# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 22:34:24 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 6-{2-amino-6-[(3R)-3-methylmorpholin-4-yl]pyrimidin-4-yl}-2H-indazol-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1COCCN1c2cc(nc(N)n2)c3ccc4c(N)[nH]nc4c3
#
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
 3Q2  3Q2  6-{2-amino-6-[(3R)-3-methylmorpholin-4-yl]pyrimidin-4-yl}-2H-indazol-3-amine  ligand  43  24  .  2021-08-04  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3Q2
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
 3Q2  C1    C  CR16  0  -0.279  -3.2067  -1.7439   0.2939
 3Q2  C2    C  CR16  0  -0.344  -1.9295  -1.2667   0.3787
 3Q2  C3    C  CR16  0  -0.350  -2.6375   1.0181  -0.0823
 3Q2  C4    C  CR16  0  -0.498   0.8355  -0.2380   0.0773
 3Q2  C5    C  CR56  0  -0.141  -4.2420  -0.8360   0.0026
 3Q2  C6    C  CR6   0   0.044  -1.6346   0.1205   0.1880
 3Q2  C7    C  CR56  0   0.279  -3.9658   0.5465  -0.1887
 3Q2  C8    C  CR6   0   0.284  -0.2382   0.6086   0.2836
 3Q2  C9    C  CR6   0   0.597   2.1257   0.3222   0.1933
 3Q2  C10   C  CR5   0   0.511  -5.6303  -0.9350  -0.1660
 3Q2  C11   C  CR6   0   0.524   1.1718   2.3482   0.6069
 3Q2  C12   C  CH2   0  -0.324   3.2096  -1.8068  -0.3466
 3Q2  C13   C  CH2   0  -0.185   4.4325  -2.5564   0.1513
 3Q2  C14   C  CH2   0  -0.186   5.6627  -0.6255   0.3736
 3Q2  C15   C  CH1   0  -0.130   4.5409   0.2623  -0.1435
 3Q2  C16   C  CH3   0  -0.664   4.7324   0.6636  -1.6032
 3Q2  N17   N  N     0  -0.514  -0.0828   1.9061   0.5530
 3Q2  N18   N  N     0  -0.523   2.2739   1.6202   0.4494
 3Q2  N19   N  NR15  0  -0.475  -6.0383   0.3103  -0.4282
 3Q2  N20   N  N     0  -0.352  -5.0661   1.2436  -0.4538
 3Q2  N21   N  NT    0  -0.510   3.2588  -0.4146   0.0644
 3Q2  N22   N  NH2   0  -0.845  -6.4690  -2.0025  -0.0287
 3Q2  N23   N  NH2   0  -0.827   1.3443   3.6736   0.8159
 3Q2  O24   O  O2    0  -0.479   5.6317  -1.9111  -0.2008
 3Q2  H1    H  HCR6  0   0.253  -3.4085  -2.7956   0.4568
 3Q2  H2    H  HCR6  0   0.243  -1.1315  -1.9534   0.6254
 3Q2  H3    H  HCR6  0   0.250  -2.4163   2.0682  -0.2186
 3Q2  H4    H  HCR6  0   0.262   0.6811  -1.2685  -0.1952
 3Q2  H12   H  HCH2  0   0.239   3.1217  -1.8965  -1.4358
 3Q2  H12A  H  HCH2  0   0.263   2.3398  -2.2949   0.0895
 3Q2  H13   H  HCH2  0   0.208   4.3673  -2.6679   1.2429
 3Q2  H13A  H  HCH2  0   0.247   4.4451  -3.5547  -0.2875
 3Q2  H14   H  HCH2  0   0.240   6.6255  -0.1755   0.1268
 3Q2  H14A  H  HCH2  0   0.218   5.5932  -0.6970   1.4686
 3Q2  H15   H  HCH1  0   0.269   4.5410   1.1612   0.4706
 3Q2  H16   H  HCH3  0   0.229   4.7386  -0.1996  -2.2689
 3Q2  H16A  H  HCH3  0   0.237   3.9359   1.3345  -1.9243
 3Q2  H16B  H  HCH3  0   0.232   5.6799   1.1895  -1.7290
 3Q2  HN22  H  HNH2  0   0.398  -6.0249  -2.8995  -0.1456
 3Q2  HN2A  H  HNH2  0   0.397  -7.3377  -1.9545  -0.5393
 3Q2  HN23  H  HNH2  0   0.389   2.2570   4.0010   1.0796
