# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 09:17:16 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 1-tert-butyl-3-(4-methylphenyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)c2nn(c3ncnc(N)c23)C(C)(C)C
#
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
 PP1  PP1  1-tert-butyl-3-(4-methylphenyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine  ligand  40  21  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PP1
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
 PP1  N1    N  NR5   0  -0.374   0.6686  -0.0451  -1.8410
 PP1  C2    C  CR16  0   0.048  -2.7637   0.1190  -2.5599
 PP1  N3    N  N     0  -0.466  -1.4962   0.0362  -2.9013
 PP1  C4    C  CR56  0   0.589  -0.6799   0.0126  -1.8404
 PP1  C5    C  CR56  0  -0.263  -1.0844   0.0529  -0.5021
 PP1  C6    C  CR6   0   0.432  -2.4750   0.2001  -0.2846
 PP1  N7    N  N     0  -0.478  -3.2915   0.2092  -1.3402
 PP1  N8    N  N     0  -0.270   1.1441  -0.0553  -0.5886
 PP1  C9    C  CR5   0   0.269   0.1268  -0.0034   0.2385
 PP1  N10   N  NH2   0  -0.818  -3.0233   0.3301   0.9252
 PP1  C11   C  CR6   0   0.023   0.3507  -0.0187   1.6878
 PP1  C12   C  CR16  0  -0.327  -0.4270  -0.8144   2.5273
 PP1  C13   C  CR16  0  -0.282  -0.1972  -0.8353   3.8954
 PP1  C14   C  CR6   0   0.091   0.8199  -0.0753   4.4664
 PP1  C15   C  CR16  0  -0.284   1.6032   0.7091   3.6198
 PP1  C16   C  CR16  0  -0.272   1.3763   0.7387   2.2540
 PP1  C24   C  CH3   0  -0.723   1.0859  -0.1198   5.9420
 PP1  C28   C  CT    0   0.061   1.5757  -0.1010  -3.0059
 PP1  C29   C  CH3   0  -0.647   3.0192  -0.1589  -2.5193
 PP1  C33   C  CH3   0  -0.649   1.2663  -1.3566  -3.8218
 PP1  C37   C  CH3   0  -0.648   1.3732   1.1566  -3.8516
 PP1  HC2   H  HCR6  0   0.253  -3.4793   0.1266  -3.3755
 PP1  H101  H  HNH2  0   0.405  -4.0117   0.5039   0.9983
 PP1  H102  H  HNH2  0   0.414  -2.4642   0.4737   1.7479
 PP1  HC12  H  HCR6  0   0.267  -1.2045  -1.4451   2.1123
 PP1  HC13  H  HCR6  0   0.253  -0.8152  -1.4627   4.5264
 PP1  HC15  H  HCR6  0   0.251   2.4013   1.3123   4.0369
 PP1  HC16  H  HCR6  0   0.251   1.9909   1.3647   1.6199
 PP1  H241  H  HCH3  0   0.251   1.8953  -0.8163   6.1709
 PP1  H242  H  HCH3  0   0.246   1.3835   0.8560   6.3251
 PP1  H243  H  HCH3  0   0.245   0.2079  -0.4479   6.4972
 PP1  H291  H  HCH3  0   0.237   3.6650  -0.1908  -3.3969
 PP1  H292  H  HCH3  0   0.239   3.2938   0.7166  -1.9322
 PP1  H293  H  HCH3  0   0.239   3.2183  -1.0486  -1.9230
 PP1  H331  H  HCH3  0   0.236   1.3694  -2.2547  -3.2112
 PP1  H332  H  HCH3  0   0.246   0.2593  -1.3328  -4.2348
 PP1  H333  H  HCH3  0   0.235   1.9691  -1.4309  -4.6522
 PP1  H371  H  HCH3  0   0.236   1.5587   2.0567  -3.2640
 PP1  H372  H  HCH3  0   0.235   2.0729   1.1502  -4.6883
