# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 08:32:54 2021
#   Inital geometry file: a 76 line input string
#   Ligand name: 5-(1-methylindol-3-yl)pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(c2cncnc2N)c3ccccc13
#
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
 JU8  JU8  5-(1-methylindol-3-yl)pyrimidin-4-amine  ligand  29  17  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JU8
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
 JU8  C4   C  CR6   0   0.447  22.4035  -18.8122  4.1701
 JU8  C5   C  CR6   0  -0.124  21.0317  -19.1618  4.0703
 JU8  C6   C  CR16  0  -0.093  20.7857  -20.4473  3.6341
 JU8  N1   N  N     0  -0.428  21.7377  -21.3317  3.3236
 JU8  N3   N  N     0  -0.450  23.3567  -19.6972  3.8701
 JU8  NAG  N  NR5   0  -0.518  18.6412  -16.7524  5.4577
 JU8  CAH  C  CR15  0  -0.077  19.8063  -17.4565  5.5031
 JU8  CAE  C  CR56  0   0.374  17.9886  -17.0568  4.2963
 JU8  CAD  C  CR16  0  -0.313  16.7729  -16.5811  3.8068
 JU8  CAC  C  CR16  0  -0.279  16.3509  -17.0579  2.5808
 JU8  CAB  C  CR16  0  -0.267  17.1208  -17.9811  1.8545
 JU8  CAA  C  CR16  0  -0.383  18.3245  -18.4492  2.3439
 JU8  CAF  C  CR56  0   0.043  18.7738  -17.9900  3.5871
 JU8  CAI  C  CR5   0  -0.028  19.9441  -18.2363  4.3816
 JU8  C2   C  CR16  0   0.048  22.9754  -20.8968  3.4688
 JU8  NAQ  N  NH2   0  -0.823  22.8025  -17.5980  4.5897
 JU8  H1   H  HCR6  0   0.262  19.7600  -20.7896  3.5385
 JU8  H2   H  HCH3  0   0.266  18.9082  -15.7531  7.2525
 JU8  H3   H  HCH3  0   0.255  18.0396  -14.8282  6.0246
 JU8  H4   H  HCH3  0   0.255  17.2264  -16.1476  6.8822
 JU8  H5   H  HCR5  0   0.298  20.4601  -17.3657  6.3574
 JU8  H6   H  HCR6  0   0.267  16.1796  -15.8652  4.3615
 JU8  H7   H  HCR6  0   0.252  15.4108  -16.7112  2.1716
 JU8  H8   H  HCR6  0   0.249  16.7633  -18.3291  0.8940
 JU8  H9   H  HCR6  0   0.246  18.9092  -19.1570  1.7692
 JU8  H10  H  HCR6  0   0.253  23.7712  -21.5953  3.2298
 JU8  H11  H  HNH2  0   0.396  23.7722  -17.3571  4.4669
 JU8  H12  H  HNH2  0   0.403  22.1499  -16.8318  4.5882
 JU8  CAP  C  CH3   0  -0.529  18.1740  -15.8204  6.4546

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
 JU8  CAB  CAA  aromatic  1.381  0.020  1.381
 JU8  CAB  CAC  aromatic  1.405  0.020  1.405
 JU8  CAA  CAF  aromatic  1.399  0.020  1.399
 JU8  N1   C6   aromatic  1.336  0.020  1.336
 JU8  N1   C2   aromatic  1.320  0.020  1.320
 JU8  C6   C5   aromatic  1.380  0.020  1.380
 JU8  CAC  CAD  aromatic  1.381  0.020  1.381
 JU8  C2   N3   aromatic  1.321  0.020  1.321
 JU8  CAF  CAI  aromatic  1.436  0.020  1.436
 JU8  CAF  CAE  aromatic  1.411  0.020  1.411
 JU8  C5   CAI  single    1.462  0.020  1.462
 JU8  C5   C4   aromatic  1.419  0.020  1.419
 JU8  CAD  CAE  aromatic  1.394  0.020  1.394
 JU8  CAI  CAH  aromatic  1.373  0.020  1.373
