# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 10:59:13 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: 4-[6,7-bis(chloranyl)-1~{H}-indol-3-yl]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nccc(n1)c2c[nH]c3c(Cl)c(Cl)ccc23
#
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
 JQW  JQW  4-[6,7-bis(chloranyl)-1~{H}-indol-3-yl]pyrimidin-2-amine  ligand  26  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JQW
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
 JQW  C4   C   CR6   0   0.253  -2.5318  -0.5703  -0.0162
 JQW  C5   C   CR16  0  -0.405  -3.5482  -1.5324  -0.0371
 JQW  C6   C   CR16  0  -0.028  -4.8418  -1.0558  -0.0474
 JQW  N1   N   N     0  -0.463  -5.1501   0.2344  -0.0403
 JQW  N3   N   N     0  -0.500  -2.8231   0.7261  -0.0091
 JQW  CAD  C   CR6   0  -0.073   2.4476  -0.3857   0.0060
 JQW  CAC  C   CR6   0  -0.058   2.6004   0.9870  -0.0192
 JQW  CL2  CL  CL    0  -0.103   4.1808   1.6776  -0.0263
 JQW  CAB  C   CR16  0  -0.229   1.4852   1.8349  -0.0388
 JQW  CAA  C   CR16  0  -0.378   0.2030   1.3279  -0.0341
 JQW  CAF  C   CR56  0   0.064   0.0154  -0.0581  -0.0093
 JQW  CAE  C   CR56  0   0.475   1.1516  -0.8913   0.0100
 JQW  NAG  N   NR15  0  -0.683   0.7270  -2.1860   0.0300
 JQW  CAH  C   CR15  0  -0.047  -0.6252  -2.2152   0.0225
 JQW  CAI  C   CR5   0  -0.038  -1.1257  -0.9344  -0.0015
 JQW  C2   C   CR6   0   0.535  -4.1121   1.0750  -0.0225
 JQW  NAP  N   NH2   0  -0.825  -4.3853   2.3976  -0.0513
 JQW  H1   H   HCR6  0   0.261  -3.3497  -2.5937  -0.0433
 JQW  H2   H   HCR6  0   0.268  -5.6761  -1.7493  -0.0617
 JQW  H3   H   HCR6  0   0.280   1.6426   2.9045  -0.0588
 JQW  H4   H   HCR6  0   0.267  -0.6438   1.9963  -0.0485
 JQW  H5   H   HNR5  0   0.422   1.3186  -3.0016   0.0471
 JQW  H6   H   HCR5  0   0.304  -1.1444  -3.1603   0.0355
 JQW  H7   H   HNH2  0   0.392  -5.3233   2.6939   0.1562
 JQW  H8   H   HNH2  0   0.393  -3.6491   3.0392   0.1876
 JQW  CL1  CL  CL    0  -0.085   3.7831  -1.4671   0.0311

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
 JQW  C4   C5   aromatic  1.400  0.020  1.400
 JQW  C4   N3   aromatic  1.329  0.020  1.329
 JQW  C4   CAI  single    1.453  0.020  1.453
 JQW  C5   C6   aromatic  1.379  0.020  1.379
 JQW  C6   N1   aromatic  1.327  0.020  1.327
 JQW  N1   C2   aromatic  1.336  0.020  1.336
 JQW  N3   C2   aromatic  1.336  0.020  1.336
 JQW  CAD  CAC  aromatic  1.381  0.020  1.381
 JQW  CAD  CAE  aromatic  1.391  0.020  1.391
 JQW  CAC  CL2  single    1.725  0.020  1.725
 JQW  CAC  CAB  aromatic  1.401  0.020  1.401
 JQW  CAB  CAA  aromatic  1.379  0.020  1.379
 JQW  CAA  CAF  aromatic  1.399  0.020  1.399
 JQW  CAF  CAE  aromatic  1.409  0.020  1.409