 3Q2  HN2B  H  HNH2  0   0.389   0.5601   4.2080   1.1472
 3Q2  HN19  H  HNR5  0   0.422  -6.9907   0.5953  -0.6000

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
 3Q2  C2   C1    aromatic  1.366  0.020  1.366
 3Q2  C5   C1    aromatic  1.408  0.020  1.408
 3Q2  C1   H1    single    0.930  0.020  1.080
 3Q2  C6   C2    aromatic  1.431  0.020  1.431
 3Q2  C2   H2    single    0.930  0.020  1.080
 3Q2  C3   C6    aromatic  1.373  0.020  1.373
 3Q2  C3   C7    aromatic  1.414  0.020  1.414
 3Q2  C3   H3    single    0.930  0.020  1.080
 3Q2  C9   C4    aromatic  1.411  0.020  1.411
 3Q2  C8   C4    aromatic  1.383  0.020  1.383
 3Q2  C4   H4    single    0.930  0.020  1.080
 3Q2  C7   C5    aromatic  1.423  0.020  1.423
 3Q2  C5   C10   aromatic  1.402  0.020  1.402
 3Q2  C8   C6    single    1.482  0.020  1.482
 3Q2  N20  C7    aromatic  1.329  0.020  1.329
 3Q2  N17  C8    aromatic  1.334  0.020  1.334
 3Q2  N18  C9    aromatic  1.331  0.020  1.331
 3Q2  C9   N21   single    1.358  0.020  1.358
 3Q2  N19  C10   aromatic  1.336  0.020  1.336
 3Q2  C10  N22   single    1.365  0.020  1.365
 3Q2  N23  C11   single    1.353  0.020  1.353
 3Q2  C11  N18   aromatic  1.330  0.020  1.330
 3Q2  C11  N17   aromatic  1.331  0.020  1.331
 3Q2  C13  C12   single    1.518  0.020  1.518
 3Q2  N21  C12   single    1.452  0.020  1.452
 3Q2  C12  H12   single    0.970  0.020  1.090
 3Q2  C12  H12A  single    0.970  0.020  1.090
 3Q2  C13  O24   single    1.407  0.020  1.407
 3Q2  C13  H13   single    0.970  0.020  1.090
 3Q2  C13  H13A  single    0.970  0.020  1.090
 3Q2  C14  O24   single    1.408  0.020  1.408
 3Q2  C14  C15   single    1.521  0.020  1.521
 3Q2  C14  H14   single    0.970  0.020  1.090
 3Q2  C14  H14A  single    0.970  0.020  1.090
 3Q2  N21  C15   single    1.465  0.020  1.465
 3Q2  C15  C16   single    1.526  0.020  1.526
 3Q2  C15  H15   single    0.970  0.020  1.090
 3Q2  C16  H16   single    0.970  0.020  1.090
 3Q2  C16  H16A  single    0.970  0.020  1.090
 3Q2  C16  H16B  single    0.970  0.020  1.090
 3Q2  N20  N19   aromatic  1.348  0.020  1.348
 3Q2  N22  HN22  single    0.890  0.020  1.040
 3Q2  N22  HN2A  single    0.890  0.020  1.040
 3Q2  N23  HN23  single    0.890  0.020  1.040
 3Q2  N23  HN2B  single    0.890  0.020  1.040
 3Q2  N19  HN19  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
 3Q2  H1    C1   C5    121.36  3.000
 3Q2  H1    C1   C2    120.27  3.000
 3Q2  C5    C1   C2    118.37  3.000
 3Q2  H2    C2   C6    119.60  3.000
 3Q2  H2    C2   C1    118.83  3.000
 3Q2  C6    C2   C1    121.54  3.000
 3Q2  H3    C3   C7    120.43  3.000
 3Q2  H3    C3   C6    120.67  3.000
 3Q2  C7    C3   C6    118.89  3.000
 3Q2  H4    C4   C9    122.12  3.000
 3Q2  H4    C4   C8    120.81  3.000
 3Q2  C9    C4   C8    117.03  3.000
 3Q2  C10   C5   C7    104.17  3.000
 3Q2  C10   C5   C1    135.05  3.000
 3Q2  C7    C5   C1    120.79  3.000
