# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 02:43:32 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: N~4~-(5-cyclopropyl-1H-pyrazol-3-yl)-N~2~-(1H-indazol-5-yl)-6-methylpyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(Nc2cc([nH]n2)C3CC3)nc(Nc4ccc5[nH]ncc5c4)n1
#
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
 3N7  3N7  N~4~-(5-cyclopropyl-1H-pyrazol-3-yl)-N~2~-(1H-indazol-5-yl)-6-methylpyrimidine-2,4-diamine  ligand  44  26  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3N7
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
 3N7  C1    C  CH3   0  -0.722   0.9670   4.7879  -0.0823
 3N7  C2    C  CR6   0   0.280   0.4864   3.3718  -0.0500
 3N7  C3    C  CR16  0  -0.468   1.3860   2.3171  -0.0539
 3N7  C4    C  CR6   0   0.533   0.8348   1.0328  -0.0022
 3N7  N5    N  NH1   0  -0.754   1.5535  -0.1202   0.0227
 3N7  C6    C  CR5   0   0.505   2.9207  -0.3204  -0.0150
 3N7  C7    C  CR15  0  -0.585   3.5410  -1.5767   0.1470
 3N7  C8    C  CR5   0   0.511   4.8883  -1.3125   0.0247
 3N7  N9    N  NR15  0  -0.521   4.9867   0.0103  -0.1871
 3N7  N10   N  N     0  -0.327   3.8011   0.6364  -0.2199
 3N7  C12   C  CH1   0  -0.368   6.0303  -2.2323   0.0947
 3N7  C13   C  CH2   0  -0.476   7.2011  -2.0855  -0.8422
 3N7  C14   C  CH2   0  -0.477   7.3699  -1.7775   0.6072
 3N7  N15   N  N     0  -0.533  -0.4870   0.8448   0.0360
 3N7  C16   C  CR6   0   0.584  -1.2510   1.9237   0.0242
 3N7  N17   N  NH1   0  -0.774  -2.6063   1.7898   0.0572
 3N7  C18   C  CR6   0   0.355  -3.4271   0.6641   0.0579
 3N7  C19   C  CR16  0  -0.361  -4.8205   0.9402   0.1497
 3N7  C20   C  CR16  0  -0.277  -5.7738  -0.0449   0.1521
 3N7  C21   C  CR56  0   0.396  -5.3236  -1.3665   0.0608
 3N7  N22   N  NR15  0  -0.545  -5.9710  -2.5566   0.0348
 3N7  N24   N  N     0  -0.229  -5.1295  -3.5844  -0.0633
 3N7  C25   C  CR15  0  -0.140  -3.9188  -3.0815  -0.1024
 3N7  C26   C  CR56  0  -0.059  -3.9565  -1.6630  -0.0279
 3N7  C27   C  CR16  0  -0.408  -2.9905  -0.6451  -0.0300
 3N7  N28   N  N     0  -0.511  -0.8304   3.1909  -0.0139
 3N7  H1    H  HCH3  0   0.254   0.5308   5.3200  -0.9284
 3N7  H1A   H  HCH3  0   0.256   0.6555   5.3130   0.8219
 3N7  H1B   H  HCH3  0   0.246   2.0510   4.8468  -0.1562
 3N7  H3    H  HCR6  0   0.285   2.4496   2.4811  -0.0913
 3N7  HN5   H  HNH1  0   0.409   0.9939  -0.9558   0.0979
 3N7  H7    H  HCR5  0   0.271   3.0742  -2.5309   0.3314
 3N7  H12   H  HCH1  0   0.278   5.7401  -3.2455   0.3427
 3N7  H13   H  HCH2  0   0.267   7.6402  -2.9934  -1.2336
 3N7  H13A  H  HCH2  0   0.258   7.1826  -1.2606  -1.5433
 3N7  H14   H  HCH2  0   0.255   7.4778  -0.7415   0.9049
 3N7  H14A  H  HCH2  0   0.268   7.9248  -2.4729   1.2228
 3N7  HN17  H  HNH1  0   0.403  -3.0848   2.6772   0.0675
 3N7  H19   H  HCR6  0   0.271  -5.1406   1.9733   0.2231
 3N7  H20   H  HCR6  0   0.273  -6.8248   0.2006   0.2234
 3N7  H25   H  HCR5  0   0.264  -3.0581  -3.7279  -0.1824
 3N7  H27   H  HCR6  0   0.284  -1.9407  -0.8785  -0.0992
 3N7  HN9   H  HNR5  0   0.415   5.8228   0.5538  -0.3282
 3N7  HN22  H  HNR5  0   0.415  -6.9626  -2.7244   0.0789