 PP1  H373  H  HCH3  0   0.246   0.3645   1.2103  -4.2582

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
 PP1  N1   C4    aromatic  1.350  0.020  1.350
 PP1  N1   N8    aromatic  1.340  0.020  1.340
 PP1  N1   C28   single    1.477  0.020  1.477
 PP1  C2   N3    aromatic  1.315  0.020  1.315
 PP1  C2   N7    aromatic  1.332  0.020  1.332
 PP1  C2   HC2   single    0.930  0.020  1.080
 PP1  N3   C4    aromatic  1.339  0.020  1.339
 PP1  C4   C5    aromatic  1.399  0.020  1.399
 PP1  C5   C6    aromatic  1.415  0.020  1.415
 PP1  C5   C9    aromatic  1.421  0.020  1.421
 PP1  C6   N7    aromatic  1.335  0.020  1.335
 PP1  C6   N10   single    1.335  0.020  1.335
 PP1  N8   C9    aromatic  1.312  0.020  1.312
 PP1  C9   C11   single    1.466  0.020  1.466
 PP1  N10  H101  single    0.860  0.020  1.020
 PP1  N10  H102  single    0.860  0.020  1.020
 PP1  C11  C12   aromatic  1.394  0.020  1.394
 PP1  C11  C16   aromatic  1.395  0.020  1.395
 PP1  C12  C13   aromatic  1.387  0.020  1.387
 PP1  C12  HC12  single    0.930  0.020  1.080
 PP1  C13  C14   aromatic  1.392  0.020  1.392
 PP1  C13  HC13  single    0.930  0.020  1.080
 PP1  C14  C15   aromatic  1.395  0.020  1.395
 PP1  C14  C24   single    1.500  0.020  1.500
 PP1  C15  C16   aromatic  1.385  0.020  1.385
 PP1  C15  HC15  single    0.930  0.020  1.080
 PP1  C16  HC16  single    0.930  0.020  1.080
 PP1  C24  H241  single    0.970  0.020  1.090
 PP1  C24  H242  single    0.970  0.020  1.090
 PP1  C24  H243  single    0.970  0.020  1.090
 PP1  C28  C29   single    1.524  0.020  1.524
 PP1  C28  C33   single    1.529  0.020  1.529
 PP1  C28  C37   single    1.529  0.020  1.529
 PP1  C29  H291  single    0.970  0.020  1.090
 PP1  C29  H292  single    0.970  0.020  1.090
 PP1  C29  H293  single    0.970  0.020  1.090
 PP1  C33  H331  single    0.970  0.020  1.090
 PP1  C33  H332  single    0.970  0.020  1.090
 PP1  C33  H333  single    0.970  0.020  1.090
 PP1  C37  H371  single    0.970  0.020  1.090
 PP1  C37  H372  single    0.970  0.020  1.090
 PP1  C37  H373  single    0.970  0.020  1.090

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
 PP1  C28   N1   N8    121.26  3.000
 PP1  C28   N1   C4    127.98  3.000
 PP1  N8    N1   C4    110.76  3.000
 PP1  HC2   C2   N7    115.25  3.000
 PP1  HC2   C2   N3    116.16  3.000
 PP1  N7    C2   N3    128.59  3.000
 PP1  C4    N3   C2    112.52  3.000
 PP1  C5    C4   N3    125.54  3.000
 PP1  C5    C4   N1    106.90  3.000
 PP1  N3    C4   N1    127.56  3.000
 PP1  C9    C5   C6    139.62  3.000
 PP1  C9    C5   C4    104.54  3.000
 PP1  C6    C5   C4    115.74  3.000
 PP1  N10   C6   N7    117.71  3.000
 PP1  N10   C6   C5    123.58  3.000
 PP1  N7    C6   C5    118.70  3.000
