# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 07:56:20 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: N-(3-tert-butyl-1H-pyrazol-5-yl)-2-[(2R)-2-methylpiperazin-1-yl]quinazolin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CNCCN1c2nc(Nc3[nH]nc(c3)C(C)(C)C)c4ccccc4n2
#
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
 LBD  LBD  N-(3-tert-butyl-1H-pyrazol-5-yl)-2-[(2R)-2-methylpiperazin-1-yl]quinazolin-4-amine  ligand  54  27  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_LBD
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
 LBD  C01  C  CH3   0  -0.659   3.0491  -3.3144  -1.4482
 LBD  C02  C  CH1   0  -0.106   2.6450  -2.9547  -0.0219
 LBD  C03  C  CH2   0  -0.287   2.2939  -4.1721   0.8279
 LBD  C05  C  CH2   0  -0.293  -0.0350  -3.8242   0.5428
 LBD  C06  C  CH2   0  -0.320   0.2263  -2.5999  -0.3134
 LBD  C08  C  CR6   0   0.642   1.7403  -0.6835   0.0058
 LBD  C10  C  CR66  0   0.263   3.1761   1.0781   0.1201
 LBD  C11  C  CR16  0  -0.320   4.4948   1.5770   0.2088
 LBD  C12  C  CR16  0  -0.245   4.7302   2.9269   0.2476
 LBD  C13  C  CR16  0  -0.268   3.6658   3.8435   0.2000
 LBD  C14  C  CR16  0  -0.311   2.3756   3.3831   0.1143
 LBD  C15  C  CR66  0  -0.067   2.1106   2.0027   0.0737
 LBD  C16  C  CR6   0   0.550   0.8057   1.4013  -0.0133
 LBD  C18  C  CR5   0   0.627  -1.6093   1.8196  -0.0904
 LBD  C21  C  CR5   0   0.327  -3.6347   0.9432  -0.1326
 LBD  C22  C  CT    0  -0.190  -4.7894  -0.0235  -0.1557
 LBD  C23  C  CH3   0  -0.631  -4.6733  -0.9067  -1.4044
 LBD  C24  C  CH3   0  -0.631  -4.7201  -0.9137   1.0917
 LBD  C25  C  CH3   0  -0.637  -6.1259   0.7162  -0.1798
 LBD  C26  C  CR15  0  -0.539  -2.2625   0.6063  -0.1048
 LBD  N04  N  NH1   0  -0.597   1.0515  -4.7687   0.3817
 LBD  N07  N  NT    0  -0.506   1.5206  -2.0216   0.0004
 LBD  N09  N  N     0  -0.540   2.9831  -0.2567   0.0811
 LBD  N17  N  NH1   0  -0.778  -0.2861   2.2055  -0.0537
 LBD  N19  N  NR15  0  -0.525  -2.5696   2.7655  -0.1116
 LBD  N20  N  N     0  -0.301  -3.8033   2.2488  -0.1364
 LBD  N27  N  N     0  -0.528   0.6403   0.1080  -0.0491
 LBD  H1   H  HCH3  0   0.227   2.2465  -3.8122  -1.9914
 LBD  H2   H  HCH3  0   0.231   3.3335  -2.4187  -2.0013
 LBD  H3   H  HCH3  0   0.228   3.9101  -3.9844  -1.4387
 LBD  H4   H  HCH1  0   0.261   3.4866  -2.4589   0.4574
 LBD  H5   H  HCH2  0   0.236   3.1004  -4.9025   0.7432
 LBD  H6   H  HCH2  0   0.204   2.2515  -3.8529   1.8819
 LBD  H7   H  HCH2  0   0.195  -0.1705  -3.5032   1.5882
 LBD  H8   H  HCH2  0   0.239  -0.9713  -4.2829   0.2195
 LBD  H9   H  HCH2  0   0.229   0.1788  -2.8791  -1.3724
 LBD  H10  H  HCH2  0   0.278  -0.5484  -1.8613  -0.1399