 JU8  CAE  NAG  aromatic  1.367  0.020  1.367
 JU8  N3   C4   aromatic  1.335  0.020  1.335
 JU8  C4   NAQ  single    1.345  0.020  1.345
 JU8  CAH  NAG  aromatic  1.362  0.020  1.362
 JU8  NAG  CAP  single    1.442  0.020  1.442
 JU8  C6   H1   single    0.930  0.020  1.080
 JU8  CAP  H2   single    0.970  0.020  1.090
 JU8  CAP  H3   single    0.970  0.020  1.090
 JU8  CAP  H4   single    0.970  0.020  1.090
 JU8  CAH  H5   single    0.930  0.020  1.080
 JU8  CAD  H6   single    0.930  0.020  1.080
 JU8  CAC  H7   single    0.930  0.020  1.080
 JU8  CAB  H8   single    0.930  0.020  1.080
 JU8  CAA  H9   single    0.930  0.020  1.080
 JU8  C2   H10  single    0.930  0.020  1.080
 JU8  NAQ  H11  single    0.890  0.020  1.040
 JU8  NAQ  H12  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
 JU8  NAQ  C4   N3   117.17  3.000
 JU8  NAQ  C4   C5   122.08  3.000
 JU8  N3   C4   C5   120.74  3.000
 JU8  CAI  C5   C6   121.65  3.000
 JU8  CAI  C5   C4   123.25  3.000
 JU8  C6   C5   C4   115.10  3.000
 JU8  H1   C6   N1   116.36  3.000
 JU8  H1   C6   C5   119.35  3.000
 JU8  N1   C6   C5   124.28  3.000
 JU8  C2   N1   C6   115.12  3.000
 JU8  C2   N3   C4   117.65  3.000
 JU8  CAE  NAG  CAH  108.77  3.000
 JU8  CAH  NAG  CAP  126.02  3.000
 JU8  CAE  NAG  CAP  125.21  3.000
 JU8  H5   CAH  CAI  129.30  3.000
 JU8  H5   CAH  NAG  120.06  3.000
 JU8  CAI  CAH  NAG  110.63  3.000
 JU8  CAF  CAE  CAD  122.31  3.000
 JU8  CAD  CAE  NAG  129.71  3.000
 JU8  CAF  CAE  NAG  107.98  3.000
 JU8  H6   CAD  CAC  121.03  3.000
 JU8  H6   CAD  CAE  121.57  3.000
 JU8  CAC  CAD  CAE  117.40  3.000
 JU8  H7   CAC  CAB  119.42  3.000
 JU8  H7   CAC  CAD  119.36  3.000
 JU8  CAB  CAC  CAD  121.22  3.000
 JU8  H8   CAB  CAA  119.56  3.000
 JU8  H8   CAB  CAC  119.29  3.000
 JU8  CAA  CAB  CAC  121.15  3.000
 JU8  H9   CAA  CAF  120.83  3.000
 JU8  H9   CAA  CAB  120.26  3.000
 JU8  CAF  CAA  CAB  118.91  3.000
 JU8  CAI  CAF  CAA  134.19  3.000
 JU8  CAI  CAF  CAE  106.79  3.000
 JU8  CAA  CAF  CAE  119.00  3.000
 JU8  CAF  CAI  CAH  105.83  3.000
 JU8  CAH  CAI  C5   127.47  3.000
 JU8  CAF  CAI  C5   126.67  3.000
 JU8  H10  C2   N3   116.07  3.000
 JU8  H10  C2   N1   116.82  3.000
 JU8  N3   C2   N1   127.10  3.000
 JU8  H12  NAQ  H11  116.25  3.000
 JU8  H12  NAQ  C4   119.62  3.000
 JU8  H11  NAQ  C4   117.62  3.000
 JU8  H4   CAP  H3   108.72  3.000
 JU8  H4   CAP  H2   108.55  3.000
 JU8  H3   CAP  H2   108.47  3.000
 JU8  H4   CAP  NAG  111.03  3.000
 JU8  H3   CAP  NAG  110.82  3.000
 JU8  H2   CAP  NAG  109.19  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
 JU8  CONST_01  N1   C6   C5   C4     0.00   0.0  0
 JU8  CONST_04  N1   C2   N3   C4     0.00   0.0  0
 JU8  CONST_05  C2   N1   C6   C5     0.00   0.0  0
 JU8  CONST_06  CAA  CAF  CAI  C5     0.00   0.0  0
