# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 22:42:31 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: N-(4-methoxyphenyl)-4-[3-(pyridin-3-yl)-1H-pyrazol-4-yl]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(Nc2nccc(n2)c3c[nH]nc3c4cccnc4)cc1
#
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
 9TO  9TO  N-(4-methoxyphenyl)-4-[3-(pyridin-3-yl)-1H-pyrazol-4-yl]pyrimidin-2-amine  ligand  42  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9TO
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
 9TO  C20  C  CR16  0  -0.085   3.7114  -2.2672   0.8067
 9TO  C22  C  CR16  0  -0.070   2.4991  -3.7841  -0.3766
 9TO  C23  C  CR16  0  -0.323   2.0386  -2.8086  -1.2493
 9TO  C24  C  CR16  0  -0.169   2.4516  -1.5016  -1.0609
 9TO  C25  C  CR16  0  -0.340  -3.1965  -1.2956   0.5344
 9TO  C26  C  CR16  0  -0.328  -4.5587  -1.5055   0.5133
 9TO  C01  C  CH3   0  -0.434  -7.6559   0.2261  -0.2635
 9TO  C03  C  CR6   0   0.361  -5.4275  -0.4866   0.1180
 9TO  C04  C  CR16  0  -0.369  -4.8871   0.7372  -0.2540
 9TO  C05  C  CR16  0  -0.303  -3.5106   0.9484  -0.2333
 9TO  C06  C  CR6   0   0.340  -2.6415  -0.0638   0.1629
 9TO  C08  C  CR6   0   0.596  -0.4075   1.0726  -0.0227
 9TO  C10  C  CR16  0   0.002   0.0253   3.1919  -0.6465
 9TO  C11  C  CR16  0  -0.407   1.3788   2.9978  -0.4826
 9TO  C12  C  CR6   0   0.219   1.7734   1.7264  -0.0484
 9TO  C14  C  CR5   0  -0.169   3.1753   1.4025   0.1782
 9TO  C15  C  CR15  0   0.024   4.1759   2.3120   0.4656
 9TO  C18  C  CR5   0   0.257   3.8277   0.1419   0.2386
 9TO  C19  C  CR6   0  -0.025   3.3089  -1.2083  -0.0045
 9TO  N09  N  N     0  -0.472  -0.8824   2.2459  -0.4281
 9TO  N13  N  N     0  -0.489   0.8798   0.7798   0.1853
 9TO  N16  N  NR15  0  -0.425   5.2845   1.6020   0.6763
 9TO  N17  N  N     0  -0.275   5.1056   0.2951   0.5393
 9TO  N21  N  N     0  -0.404   3.3213  -3.5231   0.6322
 9TO  H1   H  HCR6  0   0.258   4.3770  -2.0796   1.6424
 9TO  H2   H  HCR6  0   0.264   2.1933  -4.8171  -0.5004
 9TO  H3   H  HCR6  0   0.271   1.3786  -3.0722  -2.0642
 9TO  H4   H  HCR6  0   0.264   2.1239  -0.7242  -1.7371
 9TO  H5   H  HCR6  0   0.267  -2.5479  -2.1058   0.8478
 9TO  H6   H  HCR6  0   0.264  -4.9579  -2.4679   0.8085
 9TO  H7   H  HCH3  0   0.225  -7.4965   0.5427  -1.2980
 9TO  H8   H  HCH3  0   0.258  -8.6507  -0.2053  -0.1809
 9TO  H9   H  HCH3  0   0.225  -7.6003   1.1062   0.3835
 9TO  H10  H  HCR6  0   0.276  -5.5159   1.5591  -0.5695
 9TO  H11  H  HCR6  0   0.286  -3.1273   1.9104  -0.5304
 9TO  H12  H  HCR6  0   0.272  -0.3549   4.1513  -0.9789
 9TO  H13  H  HCR6  0   0.269   2.0885   3.7838  -0.6929
 9TO  H14  H  HCR5  0   0.305   4.1595   3.3857   0.5575
 9TO  H15  H  HNH1  0   0.401  -0.7710  -0.7956   0.5288
 9TO  H16  H  HNR5  0   0.431   6.1975   1.9610   0.9078
 9TO  N07  N  NH1   0  -0.773  -1.2518   0.0363   0.2222
