# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 02:04:20 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 6-(2-aminopyrimidin-4-yl)-1H-indazol-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nccc(n1)c2ccc3c(N)n[nH]c3c2
#
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
 JMZ  JMZ  6-(2-aminopyrimidin-4-yl)-1H-indazol-3-amine  ligand  27  17  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JMZ
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
 JMZ  C4    C  CR16  0  -0.020   3.8027  -1.4473  -0.3021
 JMZ  C5    C  CR16  0  -0.336  -0.4443   0.7994  -0.2046
 JMZ  C6    C  CR6   0   0.042   0.2173  -0.4019  -0.0246
 JMZ  C7    C  CR56  0  -0.126  -2.5621  -0.4148  -0.0064
 JMZ  C8    C  CR6   0   0.289   1.6968  -0.4166  -0.0383
 JMZ  C10   C  CR5   0   0.353  -3.9314  -0.0096  -0.0650
 JMZ  N12   N  NH2   0  -0.847  -5.0303  -0.8359   0.0078
 JMZ  C1    C  CR16  0  -0.334  -0.5056  -1.6048   0.1697
 JMZ  C2    C  CR16  0  -0.285  -1.8805  -1.6202   0.1832
 JMZ  C3    C  CR16  0  -0.399   2.4243  -1.5744  -0.3081
 JMZ  C9    C  CR56  0   0.464  -1.8405   0.7754  -0.2010
 JMZ  C11   C  CR6   0   0.542   3.6446   0.7477   0.1821
 JMZ  N13   N  NH2   0  -0.823   4.2550   1.9163   0.4599
 JMZ  N14   N  NR15  0  -0.575  -2.7572   1.7483  -0.3687
 JMZ  N15   N  N     0  -0.455   4.4300  -0.3099  -0.0586
 JMZ  N16   N  N     0  -0.486   2.3109   0.7357   0.2011
 JMZ  N17   N  N     0  -0.281  -4.0206   1.2799  -0.2721
 JMZ  H4    H  HCR6  0   0.271   4.4288  -2.3085  -0.5106
 JMZ  HN12  H  HNH2  0   0.383  -4.9285  -1.5973   0.6614
 JMZ  HN1A  H  HNH2  0   0.377  -5.8972  -0.3453   0.1702
 JMZ  H1    H  HCR6  0   0.253   0.0284  -2.5301   0.3368
 JMZ  H2    H  HCR6  0   0.257  -2.4131  -2.5485   0.3463
 JMZ  H3    H  HCR6  0   0.267   1.9605  -2.5209  -0.5379
 JMZ  HN13  H  HNH2  0   0.395   5.2392   2.0035   0.2754
 JMZ  HN1B  H  HNH2  0   0.395   3.7116   2.7619   0.4582
 JMZ  HN14  H  HNR5  0   0.411  -2.6015   2.7331  -0.4976
 JMZ  H5    H  HCR6  0   0.267   0.1063   1.7186  -0.3518

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
 JMZ  C4   C3    aromatic  1.384  0.020  1.384
 JMZ  C4   N15   aromatic  1.322  0.020  1.322
 JMZ  C5   C6    aromatic  1.383  0.020  1.383
 JMZ  C5   C9    aromatic  1.396  0.020  1.396
 JMZ  C6   C8    single    1.480  0.020  1.480
 JMZ  C6   C1    aromatic  1.417  0.020  1.417
 JMZ  C7   C10   aromatic  1.429  0.020  1.429
 JMZ  C7   C2    aromatic  1.398  0.020  1.398
 JMZ  C7   C9    aromatic  1.405  0.020  1.405
 JMZ  C8   C3    aromatic  1.394  0.020  1.394
 JMZ  C8   N16   aromatic  1.328  0.020  1.328
 JMZ  C10  N12   single    1.377  0.020  1.377
 JMZ  C10  N17   aromatic  1.309  0.020  1.309
 JMZ  C1   C2    aromatic  1.375  0.020  1.375
