# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 07:49:11 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: 4-(1~{H}-indol-3-yl)pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nccc(n1)c2c[nH]c3ccccc23
#
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
 V5T  V5T  "4-(1~{H}-indol-3-yl)pyrimidin-2-amine"
  ligand  26  16  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_V5T
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
 V5T  C4   C  CR6   0   0.248  20.7852  -19.4094  3.3791
 V5T  C5   C  CR16  0  -0.405  22.0773  -19.5955  3.8909
 V5T  C6   C  CR16  0  -0.030  22.8560  -20.5442  3.2650
 V5T  N1   N  N     0  -0.463  22.4473  -21.2684  2.2306
 V5T  N3   N  N     0  -0.501  20.3626  -20.1263  2.3413
 V5T  CAD  C  CR16  0  -0.296  16.7673  -16.5907  4.3171
 V5T  CAC  C  CR16  0  -0.280  15.9394  -17.0756  3.3242
 V5T  CAB  C  CR16  0  -0.255  16.3770  -18.0802  2.4477
 V5T  CAA  C  CR16  0  -0.375  17.6457  -18.6193  2.5444
 V5T  CAF  C  CR56  0   0.059  18.5109  -18.1470  3.5399
 V5T  CAE  C  CR56  0   0.351  18.0441  -17.1377  4.4082
 V5T  NAG  N  NR15  0  -0.680  19.0553  -16.8456  5.2840
 V5T  CAH  C  CR15  0  -0.052  20.1302  -17.6147  5.0124
 V5T  CAI  C  CR5   0  -0.046  19.8622  -18.4437  3.9454
 V5T  C2   C  CR6   0   0.532  21.2025  -21.0210  1.8147
 V5T  NAP  N  NH2   0  -0.826  20.7363  -21.7641  0.7869
 V5T  H1   H  HCR6  0   0.257  22.4616  -19.0346  4.7295
 V5T  H2   H  HCR6  0   0.263  23.8663  -20.7333  3.6134
 V5T  H4   H  HCR6  0   0.250  14.9397  -16.6747  3.2207
 V5T  H5   H  HCR6  0   0.246  15.7040  -18.4402  1.6799
 V5T  H6   H  HCR6  0   0.247  17.9683  -19.3931  1.8638
 V5T  H7   H  HNR5  0   0.417  19.0124  -16.1575  6.0187
 V5T  H8   H  HCR5  0   0.296  21.0271  -17.5190  5.6035
 V5T  H9   H  HNH2  0   0.391  19.8992  -21.4628  0.3185
 V5T  H10  H  HNH2  0   0.390  21.3955  -22.2897  0.2393
 V5T  H3   H  HCR6  0   0.262  16.4385  -15.8159  4.9978

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
 V5T  NAP  C2   single    1.351  0.020  1.351
 V5T  C2   N3   aromatic  1.335  0.020  1.335
 V5T  C2   N1   aromatic  1.336  0.020  1.336
 V5T  N3   C4   aromatic  1.330  0.020  1.330
 V5T  N1   C6   aromatic  1.327  0.020  1.327
 V5T  CAB  CAA  aromatic  1.382  0.020  1.382
 V5T  CAB  CAC  aromatic  1.403  0.020  1.403
 V5T  CAA  CAF  aromatic  1.401  0.020  1.401
 V5T  C4   CAI  single    1.451  0.020  1.451
 V5T  C4   C5   aromatic  1.402  0.020  1.402
 V5T  CAC  CAD  aromatic  1.381  0.020  1.381
 V5T  C6   C5   aromatic  1.378  0.020  1.378
 V5T  CAF  CAI  aromatic  1.442  0.020  1.442
 V5T  CAF  CAE  aromatic  1.411  0.020  1.411
 V5T  CAI  CAH  aromatic  1.377  0.020  1.377
 V5T  CAD  CAE  aromatic  1.392  0.020  1.392
 V5T  CAE  NAG  aromatic  1.369  0.020  1.369
 V5T  CAH  NAG  aromatic  1.349  0.020  1.349
 V5T  C5   H1   single    0.930  0.020  1.080
