# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 10:42:12 2022
#   Inital geometry file: a 125 line input string
#   Ligand name: methyl ~{N}-[4,6-bis(azanyl)-2-[1-[(2-fluorophenyl)methyl]pyrazolo[3,4-b]pyridin-3-yl]pyrimidin-5-yl]-~{N}-methyl-carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)N(C)c1c(N)nc(nc1N)c2nn(Cc3ccccc3F)c4ncccc24
#
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
 GZO  GZO  'methyl ~{N}-[4,6-bis(azanyl)-2-[1-[(2-fluorophenyl)methyl]pyrazolo[3,4-b]pyridin-3-yl]pyrimidin-5-yl]-~{N}-methyl-carbamate'  ligand  50  31  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_GZO
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
 GZO  C12  C  CR56  0  -0.121   99.8570  102.5866  114.3461
 GZO  C13  C  CR56  0   0.577   98.4926  102.8994  114.4624
 GZO  C14  C  CH2   0  -0.395   97.2376  104.9512  115.1933
 GZO  C15  C  CR5   0   0.175  100.5197  103.7670  114.7913
 GZO  C16  C  CR6   0  -0.076   97.1066  106.0627  114.1879
 GZO  C17  C  CR6   0   0.352  101.9623  104.0266  114.8701
 GZO  C18  C  CR16  0  -0.228  100.1782  101.3175  113.8582
 GZO  C19  C  CR6   0   0.034  104.5838  104.4537  114.9735
 GZO  C20  C  CR16  0  -0.339   99.1253  100.4900  113.5292
 GZO  C21  C  CR6   0   0.528   97.5513  107.3479  114.4538
 GZO  C22  C  CR16  0  -0.270   96.5598  105.8222  112.9297
 GZO  C23  C  CR6   0   0.503  104.0632  103.2030  114.6307
 GZO  C24  C  CR6   0   0.486  103.6628  105.4659  115.2660
 GZO  C25  C  CR16  0  -0.067   97.8006  100.9326  113.6893
 GZO  C26  C  CR16  0  -0.401   97.4678  108.3739  113.5315
 GZO  C27  C  CR16  0  -0.254   96.4648  106.8298  111.9822
 GZO  C28  C  CR16  0  -0.244   96.9205  108.1064  112.2854
 GZO  C29  C  CH3   0  -0.530  106.5639  105.2196  113.7521
 GZO  C30  C  C     0   0.726  106.7551  104.4332  116.0596
 GZO  C31  C  CH3   0  -0.411  106.7326  103.6731  118.2786
 GZO  F01  F  F     0  -0.310   98.0806  107.6150  115.6585
 GZO  N04  N  NR5   0  -0.361   98.4265  104.1604  114.9579
 GZO  N05  N  N     0  -0.246   99.6358  104.6751  115.1412
 GZO  N06  N  N     0  -0.434   97.4638  102.1220  114.1510
 GZO  N07  N  N     0  -0.515  102.7383  102.9965  114.5794
 GZO  N08  N  N     0  -0.491  102.3424  105.2450  115.2122
 GZO  N09  N  NT    0  -0.582  105.9725  104.7072  114.9786
 GZO  N10  N  NH2   0  -0.838  104.8524  102.1470  114.3684
 GZO  N11  N  NH2   0  -0.835  104.0613  106.7103  115.5799
 GZO  O02  O  O2    0  -0.466  106.0288  103.9850  117.0810
 GZO  O03  O  O     0  -0.501  107.9572  104.5809  116.0955
 GZO  H1   H  HCH2  0   0.293   97.2607  105.3225  116.2165
 GZO  H2   H  HCH2  0   0.293   96.3892  104.2740  115.1120
 GZO  H3   H  HCR6  0   0.270  101.2047  101.0008  113.7447
 GZO  H4   H  HCR6  0   0.272   99.3027   99.4955  113.1446
 GZO  H5   H  HCR6  0   0.266   96.2030  104.8259  112.6960