 JQW  CAF  CAI  aromatic  1.439  0.020  1.439
 JQW  CAE  NAG  aromatic  1.363  0.020  1.363
 JQW  NAG  CAH  aromatic  1.353  0.020  1.353
 JQW  CAH  CAI  aromatic  1.375  0.020  1.375
 JQW  C2   NAP  single    1.351  0.020  1.351
 JQW  CAD  CL1  single    1.719  0.020  1.719
 JQW  C5   H1   single    0.930  0.020  1.080
 JQW  C6   H2   single    0.930  0.020  1.080
 JQW  CAB  H3   single    0.930  0.020  1.080
 JQW  CAA  H4   single    0.930  0.020  1.080
 JQW  NAG  H5   single    0.860  0.020  1.020
 JQW  CAH  H6   single    0.930  0.020  1.080
 JQW  NAP  H7   single    0.890  0.020  1.040
 JQW  NAP  H8   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
 JQW  CAI  C4   N3   117.17  3.000
 JQW  CAI  C4   C5   122.06  3.000
 JQW  N3   C4   C5   120.77  3.000
 JQW  H1   C5   C6   120.81  3.000
 JQW  H1   C5   C4   122.84  3.000
 JQW  C6   C5   C4   116.35  3.000
 JQW  H2   C6   N1   116.30  3.000
 JQW  H2   C6   C5   120.05  3.000
 JQW  N1   C6   C5   123.66  3.000
 JQW  C2   N1   C6   115.56  3.000
 JQW  C2   N3   C4   117.80  3.000
 JQW  CAE  CAD  CAC  117.66  3.000
 JQW  CAE  CAD  CL1  119.68  3.000
 JQW  CAC  CAD  CL1  122.65  3.000
 JQW  CAB  CAC  CL2  119.14  3.000
 JQW  CAB  CAC  CAD  120.90  3.000
 JQW  CL2  CAC  CAD  119.96  3.000
 JQW  H3   CAB  CAA  119.95  3.000
 JQW  H3   CAB  CAC  118.88  3.000
 JQW  CAA  CAB  CAC  121.17  3.000
 JQW  H4   CAA  CAF  120.59  3.000
 JQW  H4   CAA  CAB  120.13  3.000
 JQW  CAF  CAA  CAB  119.28  3.000
 JQW  CAI  CAF  CAE  106.22  3.000
 JQW  CAI  CAF  CAA  135.23  3.000
 JQW  CAE  CAF  CAA  118.56  3.000
 JQW  NAG  CAE  CAF  108.11  3.000
 JQW  NAG  CAE  CAD  129.47  3.000
 JQW  CAF  CAE  CAD  122.42  3.000
 JQW  H5   NAG  CAH  124.72  3.000
 JQW  H5   NAG  CAE  125.90  3.000
 JQW  CAH  NAG  CAE  109.38  3.000
 JQW  H6   CAH  CAI  129.87  3.000
 JQW  H6   CAH  NAG  120.01  3.000
 JQW  CAI  CAH  NAG  110.11  3.000
 JQW  CAH  CAI  CAF  106.18  3.000
 JQW  CAH  CAI  C4   125.86  3.000
 JQW  CAF  CAI  C4   127.96  3.000
 JQW  NAP  C2   N3   116.82  3.000
 JQW  NAP  C2   N1   117.30  3.000
 JQW  N3   C2   N1   125.86  3.000
 JQW  H8   NAP  H7   116.49  3.000
 JQW  H8   NAP  C2   118.15  3.000
 JQW  H7   NAP  C2   118.22  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
 JQW  CONST_01  N1   C6   C5   C4     0.00  0.0  0
 JQW  CONST_02  N1   C2   N3   C4     0.00  0.0  0
 JQW  CONST_03  CAA  CAF  CAI  C4     0.00  0.0  0
 JQW  CONST_04  CAE  CAF  CAI  C4   180.00  0.0  0
 JQW  CONST_05  NAG  CAH  CAI  C4   180.00  0.0  0
 JQW  CONST_06  C2   N3   C4   C5     0.00  0.0  0
 JQW  CONST_07  CAF  CAI  C4   C5   180.00  0.0  0
 JQW  CONST_08  CAH  CAI  C4   C5     0.00  0.0  0
 JQW  CONST_09  C2   N1   C6   C5     0.00  0.0  0