 PP1  C6    N7   C2    118.78  3.000
 PP1  C9    N8   N1    108.29  3.000
 PP1  C11   C9   N8    120.28  3.000
 PP1  C11   C9   C5    130.21  3.000
 PP1  N8    C9   C5    109.51  3.000
 PP1  H102  N10  H101  117.53  3.000
 PP1  H102  N10  C6    121.83  3.000
 PP1  H101  N10  C6    119.09  3.000
 PP1  C16   C11  C12   118.40  3.000
 PP1  C16   C11  C9    120.51  3.000
 PP1  C12   C11  C9    121.06  3.000
 PP1  HC12  C12  C13   119.19  3.000
 PP1  HC12  C12  C11   120.12  3.000
 PP1  C13   C12  C11   120.67  3.000
 PP1  HC13  C13  C14   119.61  3.000
 PP1  HC13  C13  C12   119.25  3.000
 PP1  C14   C13  C12   121.14  3.000
 PP1  C24   C14  C15   120.94  3.000
 PP1  C24   C14  C13   121.12  3.000
 PP1  C15   C14  C13   117.93  3.000
 PP1  HC15  C15  C16   119.23  3.000
 PP1  HC15  C15  C14   119.54  3.000
 PP1  C16   C15  C14   121.23  3.000
 PP1  HC16  C16  C15   119.81  3.000
 PP1  HC16  C16  C11   119.58  3.000
 PP1  C15   C16  C11   120.61  3.000
 PP1  H243  C24  H242  108.10  3.000
 PP1  H243  C24  H241  107.37  3.000
 PP1  H242  C24  H241  107.16  3.000
 PP1  H243  C24  C14   111.55  3.000
 PP1  H242  C24  C14   111.57  3.000
 PP1  H241  C24  C14   110.88  3.000
 PP1  C37   C28  C33   110.70  3.000
 PP1  C37   C28  C29   109.46  3.000
 PP1  C33   C28  C29   109.31  3.000
 PP1  C37   C28  N1    108.89  3.000
 PP1  C33   C28  N1    109.12  3.000
 PP1  C29   C28  N1    109.34  3.000
 PP1  H293  C29  H292  108.38  3.000
 PP1  H293  C29  H291  107.97  3.000
 PP1  H292  C29  H291  107.94  3.000
 PP1  H293  C29  C28   112.26  3.000
 PP1  H292  C29  C28   112.35  3.000
 PP1  H291  C29  C28   107.77  3.000
 PP1  H333  C33  H332  107.98  3.000
 PP1  H333  C33  H331  108.01  3.000
 PP1  H332  C33  H331  108.53  3.000
 PP1  H333  C33  C28   109.39  3.000
 PP1  H332  C33  C28   111.81  3.000
 PP1  H331  C33  C28   111.00  3.000
 PP1  H373  C37  H372  107.95  3.000
 PP1  H373  C37  H371  108.54  3.000
 PP1  H372  C37  H371  108.00  3.000
 PP1  H373  C37  C28   111.70  3.000
 PP1  H372  C37  C28   109.55  3.000
 PP1  H371  C37  C28   110.99  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
 PP1  CONST_01  C2    N3   C4   N1    180.00   0.0  0
 PP1  CONST_02  C6    C5   C4   N1    180.00   0.0  0
 PP1  CONST_03  C9    C5   C4   N1      0.00   0.0  0
 PP1  CONST_04  C5    C9   N8   N1      0.00   0.0  0
 PP1  CONST_05  C11   C9   N8   N1    180.00   0.0  0
 PP1  CONST_06  C5    C4   N3   C2      0.00   0.0  0
 PP1  CONST_07  C5    C6   N7   C2      0.00   0.0  0
 PP1  CONST_08  C6    N7   C2   N3      0.00   0.0  0
 PP1  CONST_09  N8    N1   C4   N3    180.00   0.0  0
 PP1  CONST_10  C6    C5   C4   N3      0.00   0.0  0
 PP1  CONST_11  C9    C5   C4   N3    180.00   0.0  0
 PP1  CONST_12  C9    N8   N1   C4      0.00   0.0  0
