# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 10:24:39 2021
#   Inital geometry file: a 76 line input string
#   Ligand name: 5-[6,7-bis(chloranyl)-1-methyl-indol-3-yl]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(c2ccc(Cl)c(Cl)c12)c3cncnc3N
#
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
 JTQ  JTQ  5-[6,7-bis(chloranyl)-1-methyl-indol-3-yl]pyrimidin-4-amine  ligand  29  19  .  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_JTQ
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
 JTQ  C4   C   CR6   0   0.455  22.1630  -19.4047  5.4161
 JTQ  C5   C   CR6   0  -0.141  21.5379  -18.7323  4.3355
 JTQ  C6   C   CR16  0  -0.080  22.0469  -19.0200  3.0870
 JTQ  N1   N   N     0  -0.430  23.0603  -19.8614  2.8661
 JTQ  N3   N   N     0  -0.450  23.1815  -20.2407  5.1985
 JTQ  CAD  C   CR6   0  -0.075  17.0737  -16.5986  3.8255
 JTQ  CAC  C   CR6   0  -0.048  16.5697  -17.5159  2.9196
 JTQ  CL2  CL  CL    0  -0.103  14.9680  -17.3263  2.3030
 JTQ  CAB  C   CR16  0  -0.242  17.3243  -18.6111  2.4798
 JTQ  CAA  C   CR16  0  -0.378  18.6061  -18.8010  2.9400
 JTQ  CAF  C   CR56  0   0.025  19.1449  -17.8905  3.8506
 JTQ  CAE  C   CR56  0   0.497  18.3763  -16.7908  4.3001
 JTQ  NAG  N   NR5   0  -0.530  19.1384  -16.0871  5.1924
 JTQ  CAP  C   CH3   0  -0.527  18.8070  -14.8771  5.9194
 JTQ  CAH  C   CR15  0  -0.075  20.3476  -16.7093  5.3113
 JTQ  CAI  C   CR5   0  -0.002  20.4104  -17.8172  4.5123
 JTQ  C2   C   CR16  0   0.052  23.5702  -20.4196  3.9490
 JTQ  NAQ  N   NH2   0  -0.822  21.7792  -19.2172  6.6894
 JTQ  H1   H   HCR6  0   0.264  21.6177  -18.5384  2.2137
 JTQ  H2   H   HCR6  0   0.281  16.8855  -19.3044  1.7760
 JTQ  H3   H   HCR6  0   0.260  19.1813  -19.6506  2.5956
 JTQ  H4   H   HCH3  0   0.265  19.6617  -14.6159  6.5367
 JTQ  H5   H   HCH3  0   0.260  18.6077  -14.0506  5.2415
 JTQ  H6   H   HCH3  0   0.261  17.9492  -15.0260  6.5704
 JTQ  H7   H   HCR5  0   0.307  21.1010  -16.2920  5.9617
 JTQ  H8   H   HCR6  0   0.255  24.3998  -21.1041  3.8017
 JTQ  H9   H   HNH2  0   0.398  22.1328  -19.8488  7.3886
 JTQ  H10  H   HNH2  0   0.405  20.8981  -18.7742  6.8890
 JTQ  CL1  CL  CL    0  -0.083  16.1042  -15.2709  4.3380

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
 JTQ  CL2  CAC  single    1.727  0.020  1.727
 JTQ  CAB  CAC  aromatic  1.401  0.020  1.401
 JTQ  CAB  CAA  aromatic  1.375  0.020  1.375
 JTQ  CAC  CAD  aromatic  1.384  0.020  1.384
 JTQ  CAA  CAF  aromatic  1.396  0.020  1.396
 JTQ  N1   C6   aromatic  1.336  0.020  1.336
 JTQ  N1   C2   aromatic  1.321  0.020  1.321
 JTQ  C6   C5   aromatic  1.379  0.020  1.379
 JTQ  CAD  CAE  aromatic  1.400  0.020  1.400
 JTQ  CAD  CL1  single    1.722  0.020  1.722
 JTQ  CAF  CAE  aromatic  1.415  0.020  1.415
 JTQ  CAF  CAI  aromatic  1.430  0.020  1.430
 JTQ  C2   N3   aromatic  1.321  0.020  1.321
 JTQ  CAE  NAG  aromatic  1.368  0.020  1.368