 LBD  H11  H  HCR6  0   0.256   5.3103   0.8662   0.2448
 LBD  H12  H  HCR6  0   0.262   5.7469   3.2923   0.3170
 LBD  H13  H  HCR6  0   0.262   3.8609   4.9066   0.2310
 LBD  H14  H  HCR6  0   0.253   1.5757   4.1123   0.0802
 LBD  H15  H  HCH3  0   0.222  -3.7394  -1.4723  -1.4101
 LBD  H16  H  HCH3  0   0.227  -5.4942  -1.6259  -1.4412
 LBD  H17  H  HCH3  0   0.228  -4.7063  -0.3098  -2.3176
 LBD  H18  H  HCH3  0   0.228  -4.7821  -0.3223   2.0069
 LBD  H19  H  HCH3  0   0.227  -5.5454  -1.6286   1.0949
 LBD  H20  H  HCH3  0   0.222  -3.7896  -1.4838   1.1260
 LBD  H21  H  HCH3  0   0.225  -6.2197   1.3479  -1.0638
 LBD  H22  H  HCH3  0   0.225  -6.9476  -0.0021  -0.1935
 LBD  H23  H  HCH3  0   0.225  -6.2513   1.3515   0.6977
 LBD  H24  H  HCR5  0   0.279  -1.8239  -0.3715  -0.0969
 LBD  H25  H  HNH1  0   0.356   0.8613  -5.6044   0.9185
 LBD  H27  H  HNH1  0   0.428  -0.1278   3.1998  -0.0365
 LBD  H28  H  HNR5  0   0.417  -2.4464   3.7656  -0.1048

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
 LBD  C12  C13  aromatic  1.405  0.020  1.405
 LBD  C12  C11  aromatic  1.371  0.020  1.371
 LBD  C13  C14  aromatic  1.373  0.020  1.373
 LBD  C11  C10  aromatic  1.413  0.020  1.413
 LBD  C14  C15  aromatic  1.406  0.020  1.406
 LBD  C10  C15  aromatic  1.412  0.020  1.412
 LBD  C10  N09  aromatic  1.349  0.020  1.349
 LBD  C15  C16  aromatic  1.439  0.020  1.439
 LBD  N09  C08  aromatic  1.316  0.020  1.316
 LBD  C16  N17  single    1.357  0.020  1.357
 LBD  C16  N27  aromatic  1.304  0.020  1.304
 LBD  C08  N27  aromatic  1.356  0.020  1.356
 LBD  C08  N07  single    1.356  0.020  1.356
 LBD  N17  C18  single    1.379  0.020  1.379
 LBD  C06  N07  single    1.452  0.020  1.452
 LBD  C06  C05  single    1.517  0.020  1.517
 LBD  N07  C02  single    1.461  0.020  1.461
 LBD  C05  N04  single    1.449  0.020  1.449
 LBD  C18  N19  aromatic  1.348  0.020  1.348
 LBD  C18  C26  aromatic  1.378  0.020  1.378
 LBD  N19  N20  aromatic  1.338  0.020  1.338
 LBD  C02  C01  single    1.525  0.020  1.525
 LBD  C02  C03  single    1.526  0.020  1.526
 LBD  C26  C21  aromatic  1.413  0.020  1.413
 LBD  N04  C03  single    1.449  0.020  1.449
 LBD  N20  C21  aromatic  1.316  0.020  1.316
 LBD  C21  C22  single    1.506  0.020  1.506
 LBD  C22  C24  single    1.534  0.020  1.534
 LBD  C22  C25  single    1.528  0.020  1.528
 LBD  C22  C23  single    1.534  0.020  1.534
 LBD  C01  H1   single    0.970  0.020  1.090
 LBD  C01  H2   single    0.970  0.020  1.090
 LBD  C01  H3   single    0.970  0.020  1.090
 LBD  C02  H4   single    0.970  0.020  1.090
 LBD  C03  H5   single    0.970  0.020  1.090