 GZO  H6   H  HCR6  0   0.266   96.9838  100.2717  113.4227
 GZO  H7   H  HCR6  0   0.279   97.8262  109.3630  113.7857
 GZO  H8   H  HCR6  0   0.262   96.0350  106.6211  111.0119
 GZO  H9   H  HCR6  0   0.269   96.8496  108.9000  111.5535
 GZO  H10  H  HCH3  0   0.258  107.5698  105.5826  113.9397
 GZO  H11  H  HCH3  0   0.244  106.6108  104.4481  112.9814
 GZO  H12  H  HCH3  0   0.248  105.9644  106.0476  113.3763
 GZO  H13  H  HCH3  0   0.248  105.9824  103.3133  118.9771
 GZO  H14  H  HCH3  0   0.235  107.4766  102.8930  118.1182
 GZO  H15  H  HCH3  0   0.234  107.2203  104.5523  118.6995
 GZO  H16  H  HNH2  0   0.397  104.4300  101.3207  113.9807
 GZO  H17  H  HNH2  0   0.404  105.8401  102.2608  114.2211
 GZO  H18  H  HNH2  0   0.395  103.3738  107.3640  115.9133
 GZO  H19  H  HNH2  0   0.404  105.0214  106.9036  115.8053

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
 GZO  C27  C28  aromatic  1.389  0.020  1.389
 GZO  C27  C22  aromatic  1.386  0.020  1.386
 GZO  C28  C26  aromatic  1.387  0.020  1.387
 GZO  C22  C16  aromatic  1.393  0.020  1.393
 GZO  C20  C25  aromatic  1.406  0.020  1.406
 GZO  C20  C18  aromatic  1.379  0.020  1.379
 GZO  C25  N06  aromatic  1.319  0.020  1.319
 GZO  C26  C21  aromatic  1.382  0.020  1.382
 GZO  C18  C12  aromatic  1.397  0.020  1.397
 GZO  N06  C13  aromatic  1.327  0.020  1.327
 GZO  C29  N09  single    1.455  0.020  1.455
 GZO  C16  C21  aromatic  1.386  0.020  1.386
 GZO  C16  C14  single    1.504  0.020  1.504
 GZO  C12  C13  aromatic  1.405  0.020  1.405
 GZO  C12  C15  aromatic  1.425  0.020  1.425
 GZO  C13  N04  aromatic  1.356  0.020  1.356
 GZO  C21  F01  single    1.343  0.020  1.343
 GZO  N10  C23  single    1.344  0.020  1.344
 GZO  N07  C23  aromatic  1.342  0.020  1.342
 GZO  N07  C17  aromatic  1.322  0.020  1.322
 GZO  C23  C19  aromatic  1.397  0.020  1.397
 GZO  C15  C17  single    1.468  0.020  1.468
 GZO  C15  N05  aromatic  1.315  0.020  1.315
 GZO  N04  C14  single    1.447  0.020  1.447
 GZO  N04  N05  aromatic  1.327  0.020  1.327
 GZO  C17  N08  aromatic  1.321  0.020  1.321
 GZO  C19  N09  single    1.412  0.020  1.412
 GZO  C19  C24  aromatic  1.399  0.020  1.399
 GZO  N09  C30  single    1.362  0.020  1.362
 GZO  N08  C24  aromatic  1.340  0.020  1.340
 GZO  C24  N11  single    1.344  0.020  1.344
 GZO  O03  C30  double    1.212  0.020  1.212
 GZO  C30  O02  single    1.331  0.020  1.331
 GZO  O02  C31  single    1.424  0.020  1.424
 GZO  C14  H1   single    0.970  0.020  1.090
 GZO  C14  H2   single    0.970  0.020  1.090
 GZO  C18  H3   single    0.930  0.020  1.080
 GZO  C20  H4   single    0.930  0.020  1.080
 GZO  C22  H5   single    0.930  0.020  1.080
 GZO  C25  H6   single    0.930  0.020  1.080
 GZO  C26  H7   single    0.930  0.020  1.080
 GZO  C27  H8   single    0.930  0.020  1.080
 GZO  C28  H9   single    0.930  0.020  1.080