 PP1  CONST_13  N7    C2   N3   C4      0.00   0.0  0
 PP1  CONST_14  N7    C6   C5   C4      0.00   0.0  0
 PP1  CONST_15  N8    C9   C5   C4      0.00   0.0  0
 PP1  CONST_16  C11   C9   C5   C4    180.00   0.0  0
 PP1  CONST_17  N8    N1   C4   C5      0.00   0.0  0
 PP1  CONST_20  N8    C9   C5   C6    180.00   0.0  0
 PP1  CONST_21  C11   C9   C5   C6      0.00   0.0  0
 PP1  CONST_22  C9    C5   C6   N7    180.00   0.0  0
 PP1  CONST_25  C13   C12  C11  C9    180.00   0.0  0
 PP1  CONST_26  C15   C16  C11  C9    180.00   0.0  0
 PP1  CONST_27  C14   C13  C12  C11     0.00   0.0  0
 PP1  CONST_28  C14   C15  C16  C11     0.00   0.0  0
 PP1  CONST_29  C15   C16  C11  C12     0.00   0.0  0
 PP1  CONST_30  C15   C14  C13  C12     0.00   0.0  0
 PP1  CONST_31  C16   C11  C12  C13     0.00   0.0  0
 PP1  CONST_32  C16   C15  C14  C13     0.00   0.0  0
 PP1  CONST_33  N10   C6   N7   C2    180.00   0.0  0
 PP1  CONST_34  C28   N1   C4   N3      0.00   0.0  0
 PP1  CONST_35  N10   C6   C5   C4    180.00   0.0  0
 PP1  CONST_36  C28   N1   C4   C5    180.00   0.0  0
 PP1  CONST_37  N10   C6   C5   C9      0.00   0.0  0
 PP1  CONST_38  C28   N1   N8   C9    180.00   0.0  0
 PP1  CONST_39  C24   C14  C13  C12   180.00   0.0  0
 PP1  CONST_40  C24   C14  C15  C16   180.00   0.0  0
 PP1  CONST_41  HC2   C2   N3   C4    180.00   0.0  0
 PP1  CONST_42  HC12  C12  C11  C9      0.00   0.0  0
 PP1  CONST_43  HC16  C16  C11  C9      0.00   0.0  0
 PP1  CONST_44  HC13  C13  C12  C11   180.00   0.0  0
 PP1  CONST_45  HC15  C15  C16  C11   180.00   0.0  0
 PP1  CONST_46  H101  N10  C6   C5    180.00   0.0  0
 PP1  CONST_47  H102  N10  C6   C5      0.00   0.0  0
 PP1  Var_01    C29   C28  N1   C4   -179.87  30.0  2
 PP1  Var_02    H241  C24  C14  C13    96.82  30.0  2
 PP1  Var_03    H291  C29  C28  N1   -179.53  30.0  3
 PP1  Var_04    H331  C33  C28  N1    -57.84  30.0  3
 PP1  Var_05    H371  C37  C28  N1     58.05  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
 PP1  plan-1  C9    0.020
 PP1  plan-1  C11   0.020
 PP1  plan-1  C12   0.020
 PP1  plan-1  C13   0.020
 PP1  plan-1  C14   0.020
 PP1  plan-1  C15   0.020
 PP1  plan-1  C16   0.020
 PP1  plan-1  C24   0.020
 PP1  plan-1  HC12  0.020
 PP1  plan-1  HC13  0.020
 PP1  plan-1  HC15  0.020
 PP1  plan-1  HC16  0.020
 PP1  plan-2  N1    0.020
 PP1  plan-2  C2    0.020
 PP1  plan-2  N3    0.020
 PP1  plan-2  C4    0.020
 PP1  plan-2  C5    0.020
 PP1  plan-2  C6    0.020
 PP1  plan-2  N7    0.020
 PP1  plan-2  N8    0.020
 PP1  plan-2  C9    0.020
 PP1  plan-2  N10   0.020
 PP1  plan-2  C11   0.020
 PP1  plan-2  C28   0.020
 PP1  plan-2  HC2   0.020
 PP1  plan-3  C6    0.020
 PP1  plan-3  N10   0.020
 PP1  plan-3  H101  0.020
 PP1  plan-3  H102  0.020