 V5T  C6   H2   single    0.930  0.020  1.080
 V5T  CAD  H3   single    0.930  0.020  1.080
 V5T  CAC  H4   single    0.930  0.020  1.080
 V5T  CAB  H5   single    0.930  0.020  1.080
 V5T  CAA  H6   single    0.930  0.020  1.080
 V5T  NAG  H7   single    0.860  0.020  1.020
 V5T  CAH  H8   single    0.930  0.020  1.080
 V5T  NAP  H9   single    0.890  0.020  1.040
 V5T  NAP  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
 V5T  CAI  C4   N3   117.46  3.000
 V5T  CAI  C4   C5   122.15  3.000
 V5T  N3   C4   C5   120.39  3.000
 V5T  H1   C5   C6   120.63  3.000
 V5T  H1   C5   C4   122.86  3.000
 V5T  C6   C5   C4   116.51  3.000
 V5T  H2   C6   N1   116.22  3.000
 V5T  H2   C6   C5   120.02  3.000
 V5T  N1   C6   C5   123.77  3.000
 V5T  C2   N1   C6   115.38  3.000
 V5T  C2   N3   C4   117.96  3.000
 V5T  H3   CAD  CAE  121.24  3.000
 V5T  H3   CAD  CAC  121.43  3.000
 V5T  CAE  CAD  CAC  117.33  3.000
 V5T  H4   CAC  CAB  119.58  3.000
 V5T  H4   CAC  CAD  119.52  3.000
 V5T  CAB  CAC  CAD  120.90  3.000
 V5T  H5   CAB  CAA  119.38  3.000
 V5T  H5   CAB  CAC  119.16  3.000
 V5T  CAA  CAB  CAC  121.46  3.000
 V5T  H6   CAA  CAF  120.33  3.000
 V5T  H6   CAA  CAB  120.65  3.000
 V5T  CAF  CAA  CAB  119.02  3.000
 V5T  CAI  CAF  CAE  106.51  3.000
 V5T  CAE  CAF  CAA  118.31  3.000
 V5T  CAI  CAF  CAA  135.18  3.000
 V5T  NAG  CAE  CAF  107.57  3.000
 V5T  NAG  CAE  CAD  129.45  3.000
 V5T  CAF  CAE  CAD  122.98  3.000
 V5T  H7   NAG  CAH  124.75  3.000
 V5T  H7   NAG  CAE  125.49  3.000
 V5T  CAH  NAG  CAE  109.75  3.000
 V5T  H8   CAH  CAI  129.78  3.000
 V5T  H8   CAH  NAG  120.10  3.000
 V5T  CAI  CAH  NAG  110.12  3.000
 V5T  CAH  CAI  CAF  106.04  3.000
 V5T  CAH  CAI  C4   125.39  3.000
 V5T  CAF  CAI  C4   128.57  3.000
 V5T  NAP  C2   N3   116.83  3.000
 V5T  N3   C2   N1   125.99  3.000
 V5T  NAP  C2   N1   117.17  3.000
 V5T  H10  NAP  H9   116.68  3.000
 V5T  H10  NAP  C2   118.39  3.000
 V5T  H9   NAP  C2   118.48  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
 V5T  CONST_01  N1   C2   N3   C4     0.00  0.0  0
 V5T  CONST_02  CAA  CAF  CAI  C4     0.00  0.0  0
 V5T  CONST_03  CAE  CAF  CAI  C4   180.00  0.0  0
 V5T  CONST_04  NAG  CAH  CAI  C4   180.00  0.0  0
 V5T  CONST_05  N1   C6   C5   C4     0.00  0.0  0
 V5T  CONST_06  C2   N3   C4   C5     0.00  0.0  0
 V5T  CONST_07  CAF  CAI  C4   C5   180.00  0.0  0
 V5T  CONST_08  CAH  CAI  C4   C5     0.00  0.0  0
 V5T  CONST_09  C2   N1   C6   C5     0.00  0.0  0
 V5T  CONST_10  N3   C2   N1   C6     0.00  0.0  0
 V5T  CONST_11  N3   C4   C5   C6     0.00  0.0  0
 V5T  CONST_12  CAI  C4   C5   C6   180.00  0.0  0
 V5T  CONST_13  CAF  CAI  C4   N3     0.00  0.0  0
 V5T  CONST_14  CAH  CAI  C4   N3   180.00  0.0  0
 V5T  CONST_15  CAA  CAB  CAC  CAD    0.00  0.0  0
 V5T  CONST_16  CAA  CAF  CAE  CAD    0.00  0.0  0