 JMZ  C9   N14   aromatic  1.347  0.020  1.347
 JMZ  C11  N13   single    1.347  0.020  1.347
 JMZ  C11  N15   aromatic  1.339  0.020  1.339
 JMZ  C11  N16   aromatic  1.334  0.020  1.334
 JMZ  N14  N17   aromatic  1.351  0.020  1.351
 JMZ  C4   H4    single    0.930  0.020  1.080
 JMZ  C5   H5    single    0.930  0.020  1.080
 JMZ  N12  HN12  single    0.890  0.020  1.040
 JMZ  N12  HN1A  single    0.890  0.020  1.040
 JMZ  C1   H1    single    0.930  0.020  1.080
 JMZ  C2   H2    single    0.930  0.020  1.080
 JMZ  C3   H3    single    0.930  0.020  1.080
 JMZ  N13  HN13  single    0.890  0.020  1.040
 JMZ  N13  HN1B  single    0.890  0.020  1.040
 JMZ  N14  HN14  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
 JMZ  H4    C4   N15   116.40  3.000
 JMZ  H4    C4   C3    120.07  3.000
 JMZ  N15   C4   C3    123.54  3.000
 JMZ  H5    C5   C9    121.60  3.000
 JMZ  H5    C5   C6    120.82  3.000
 JMZ  C9    C5   C6    117.58  3.000
 JMZ  C1    C6   C8    120.20  3.000
 JMZ  C1    C6   C5    120.74  3.000
 JMZ  C8    C6   C5    119.06  3.000
 JMZ  C9    C7   C2    119.92  3.000
 JMZ  C9    C7   C10   104.25  3.000
 JMZ  C2    C7   C10   135.83  3.000
 JMZ  N16   C8   C3    120.97  3.000
 JMZ  N16   C8   C6    116.89  3.000
 JMZ  C3    C8   C6    122.14  3.000
 JMZ  N17   C10  N12   123.04  3.000
 JMZ  N17   C10  C7    110.55  3.000
 JMZ  N12   C10  C7    126.33  3.000
 JMZ  HN1A  N12  HN12  110.45  3.000
 JMZ  HN1A  N12  C10   113.73  3.000
 JMZ  HN12  N12  C10   114.00  3.000
 JMZ  H1    C1   C2    118.86  3.000
 JMZ  H1    C1   C6    119.72  3.000
 JMZ  C2    C1   C6    121.40  3.000
 JMZ  H2    C2   C1    120.20  3.000
 JMZ  H2    C2   C7    121.33  3.000
 JMZ  C1    C2   C7    118.47  3.000
 JMZ  H3    C3   C8    123.07  3.000
 JMZ  H3    C3   C4    120.63  3.000
 JMZ  C8    C3   C4    116.28  3.000
 JMZ  N14   C9   C7    106.23  3.000
 JMZ  N14   C9   C5    131.88  3.000
 JMZ  C7    C9   C5    121.89  3.000
 JMZ  N16   C11  N15   125.59  3.000
 JMZ  N16   C11  N13   117.25  3.000
 JMZ  N15   C11  N13   117.15  3.000
 JMZ  HN1B  N13  HN13  117.13  3.000
 JMZ  HN1B  N13  C11   118.97  3.000
 JMZ  HN13  N13  C11   118.76  3.000
 JMZ  HN14  N14  N17   119.58  3.000
 JMZ  HN14  N14  C9    128.18  3.000
 JMZ  N17   N14  C9    112.15  3.000
 JMZ  C11   N15  C4    115.75  3.000
 JMZ  C11   N16  C8    117.89  3.000
 JMZ  N14   N17  C10   106.81  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
 JMZ  CONST_01  C6    C8   C3   C4   180.00  0.0  0
 JMZ  CONST_02  N16   C8   C3   C4     0.00  0.0  0
 JMZ  CONST_03  N16   C11  N15  C4     0.00  0.0  0
 JMZ  CONST_06  C2    C1   C6   C5     0.00  0.0  0
 JMZ  CONST_07  C10   C7   C9   C5   180.00  0.0  0
 JMZ  CONST_08  C2    C7   C9   C5     0.00  0.0  0
