# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 08:07:30 2021
#   Inital geometry file: a 76 line input string
#   Ligand name: 4-(1-methylindol-3-yl)pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(c2ccnc(N)n2)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
 JUW  JUW  4-(1-methylindol-3-yl)pyrimidin-2-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_JUW
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
 JUW  C4   C  CR6   0   0.246  21.1398  -19.6177  3.4741
 JUW  C5   C  CR16  0  -0.410  22.4526  -19.8341  3.9168
 JUW  C6   C  CR16  0  -0.031  23.1400  -20.8680  3.3196
 JUW  N1   N  N     0  -0.467  22.6299  -21.6395  2.3670
 JUW  N3   N  N     0  -0.499  20.6157  -20.3823  2.5198
 JUW  NAG  N  NR5   0  -0.521  19.6482  -16.8426  5.2972
 JUW  CAH  C  CR15  0  -0.056  20.6599  -17.6957  5.0241
 JUW  CAE  C  CR56  0   0.364  18.5872  -17.1343  4.4768
 JUW  CAD  C  CR16  0  -0.308  17.3413  -16.5172  4.4013
 JUW  CAC  C  CR16  0  -0.280  16.4453  -17.0112  3.4723
 JUW  CAB  C  CR16  0  -0.259  16.7859  -18.0901  2.6433
 JUW  CAA  C  CR16  0  -0.377  18.0245  -18.6987  2.7240
 JUW  CAF  C  CR56  0   0.061  18.9541  -18.2206  3.6553
 JUW  CAI  C  CR5   0  -0.050  20.3012  -18.5707  4.0221
 JUW  C2   C  CR6   0   0.531  21.3771  -21.3508  2.0056
 JUW  NAP  N  NH2   0  -0.827  20.8377  -22.0837  1.0060
 JUW  H1   H  HCR6  0   0.258  22.9168  -19.2348  4.6857
 JUW  H2   H  HCR6  0   0.265  24.1580  -21.0894  3.6227
 JUW  H3   H  HCH3  0   0.269  20.6177  -15.8078  6.8083
 JUW  H4   H  HCH3  0   0.259  19.5429  -14.8164  5.8168
 JUW  H5   H  HCH3  0   0.259  18.8681  -15.9357  7.0143
 JUW  H6   H  HCR5  0   0.300  21.5871  -17.6238  5.5717
 JUW  H7   H  HCR6  0   0.268  17.0772  -15.6846  5.0411
 JUW  H8   H  HCR6  0   0.253  15.4659  -16.5595  3.3847
 JUW  H9   H  HCR6  0   0.248  16.0609  -18.4549  1.9270
 JUW  H10  H  HCR6  0   0.252  18.2739  -19.5319  2.0838
 JUW  H11  H  HNH2  0   0.391  21.2882  -22.9463  0.7534
 JUW  H12  H  HNH2  0   0.392  19.8431  -22.0386  0.8665
 JUW  CAQ  C  CH3   0  -0.530  19.6655  -15.7917  6.2865

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
 JUW  NAP  C2   single    1.352  0.020  1.352
 JUW  C2   N1   aromatic  1.335  0.020  1.335
 JUW  C2   N3   aromatic  1.335  0.020  1.335
 JUW  N1   C6   aromatic  1.328  0.020  1.328
 JUW  N3   C4   aromatic  1.330  0.020  1.330
 JUW  CAB  CAA  aromatic  1.382  0.020  1.382
 JUW  CAB  CAC  aromatic  1.403  0.020  1.403
 JUW  CAA  CAF  aromatic  1.400  0.020  1.400
 JUW  C6   C5   aromatic  1.378  0.020  1.378
 JUW  C4   C5   aromatic  1.402  0.020  1.402
 JUW  C4   CAI  single    1.449  0.020  1.449
 JUW  CAC  CAD  aromatic  1.382  0.020  1.382
 JUW  CAF  CAI  aromatic  1.439  0.020  1.439
 JUW  CAF  CAE  aromatic  1.411  0.020  1.411
 JUW  CAI  CAH  aromatic  1.378  0.020  1.378
 JUW  CAD  CAE  aromatic  1.392  0.020  1.392