 JTQ  C5   CAI  single    1.463  0.020  1.463
 JTQ  C5   C4   aromatic  1.418  0.020  1.418
 JTQ  CAI  CAH  aromatic  1.367  0.020  1.367
 JTQ  NAG  CAH  aromatic  1.365  0.020  1.365
 JTQ  NAG  CAP  single    1.450  0.020  1.450
 JTQ  N3   C4   aromatic  1.336  0.020  1.336
 JTQ  C4   NAQ  single    1.343  0.020  1.343
 JTQ  C6   H1   single    0.930  0.020  1.080
 JTQ  CAB  H2   single    0.930  0.020  1.080
 JTQ  CAA  H3   single    0.930  0.020  1.080
 JTQ  CAP  H4   single    0.970  0.020  1.090
 JTQ  CAP  H5   single    0.970  0.020  1.090
 JTQ  CAP  H6   single    0.970  0.020  1.090
 JTQ  CAH  H7   single    0.930  0.020  1.080
 JTQ  C2   H8   single    0.930  0.020  1.080
 JTQ  NAQ  H9   single    0.890  0.020  1.040
 JTQ  NAQ  H10  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
 JTQ  NAQ  C4   N3   117.37  3.000
 JTQ  NAQ  C4   C5   122.03  3.000
 JTQ  N3   C4   C5   120.59  3.000
 JTQ  CAI  C5   C6   121.64  3.000
 JTQ  CAI  C5   C4   122.98  3.000
 JTQ  C6   C5   C4   115.37  3.000
 JTQ  H1   C6   N1   116.51  3.000
 JTQ  H1   C6   C5   119.34  3.000
 JTQ  N1   C6   C5   124.15  3.000
 JTQ  C2   N1   C6   115.06  3.000
 JTQ  C2   N3   C4   117.61  3.000
 JTQ  CAE  CAD  CAC  118.02  3.000
 JTQ  CAE  CAD  CL1  121.93  3.000
 JTQ  CAC  CAD  CL1  120.05  3.000
 JTQ  CAB  CAC  CL2  118.25  3.000
 JTQ  CAB  CAC  CAD  121.83  3.000
 JTQ  CL2  CAC  CAD  119.91  3.000
 JTQ  H2   CAB  CAA  120.51  3.000
 JTQ  H2   CAB  CAC  119.15  3.000
 JTQ  CAA  CAB  CAC  120.33  3.000
 JTQ  H3   CAA  CAF  120.96  3.000
 JTQ  H3   CAA  CAB  119.83  3.000
 JTQ  CAF  CAA  CAB  119.21  3.000
 JTQ  CAI  CAF  CAE  107.09  3.000
 JTQ  CAI  CAF  CAA  132.60  3.000
 JTQ  CAE  CAF  CAA  120.30  3.000
 JTQ  NAG  CAE  CAF  107.71  3.000
 JTQ  NAG  CAE  CAD  131.98  3.000
 JTQ  CAF  CAE  CAD  120.30  3.000
 JTQ  CAH  NAG  CAP  122.63  3.000
 JTQ  CAP  NAG  CAE  128.96  3.000
 JTQ  CAH  NAG  CAE  108.41  3.000
 JTQ  H6   CAP  H5   109.44  3.000
 JTQ  H6   CAP  H4   108.27  3.000
 JTQ  H5   CAP  H4   108.41  3.000
 JTQ  H6   CAP  NAG  111.49  3.000
 JTQ  H5   CAP  NAG  111.33  3.000
 JTQ  H4   CAP  NAG  107.80  3.000
 JTQ  H7   CAH  CAI  129.30  3.000
 JTQ  H7   CAH  NAG  119.64  3.000
 JTQ  CAI  CAH  NAG  111.05  3.000
 JTQ  CAH  CAI  CAF  105.74  3.000
 JTQ  CAH  CAI  C5   127.80  3.000
 JTQ  CAF  CAI  C5   126.45  3.000
 JTQ  H8   C2   N3   116.02  3.000
 JTQ  H8   C2   N1   116.76  3.000
 JTQ  N3   C2   N1   127.22  3.000
 JTQ  H10  NAQ  H9   116.50  3.000
 JTQ  H10  NAQ  C4   119.98  3.000
 JTQ  H9   NAQ  C4   118.07  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
 JTQ  CONST_01  N1   C6   C5   C4     0.00   0.0  0
 JTQ  CONST_04  N1   C2   N3   C4     0.00   0.0  0
 JTQ  CONST_05  C2   N1   C6   C5     0.00   0.0  0
 JTQ  CONST_06  CAA  CAF  CAI  C5     0.00   0.0  0
 JTQ  CONST_07  CAE  CAF  CAI  C5   180.00   0.0  0
 JTQ  CONST_08  NAG  CAH  CAI  C5   180.00   0.0  0