 JMZ  CONST_09  N17   N14  C9   C5   180.00  0.0  0
 JMZ  CONST_10  C7    C9   C5   C6     0.00  0.0  0
 JMZ  CONST_11  N14   C9   C5   C6   180.00  0.0  0
 JMZ  CONST_12  C11   N16  C8   C6   180.00  0.0  0
 JMZ  CONST_13  C7    C2   C1   C6     0.00  0.0  0
 JMZ  CONST_14  N14   N17  C10  C7     0.00  0.0  0
 JMZ  CONST_15  N17   N14  C9   C7     0.00  0.0  0
 JMZ  CONST_16  C9    C5   C6   C8   180.00  0.0  0
 JMZ  CONST_17  C2    C1   C6   C8   180.00  0.0  0
 JMZ  CONST_18  N15   C4   C3   C8     0.00  0.0  0
 JMZ  CONST_19  N15   C11  N16  C8     0.00  0.0  0
 JMZ  CONST_20  C1    C2   C7   C10  180.00  0.0  0
 JMZ  CONST_21  N14   C9   C7   C10    0.00  0.0  0
 JMZ  CONST_22  C9    N14  N17  C10    0.00  0.0  0
 JMZ  CONST_23  C9    C5   C6   C1     0.00  0.0  0
 JMZ  CONST_26  C9    C7   C2   C1     0.00  0.0  0
 JMZ  CONST_27  N17   C10  C7   C2   180.00  0.0  0
 JMZ  CONST_28  N14   C9   C7   C2   180.00  0.0  0
 JMZ  CONST_29  C11   N15  C4   C3     0.00  0.0  0
 JMZ  CONST_30  C11   N16  C8   C3     0.00  0.0  0
 JMZ  CONST_31  N17   C10  C7   C9     0.00  0.0  0
 JMZ  CONST_32  N13   C11  N15  C4   180.00  0.0  0
 JMZ  CONST_33  N13   C11  N16  C8   180.00  0.0  0
 JMZ  CONST_34  C2    C7   C10  N12    0.00  0.0  0
 JMZ  CONST_35  C9    C7   C10  N12  180.00  0.0  0
 JMZ  CONST_36  N14   N17  C10  N12  180.00  0.0  0
 JMZ  CONST_37  H1    C1   C6   C5   180.00  0.0  0
 JMZ  CONST_38  HN14  N14  C9   C5     0.00  0.0  0
 JMZ  CONST_39  H3    C3   C8   C6     0.00  0.0  0
 JMZ  CONST_40  H2    C2   C1   C6   180.00  0.0  0
 JMZ  CONST_41  H5    C5   C9   C7   180.00  0.0  0
 JMZ  CONST_42  H4    C4   C3   C8   180.00  0.0  0
 JMZ  CONST_44  HN1A  N12  C10  C7   180.00  0.0  0
 JMZ  CONST_45  HN13  N13  C11  N15    0.00  0.0  0
 JMZ  CONST_46  HN1B  N13  C11  N15  180.00  0.0  0

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
 JMZ  plan-1  C4    0.020
 JMZ  plan-1  C6    0.020
 JMZ  plan-1  C8    0.020
 JMZ  plan-1  C3    0.020
 JMZ  plan-1  C11   0.020
 JMZ  plan-1  N13   0.020
 JMZ  plan-1  N15   0.020
 JMZ  plan-1  N16   0.020
 JMZ  plan-1  H4    0.020
 JMZ  plan-1  H3    0.020
 JMZ  plan-2  C5    0.020
 JMZ  plan-2  C6    0.020
 JMZ  plan-2  C7    0.020
 JMZ  plan-2  C8    0.020
 JMZ  plan-2  C10   0.020
 JMZ  plan-2  N12   0.020
 JMZ  plan-2  C1    0.020
 JMZ  plan-2  C2    0.020
 JMZ  plan-2  C9    0.020
 JMZ  plan-2  N14   0.020
 JMZ  plan-2  N17   0.020
 JMZ  plan-2  H1    0.020
 JMZ  plan-2  H2    0.020
 JMZ  plan-2  HN14  0.020
 JMZ  plan-2  H5    0.020
 JMZ  plan-3  C10   0.020
 JMZ  plan-3  N12   0.020
 JMZ  plan-3  HN12  0.020
 JMZ  plan-3  HN1A  0.020
 JMZ  plan-4  C11   0.020
 JMZ  plan-4  N13   0.020
 JMZ  plan-4  HN13  0.020
 JMZ  plan-4  HN1B  0.020