 LBD  C03  H6   single    0.970  0.020  1.090
 LBD  C05  H7   single    0.970  0.020  1.090
 LBD  C05  H8   single    0.970  0.020  1.090
 LBD  C06  H9   single    0.970  0.020  1.090
 LBD  C06  H10  single    0.970  0.020  1.090
 LBD  C11  H11  single    0.930  0.020  1.080
 LBD  C12  H12  single    0.930  0.020  1.080
 LBD  C13  H13  single    0.930  0.020  1.080
 LBD  C14  H14  single    0.930  0.020  1.080
 LBD  C23  H15  single    0.970  0.020  1.090
 LBD  C23  H16  single    0.970  0.020  1.090
 LBD  C23  H17  single    0.970  0.020  1.090
 LBD  C24  H18  single    0.970  0.020  1.090
 LBD  C24  H19  single    0.970  0.020  1.090
 LBD  C24  H20  single    0.970  0.020  1.090
 LBD  C25  H21  single    0.970  0.020  1.090
 LBD  C25  H22  single    0.970  0.020  1.090
 LBD  C25  H23  single    0.970  0.020  1.090
 LBD  C26  H24  single    0.930  0.020  1.080
 LBD  N04  H25  single    0.890  0.020  1.040
 LBD  N17  H27  single    0.860  0.020  1.020
 LBD  N19  H28  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
 LBD  H3   C01  H2   107.64  3.000
 LBD  H3   C01  H1   107.77  3.000
 LBD  H2   C01  H1   108.33  3.000
 LBD  H3   C01  C02  110.23  3.000
 LBD  H2   C01  C02  110.47  3.000
 LBD  H1   C01  C02  112.26  3.000
 LBD  H4   C02  N07  107.31  3.000
 LBD  H4   C02  C03  107.23  3.000
 LBD  N07  C02  C03  108.90  3.000
 LBD  H4   C02  C01  108.33  3.000
 LBD  C03  C02  C01  113.18  3.000
 LBD  N07  C02  C01  111.63  3.000
 LBD  H6   C03  H5   107.25  3.000
 LBD  H6   C03  N04  112.38  3.000
 LBD  H5   C03  N04  109.52  3.000
 LBD  H6   C03  C02  108.09  3.000
 LBD  H5   C03  C02  108.71  3.000
 LBD  N04  C03  C02  110.76  3.000
 LBD  H8   C05  H7   107.34  3.000
 LBD  H8   C05  N04  109.66  3.000
 LBD  H7   C05  N04  112.81  3.000
 LBD  H8   C05  C06  108.65  3.000
 LBD  H7   C05  C06  108.75  3.000
 LBD  N04  C05  C06  109.53  3.000
 LBD  H10  C06  H9   107.29  3.000
 LBD  H10  C06  N07  109.33  3.000
 LBD  H9   C06  N07  110.42  3.000
 LBD  H10  C06  C05  109.66  3.000
 LBD  H9   C06  C05  109.40  3.000
 LBD  N07  C06  C05  110.67  3.000
 LBD  N27  C08  N09  125.37  3.000
 LBD  N27  C08  N07  116.38  3.000
 LBD  N09  C08  N07  118.24  3.000
 LBD  N09  C10  C15  122.63  3.000
 LBD  N09  C10  C11  118.99  3.000
 LBD  C15  C10  C11  118.38  3.000
 LBD  H11  C11  C12  121.08  3.000
 LBD  H11  C11  C10  118.26  3.000
 LBD  C12  C11  C10  120.65  3.000
 LBD  H12  C12  C13  119.56  3.000
 LBD  H12  C12  C11  119.70  3.000
 LBD  C13  C12  C11  120.74  3.000
 LBD  H13  C13  C14  120.08  3.000
 LBD  H13  C13  C12  120.23  3.000
 LBD  C14  C13  C12  119.69  3.000
 LBD  H14  C14  C15  121.39  3.000
 LBD  H14  C14  C13  118.06  3.000