 V5T  CONST_17  CAI  CAF  CAE  CAD  180.00  0.0  0
 V5T  CONST_18  CAH  NAG  CAE  CAD  180.00  0.0  0
 V5T  CONST_19  CAF  CAA  CAB  CAC    0.00  0.0  0
 V5T  CONST_20  CAF  CAE  CAD  CAC    0.00  0.0  0
 V5T  CONST_21  NAG  CAE  CAD  CAC  180.00  0.0  0
 V5T  CONST_22  CAI  CAF  CAA  CAB  180.00  0.0  0
 V5T  CONST_23  CAE  CAF  CAA  CAB    0.00  0.0  0
 V5T  CONST_24  CAE  CAD  CAC  CAB    0.00  0.0  0
 V5T  CONST_25  CAH  CAI  CAF  CAA  180.00  0.0  0
 V5T  CONST_26  NAG  CAE  CAF  CAA  180.00  0.0  0
 V5T  CONST_27  NAG  CAH  CAI  CAF    0.00  0.0  0
 V5T  CONST_28  CAH  NAG  CAE  CAF    0.00  0.0  0
 V5T  CONST_29  CAH  CAI  CAF  CAE    0.00  0.0  0
 V5T  CONST_30  CAI  CAH  NAG  CAE    0.00  0.0  0
 V5T  CONST_31  CAI  CAF  CAE  NAG    0.00  0.0  0
 V5T  CONST_32  C2   N3   C4   CAI  180.00  0.0  0
 V5T  CONST_33  NAP  C2   N3   C4   180.00  0.0  0
 V5T  CONST_34  NAP  C2   N1   C6   180.00  0.0  0
 V5T  CONST_35  H8   CAH  CAI  C4     0.00  0.0  0
 V5T  CONST_36  H2   C6   C5   C4   180.00  0.0  0
 V5T  CONST_37  H1   C5   C6   N1   180.00  0.0  0
 V5T  CONST_38  H1   C5   C4   N3   180.00  0.0  0
 V5T  CONST_39  H5   CAB  CAC  CAD  180.00  0.0  0
 V5T  CONST_40  H7   NAG  CAE  CAD    0.00  0.0  0
 V5T  CONST_41  H6   CAA  CAB  CAC  180.00  0.0  0
 V5T  CONST_42  H3   CAD  CAC  CAB  180.00  0.0  0
 V5T  CONST_43  H4   CAC  CAB  CAA  180.00  0.0  0
 V5T  CONST_44  H5   CAB  CAA  CAF  180.00  0.0  0
 V5T  CONST_45  H8   CAH  CAI  CAF  180.00  0.0  0
 V5T  CONST_46  H3   CAD  CAE  CAF  180.00  0.0  0
 V5T  CONST_47  H7   NAG  CAE  CAF  180.00  0.0  0
 V5T  CONST_48  H6   CAA  CAF  CAE  180.00  0.0  0
 V5T  CONST_49  H4   CAC  CAD  CAE  180.00  0.0  0
 V5T  CONST_50  H8   CAH  NAG  CAE  180.00  0.0  0
 V5T  CONST_51  H3   CAD  CAE  NAG    0.00  0.0  0
 V5T  CONST_52  H1   C5   C4   CAI    0.00  0.0  0
 V5T  CONST_53  H6   CAA  CAF  CAI    0.00  0.0  0
 V5T  CONST_54  H7   NAG  CAH  CAI  180.00  0.0  0
 V5T  CONST_55  H2   C6   N1   C2   180.00  0.0  0
 V5T  CONST_56  H9   NAP  C2   N1   180.00  0.0  0
 V5T  CONST_59  H10  NAP  C2   N3   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
 V5T  plan-1  C4   0.020
 V5T  plan-1  C5   0.020
 V5T  plan-1  C6   0.020
 V5T  plan-1  N1   0.020
 V5T  plan-1  N3   0.020
 V5T  plan-1  CAI  0.020
 V5T  plan-1  C2   0.020
 V5T  plan-1  NAP  0.020
 V5T  plan-1  H1   0.020
 V5T  plan-1  H2   0.020
 V5T  plan-2  C4   0.020
 V5T  plan-2  CAD  0.020
 V5T  plan-2  CAC  0.020
 V5T  plan-2  CAB  0.020
 V5T  plan-2  CAA  0.020
 V5T  plan-2  CAF  0.020
 V5T  plan-2  CAE  0.020
 V5T  plan-2  NAG  0.020
 V5T  plan-2  CAH  0.020
 V5T  plan-2  CAI  0.020
 V5T  plan-2  H4   0.020
 V5T  plan-2  H5   0.020
 V5T  plan-2  H6   0.020
 V5T  plan-2  H7   0.020
 V5T  plan-2  H8   0.020
 V5T  plan-2  H3   0.020
 V5T  plan-3  C2   0.020
 V5T  plan-3  NAP  0.020
 V5T  plan-3  H9   0.020
 V5T  plan-3  H10  0.020

