# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 03:29:35 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 3-[(4-amino-1-tert-butyl-1H-pyrazolo[3,4-d]pyrimidin-3-yl)methyl]phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)n1nc(Cc2cccc(O)c2)c3c(N)ncnc13
#
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
 RB1  RB1  3-[(4-amino-1-tert-butyl-1H-pyrazolo[3,4-d]pyrimidin-3-yl)methyl]phenol  ligand  41  22  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RB1
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
 RB1  C20   C  CH3   0  -0.648   3.1868   2.9715  -0.7240
 RB1  C19   C  CT    0   0.062   3.3864   1.6264  -0.0345
 RB1  C21   C  CH3   0  -0.647   4.5605   0.8940  -0.6837
 RB1  C22   C  CH3   0  -0.649   3.6463   1.8527   1.4552
 RB1  N7    N  NR5   0  -0.381   2.1633   0.8143  -0.1924
 RB1  N8    N  N     0  -0.274   1.1034   1.2767  -0.8784
 RB1  C3    C  CR56  0   0.592   1.9180  -0.4247   0.2820
 RB1  N2    N  N     0  -0.464   2.7395  -1.2118   0.9889
 RB1  C1    C  CR16  0   0.051   2.1950  -2.3727   1.2853
 RB1  N6    N  N     0  -0.479   0.9754  -2.8187   0.9909
 RB1  C5    C  CR6   0   0.427   0.1551  -2.0294   0.2942
 RB1  N10   N  NH2   0  -0.821  -1.0643  -2.4942   0.0026
 RB1  C4    C  CR56  0  -0.251   0.6206  -0.7613  -0.1168
 RB1  C9    C  CR5   0   0.302   0.1682   0.3620  -0.8567
 RB1  C11   C  CH2   0  -0.607  -1.1286   0.5714  -1.5636
 RB1  C12   C  CR6   0   0.088  -2.3278   0.5594  -0.6452
 RB1  C13   C  CR16  0  -0.458  -3.4845  -0.1107  -1.0340
 RB1  C17   C  CR16  0  -0.304  -2.2997   1.2197   0.5793
 RB1  C16   C  CR16  0  -0.227  -3.4238   1.2067   1.3934
 RB1  C15   C  CR16  0  -0.350  -4.5782   0.5412   1.0113
 RB1  C14   C  CR6   0   0.375  -4.6098  -0.1235  -0.2114
 RB1  O18   O  OH1   0  -0.631  -5.7445  -0.7647  -0.5515
 RB1  H201  H  HCH3  0   0.238   2.9986   2.8627  -1.7913
 RB1  H202  H  HCH3  0   0.238   2.3659   3.5397  -0.2875
 RB1  H203  H  HCH3  0   0.237   4.1001   3.5538  -0.6011
 RB1  H211  H  HCH3  0   0.234   5.4519   1.5209  -0.6384
 RB1  H212  H  HCH3  0   0.245   4.7837  -0.0429  -0.1757
 RB1  H213  H  HCH3  0   0.235   4.3542   0.6809  -1.7335
 RB1  H221  H  HCH3  0   0.235   2.7936   2.3404   1.9295
 RB1  H222  H  HCH3  0   0.246   3.8455   0.9172   1.9754
 RB1  H223  H  HCH3  0   0.234   4.5152   2.4998   1.5800
 RB1  H1    H  HCR6  0   0.252   2.8156  -3.0607   1.8506
 RB1  H101  H  HNH2  0   0.416  -1.7907  -1.8810  -0.3267
 RB1  H102  H  HNH2  0   0.402  -1.3600  -3.3599   0.4225
 RB1  H111  H  HCH2  0   0.287  -1.0801   1.5282  -2.0900
 RB1  H112  H  HCH2  0   0.270  -1.2533  -0.1953  -2.3329
 RB1  H13   H  HCR6  0   0.277  -3.5078  -0.6272  -1.9893
 RB1  H17   H  HCR6  0   0.249  -1.4063   1.7419   0.8982
 RB1  H16   H  HCR6  0   0.259  -3.4035   1.7232   2.3445