 9TO  O02  O  O2    0  -0.475  -6.7460  -0.7789   0.1303

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
 9TO  N16  C15  aromatic  1.333  0.020  1.333
 9TO  N16  N17  aromatic  1.326  0.020  1.326
 9TO  C15  C14  aromatic  1.382  0.020  1.382
 9TO  N17  C18  aromatic  1.322  0.020  1.322
 9TO  C11  C10  aromatic  1.377  0.020  1.377
 9TO  C11  C12  aromatic  1.400  0.020  1.400
 9TO  C10  N09  aromatic  1.329  0.020  1.329
 9TO  C14  C18  aromatic  1.421  0.020  1.421
 9TO  C14  C12  single    1.457  0.020  1.457
 9TO  C20  N21  aromatic  1.327  0.020  1.327
 9TO  C20  C19  aromatic  1.393  0.020  1.393
 9TO  C18  C19  single    1.467  0.020  1.467
 9TO  C12  N13  aromatic  1.323  0.020  1.323
 9TO  N09  C08  aromatic  1.329  0.020  1.329
 9TO  N13  C08  aromatic  1.336  0.020  1.336
 9TO  C08  N07  single    1.359  0.020  1.359
 9TO  N21  C22  aromatic  1.327  0.020  1.327
 9TO  C19  C24  aromatic  1.392  0.020  1.392
 9TO  N07  C06  single    1.395  0.020  1.395
 9TO  C06  C25  aromatic  1.401  0.020  1.401
 9TO  C06  C05  aromatic  1.392  0.020  1.392
 9TO  C22  C23  aromatic  1.388  0.020  1.388
 9TO  C25  C26  aromatic  1.378  0.020  1.378
 9TO  C05  C04  aromatic  1.393  0.020  1.393
 9TO  C24  C23  aromatic  1.384  0.020  1.384
 9TO  C01  O02  single    1.412  0.020  1.412
 9TO  C26  C03  aromatic  1.396  0.020  1.396
 9TO  C04  C03  aromatic  1.389  0.020  1.389
 9TO  C03  O02  single    1.351  0.020  1.351
 9TO  C20  H1   single    0.930  0.020  1.080
 9TO  C22  H2   single    0.930  0.020  1.080
 9TO  C23  H3   single    0.930  0.020  1.080
 9TO  C24  H4   single    0.930  0.020  1.080
 9TO  C25  H5   single    0.930  0.020  1.080
 9TO  C26  H6   single    0.930  0.020  1.080
 9TO  C01  H7   single    0.970  0.020  1.090
 9TO  C01  H8   single    0.970  0.020  1.090
 9TO  C01  H9   single    0.970  0.020  1.090
 9TO  C04  H10  single    0.930  0.020  1.080
 9TO  C05  H11  single    0.930  0.020  1.080
 9TO  C10  H12  single    0.930  0.020  1.080
 9TO  C11  H13  single    0.930  0.020  1.080
 9TO  C15  H14  single    0.930  0.020  1.080
 9TO  N07  H15  single    0.860  0.020  1.020
 9TO  N16  H16  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
 9TO  H1   C20  N21  116.46  3.000
 9TO  H1   C20  C19  119.63  3.000
 9TO  N21  C20  C19  123.92  3.000
 9TO  H2   C22  N21  116.66  3.000
 9TO  H2   C22  C23  120.29  3.000
 9TO  N21  C22  C23  123.05  3.000
 9TO  H3   C23  C24  121.01  3.000
 9TO  H3   C23  C22  120.34  3.000
 9TO  C24  C23  C22  118.65  3.000
 9TO  H4   C24  C19  120.65  3.000
 9TO  H4   C24  C23  120.24  3.000
 9TO  C19  C24  C23  119.10  3.000
 9TO  H5   C25  C06  119.79  3.000
 9TO  H5   C25  C26  118.80  3.000
 9TO  C06  C25  C26  121.41  3.000
 9TO  H6   C26  C03  119.76  3.000
 9TO  H6   C26  C25  119.70  3.000
 9TO  C03  C26  C25  120.54  3.000
 9TO  H9   C01  H8   108.71  3.000
 9TO  H9   C01  H7   108.62  3.000
