25  single    0.890  0.020  1.040
 B8O  N21  H26  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
 B8O  H1   C7   C12  107.72  3.000
 B8O  H1   C7   C4   107.97  3.000
 B8O  C12  C7   C4   112.01  3.000
 B8O  H1   C7   C8   107.22  3.000
 B8O  C4   C7   C8   111.55  3.000
 B8O  C12  C7   C8   110.16  3.000
 B8O  H3   C8   H2   106.69  3.000
 B8O  H3   C8   N9   108.80  3.000
 B8O  H2   C8   N9   111.28  3.000
 B8O  H3   C8   C7   109.36  3.000
 B8O  H2   C8   C7   109.53  3.000
 B8O  N9   C8   C7   111.06  3.000
 B8O  O25  C6   C1   121.91  3.000
 B8O  C1   C6   C5   119.70  3.000
 B8O  O25  C6   C5   118.39  3.000
 B8O  H5   C10  H4   107.30  3.000
 B8O  H5   C10  C11  109.21  3.000
 B8O  H4   C10  C11  108.62  3.000
 B8O  H5   C10  N9   109.08  3.000
 B8O  H4   C10  N9   111.93  3.000
 B8O  C11  C10  N9   110.61  3.000
 B8O  C14  N9   C10  111.60  3.000
 B8O  C14  N9   C8   111.53  3.000
 B8O  C10  N9   C8   111.24  3.000
 B8O  H7   C5   C4   120.16  3.000
 B8O  H7   C5   C6   118.39  3.000
 B8O  C4   C5   C6   121.45  3.000
 B8O  C3   C4   C5   118.26  3.000
 B8O  C3   C4   C7   121.51  3.000
 B8O  C5   C4   C7   120.23  3.000
 B8O  O28  C1   C2   118.88  3.000
 B8O  C2   C1   C6   119.16  3.000
 B8O  O28  C1   C6   121.95  3.000
 B8O  H8   C3   C2   118.75  3.000
 B8O  H8   C3   C4   120.45  3.000
 B8O  C2   C3   C4   120.80  3.000
 B8O  H9   C2   C3   120.44  3.000
 B8O  H9   C2   C1   118.94  3.000
 B8O  C3   C2   C1   120.62  3.000
 B8O  H10  C11  N13  107.95  3.000
 B8O  H10  C11  C12  109.16  3.000
 B8O  N13  C11  C12  109.33  3.000
 B8O  H10  C11  C10  108.46  3.000
 B8O  C12  C11  C10  110.18  3.000
 B8O  N13  C11  C10  111.70  3.000
 B8O  H12  C12  H11  107.19  3.000
 B8O  H12  C12  C11  109.25  3.000
 B8O  H11  C12  C11  110.30  3.000
 B8O  H12  C12  C7   109.51  3.000
 B8O  H11  C12  C7   110.29  3.000
 B8O  C11  C12  C7   110.23  3.000
 B8O  H15  C14  H14  107.79  3.000
 B8O  H15  C14  H13  107.67  3.000
 B8O  H14  C14  H13  107.85  3.000
 B8O  H15  C14  N9   113.25  3.000
 B8O  H14  C14  N9   110.03  3.000
 B8O  H13  C14  N9   110.06  3.000
 B8O  N20  C15  N16  124.32  3.000
 B8O  N20  C15  N13  119.27  3.000
 B8O  N16  C15  N13  116.38  3.000
 B8O  O24  C17  N16  121.92  3.000
 B8O  N16  C17  C18  111.84  3.000
 B8O  O24  C17  C18  126.23  3.000
 B8O  N21  C18  C19  108.43  3.000
 B8O  C19  C18  C17  122.19  3.000
 B8O  N21  C18  C17  129.39  3.000
 B8O  N20  C19  C23  130.11  3.000
 B8O  C23  C19  C18  106.98  3.000
 B8O  N20  C19  C18  122.91  3.000
 B8O  H16  C22  N21  120.69  3.000
 B8O  H16  C22  C23  129.54  3.000
 B8O  N21  C22  C23  109.78  3.000
 B8O  H17  C23  C22  126.33  3.000
 B8O  H17  C23  C19  127.44  3.000
 B8O  C22  C23  C19  106.24  3.000
 B8O  H19  C26  H18  108.36  3.000
 B8O  H19  C26  O25  107.21  3.000
 B8O  H18  C26  O25  110.11  3.000
 B8O  H19  C26  C27  110.33  3.000
 B8O  H18  C26  C27  110.44  3.000
 B8O  O25  C26  C27  110.31  3.000
 B8O  H21  C27  H20  108.35  3.000
 B8O  H21  C27  O28  107.29  3.000
 B8O  H20  C27  O28  110.11  3.000
 B8O  H21  C27  C26  110.40  3.000
 B8O  H20  C27  C26  110.33  3.000
 B8O  O28  C27  C26  110.30  3.000
 B8O  H25  N13  C15  118.81  3.000
 B8O  H25  N13  C11  115.58  3.000
 B8O  C15  N13  C11  122.12  3.000
 B8O  C29  N16  C17  117.69  3.000
 B8O  C17  N16  C15  122.67  3.000
 B8O  C29  N16  C15  119.65  3.000