 GZO  C29  H10  single    0.970  0.020  1.090
 GZO  C29  H11  single    0.970  0.020  1.090
 GZO  C29  H12  single    0.970  0.020  1.090
 GZO  C31  H13  single    0.970  0.020  1.090
 GZO  C31  H14  single    0.970  0.020  1.090
 GZO  C31  H15  single    0.970  0.020  1.090
 GZO  N10  H16  single    0.890  0.020  1.040
 GZO  N10  H17  single    0.890  0.020  1.040
 GZO  N11  H18  single    0.890  0.020  1.040
 GZO  N11  H19  single    0.890  0.020  1.040

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
 GZO  C18  C12  C15  138.99  3.000
 GZO  C15  C12  C13  103.97  3.000
 GZO  C18  C12  C13  117.04  3.000
 GZO  N06  C13  N04  126.35  3.000
 GZO  N04  C13  C12  106.54  3.000
 GZO  N06  C13  C12  127.11  3.000
 GZO  H2   C14  H1   107.39  3.000
 GZO  H2   C14  N04  106.75  3.000
 GZO  H1   C14  N04  108.77  3.000
 GZO  H2   C14  C16  109.99  3.000
 GZO  H1   C14  C16  112.21  3.000
 GZO  N04  C14  C16  111.50  3.000
 GZO  N05  C15  C17  121.62  3.000
 GZO  N05  C15  C12  110.03  3.000
 GZO  C17  C15  C12  128.34  3.000
 GZO  C22  C16  C21  117.36  3.000
 GZO  C21  C16  C14  121.94  3.000
 GZO  C22  C16  C14  120.68  3.000
 GZO  N08  C17  N07  127.34  3.000
 GZO  N08  C17  C15  117.37  3.000
 GZO  N07  C17  C15  115.29  3.000
 GZO  H3   C18  C20  121.64  3.000
 GZO  H3   C18  C12  121.44  3.000
 GZO  C20  C18  C12  116.93  3.000
 GZO  N09  C19  C24  121.11  3.000
 GZO  C24  C19  C23  116.97  3.000
 GZO  N09  C19  C23  121.88  3.000
 GZO  H4   C20  C25  119.00  3.000
 GZO  H4   C20  C18  120.78  3.000
 GZO  C25  C20  C18  120.22  3.000
 GZO  F01  C21  C26  118.35  3.000
 GZO  F01  C21  C16  118.89  3.000
 GZO  C26  C21  C16  122.75  3.000
 GZO  H5   C22  C27  119.88  3.000
 GZO  H5   C22  C16  118.87  3.000
 GZO  C27  C22  C16  121.25  3.000
 GZO  N10  C23  N07  116.83  3.000
 GZO  N07  C23  C19  120.99  3.000
 GZO  N10  C23  C19  122.16  3.000
 GZO  N11  C24  N08  117.01  3.000
 GZO  N11  C24  C19  121.57  3.000
 GZO  N08  C24  C19  121.40  3.000
 GZO  H6   C25  N06  116.32  3.000
 GZO  H6   C25  C20  119.34  3.000
 GZO  N06  C25  C20  124.34  3.000
 GZO  H7   C26  C28  121.20  3.000
 GZO  H7   C26  C21  120.11  3.000
 GZO  C28  C26  C21  118.70  3.000
 GZO  H8   C27  C28  120.24  3.000
 GZO  H8   C27  C22  120.01  3.000
 GZO  C28  C27  C22  119.76  3.000
 GZO  H9   C28  C27  120.33  3.000
 GZO  H9   C28  C26  119.49  3.000
 GZO  C27  C28  C26  120.19  3.000
 GZO  H12  C29  H11  108.50  3.000
 GZO  H12  C29  H10  108.38  3.000
 GZO  H11  C29  H10  108.58  3.000
 GZO  H12  C29  N09  109.57  3.000
 GZO  H11  C29  N09  111.34  3.000
 GZO  H10  C29  N09  110.41  3.000
 GZO  O03  C30  O02  124.03  3.000
 GZO  O02  C30  N09  111.29  3.000
 GZO  O03  C30  N09  124.67  3.000
 GZO  H15  C31  H14  109.19  3.000
 GZO  H15  C31  H13  109.14  3.000
 GZO  H14  C31  H13  109.21  3.000
 GZO  H15  C31  O02  111.68  3.000