 JTQ  CONST_09  C2   N3   C4   C5     0.00   0.0  0
 JTQ  CONST_10  N3   C2   N1   C6     0.00   0.0  0
 JTQ  CONST_13  N3   C4   C5   C6     0.00   0.0  0
 JTQ  CONST_14  CAI  C5   C6   N1   180.00   0.0  0
 JTQ  CONST_15  CAI  C5   C4   N3   180.00   0.0  0
 JTQ  CONST_16  CAA  CAB  CAC  CAD    0.00   0.0  0
 JTQ  CONST_17  CAA  CAF  CAE  CAD    0.00   0.0  0
 JTQ  CONST_18  CAI  CAF  CAE  CAD  180.00   0.0  0
 JTQ  CONST_19  CAH  NAG  CAE  CAD  180.00   0.0  0
 JTQ  CONST_20  CAF  CAA  CAB  CAC    0.00   0.0  0
 JTQ  CONST_21  CAF  CAE  CAD  CAC    0.00   0.0  0
 JTQ  CONST_22  NAG  CAE  CAD  CAC  180.00   0.0  0
 JTQ  CONST_23  CAE  CAD  CAC  CAB    0.00   0.0  0
 JTQ  CONST_24  CAE  CAF  CAA  CAB    0.00   0.0  0
 JTQ  CONST_25  CAI  CAF  CAA  CAB  180.00   0.0  0
 JTQ  CONST_26  NAG  CAE  CAF  CAA  180.00   0.0  0
 JTQ  CONST_27  CAH  CAI  CAF  CAA  180.00   0.0  0
 JTQ  CONST_28  CAH  NAG  CAE  CAF    0.00   0.0  0
 JTQ  CONST_29  NAG  CAH  CAI  CAF    0.00   0.0  0
 JTQ  CONST_30  CAH  CAI  CAF  CAE    0.00   0.0  0
 JTQ  CONST_31  CAI  CAH  NAG  CAE    0.00   0.0  0
 JTQ  CONST_32  CAI  CAF  CAE  NAG    0.00   0.0  0
 JTQ  CONST_33  NAQ  C4   C5   C6   180.00   0.0  0
 JTQ  CONST_34  CAB  CAC  CAD  CL1  180.00   0.0  0
 JTQ  CONST_35  CAF  CAE  CAD  CL1  180.00   0.0  0
 JTQ  CONST_36  NAG  CAE  CAD  CL1    0.00   0.0  0
 JTQ  CONST_37  CAP  NAG  CAE  CAD    0.00   0.0  0
 JTQ  CONST_38  CAA  CAB  CAC  CL2  180.00   0.0  0
 JTQ  CONST_39  CAE  CAD  CAC  CL2  180.00   0.0  0
 JTQ  CONST_40  CAP  NAG  CAE  CAF  180.00   0.0  0
 JTQ  CONST_41  CAI  CAH  NAG  CAP  180.00   0.0  0
 JTQ  CONST_42  NAQ  C4   C5   CAI    0.00   0.0  0
 JTQ  CONST_43  NAQ  C4   N3   C2   180.00   0.0  0
 JTQ  CONST_44  H1   C6   C5   C4   180.00   0.0  0
 JTQ  CONST_45  H8   C2   N3   C4   180.00   0.0  0
 JTQ  CONST_46  H7   CAH  CAI  C5     0.00   0.0  0
 JTQ  CONST_47  H2   CAB  CAC  CAD  180.00   0.0  0
 JTQ  CONST_48  H3   CAA  CAB  CAC  180.00   0.0  0
 JTQ  CONST_49  H9   NAQ  C4   C5   180.00   0.0  0
 JTQ  Var_01    H4   CAP  NAG  CAE  179.79  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
 JTQ  plan-1  C4   0.020
 JTQ  plan-1  C5   0.020
 JTQ  plan-1  C6   0.020
 JTQ  plan-1  N1   0.020
 JTQ  plan-1  N3   0.020
 JTQ  plan-1  CAI  0.020
 JTQ  plan-1  C2   0.020
 JTQ  plan-1  NAQ  0.020
 JTQ  plan-1  H1   0.020
 JTQ  plan-1  H8   0.020
 JTQ  plan-2  C5   0.020
 JTQ  plan-2  CAD  0.020
 JTQ  plan-2  CAC  0.020
 JTQ  plan-2  CL2  0.020
 JTQ  plan-2  CAB  0.020
 JTQ  plan-2  CAA  0.020
 JTQ  plan-2  CAF  0.020
 JTQ  plan-2  CAE  0.020
 JTQ  plan-2  NAG  0.020
 JTQ  plan-2  CAP  0.020
 JTQ  plan-2  CAH  0.020
 JTQ  plan-2  CAI  0.020
 JTQ  plan-2  H2   0.020
 JTQ  plan-2  H3   0.020
 JTQ  plan-2  H7   0.020
 JTQ  plan-2  CL1  0.020
 JTQ  plan-3  C4   0.020
 JTQ  plan-3  NAQ  0.020
 JTQ  plan-3  H9   0.020
 JTQ  plan-3  H10  0.020