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
 3N7  C1   C2    single    1.496  0.020  1.496
 3N7  C1   H1    single    0.970  0.020  1.090
 3N7  C1   H1A   single    0.970  0.020  1.090
 3N7  C1   H1B   single    0.970  0.020  1.090
 3N7  N28  C2    aromatic  1.330  0.020  1.330
 3N7  C2   C3    aromatic  1.386  0.020  1.386
 3N7  C3   C4    aromatic  1.399  0.020  1.399
 3N7  C3   H3    single    0.930  0.020  1.080
 3N7  N15  C4    aromatic  1.336  0.020  1.336
 3N7  C4   N5    single    1.359  0.020  1.359
 3N7  N5   C6    single    1.382  0.020  1.382
 3N7  N5   HN5   single    0.860  0.020  1.020
 3N7  C7   C6    aromatic  1.410  0.020  1.410
 3N7  C6   N10   aromatic  1.316  0.020  1.316
 3N7  C7   C8    aromatic  1.378  0.020  1.378
 3N7  C7   H7    single    0.930  0.020  1.080
 3N7  C12  C8    single    1.468  0.020  1.468
 3N7  C8   N9    aromatic  1.343  0.020  1.343
 3N7  N10  N9    aromatic  1.341  0.020  1.341
 3N7  C14  C12   single    1.505  0.020  1.505
 3N7  C12  C13   single    1.507  0.020  1.507
 3N7  C12  H12   single    0.970  0.020  1.090
 3N7  C14  C13   single    1.491  0.020  1.491
 3N7  C13  H13   single    0.970  0.020  1.090
 3N7  C13  H13A  single    0.970  0.020  1.090
 3N7  C14  H14   single    0.970  0.020  1.090
 3N7  C14  H14A  single    0.970  0.020  1.090
 3N7  C16  N15   aromatic  1.322  0.020  1.322
 3N7  N17  C16   single    1.362  0.020  1.362
 3N7  N28  C16   aromatic  1.336  0.020  1.336
 3N7  N17  C18   single    1.393  0.020  1.393
 3N7  N17  HN17  single    0.860  0.020  1.020
 3N7  C27  C18   aromatic  1.383  0.020  1.383
 3N7  C18  C19   aromatic  1.423  0.020  1.423
 3N7  C19  C20   aromatic  1.371  0.020  1.371
 3N7  C19  H19   single    0.930  0.020  1.080
 3N7  C21  C20   aromatic  1.399  0.020  1.399
 3N7  C20  H20   single    0.930  0.020  1.080
 3N7  C26  C21   aromatic  1.402  0.020  1.402
 3N7  N22  C21   aromatic  1.355  0.020  1.355
 3N7  N24  N22   aromatic  1.332  0.020  1.332
 3N7  C25  N24   aromatic  1.312  0.020  1.312
 3N7  C25  C26   aromatic  1.421  0.020  1.421
 3N7  C25  H25   single    0.930  0.020  1.080
 3N7  C27  C26   aromatic  1.403  0.020  1.403
 3N7  C27  H27   single    0.930  0.020  1.080
 3N7  N9   HN9   single    0.860  0.020  1.020
 3N7  N22  HN22  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
 3N7  H1B   C1   H1A  108.34  3.000
 3N7  H1B   C1   H1   108.62  3.000
 3N7  H1A   C1   H1   107.09  3.000
 3N7  H1B   C1   C2   111.88  3.000
 3N7  H1A   C1   C2   110.25  3.000
 3N7  H1    C1   C2   110.50  3.000
 3N7  N28   C2   C3   122.63  3.000
 3N7  C3    C2   C1   120.78  3.000
 3N7  N28   C2   C1   116.59  3.000
 3N7  H3    C3   C4   122.03  3.000
 3N7  H3    C3   C2   121.68  3.000
 3N7  C4    C3   C2   116.29  3.000
 3N7  N15   C4   N5   113.79  3.000
 3N7  N5    C4   C3   124.85  3.000
 3N7  N15   C4   C3   121.36  3.000
 3N7  HN5   N5   C6   115.52  3.000
 3N7  HN5   N5   C4   114.27  3.000
 3N7  C6    N5   C4   130.20  3.000
 3N7  N10   C6   C7   111.79  3.000
 3N7  N10   C6   N5   124.09  3.000
 3N7  C7    C6   N5   124.11  3.000