 3Q2  C8    C6   C3    119.05  3.000
 3Q2  C8    C6   C2    120.31  3.000
 3Q2  C3    C6   C2    120.63  3.000
 3Q2  N20   C7   C5    112.07  3.000
 3Q2  N20   C7   C3    128.16  3.000
 3Q2  C5    C7   C3    119.77  3.000
 3Q2  N17   C8   C6    116.29  3.000
 3Q2  N17   C8   C4    122.35  3.000
 3Q2  C6    C8   C4    121.35  3.000
 3Q2  N21   C9   N18   117.03  3.000
 3Q2  N21   C9   C4    122.66  3.000
 3Q2  N18   C9   C4    120.31  3.000
 3Q2  N22   C10  N19   124.13  3.000
 3Q2  N22   C10  C5    130.68  3.000
 3Q2  N19   C10  C5    105.08  3.000
 3Q2  N23   C11  N18   116.67  3.000
 3Q2  N18   C11  N17   126.46  3.000
 3Q2  N23   C11  N17   116.86  3.000
 3Q2  H12A  C12  H12   107.29  3.000
 3Q2  H12A  C12  N21   110.09  3.000
 3Q2  H12   C12  N21   111.24  3.000
 3Q2  H12A  C12  C13   106.90  3.000
 3Q2  H12   C12  C13   110.49  3.000
 3Q2  N21   C12  C13   110.68  3.000
 3Q2  H13A  C13  H13   107.91  3.000
 3Q2  H13A  C13  O24   108.02  3.000
 3Q2  H13   C13  O24   110.23  3.000
 3Q2  H13A  C13  C12   109.22  3.000
 3Q2  H13   C13  C12   109.14  3.000
 3Q2  O24   C13  C12   112.21  3.000
 3Q2  H14A  C14  H14   107.93  3.000
 3Q2  H14A  C14  O24   110.21  3.000
 3Q2  H14   C14  O24   107.68  3.000
 3Q2  H14A  C14  C15   109.26  3.000
 3Q2  H14   C14  C15   109.46  3.000
 3Q2  O24   C14  C15   112.20  3.000
 3Q2  H15   C15  N21   107.56  3.000
 3Q2  H15   C15  C16   108.81  3.000
 3Q2  N21   C15  C16   111.55  3.000
 3Q2  H15   C15  C14   106.86  3.000
 3Q2  C16   C15  C14   112.71  3.000
 3Q2  N21   C15  C14   109.12  3.000
 3Q2  H16B  C16  H16A  107.70  3.000
 3Q2  H16B  C16  H16   107.84  3.000
 3Q2  H16A  C16  H16   108.16  3.000
 3Q2  H16B  C16  C15   110.25  3.000
 3Q2  H16A  C16  C15   110.61  3.000
 3Q2  H16   C16  C15   112.12  3.000
 3Q2  C11   N17  C8    116.16  3.000
 3Q2  C11   N18  C9    117.65  3.000
 3Q2  HN19  N19  N20   118.82  3.000
 3Q2  HN19  N19  C10   125.80  3.000
 3Q2  N20   N19  C10   115.38  3.000
 3Q2  N19   N20  C7    103.30  3.000
 3Q2  C15   N21  C12   115.63  3.000
 3Q2  C15   N21  C9    119.55  3.000
 3Q2  C12   N21  C9    121.25  3.000
 3Q2  HN2A  N22  HN22  111.30  3.000
 3Q2  HN2A  N22  C10   116.18  3.000
 3Q2  HN22  N22  C10   114.44  3.000
 3Q2  HN2B  N23  HN23  116.67  3.000
 3Q2  HN2B  N23  C11   118.19  3.000
 3Q2  HN23  N23  C11   118.40  3.000
 3Q2  C14   O24  C13   109.60  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
 3Q2  CONST_01  C3    C6   C2   C1      0.00   0.0  0
 3Q2  CONST_02  C8    C6   C2   C1    180.00   0.0  0
 3Q2  CONST_03  C3    C7   C5   C1      0.00   0.0  0
 3Q2  CONST_04  N20   C7   C5   C1    180.00   0.0  0
 3Q2  CONST_05  N19   C10  C5   C1    180.00   0.0  0
 3Q2  CONST_06  C7    C5   C1   C2      0.00   0.0  0
 3Q2  CONST_07  C10   C5   C1   C2    180.00   0.0  0
 3Q2  CONST_08  C7    C3   C6   C2      0.00   0.0  0
 3Q2  CONST_13  C10   C5   C7   C3    180.00   0.0  0