 LBD  C15  C14  C13  120.55  3.000
 LBD  C16  C15  C14  125.64  3.000
 LBD  C16  C15  C10  114.37  3.000
 LBD  C14  C15  C10  119.99  3.000
 LBD  N27  C16  N17  119.00  3.000
 LBD  N27  C16  C15  122.07  3.000
 LBD  N17  C16  C15  118.93  3.000
 LBD  N19  C18  N17  119.19  3.000
 LBD  N19  C18  C26  106.26  3.000
 LBD  N17  C18  C26  134.56  3.000
 LBD  N20  C21  C26  111.16  3.000
 LBD  N20  C21  C22  122.57  3.000
 LBD  C26  C21  C22  126.28  3.000
 LBD  C25  C22  C24  109.47  3.000
 LBD  C25  C22  C23  109.40  3.000
 LBD  C24  C22  C23  108.93  3.000
 LBD  C23  C22  C21  108.91  3.000
 LBD  C25  C22  C21  111.11  3.000
 LBD  C24  C22  C21  108.98  3.000
 LBD  H17  C23  H16  108.01  3.000
 LBD  H17  C23  H15  107.75  3.000
 LBD  H16  C23  H15  107.56  3.000
 LBD  H17  C23  C22  111.34  3.000
 LBD  H16  C23  C22  110.47  3.000
 LBD  H15  C23  C22  111.55  3.000
 LBD  H20  C24  H19  107.59  3.000
 LBD  H20  C24  H18  107.76  3.000
 LBD  H19  C24  H18  108.02  3.000
 LBD  H20  C24  C22  111.54  3.000
 LBD  H19  C24  C22  110.38  3.000
 LBD  H18  C24  C22  111.40  3.000
 LBD  H23  C25  H22  107.87  3.000
 LBD  H23  C25  H21  107.75  3.000
 LBD  H22  C25  H21  107.84  3.000
 LBD  H23  C25  C22  111.71  3.000
 LBD  H22  C25  C22  109.89  3.000
 LBD  H21  C25  C22  111.62  3.000
 LBD  H24  C26  C21  127.96  3.000
 LBD  H24  C26  C18  127.53  3.000
 LBD  C21  C26  C18  104.51  3.000
 LBD  H25  N04  C05  109.80  3.000
 LBD  H25  N04  C03  109.77  3.000
 LBD  C05  N04  C03  109.90  3.000
 LBD  C08  N07  C06  122.57  3.000
 LBD  C06  N07  C02  115.36  3.000
 LBD  C08  N07  C02  120.37  3.000
 LBD  C10  N09  C08  117.22  3.000
 LBD  H27  N17  C18  115.32  3.000
 LBD  H27  N17  C16  117.28  3.000
 LBD  C18  N17  C16  127.39  3.000
 LBD  H28  N19  N20  119.75  3.000
 LBD  H28  N19  C18  127.53  3.000
 LBD  N20  N19  C18  112.72  3.000
 LBD  N19  N20  C21  105.36  3.000
 LBD  C16  N27  C08  118.34  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
 LBD  CONST_01  C11  C10  N09  C08   180.00   0.0  0
 LBD  CONST_02  C15  C10  N09  C08     0.00   0.0  0
 LBD  CONST_03  C15  C16  N27  C08     0.00   0.0  0
 LBD  CONST_04  C13  C12  C11  C10     0.00   0.0  0
 LBD  CONST_05  C13  C14  C15  C10     0.00   0.0  0
 LBD  CONST_06  N27  C16  C15  C10     0.00   0.0  0
 LBD  CONST_07  N27  C08  N09  C10     0.00   0.0  0
 LBD  CONST_08  C14  C13  C12  C11     0.00   0.0  0
 LBD  CONST_09  C14  C15  C10  C11     0.00   0.0  0
 LBD  CONST_10  C16  C15  C10  C11   180.00   0.0  0
 LBD  CONST_11  C15  C14  C13  C12     0.00   0.0  0
 LBD  CONST_12  C15  C10  C11  C12     0.00   0.0  0
 LBD  CONST_13  N09  C10  C11  C12   180.00   0.0  0