 JU8  CONST_07  CAE  CAF  CAI  C5   180.00   0.0  0
 JU8  CONST_08  NAG  CAH  CAI  C5   180.00   0.0  0
 JU8  CONST_09  C2   N3   C4   C5     0.00   0.0  0
 JU8  CONST_10  N3   C2   N1   C6     0.00   0.0  0
 JU8  CONST_13  N3   C4   C5   C6     0.00   0.0  0
 JU8  CONST_14  CAI  C5   C6   N1   180.00   0.0  0
 JU8  CONST_15  CAI  C5   C4   N3   180.00   0.0  0
 JU8  CONST_16  CAA  CAF  CAE  NAG  180.00   0.0  0
 JU8  CONST_17  CAI  CAF  CAE  NAG    0.00   0.0  0
 JU8  CONST_18  CAC  CAD  CAE  NAG  180.00   0.0  0
 JU8  CONST_19  CAF  CAI  CAH  NAG    0.00   0.0  0
 JU8  CONST_20  CAA  CAF  CAI  CAH  180.00   0.0  0
 JU8  CONST_21  CAE  CAF  CAI  CAH    0.00   0.0  0
 JU8  CONST_22  CAF  CAE  NAG  CAH    0.00   0.0  0
 JU8  CONST_23  CAD  CAE  NAG  CAH  180.00   0.0  0
 JU8  CONST_24  CAB  CAA  CAF  CAE    0.00   0.0  0
 JU8  CONST_25  CAB  CAC  CAD  CAE    0.00   0.0  0
 JU8  CONST_26  CAI  CAH  NAG  CAE    0.00   0.0  0
 JU8  CONST_27  CAA  CAB  CAC  CAD    0.00   0.0  0
 JU8  CONST_28  CAA  CAF  CAE  CAD    0.00   0.0  0
 JU8  CONST_29  CAI  CAF  CAE  CAD  180.00   0.0  0
 JU8  CONST_30  CAF  CAA  CAB  CAC    0.00   0.0  0
 JU8  CONST_31  CAF  CAE  CAD  CAC    0.00   0.0  0
 JU8  CONST_32  CAI  CAF  CAA  CAB  180.00   0.0  0
 JU8  CONST_33  NAQ  C4   C5   C6   180.00   0.0  0
 JU8  CONST_34  CAF  CAE  NAG  CAP  180.00   0.0  0
 JU8  CONST_35  CAD  CAE  NAG  CAP    0.00   0.0  0
 JU8  CONST_36  CAI  CAH  NAG  CAP  180.00   0.0  0
 JU8  CONST_37  NAQ  C4   C5   CAI    0.00   0.0  0
 JU8  CONST_38  NAQ  C4   N3   C2   180.00   0.0  0
 JU8  CONST_39  H1   C6   C5   C4   180.00   0.0  0
 JU8  CONST_40  H10  C2   N3   C4   180.00   0.0  0
 JU8  CONST_41  H5   CAH  CAI  C5     0.00   0.0  0
 JU8  CONST_42  H6   CAD  CAE  NAG    0.00   0.0  0
 JU8  CONST_43  H9   CAA  CAF  CAE  180.00   0.0  0
 JU8  CONST_44  H7   CAC  CAD  CAE  180.00   0.0  0
 JU8  CONST_45  H8   CAB  CAC  CAD  180.00   0.0  0
 JU8  CONST_46  H11  NAQ  C4   C5   180.00   0.0  0
 JU8  Var_01    H2   CAP  NAG  CAH    0.78  30.0  2

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
 JU8  plan-1  C4   0.020
 JU8  plan-1  C5   0.020
 JU8  plan-1  C6   0.020
 JU8  plan-1  N1   0.020
 JU8  plan-1  N3   0.020
 JU8  plan-1  CAI  0.020
 JU8  plan-1  C2   0.020
 JU8  plan-1  NAQ  0.020
 JU8  plan-1  H1   0.020
 JU8  plan-1  H10  0.020
 JU8  plan-2  C5   0.020
 JU8  plan-2  NAG  0.020
 JU8  plan-2  CAH  0.020
 JU8  plan-2  CAE  0.020
 JU8  plan-2  CAD  0.020
 JU8  plan-2  CAC  0.020
 JU8  plan-2  CAB  0.020
 JU8  plan-2  CAA  0.020
 JU8  plan-2  CAF  0.020
 JU8  plan-2  CAI  0.020
 JU8  plan-2  H5   0.020
 JU8  plan-2  H6   0.020
 JU8  plan-2  H7   0.020
 JU8  plan-2  H8   0.020
 JU8  plan-2  H9   0.020
 JU8  plan-2  CAP  0.020
 JU8  plan-3  C4   0.020
 JU8  plan-3  NAQ  0.020
 JU8  plan-3  H11  0.020
 JU8  plan-3  H12  0.020