 3N7  H7    C7   C8   127.45  3.000
 3N7  H7    C7   C6   128.14  3.000
 3N7  C8    C7   C6   104.41  3.000
 3N7  C12   C8   N9   124.58  3.000
 3N7  N9    C8   C7   105.93  3.000
 3N7  C12   C8   C7   129.49  3.000
 3N7  HN9   N9   N10  118.59  3.000
 3N7  HN9   N9   C8   127.91  3.000
 3N7  N10   N9   C8   113.50  3.000
 3N7  N9    N10  C6   104.37  3.000
 3N7  H12   C12  C14  116.32  3.000
 3N7  H12   C12  C13  116.23  3.000
 3N7  C14   C12  C13   59.37  3.000
 3N7  H12   C12  C8   112.88  3.000
 3N7  C13   C12  C8   120.92  3.000
 3N7  C14   C12  C8   121.29  3.000
 3N7  H13A  C13  H13  114.33  3.000
 3N7  H13A  C13  C14  118.29  3.000
 3N7  H13   C13  C14  118.62  3.000
 3N7  H13A  C13  C12  117.62  3.000
 3N7  H13   C13  C12  117.29  3.000
 3N7  C14   C13  C12   60.25  3.000
 3N7  H14A  C14  H14  114.03  3.000
 3N7  H14A  C14  C13  118.57  3.000
 3N7  H14   C14  C13  118.41  3.000
 3N7  H14A  C14  C12  117.14  3.000
 3N7  H14   C14  C12  118.13  3.000
 3N7  C13   C14  C12   60.38  3.000
 3N7  C16   N15  C4   117.17  3.000
 3N7  N28   C16  N17  114.03  3.000
 3N7  N28   C16  N15  126.34  3.000
 3N7  N17   C16  N15  119.63  3.000
 3N7  HN17  N17  C18  115.56  3.000
 3N7  HN17  N17  C16  112.70  3.000
 3N7  C18   N17  C16  131.73  3.000
 3N7  C27   C18  C19  119.79  3.000
 3N7  C19   C18  N17  114.83  3.000
 3N7  C27   C18  N17  125.37  3.000
 3N7  H19   C19  C20  118.64  3.000
 3N7  H19   C19  C18  118.58  3.000
 3N7  C20   C19  C18  122.78  3.000
 3N7  H20   C20  C21  122.09  3.000
 3N7  H20   C20  C19  120.84  3.000
 3N7  C21   C20  C19  117.06  3.000
 3N7  C26   C21  N22  106.20  3.000
 3N7  N22   C21  C20  132.62  3.000
 3N7  C26   C21  C20  121.18  3.000
 3N7  HN22  N22  N24  119.79  3.000
 3N7  HN22  N22  C21  128.04  3.000
 3N7  N24   N22  C21  112.17  3.000
 3N7  C25   N24  N22  106.82  3.000
 3N7  H25   C25  C26  128.53  3.000
 3N7  H25   C25  N24  120.57  3.000
 3N7  C26   C25  N24  110.90  3.000
 3N7  C27   C26  C25  134.89  3.000
 3N7  C27   C26  C21  121.20  3.000
 3N7  C25   C26  C21  103.91  3.000
 3N7  H27   C27  C26  120.90  3.000
 3N7  H27   C27  C18  121.11  3.000
 3N7  C26   C27  C18  117.98  3.000
 3N7  C16   N28  C2   116.21  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
 3N7  CONST_01  N15   C16  N28  C2      0.00   0.0  0
 3N7  CONST_02  N15   C4   C3   C2      0.00   0.0  0
 3N7  CONST_03  C16   N28  C2   C3      0.00   0.0  0
 3N7  CONST_04  C16   N15  C4   C3      0.00   0.0  0
 3N7  CONST_05  N28   C2   C3   C4      0.00   0.0  0
 3N7  CONST_06  N28   C16  N15  C4      0.00   0.0  0
 3N7  CONST_07  N9    C8   C7   C6      0.00   0.0  0
 3N7  CONST_08  C8    N9   N10  C6      0.00   0.0  0
 3N7  CONST_09  N9    N10  C6   C7      0.00   0.0  0
 3N7  CONST_10  N10   N9   C8   C7      0.00   0.0  0
 3N7  CONST_11  N10   C6   C7   C8      0.00   0.0  0
 3N7  CONST_12  C21   C26  C27  C18     0.00   0.0  0
 3N7  CONST_13  C25   C26  C27  C18   180.00   0.0  0
 3N7  CONST_14  C21   C20  C19  C18     0.00   0.0  0
 3N7  CONST_15  C26   C27  C18  C19     0.00   0.0  0
 3N7  CONST_16  C26   C21  C20  C19     0.00   0.0  0