 LBD  CONST_14  C16  C15  C14  C13   180.00   0.0  0
 LBD  CONST_15  N09  C10  C15  C14   180.00   0.0  0
 LBD  CONST_16  N27  C16  C15  C14   180.00   0.0  0
 LBD  CONST_17  N09  C10  C15  C16     0.00   0.0  0
 LBD  CONST_18  N09  C08  N27  C16     0.00   0.0  0
 LBD  CONST_19  C21  N20  N19  C18     0.00   0.0  0
 LBD  CONST_20  N20  C21  C26  C18     0.00   0.0  0
 LBD  CONST_21  N19  C18  C26  C21     0.00   0.0  0
 LBD  CONST_22  N20  N19  C18  C26     0.00   0.0  0
 LBD  CONST_23  N19  N20  C21  C26     0.00   0.0  0
 LBD  CONST_24  N07  C08  N09  C10   180.00   0.0  0
 LBD  CONST_25  N07  C08  N27  C16   180.00   0.0  0
 LBD  CONST_26  N17  C16  N27  C08   180.00   0.0  0
 LBD  CONST_27  N17  C16  C15  C10   180.00   0.0  0
 LBD  CONST_28  N17  C16  C15  C14     0.00   0.0  0
 LBD  CONST_29  C22  C21  C26  C18   180.00   0.0  0
 LBD  CONST_30  N17  C18  C26  C21   180.00   0.0  0
 LBD  CONST_31  N19  N20  C21  C22   180.00   0.0  0
 LBD  CONST_32  N20  N19  C18  N17   180.00   0.0  0
 LBD  CONST_33  H12  C12  C11  C10   180.00   0.0  0
 LBD  CONST_34  H14  C14  C15  C10   180.00   0.0  0
 LBD  CONST_35  H13  C13  C12  C11   180.00   0.0  0
 LBD  CONST_36  H11  C11  C12  C13   180.00   0.0  0
 LBD  CONST_37  H28  N19  N20  C21   180.00   0.0  0
 LBD  CONST_38  H24  C26  C18  N19   180.00   0.0  0
 LBD  Var_01    N09  C08  N07  C02    -4.47  30.0  1
 LBD  Var_02    C05  C06  N07  C02    51.57  30.0  1
 LBD  Var_03    C05  N04  C03  C02   -62.47  30.0  1
 LBD  Var_04    C06  C05  N04  C03    61.70  30.0  1
 LBD  Var_05    N07  C06  C05  N04   -55.22  30.0  1
 LBD  Var_06    C18  N17  C16  C15  -177.60  30.0  2
 LBD  Var_07    N19  C18  N17  C16   179.19  30.0  2
 LBD  Var_08    C26  C21  C22  C23   -59.55  30.0  3
 LBD  Var_09    H18  C24  C22  C21    60.33  30.0  3
 LBD  Var_10    H21  C25  C22  C21    60.57  30.0  3
 LBD  Var_11    H15  C23  C22  C21    59.83  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
 LBD  chir_01  C02  N07  C01  C03  positiv

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
 LBD  plan-1  C18  0.020
 LBD  plan-1  C21  0.020
 LBD  plan-1  C22  0.020
 LBD  plan-1  C26  0.020
 LBD  plan-1  N17  0.020
 LBD  plan-1  N19  0.020
 LBD  plan-1  N20  0.020
 LBD  plan-1  H24  0.020
 LBD  plan-1  H28  0.020
 LBD  plan-2  C08  0.020
 LBD  plan-2  C10  0.020
 LBD  plan-2  C11  0.020
 LBD  plan-2  C12  0.020
 LBD  plan-2  C13  0.020
 LBD  plan-2  C14  0.020
 LBD  plan-2  C15  0.020
 LBD  plan-2  C16  0.020
 LBD  plan-2  N07  0.020
 LBD  plan-2  N09  0.020
 LBD  plan-2  N17  0.020
 LBD  plan-2  N27  0.020
 LBD  plan-2  H11  0.020
 LBD  plan-2  H12  0.020
 LBD  plan-2  H13  0.020
 LBD  plan-2  H14  0.020