 GZO  H14  C31  O02  111.74  3.000
 GZO  H13  C31  O02  105.78  3.000
 GZO  N05  N04  C14  120.95  3.000
 GZO  N05  N04  C13  111.51  3.000
 GZO  C14  N04  C13  127.40  3.000
 GZO  N04  N05  C15  107.94  3.000
 GZO  C25  N06  C13  114.36  3.000
 GZO  C23  N07  C17  116.82  3.000
 GZO  C24  N08  C17  116.48  3.000
 GZO  C30  N09  C29  120.42  3.000
 GZO  C30  N09  C19  122.13  3.000
 GZO  C29  N09  C19  117.39  3.000
 GZO  H17  N10  H16  116.70  3.000
 GZO  H17  N10  C23  121.11  3.000
 GZO  H16  N10  C23  118.30  3.000
 GZO  H19  N11  H18  116.98  3.000
 GZO  H19  N11  C24  120.92  3.000
 GZO  H18  N11  C24  118.48  3.000
 GZO  C31  O02  C30  116.71  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
 GZO  CONST_01  C25  C20  C18  C12     0.00   0.0  0
 GZO  CONST_02  C25  N06  C13  C12     0.00   0.0  0
 GZO  CONST_03  N05  N04  C13  C12     0.00   0.0  0
 GZO  CONST_04  N07  C17  C15  C12     0.00   0.0  0
 GZO  CONST_05  N08  C17  C15  C12   180.00   0.0  0
 GZO  CONST_06  N04  N05  C15  C12     0.00   0.0  0
 GZO  CONST_07  C20  C25  N06  C13     0.00   0.0  0
 GZO  CONST_08  C20  C18  C12  C13     0.00   0.0  0
 GZO  CONST_09  C17  C15  C12  C13   180.00   0.0  0
 GZO  CONST_10  N05  C15  C12  C13     0.00   0.0  0
 GZO  CONST_11  C15  N05  N04  C13     0.00   0.0  0
 GZO  CONST_12  C20  C18  C12  C15   180.00   0.0  0
 GZO  CONST_13  N06  C13  C12  C15   180.00   0.0  0
 GZO  CONST_14  N04  C13  C12  C15     0.00   0.0  0
 GZO  CONST_15  C23  N07  C17  C15   180.00   0.0  0
 GZO  CONST_16  C24  N08  C17  C15   180.00   0.0  0
 GZO  CONST_17  C28  C27  C22  C16     0.00   0.0  0
 GZO  CONST_18  C28  C26  C21  C16     0.00   0.0  0
 GZO  CONST_19  C19  C23  N07  C17     0.00   0.0  0
 GZO  CONST_20  C18  C12  C15  C17     0.00   0.0  0
 GZO  CONST_21  N04  N05  C15  C17   180.00   0.0  0
 GZO  CONST_22  C19  C24  N08  C17     0.00   0.0  0
 GZO  CONST_23  N06  C25  C20  C18     0.00   0.0  0
 GZO  CONST_24  N06  C13  C12  C18     0.00   0.0  0
 GZO  CONST_25  N04  C13  C12  C18   180.00   0.0  0
 GZO  CONST_26  N05  C15  C12  C18   180.00   0.0  0
 GZO  CONST_27  C27  C28  C26  C21     0.00   0.0  0
 GZO  CONST_28  C27  C22  C16  C21     0.00   0.0  0
 GZO  CONST_29  C26  C28  C27  C22     0.00   0.0  0
 GZO  CONST_30  C26  C21  C16  C22     0.00   0.0  0
 GZO  CONST_31  N08  C17  N07  C23     0.00   0.0  0
 GZO  CONST_32  N08  C24  C19  C23     0.00   0.0  0
 GZO  CONST_33  N07  C23  C19  C24     0.00   0.0  0
 GZO  CONST_34  N07  C17  N08  C24     0.00   0.0  0
 GZO  CONST_35  N04  C13  N06  C25   180.00   0.0  0
 GZO  CONST_36  N07  C17  C15  N05   180.00   0.0  0
 GZO  CONST_37  N08  C17  C15  N05     0.00   0.0  0
 GZO  CONST_38  N06  C13  N04  N05   180.00   0.0  0
 GZO  CONST_39  C14  N04  C13  C12   180.00   0.0  0
 GZO  CONST_40  C27  C22  C16  C14   180.00   0.0  0
 GZO  CONST_41  C26  C21  C16  C14   180.00   0.0  0