 3Q2  CONST_14  N19   N20  C7   C3    180.00   0.0  0
 3Q2  CONST_15  C11   N18  C9   C4      0.00   0.0  0
 3Q2  CONST_16  C11   N17  C8   C4      0.00   0.0  0
 3Q2  CONST_17  C6    C2   C1   C5      0.00   0.0  0
 3Q2  CONST_18  C6    C3   C7   C5      0.00   0.0  0
 3Q2  CONST_19  N19   N20  C7   C5      0.00   0.0  0
 3Q2  CONST_20  N20   N19  C10  C5      0.00   0.0  0
 3Q2  CONST_21  N20   C7   C3   C6    180.00   0.0  0
 3Q2  CONST_22  C9    C4   C8   C6    180.00   0.0  0
 3Q2  CONST_23  C11   N17  C8   C6    180.00   0.0  0
 3Q2  CONST_24  C8    C6   C3   C7    180.00   0.0  0
 3Q2  CONST_25  N19   C10  C5   C7      0.00   0.0  0
 3Q2  CONST_26  C10   N19  N20  C7      0.00   0.0  0
 3Q2  CONST_27  N18   C9   C4   C8      0.00   0.0  0
 3Q2  CONST_28  N18   C11  N17  C8      0.00   0.0  0
 3Q2  CONST_29  N17   C8   C4   C9      0.00   0.0  0
 3Q2  CONST_30  N17   C11  N18  C9      0.00   0.0  0
 3Q2  CONST_31  N20   C7   C5   C10     0.00   0.0  0
 3Q2  CONST_32  N21   C9   C4   C8    180.00   0.0  0
 3Q2  CONST_33  N21   C9   N18  C11   180.00   0.0  0
 3Q2  CONST_34  N22   C10  C5   C1      0.00   0.0  0
 3Q2  CONST_35  N22   C10  C5   C7    180.00   0.0  0
 3Q2  CONST_36  N23   C11  N17  C8    180.00   0.0  0
 3Q2  CONST_37  N23   C11  N18  C9    180.00   0.0  0
 3Q2  CONST_38  N22   C10  N19  N20   180.00   0.0  0
 3Q2  CONST_39  H3    C3   C6   C2    180.00   0.0  0
 3Q2  CONST_40  H2    C2   C6   C3    180.00   0.0  0
 3Q2  CONST_41  HN19  N19  C10  C5    180.00   0.0  0
 3Q2  CONST_42  H1    C1   C2   C6    180.00   0.0  0
 3Q2  CONST_43  H4    C4   C8   C6      0.00   0.0  0
 3Q2  CONST_46  HN23  N23  C11  N17   180.00   0.0  0
 3Q2  Var_01    C12   N21  C9   C4      6.78  30.0  2
 3Q2  Var_02    C13   C12  N21  C9   -155.15  30.0  1
 3Q2  Var_03    C15   C14  O24  C13   -62.51  30.0  1
 3Q2  Var_04    O24   C13  C12  N21   -52.16  30.0  1
 3Q2  Var_05    H13   C13  O24  C14   -61.11  30.0  1

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
 3Q2  chir_01  C15  C14  N21  C16  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
 3Q2  plan-1  C4    0.020
 3Q2  plan-1  C6    0.020
 3Q2  plan-1  C8    0.020
 3Q2  plan-1  C9    0.020
 3Q2  plan-1  C11   0.020
 3Q2  plan-1  N17   0.020
 3Q2  plan-1  N18   0.020
 3Q2  plan-1  N21   0.020
 3Q2  plan-1  N23   0.020
 3Q2  plan-1  H4    0.020
 3Q2  plan-2  C1    0.020
 3Q2  plan-2  C2    0.020
 3Q2  plan-2  C3    0.020
 3Q2  plan-2  C5    0.020
 3Q2  plan-2  C6    0.020
 3Q2  plan-2  C7    0.020
 3Q2  plan-2  C8    0.020
 3Q2  plan-2  C10   0.020
 3Q2  plan-2  N19   0.020
 3Q2  plan-2  N20   0.020
 3Q2  plan-2  N22   0.020
 3Q2  plan-2  H1    0.020
 3Q2  plan-2  H2    0.020
 3Q2  plan-2  H3    0.020
 3Q2  plan-2  HN19  0.020
 3Q2  plan-3  C10   0.020
 3Q2  plan-3  N22   0.020
 3Q2  plan-3  HN22  0.020
 3Q2  plan-3  HN2A  0.020
 3Q2  plan-4  C11   0.020
 3Q2  plan-4  N23   0.020
 3Q2  plan-4  HN23  0.020
 3Q2  plan-4  HN2B  0.020