 9TO  H8   C01  H7   108.66  3.000
 9TO  H9   C01  O02  112.03  3.000
 9TO  H8   C01  O02  106.62  3.000
 9TO  H7   C01  O02  112.08  3.000
 9TO  O02  C03  C04  124.96  3.000
 9TO  O02  C03  C26  116.55  3.000
 9TO  C04  C03  C26  118.49  3.000
 9TO  H10  C04  C05  117.62  3.000
 9TO  H10  C04  C03  121.44  3.000
 9TO  C05  C04  C03  120.95  3.000
 9TO  H11  C05  C06  120.38  3.000
 9TO  H11  C05  C04  118.88  3.000
 9TO  C06  C05  C04  120.74  3.000
 9TO  N07  C06  C05  125.60  3.000
 9TO  C05  C06  C25  117.87  3.000
 9TO  N07  C06  C25  116.52  3.000
 9TO  N13  C08  N09  125.81  3.000
 9TO  N13  C08  N07  113.79  3.000
 9TO  N09  C08  N07  120.41  3.000
 9TO  H12  C10  N09  116.15  3.000
 9TO  H12  C10  C11  120.39  3.000
 9TO  N09  C10  C11  123.46  3.000
 9TO  H13  C11  C12  122.42  3.000
 9TO  H13  C11  C10  121.35  3.000
 9TO  C12  C11  C10  116.22  3.000
 9TO  N13  C12  C14  117.62  3.000
 9TO  N13  C12  C11  120.95  3.000
 9TO  C14  C12  C11  121.43  3.000
 9TO  C18  C14  C15  104.04  3.000
 9TO  C18  C14  C12  130.23  3.000
 9TO  C15  C14  C12  125.64  3.000
 9TO  H14  C15  N16  121.99  3.000
 9TO  H14  C15  C14  131.46  3.000
 9TO  N16  C15  C14  106.52  3.000
 9TO  N17  C18  C19  119.11  3.000
 9TO  C19  C18  C14  130.34  3.000
 9TO  N17  C18  C14  110.53  3.000
 9TO  C18  C19  C24  122.53  3.000
 9TO  C24  C19  C20  117.37  3.000
 9TO  C18  C19  C20  120.06  3.000
 9TO  C10  N09  C08  115.75  3.000
 9TO  C12  N13  C08  117.81  3.000
 9TO  H16  N16  N17  119.79  3.000
 9TO  H16  N16  C15  126.85  3.000
 9TO  N17  N16  C15  113.35  3.000
 9TO  N16  N17  C18  105.56  3.000
 9TO  C22  N21  C20  117.92  3.000
 9TO  H15  N07  C08  112.80  3.000
 9TO  H15  N07  C06  115.39  3.000
 9TO  C08  N07  C06  131.78  3.000
 9TO  C03  O02  C01  118.21  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
 9TO  CONST_01  C23  C22  N21  C20     0.00   0.0  0
 9TO  CONST_04  C23  C24  C19  C20     0.00   0.0  0
 9TO  CONST_05  C19  C20  N21  C22     0.00   0.0  0
 9TO  CONST_06  C19  C24  C23  C22     0.00   0.0  0
 9TO  CONST_07  C18  C19  C24  C23   180.00   0.0  0
 9TO  CONST_08  N21  C20  C19  C24     0.00   0.0  0
 9TO  CONST_11  N21  C22  C23  C24     0.00   0.0  0
 9TO  CONST_12  C04  C05  C06  C25     0.00   0.0  0
 9TO  CONST_13  C04  C03  C26  C25     0.00   0.0  0
 9TO  CONST_14  C05  C06  C25  C26     0.00   0.0  0
 9TO  CONST_15  C05  C04  C03  C26     0.00   0.0  0
 9TO  CONST_16  C06  C25  C26  C03     0.00   0.0  0
 9TO  CONST_17  C06  C05  C04  C03     0.00   0.0  0
 9TO  CONST_18  C11  C10  N09  C08     0.00   0.0  0
 9TO  CONST_19  C11  C12  N13  C08     0.00   0.0  0
 9TO  CONST_20  C14  C12  N13  C08   180.00   0.0  0
 9TO  CONST_21  C14  C12  C11  C10   180.00   0.0  0
 9TO  CONST_22  N13  C12  C11  C10     0.00   0.0  0
 9TO  CONST_23  N13  C08  N09  C10     0.00   0.0  0
 9TO  CONST_26  N09  C10  C11  C12     0.00   0.0  0