 RB1  H15   H  HCR6  0   0.264  -5.4495   0.5329   1.6539
 RB1  H18   H  HOH1  0   0.475  -5.6510  -1.1812  -1.4156

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
 RB1  C20  C19   single    1.525  0.020  1.525
 RB1  C20  H201  single    0.970  0.020  1.090
 RB1  C20  H202  single    0.970  0.020  1.090
 RB1  C20  H203  single    0.970  0.020  1.090
 RB1  C19  C21   single    1.529  0.020  1.529
 RB1  C19  C22   single    1.529  0.020  1.529
 RB1  C19  N7    single    1.477  0.020  1.477
 RB1  C21  H211  single    0.970  0.020  1.090
 RB1  C21  H212  single    0.970  0.020  1.090
 RB1  C21  H213  single    0.970  0.020  1.090
 RB1  C22  H221  single    0.970  0.020  1.090
 RB1  C22  H222  single    0.970  0.020  1.090
 RB1  C22  H223  single    0.970  0.020  1.090
 RB1  N7   N8    aromatic  1.345  0.020  1.345
 RB1  N7   C3    aromatic  1.349  0.020  1.349
 RB1  N8   C9    aromatic  1.308  0.020  1.308
 RB1  C3   N2    aromatic  1.339  0.020  1.339
 RB1  C3   C4    aromatic  1.398  0.020  1.398
 RB1  N2   C1    aromatic  1.316  0.020  1.316
 RB1  C1   N6    aromatic  1.332  0.020  1.332
 RB1  C1   H1    single    0.930  0.020  1.080
 RB1  N6   C5    aromatic  1.335  0.020  1.335
 RB1  C5   N10   single    1.337  0.020  1.337
 RB1  C5   C4    aromatic  1.412  0.020  1.412
 RB1  N10  H101  single    0.890  0.020  1.040
 RB1  N10  H102  single    0.890  0.020  1.040
 RB1  C4   C9    aromatic  1.419  0.020  1.419
 RB1  C9   C11   single    1.492  0.020  1.492
 RB1  C11  C12   single    1.511  0.020  1.511
 RB1  C11  H111  single    0.970  0.020  1.090
 RB1  C11  H112  single    0.970  0.020  1.090
 RB1  C12  C13   aromatic  1.392  0.020  1.392
 RB1  C12  C17   aromatic  1.391  0.020  1.391
 RB1  C13  C14   aromatic  1.394  0.020  1.394
 RB1  C13  H13   single    0.930  0.020  1.080
 RB1  C17  C16   aromatic  1.388  0.020  1.388
 RB1  C17  H17   single    0.930  0.020  1.080
 RB1  C16  C15   aromatic  1.386  0.020  1.386
 RB1  C16  H16   single    0.930  0.020  1.080
 RB1  C15  C14   aromatic  1.392  0.020  1.392
 RB1  C15  H15   single    0.930  0.020  1.080
 RB1  C14  O18   single    1.347  0.020  1.347
 RB1  O18  H18   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
 RB1  H203  C20  H202  107.91  3.000
 RB1  H203  C20  H201  107.97  3.000
 RB1  H202  C20  H201  108.33  3.000
 RB1  H203  C20  C19   108.10  3.000
 RB1  H202  C20  C19   112.18  3.000
 RB1  H201  C20  C19   112.19  3.000
 RB1  N7    C19  C22   109.05  3.000
 RB1  N7    C19  C21   109.11  3.000
 RB1  C22   C19  C21   110.74  3.000
 RB1  N7    C19  C20   109.17  3.000
 RB1  C22   C19  C20   109.41  3.000
 RB1  C21   C19  C20   109.34  3.000
 RB1  H213  C21  H212  108.64  3.000
 RB1  H213  C21  H211  107.87  3.000
 RB1  H212  C21  H211  107.92  3.000
 RB1  H213  C21  C19   110.91  3.000