 JQW  CONST_10  N3   C4   C5   C6     0.00  0.0  0
 JQW  CONST_11  CAI  C4   C5   C6   180.00  0.0  0
 JQW  CONST_12  N3   C2   N1   C6     0.00  0.0  0
 JQW  CONST_13  CAF  CAI  C4   N3     0.00  0.0  0
 JQW  CONST_14  CAH  CAI  C4   N3   180.00  0.0  0
 JQW  CONST_15  CAA  CAB  CAC  CAD    0.00  0.0  0
 JQW  CONST_16  CAA  CAF  CAE  CAD    0.00  0.0  0
 JQW  CONST_17  CAI  CAF  CAE  CAD  180.00  0.0  0
 JQW  CONST_18  CAH  NAG  CAE  CAD  180.00  0.0  0
 JQW  CONST_19  CAF  CAE  CAD  CAC    0.00  0.0  0
 JQW  CONST_20  NAG  CAE  CAD  CAC  180.00  0.0  0
 JQW  CONST_21  CAF  CAA  CAB  CAC    0.00  0.0  0
 JQW  CONST_22  CAE  CAD  CAC  CAB    0.00  0.0  0
 JQW  CONST_23  CAE  CAF  CAA  CAB    0.00  0.0  0
 JQW  CONST_24  CAI  CAF  CAA  CAB  180.00  0.0  0
 JQW  CONST_25  NAG  CAE  CAF  CAA  180.00  0.0  0
 JQW  CONST_26  CAH  CAI  CAF  CAA  180.00  0.0  0
 JQW  CONST_27  CAH  NAG  CAE  CAF    0.00  0.0  0
 JQW  CONST_28  NAG  CAH  CAI  CAF    0.00  0.0  0
 JQW  CONST_29  CAH  CAI  CAF  CAE    0.00  0.0  0
 JQW  CONST_30  CAI  CAH  NAG  CAE    0.00  0.0  0
 JQW  CONST_31  CAI  CAF  CAE  NAG    0.00  0.0  0
 JQW  CONST_32  C2   N3   C4   CAI  180.00  0.0  0
 JQW  CONST_33  NAP  C2   N3   C4   180.00  0.0  0
 JQW  CONST_34  NAP  C2   N1   C6   180.00  0.0  0
 JQW  CONST_35  CAB  CAC  CAD  CL1  180.00  0.0  0
 JQW  CONST_36  CAF  CAE  CAD  CL1  180.00  0.0  0
 JQW  CONST_37  NAG  CAE  CAD  CL1    0.00  0.0  0
 JQW  CONST_38  CAE  CAD  CAC  CL2  180.00  0.0  0
 JQW  CONST_39  CAA  CAB  CAC  CL2  180.00  0.0  0
 JQW  CONST_40  H2   C6   C5   C4   180.00  0.0  0
 JQW  CONST_41  H6   CAH  CAI  C4     0.00  0.0  0
 JQW  CONST_42  H1   C5   C6   N1   180.00  0.0  0
 JQW  CONST_43  H3   CAB  CAC  CAD  180.00  0.0  0
 JQW  CONST_44  H5   NAG  CAE  CAD    0.00  0.0  0
 JQW  CONST_45  H4   CAA  CAB  CAC  180.00  0.0  0
 JQW  CONST_47  H8   NAP  C2   N1   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
 JQW  plan-1  C4   0.020
 JQW  plan-1  C5   0.020
 JQW  plan-1  C6   0.020
 JQW  plan-1  N1   0.020
 JQW  plan-1  N3   0.020
 JQW  plan-1  CAI  0.020
 JQW  plan-1  C2   0.020
 JQW  plan-1  NAP  0.020
 JQW  plan-1  H1   0.020
 JQW  plan-1  H2   0.020
 JQW  plan-2  C4   0.020
 JQW  plan-2  CAD  0.020
 JQW  plan-2  CAC  0.020
 JQW  plan-2  CL2  0.020
 JQW  plan-2  CAB  0.020
 JQW  plan-2  CAA  0.020
 JQW  plan-2  CAF  0.020
 JQW  plan-2  CAE  0.020
 JQW  plan-2  NAG  0.020
 JQW  plan-2  CAH  0.020
 JQW  plan-2  CAI  0.020
 JQW  plan-2  H3   0.020
 JQW  plan-2  H4   0.020
 JQW  plan-2  H5   0.020
 JQW  plan-2  H6   0.020
 JQW  plan-2  CL1  0.020
 JQW  plan-3  C2   0.020
 JQW  plan-3  NAP  0.020
 JQW  plan-3  H7   0.020
 JQW  plan-3  H8   0.020