 9TO  CONST_27  N16  C15  C14  C12   180.00   0.0  0
 9TO  CONST_28  N17  C18  C14  C12   180.00   0.0  0
 9TO  CONST_29  C19  C18  C14  C12     0.00   0.0  0
 9TO  CONST_30  N09  C08  N13  C12     0.00   0.0  0
 9TO  CONST_31  N17  N16  C15  C14     0.00   0.0  0
 9TO  CONST_32  N16  N17  C18  C14     0.00   0.0  0
 9TO  CONST_33  C18  N17  N16  C15     0.00   0.0  0
 9TO  CONST_34  N17  C18  C14  C15     0.00   0.0  0
 9TO  CONST_35  C19  C18  C14  C15   180.00   0.0  0
 9TO  CONST_37  N16  C15  C14  C18     0.00   0.0  0
 9TO  CONST_39  N21  C20  C19  C18   180.00   0.0  0
 9TO  CONST_40  N16  N17  C18  C19   180.00   0.0  0
 9TO  CONST_41  O02  C03  C26  C25   180.00   0.0  0
 9TO  CONST_42  N07  C06  C25  C26   180.00   0.0  0
 9TO  CONST_43  N07  C06  C05  C04   180.00   0.0  0
 9TO  CONST_44  O02  C03  C04  C05   180.00   0.0  0
 9TO  CONST_45  N07  C08  N09  C10   180.00   0.0  0
 9TO  CONST_46  N07  C08  N13  C12   180.00   0.0  0
 9TO  CONST_47  H2   C22  N21  C20   180.00   0.0  0
 9TO  CONST_48  H4   C24  C19  C20   180.00   0.0  0
 9TO  CONST_49  H1   C20  N21  C22   180.00   0.0  0
 9TO  CONST_50  H11  C05  C06  C25   180.00   0.0  0
 9TO  CONST_51  H10  C04  C03  C26   180.00   0.0  0
 9TO  CONST_52  H5   C25  C26  C03   180.00   0.0  0
 9TO  CONST_53  H6   C26  C03  C04   180.00   0.0  0
 9TO  CONST_54  H12  C10  N09  C08   180.00   0.0  0
 9TO  CONST_55  H14  C15  C14  C12     0.00   0.0  0
 9TO  CONST_56  H16  N16  C15  C14   180.00   0.0  0
 9TO  CONST_57  H13  C11  C12  C14     0.00   0.0  0
 9TO  CONST_58  H3   C23  C24  C19   180.00   0.0  0
 9TO  Var_01    C08  N07  C06  C25  -177.73  30.0  2
 9TO  Var_02    N09  C08  N07  C06    -1.79  30.0  1
 9TO  Var_03    C04  C03  O02  C01     0.06  30.0  3
 9TO  Var_04    H7   C01  O02  C03    61.37  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
 9TO  plan-1  C12  0.020
 9TO  plan-1  C14  0.020
 9TO  plan-1  C15  0.020
 9TO  plan-1  C18  0.020
 9TO  plan-1  C19  0.020
 9TO  plan-1  N16  0.020
 9TO  plan-1  N17  0.020
 9TO  plan-1  H14  0.020
 9TO  plan-1  H16  0.020
 9TO  plan-2  C20  0.020
 9TO  plan-2  C22  0.020
 9TO  plan-2  C23  0.020
 9TO  plan-2  C24  0.020
 9TO  plan-2  C18  0.020
 9TO  plan-2  C19  0.020
 9TO  plan-2  N21  0.020
 9TO  plan-2  H1   0.020
 9TO  plan-2  H2   0.020
 9TO  plan-2  H3   0.020
 9TO  plan-2  H4   0.020
 9TO  plan-3  C25  0.020
 9TO  plan-3  C26  0.020
 9TO  plan-3  C03  0.020
 9TO  plan-3  C04  0.020
 9TO  plan-3  C05  0.020
 9TO  plan-3  C06  0.020
 9TO  plan-3  H5   0.020
 9TO  plan-3  H6   0.020
 9TO  plan-3  H10  0.020
 9TO  plan-3  H11  0.020
 9TO  plan-3  N07  0.020
 9TO  plan-3  O02  0.020
 9TO  plan-4  C08  0.020
 9TO  plan-4  C10  0.020
 9TO  plan-4  C11  0.020
 9TO  plan-4  C12  0.020
 9TO  plan-4  C14  0.020
 9TO  plan-4  N09  0.020
 9TO  plan-4  N13  0.020
 9TO  plan-4  H12  0.020
 9TO  plan-4  H13  0.020
 9TO  plan-4  N07  0.020