 RB1  H212  C21  C19   111.81  3.000
 RB1  H211  C21  C19   109.56  3.000
 RB1  H223  C22  H222  108.03  3.000
 RB1  H223  C22  H221  107.92  3.000
 RB1  H222  C22  H221  108.63  3.000
 RB1  H223  C22  C19   109.56  3.000
 RB1  H222  C22  C19   111.68  3.000
 RB1  H221  C22  C19   110.91  3.000
 RB1  C3    N7   N8    110.60  3.000
 RB1  C3    N7   C19   128.18  3.000
 RB1  N8    N7   C19   121.22  3.000
 RB1  C9    N8   N7    108.34  3.000
 RB1  C4    C3   N2    125.32  3.000
 RB1  C4    C3   N7    106.83  3.000
 RB1  N2    C3   N7    127.85  3.000
 RB1  C1    N2   C3    112.54  3.000
 RB1  H1    C1   N6    115.25  3.000
 RB1  H1    C1   N2    116.10  3.000
 RB1  N6    C1   N2    128.65  3.000
 RB1  C5    N6   C1    118.71  3.000
 RB1  C4    C5   N10   123.32  3.000
 RB1  C4    C5   N6    118.71  3.000
 RB1  N10   C5   N6    117.96  3.000
 RB1  H102  N10  H101  116.66  3.000
 RB1  H102  N10  C5    118.42  3.000
 RB1  H101  N10  C5    121.20  3.000
 RB1  C9    C4   C5    139.25  3.000
 RB1  C9    C4   C3    104.71  3.000
 RB1  C5    C4   C3    116.04  3.000
 RB1  C11   C9   C4    129.44  3.000
 RB1  C11   C9   N8    121.03  3.000
 RB1  C4    C9   N8    109.52  3.000
 RB1  H112  C11  H111  106.26  3.000
 RB1  H112  C11  C12   109.37  3.000
 RB1  H111  C11  C12   109.57  3.000
 RB1  H112  C11  C9    109.52  3.000
 RB1  H111  C11  C9    108.21  3.000
 RB1  C12   C11  C9    113.64  3.000
 RB1  C17   C12  C13   119.40  3.000
 RB1  C17   C12  C11   121.01  3.000
 RB1  C13   C12  C11   119.58  3.000
 RB1  H13   C13  C14   119.82  3.000
 RB1  H13   C13  C12   119.49  3.000
 RB1  C14   C13  C12   120.69  3.000
 RB1  H17   C17  C16   119.99  3.000
 RB1  H17   C17  C12   120.31  3.000
 RB1  C16   C17  C12   119.69  3.000
 RB1  H16   C16  C15   119.14  3.000
 RB1  H16   C16  C17   119.71  3.000
 RB1  C15   C16  C17   121.15  3.000
 RB1  H15   C15  C14   119.96  3.000
 RB1  H15   C15  C16   120.68  3.000
 RB1  C14   C15  C16   119.36  3.000
 RB1  O18   C14  C15   117.92  3.000
 RB1  O18   C14  C13   122.37  3.000
 RB1  C15   C14  C13   119.71  3.000
 RB1  H18   O18  C14   110.51  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
 RB1  CONST_01  C4    C9   N8   N7      0.00   0.0  0
 RB1  CONST_02  C1    N2   C3   N7    180.00   0.0  0
 RB1  CONST_03  C5    C4   C3   N7    180.00   0.0  0
 RB1  CONST_04  C9    C4   C3   N7      0.00   0.0  0
 RB1  CONST_05  N2    C3   N7   N8    180.00   0.0  0
 RB1  CONST_06  C4    C3   N7   N8      0.00   0.0  0
 RB1  CONST_07  C3    C4   C9   N8      0.00   0.0  0
 RB1  CONST_08  C5    C4   C9   N8    180.00   0.0  0
 RB1  CONST_09  C9    N8   N7   C3      0.00   0.0  0
 RB1  CONST_10  N6    C1   N2   C3      0.00   0.0  0
 RB1  CONST_11  N6    C5   C4   C3      0.00   0.0  0
 RB1  CONST_12  C5    C4   C3   N2      0.00   0.0  0