 JUW  CAE  NAG  aromatic  1.373  0.020  1.373
 JUW  CAH  NAG  aromatic  1.351  0.020  1.351
 JUW  NAG  CAQ  single    1.443  0.020  1.443
 JUW  C5   H1   single    0.930  0.020  1.080
 JUW  C6   H2   single    0.930  0.020  1.080
 JUW  CAQ  H3   single    0.970  0.020  1.090
 JUW  CAQ  H4   single    0.970  0.020  1.090
 JUW  CAQ  H5   single    0.970  0.020  1.090
 JUW  CAH  H6   single    0.930  0.020  1.080
 JUW  CAD  H7   single    0.930  0.020  1.080
 JUW  CAC  H8   single    0.930  0.020  1.080
 JUW  CAB  H9   single    0.930  0.020  1.080
 JUW  CAA  H10  single    0.930  0.020  1.080
 JUW  NAP  H11  single    0.890  0.020  1.040
 JUW  NAP  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
 JUW  CAI  C4   N3   117.29  3.000
 JUW  CAI  C4   C5   122.27  3.000
 JUW  N3   C4   C5   120.44  3.000
 JUW  H1   C5   C6   120.71  3.000
 JUW  H1   C5   C4   122.80  3.000
 JUW  C6   C5   C4   116.49  3.000
 JUW  H2   C6   N1   116.26  3.000
 JUW  H2   C6   C5   120.01  3.000
 JUW  N1   C6   C5   123.73  3.000
 JUW  C2   N1   C6   115.40  3.000
 JUW  C2   N3   C4   117.94  3.000
 JUW  CAE  NAG  CAH  108.90  3.000
 JUW  CAH  NAG  CAQ  126.10  3.000
 JUW  CAE  NAG  CAQ  125.00  3.000
 JUW  H6   CAH  CAI  129.41  3.000
 JUW  H6   CAH  NAG  119.91  3.000
 JUW  CAI  CAH  NAG  110.67  3.000
 JUW  CAF  CAE  CAD  122.85  3.000
 JUW  CAD  CAE  NAG  129.05  3.000
 JUW  CAF  CAE  NAG  108.10  3.000
 JUW  H7   CAD  CAC  120.92  3.000
 JUW  H7   CAD  CAE  121.81  3.000
 JUW  CAC  CAD  CAE  117.27  3.000
 JUW  H8   CAC  CAB  119.54  3.000
 JUW  H8   CAC  CAD  119.48  3.000
 JUW  CAB  CAC  CAD  120.99  3.000
 JUW  H9   CAB  CAA  119.37  3.000
 JUW  H9   CAB  CAC  119.19  3.000
 JUW  CAA  CAB  CAC  121.44  3.000
 JUW  H10  CAA  CAF  120.30  3.000
 JUW  H10  CAA  CAB  120.79  3.000
 JUW  CAF  CAA  CAB  118.91  3.000
 JUW  CAI  CAF  CAA  135.06  3.000
 JUW  CAI  CAF  CAE  106.40  3.000
 JUW  CAA  CAF  CAE  118.54  3.000
 JUW  CAF  CAI  CAH  105.93  3.000
 JUW  CAH  CAI  C4   125.68  3.000
 JUW  CAF  CAI  C4   128.39  3.000
 JUW  NAP  C2   N3   116.78  3.000
 JUW  N3   C2   N1   125.99  3.000
 JUW  NAP  C2   N1   117.21  3.000
 JUW  H12  NAP  H11  116.55  3.000
 JUW  H12  NAP  C2   118.23  3.000
 JUW  H11  NAP  C2   118.17  3.000
 JUW  H5   CAQ  H4   108.91  3.000
 JUW  H5   CAQ  H3   108.60  3.000
 JUW  H4   CAQ  H3   108.61  3.000
 JUW  H5   CAQ  NAG  110.67  3.000
 JUW  H4   CAQ  NAG  110.79  3.000
 JUW  H3   CAQ  NAG  109.21  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
 JUW  CONST_01  N1   C2   N3   C4     0.00   0.0  0
 JUW  CONST_02  N1   C6   C5   C4     0.00   0.0  0
 JUW  CONST_03  CAA  CAF  CAI  C4     0.00   0.0  0
 JUW  CONST_04  CAE  CAF  CAI  C4   180.00   0.0  0
 JUW  CONST_05  NAG  CAH  CAI  C4   180.00   0.0  0
 JUW  CONST_06  C2   N1   C6   C5     0.00   0.0  0