 B8O  C19  N20  C15  116.07  3.000
 B8O  H26  N21  C22  125.53  3.000
 B8O  H26  N21  C18  125.88  3.000
 B8O  C22  N21  C18  108.59  3.000
 B8O  C26  O25  C6   114.38  3.000
 B8O  C27  O28  C1   113.99  3.000
 B8O  H24  C29  H23  109.51  3.000
 B8O  H24  C29  H22  108.03  3.000
 B8O  H23  C29  H22  108.39  3.000
 B8O  H24  C29  N16  111.16  3.000
 B8O  H23  C29  N16  110.81  3.000
 B8O  H22  C29  N16  108.86  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
 B8O  CONST_01  C3   C4   C5   C6      0.00   0.0  0
 B8O  CONST_02  C3   C2   C1   C6      0.00   0.0  0
 B8O  CONST_03  C2   C1   C6   C5      0.00   0.0  0
 B8O  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 B8O  CONST_05  C1   C6   C5   C4      0.00   0.0  0
 B8O  CONST_06  C1   C2   C3   C4      0.00   0.0  0
 B8O  CONST_07  C23  C22  N21  C18     0.00   0.0  0
 B8O  CONST_08  C22  C23  C19  C18     0.00   0.0  0
 B8O  CONST_09  C22  N21  C18  C19     0.00   0.0  0
 B8O  CONST_10  N21  C22  C23  C19     0.00   0.0  0
 B8O  CONST_11  N21  C18  C19  C23     0.00   0.0  0
 B8O  CONST_12  C6   C5   C4   C7    180.00   0.0  0
 B8O  CONST_13  C2   C3   C4   C7    180.00   0.0  0
 B8O  CONST_14  C18  C17  N16  C15     0.00   0.0  0
 B8O  CONST_15  N20  C15  N16  C17     0.00   0.0  0
 B8O  CONST_16  N16  C15  N20  C19     0.00   0.0  0
 B8O  CONST_17  N16  C15  N13  C11   180.00   0.0  0
 B8O  CONST_18  N20  C15  N13  C11     0.00   0.0  0
 B8O  CONST_19  O24  C17  N16  C15   180.00   0.0  0
 B8O  CONST_20  N13  C15  N16  C17   180.00   0.0  0
 B8O  CONST_21  C29  N16  C17  C18   180.00   0.0  0
 B8O  CONST_22  N13  C15  N20  C19   180.00   0.0  0
 B8O  CONST_23  N20  C15  N16  C29   180.00   0.0  0
 B8O  CONST_24  H7   C5   C4   C7      0.00   0.0  0
 B8O  CONST_25  H8   C3   C4   C7      0.00   0.0  0
 B8O  CONST_26  H9   C2   C1   C6    180.00   0.0  0
 B8O  CONST_27  H26  N21  C18  C17     0.00   0.0  0
 B8O  CONST_28  H16  C22  N21  C18   180.00   0.0  0
 B8O  CONST_29  H17  C23  C19  C18   180.00   0.0  0
 B8O  CONST_30  O24  C17  N16  C29     0.00   0.0  0
 B8O  CONST_31  N13  C15  N16  C29     0.00   0.0  0
 B8O  Var_01    C10  N9   C8   C7     60.61  30.0  1
 B8O  Var_02    C11  C10  N9   C8    -61.19  30.0  1
 B8O  Var_03    C27  C26  O25  C6     43.79  30.0  1
 B8O  Var_04    C26  C27  O28  C1     45.23  30.0  1
 B8O  Var_05    O28  C27  C26  O25   -60.30  30.0  1
 B8O  Var_06    H13  C14  N9   C8     58.46  30.0  3
 B8O  Var_07    H22  C29  N16  C15  -176.99  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
 B8O  chir_01  C7   C12  C4   C8   positiv
 B8O  chir_02  C11  N13  C10  C12  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
 B8O  plan-1  C11  0.020
 B8O  plan-1  C15  0.020
 B8O  plan-1  C17  0.020
 B8O  plan-1  C18  0.020
 B8O  plan-1  C19  0.020
 B8O  plan-1  C22  0.020
 B8O  plan-1  C23  0.020
 B8O  plan-1  N13  0.020
 B8O  plan-1  N16  0.020
 B8O  plan-1  N20  0.020
 B8O  plan-1  N21  0.020
 B8O  plan-1  O24  0.020
 B8O  plan-1  H16  0.020
 B8O  plan-1  H17  0.020
 B8O  plan-1  H25  0.020
 B8O  plan-1  H26  0.020
 B8O  plan-1  C29  0.020
 B8O  plan-2  C7   0.020
 B8O  plan-2  C6   0.020
 B8O  plan-2  C5   0.020
 B8O  plan-2  C4   0.020
 B8O  plan-2  C1   0.020
 B8O  plan-2  C3   0.020
 B8O  plan-2  C2   0.020
 B8O  plan-2  O25  0.020
 B8O  plan-2  O28  0.020
 B8O  plan-2  H7   0.020
 B8O  plan-2  H8   0.020
 B8O  plan-2  H9   0.020