 RB1  CONST_13  C9    C4   C3   N2    180.00   0.0  0
 RB1  CONST_14  C5    N6   C1   N2      0.00   0.0  0
 RB1  CONST_15  C4    C3   N2   C1      0.00   0.0  0
 RB1  CONST_16  C4    C5   N6   C1      0.00   0.0  0
 RB1  CONST_17  C9    C4   C5   N6    180.00   0.0  0
 RB1  CONST_18  C15   C14  C13  C12     0.00   0.0  0
 RB1  CONST_19  C15   C16  C17  C12     0.00   0.0  0
 RB1  CONST_20  C16   C17  C12  C13     0.00   0.0  0
 RB1  CONST_21  C16   C15  C14  C13     0.00   0.0  0
 RB1  CONST_22  C14   C13  C12  C17     0.00   0.0  0
 RB1  CONST_23  C14   C15  C16  C17     0.00   0.0  0
 RB1  CONST_24  C9    N8   N7   C19   180.00   0.0  0
 RB1  CONST_25  N2    C3   N7   C19     0.00   0.0  0
 RB1  CONST_26  C4    C3   N7   C19   180.00   0.0  0
 RB1  CONST_27  C11   C9   N8   N7    180.00   0.0  0
 RB1  CONST_28  N10   C5   C4   C3    180.00   0.0  0
 RB1  CONST_29  C11   C9   C4   C3    180.00   0.0  0
 RB1  CONST_30  N10   C5   N6   C1    180.00   0.0  0
 RB1  CONST_31  C11   C9   C4   C5      0.00   0.0  0
 RB1  CONST_32  C9    C4   C5   N10     0.00   0.0  0
 RB1  CONST_33  C14   C13  C12  C11   180.00   0.0  0
 RB1  CONST_34  C16   C17  C12  C11   180.00   0.0  0
 RB1  CONST_35  O18   C14  C13  C12   180.00   0.0  0
 RB1  CONST_36  O18   C14  C15  C16   180.00   0.0  0
 RB1  CONST_37  H1    C1   N2   C3    180.00   0.0  0
 RB1  CONST_38  H16   C16  C17  C12   180.00   0.0  0
 RB1  CONST_39  H17   C17  C12  C13   180.00   0.0  0
 RB1  CONST_40  H15   C15  C14  C13   180.00   0.0  0
 RB1  CONST_41  H13   C13  C12  C17   180.00   0.0  0
 RB1  CONST_42  H101  N10  C5   N6    180.00   0.0  0
 RB1  CONST_43  H102  N10  C5   N6      0.00   0.0  0
 RB1  Var_01    C12   C11  C9   N8   -118.66  30.0  2
 RB1  Var_02    C13   C12  C11  C9   -137.68  30.0  2
 RB1  Var_03    N8    N7   C19  C20     1.08  30.0  2
 RB1  Var_04    H201  C20  C19  N7    -60.79  30.0  3
 RB1  Var_05    H211  C21  C19  N7    175.73  30.0  3
 RB1  Var_06    H221  C22  C19  N7    -57.72  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
 RB1  plan-1  C11   0.020
 RB1  plan-1  C12   0.020
 RB1  plan-1  C13   0.020
 RB1  plan-1  C17   0.020
 RB1  plan-1  C16   0.020
 RB1  plan-1  C15   0.020
 RB1  plan-1  C14   0.020
 RB1  plan-1  O18   0.020
 RB1  plan-1  H13   0.020
 RB1  plan-1  H17   0.020
 RB1  plan-1  H16   0.020
 RB1  plan-1  H15   0.020
 RB1  plan-2  C19   0.020
 RB1  plan-2  N7    0.020
 RB1  plan-2  N8    0.020
 RB1  plan-2  C3    0.020
 RB1  plan-2  N2    0.020
 RB1  plan-2  C1    0.020
 RB1  plan-2  N6    0.020
 RB1  plan-2  C5    0.020
 RB1  plan-2  N10   0.020
 RB1  plan-2  C4    0.020
 RB1  plan-2  C9    0.020
 RB1  plan-2  C11   0.020
 RB1  plan-2  H1    0.020
 RB1  plan-3  C5    0.020
 RB1  plan-3  N10   0.020
 RB1  plan-3  H101  0.020
 RB1  plan-3  H102  0.020