 GZO  CONST_42  N06  C13  N04  C14     0.00   0.0  0
 GZO  CONST_43  C15  N05  N04  C14   180.00   0.0  0
 GZO  CONST_44  N10  C23  N07  C17   180.00   0.0  0
 GZO  CONST_45  N11  C24  N08  C17   180.00   0.0  0
 GZO  CONST_46  F01  C21  C16  C22   180.00   0.0  0
 GZO  CONST_47  N11  C24  C19  C23   180.00   0.0  0
 GZO  CONST_48  N10  C23  C19  C24   180.00   0.0  0
 GZO  CONST_49  F01  C21  C26  C28   180.00   0.0  0
 GZO  CONST_50  N09  C19  C23  N07   180.00   0.0  0
 GZO  CONST_51  N09  C19  C24  N08   180.00   0.0  0
 GZO  CONST_52  H4   C20  C18  C12   180.00   0.0  0
 GZO  CONST_53  H6   C25  N06  C13   180.00   0.0  0
 GZO  CONST_54  H3   C18  C12  C13   180.00   0.0  0
 GZO  CONST_55  H8   C27  C22  C16   180.00   0.0  0
 GZO  CONST_56  H7   C26  C21  C16   180.00   0.0  0
 GZO  CONST_57  H9   C28  C26  C21   180.00   0.0  0
 GZO  CONST_58  H5   C22  C16  C21   180.00   0.0  0
 GZO  CONST_63  H16  N10  C23  C19   180.00   0.0  0
 GZO  CONST_64  H17  N10  C23  C19     0.00   0.0  0
 GZO  CONST_65  H18  N11  C24  C19   180.00   0.0  0
 GZO  CONST_66  H19  N11  C24  C19     0.00   0.0  0
 GZO  CONST_67  O03  C30  N09  C19   180.00   0.0  0
 GZO  CONST_68  O02  C30  N09  C19     0.00   0.0  0
 GZO  Var_01    C16  C14  N04  C13  -107.66  30.0  2
 GZO  Var_02    N04  C14  C16  C21   -95.85  30.0  2
 GZO  Var_03    H10  C29  N09  C19   167.25  30.0  3
 GZO  Var_04    N09  C30  O02  C31  -179.46  30.0  1
 GZO  Var_05    H13  C31  O02  C30  -179.05  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
 GZO  plan-1  C14  0.020
 GZO  plan-1  C16  0.020
 GZO  plan-1  C21  0.020
 GZO  plan-1  C22  0.020
 GZO  plan-1  C26  0.020
 GZO  plan-1  C27  0.020
 GZO  plan-1  C28  0.020
 GZO  plan-1  F01  0.020
 GZO  plan-1  H5   0.020
 GZO  plan-1  H7   0.020
 GZO  plan-1  H8   0.020
 GZO  plan-1  H9   0.020
 GZO  plan-2  C30  0.020
 GZO  plan-2  N09  0.020
 GZO  plan-2  O02  0.020
 GZO  plan-2  O03  0.020
 GZO  plan-3  C15  0.020
 GZO  plan-3  C17  0.020
 GZO  plan-3  C19  0.020
 GZO  plan-3  C23  0.020
 GZO  plan-3  C24  0.020
 GZO  plan-3  N07  0.020
 GZO  plan-3  N08  0.020
 GZO  plan-3  N09  0.020
 GZO  plan-3  N10  0.020
 GZO  plan-3  N11  0.020
 GZO  plan-4  C12  0.020
 GZO  plan-4  C13  0.020
 GZO  plan-4  C14  0.020
 GZO  plan-4  C15  0.020
 GZO  plan-4  C17  0.020
 GZO  plan-4  C18  0.020
 GZO  plan-4  C20  0.020
 GZO  plan-4  C25  0.020
 GZO  plan-4  N04  0.020
 GZO  plan-4  N05  0.020
 GZO  plan-4  N06  0.020
 GZO  plan-4  H3   0.020
 GZO  plan-4  H4   0.020
 GZO  plan-4  H6   0.020
 GZO  plan-5  C19  0.020
 GZO  plan-5  C29  0.020
 GZO  plan-5  C30  0.020
 GZO  plan-5  N09  0.020
 GZO  plan-6  C23  0.020
 GZO  plan-6  N10  0.020
 GZO  plan-6  H16  0.020
 GZO  plan-6  H17  0.020
 GZO  plan-7  C24  0.020
 GZO  plan-7  N11  0.020
 GZO  plan-7  H18  0.020
 GZO  plan-7  H19  0.020