 JUW  CONST_07  C2   N3   C4   C5     0.00   0.0  0
 JUW  CONST_08  CAF  CAI  C4   C5   180.00   0.0  0
 JUW  CONST_09  CAH  CAI  C4   C5     0.00   0.0  0
 JUW  CONST_10  N3   C2   N1   C6     0.00   0.0  0
 JUW  CONST_11  N3   C4   C5   C6     0.00   0.0  0
 JUW  CONST_12  CAI  C4   C5   C6   180.00   0.0  0
 JUW  CONST_13  CAF  CAI  C4   N3     0.00   0.0  0
 JUW  CONST_14  CAH  CAI  C4   N3   180.00   0.0  0
 JUW  CONST_15  CAA  CAF  CAE  NAG  180.00   0.0  0
 JUW  CONST_16  CAI  CAF  CAE  NAG    0.00   0.0  0
 JUW  CONST_17  CAC  CAD  CAE  NAG  180.00   0.0  0
 JUW  CONST_18  CAF  CAI  CAH  NAG    0.00   0.0  0
 JUW  CONST_19  CAA  CAF  CAI  CAH  180.00   0.0  0
 JUW  CONST_20  CAE  CAF  CAI  CAH    0.00   0.0  0
 JUW  CONST_21  CAF  CAE  NAG  CAH    0.00   0.0  0
 JUW  CONST_22  CAD  CAE  NAG  CAH  180.00   0.0  0
 JUW  CONST_23  CAB  CAA  CAF  CAE    0.00   0.0  0
 JUW  CONST_24  CAB  CAC  CAD  CAE    0.00   0.0  0
 JUW  CONST_25  CAI  CAH  NAG  CAE    0.00   0.0  0
 JUW  CONST_26  CAA  CAB  CAC  CAD    0.00   0.0  0
 JUW  CONST_27  CAA  CAF  CAE  CAD    0.00   0.0  0
 JUW  CONST_28  CAI  CAF  CAE  CAD  180.00   0.0  0
 JUW  CONST_29  CAF  CAA  CAB  CAC    0.00   0.0  0
 JUW  CONST_30  CAF  CAE  CAD  CAC    0.00   0.0  0
 JUW  CONST_31  CAI  CAF  CAA  CAB  180.00   0.0  0
 JUW  CONST_32  C2   N3   C4   CAI  180.00   0.0  0
 JUW  CONST_33  NAP  C2   N3   C4   180.00   0.0  0
 JUW  CONST_34  NAP  C2   N1   C6   180.00   0.0  0
 JUW  CONST_35  CAF  CAE  NAG  CAQ  180.00   0.0  0
 JUW  CONST_36  CAD  CAE  NAG  CAQ    0.00   0.0  0
 JUW  CONST_37  CAI  CAH  NAG  CAQ  180.00   0.0  0
 JUW  CONST_38  H2   C6   C5   C4   180.00   0.0  0
 JUW  CONST_39  H6   CAH  CAI  C4     0.00   0.0  0
 JUW  CONST_40  H1   C5   C6   N1   180.00   0.0  0
 JUW  CONST_41  H7   CAD  CAE  NAG    0.00   0.0  0
 JUW  CONST_42  H10  CAA  CAF  CAE  180.00   0.0  0
 JUW  CONST_43  H8   CAC  CAD  CAE  180.00   0.0  0
 JUW  CONST_44  H9   CAB  CAC  CAD  180.00   0.0  0
 JUW  CONST_46  H12  NAP  C2   N1   180.00   0.0  0
 JUW  Var_01    H3   CAQ  NAG  CAH   -1.71  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
 JUW  plan-1  C4   0.020
 JUW  plan-1  C5   0.020
 JUW  plan-1  C6   0.020
 JUW  plan-1  N1   0.020
 JUW  plan-1  N3   0.020
 JUW  plan-1  CAI  0.020
 JUW  plan-1  C2   0.020
 JUW  plan-1  NAP  0.020
 JUW  plan-1  H1   0.020
 JUW  plan-1  H2   0.020
 JUW  plan-2  C4   0.020
 JUW  plan-2  NAG  0.020
 JUW  plan-2  CAH  0.020
 JUW  plan-2  CAE  0.020
 JUW  plan-2  CAD  0.020
 JUW  plan-2  CAC  0.020
 JUW  plan-2  CAB  0.020
 JUW  plan-2  CAA  0.020
 JUW  plan-2  CAF  0.020
 JUW  plan-2  CAI  0.020
 JUW  plan-2  H6   0.020
 JUW  plan-2  H7   0.020
 JUW  plan-2  H8   0.020
 JUW  plan-2  H9   0.020
 JUW  plan-2  H10  0.020
 JUW  plan-2  CAQ  0.020
 JUW  plan-3  C2   0.020
 JUW  plan-3  NAP  0.020
 JUW  plan-3  H11  0.020
 JUW  plan-3  H12  0.020