 3N7  CONST_17  N22   C21  C20  C19   180.00   0.0  0
 3N7  CONST_18  C27   C18  C19  C20     0.00   0.0  0
 3N7  CONST_19  C25   C26  C21  C20   180.00   0.0  0
 3N7  CONST_20  C27   C26  C21  C20     0.00   0.0  0
 3N7  CONST_21  N24   N22  C21  C20   180.00   0.0  0
 3N7  CONST_22  N24   C25  C26  C21     0.00   0.0  0
 3N7  CONST_23  C25   N24  N22  C21     0.00   0.0  0
 3N7  CONST_24  C25   C26  C21  N22     0.00   0.0  0
 3N7  CONST_25  C27   C26  C21  N22   180.00   0.0  0
 3N7  CONST_26  C26   C25  N24  N22     0.00   0.0  0
 3N7  CONST_27  C26   C21  N22  N24     0.00   0.0  0
 3N7  CONST_28  C27   C26  C25  N24   180.00   0.0  0
 3N7  CONST_29  C12   C8   C7   C6    180.00   0.0  0
 3N7  CONST_30  C12   C8   N9   N10   180.00   0.0  0
 3N7  CONST_31  C16   N28  C2   C1    180.00   0.0  0
 3N7  CONST_32  C4    C3   C2   C1    180.00   0.0  0
 3N7  CONST_33  N17   C16  N28  C2    180.00   0.0  0
 3N7  CONST_34  N5    C4   C3   C2    180.00   0.0  0
 3N7  CONST_35  N17   C16  N15  C4    180.00   0.0  0
 3N7  CONST_36  C16   N15  C4   N5    180.00   0.0  0
 3N7  CONST_37  C8    C7   C6   N5    180.00   0.0  0
 3N7  CONST_38  N9    N10  C6   N5    180.00   0.0  0
 3N7  CONST_39  C26   C27  C18  N17   180.00   0.0  0
 3N7  CONST_40  C20   C19  C18  N17   180.00   0.0  0
 3N7  CONST_41  HN9   N9   N10  C6    180.00   0.0  0
 3N7  CONST_42  H7    C7   C8   N9    180.00   0.0  0
 3N7  CONST_43  H3    C3   C4   N15   180.00   0.0  0
 3N7  CONST_44  H20   C20  C19  C18   180.00   0.0  0
 3N7  CONST_45  H27   C27  C18  C19   180.00   0.0  0
 3N7  CONST_46  HN22  N22  C21  C20     0.00   0.0  0
 3N7  CONST_47  H19   C19  C20  C21   180.00   0.0  0
 3N7  CONST_48  H25   C25  C26  C21   180.00   0.0  0
 3N7  Var_01    C14   C12  C8   C7   -149.40  30.0  2
 3N7  Var_02    C13   C14  C12  C8   -109.81  30.0  1
 3N7  Var_03    C6    N5   C4   C3     -1.09  30.0  2
 3N7  Var_04    C7    C6   N5   C4    173.65  30.0  2
 3N7  Var_05    C18   N17  C16  N15    -2.59  30.0  2
 3N7  Var_06    C27   C18  N17  C16    -2.66  30.0  2
 3N7  Var_07    H1    C1   C2   C3    123.95  30.0  2

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
 3N7  chir_01  C12  C8  C14  C13  both

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
 3N7  plan-1  N5    0.020
 3N7  plan-1  C6    0.020
 3N7  plan-1  C7    0.020
 3N7  plan-1  C8    0.020
 3N7  plan-1  N9    0.020
 3N7  plan-1  N10   0.020
 3N7  plan-1  C12   0.020
 3N7  plan-1  H7    0.020
 3N7  plan-1  HN9   0.020
 3N7  plan-2  C1    0.020
 3N7  plan-2  C2    0.020
 3N7  plan-2  C3    0.020
 3N7  plan-2  C4    0.020
 3N7  plan-2  N5    0.020
 3N7  plan-2  N15   0.020
 3N7  plan-2  C16   0.020
 3N7  plan-2  N17   0.020
 3N7  plan-2  N28   0.020
 3N7  plan-2  H3    0.020
 3N7  plan-3  N17   0.020
 3N7  plan-3  C18   0.020
 3N7  plan-3  C19   0.020
 3N7  plan-3  C20   0.020
 3N7  plan-3  C21   0.020
 3N7  plan-3  N22   0.020
 3N7  plan-3  N24   0.020
 3N7  plan-3  C25   0.020
 3N7  plan-3  C26   0.020
 3N7  plan-3  C27   0.020
 3N7  plan-3  H19   0.020
 3N7  plan-3  H20   0.020
 3N7  plan-3  H25   0.020
 3N7  plan-3  H27   0.020
 3N7  plan-3  HN22  0.020

