# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 19:41:08 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 6-[(4-methoxybenzyl)sulfanyl]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CSc2cc(N)nc(N)n2)cc1
#
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
 AX6  AX6  6-[(4-methoxybenzyl)sulfanyl]pyrimidine-2,4-diamine  ligand  32  18  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AX6
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
 AX6  C4    C  CR6   0   0.127  -2.2183  -0.3128   0.0072
 AX6  C5    C  CR16  0  -0.434  -3.1569  -1.3268   0.0204
 AX6  C6    C  CR6   0   0.507  -4.4980  -0.9126   0.0626
 AX6  N1    N  N     0  -0.517  -4.8310   0.3796   0.0884
 AX6  N3    N  N     0  -0.501  -2.5263   0.9765   0.0344
 AX6  CAA   C  CH3   0  -0.437   6.6474  -0.4918   0.8157
 AX6  CAP   C  CR6   0   0.372   4.5497  -0.0214  -0.1876
 AX6  CAG   C  CR16  0  -0.328   3.8178   0.1844  -1.3598
 AX6  CAE   C  CR16  0  -0.270   2.4669   0.4673  -1.2951
 AX6  CAF   C  CR16  0  -0.370   3.9026   0.0630   1.0429
 AX6  CAD   C  CR16  0  -0.270   2.5434   0.3496   1.0870
 AX6  CAO   C  CR6   0   0.074   1.8065   0.5608  -0.0702
 AX6  CAI   C  CH2   0  -0.617   0.3364   0.8436  -0.0090
 AX6  SAM   S  S2    0   0.046  -0.5210  -0.7649  -0.0544
 AX6  C2    C  CR6   0   0.538  -3.8332   1.2582   0.0755
 AX6  NAC   N  NH2   0  -0.821  -4.1657   2.5662   0.1409
 AX6  NAB   N  NH2   0  -0.830  -5.5030  -1.8045   0.1040
 AX6  H5    H  HCR6  0   0.270  -2.8839  -2.3728  -0.0039
 AX6  HAA   H  HCH3  0   0.229   6.6483   0.3857   1.4674
 AX6  HAAA  H  HCH3  0   0.229   6.3119  -1.3587   1.3909
 AX6  HAAB  H  HCH3  0   0.260   7.6623  -0.6724   0.4708
 AX6  HAG   H  HCR6  0   0.263   4.3173   0.1192  -2.3186
 AX6  HAE   H  HCR6  0   0.256   1.9168   0.6265  -2.2150
 AX6  HAF   H  HCR6  0   0.279   4.4339  -0.0884   1.9726
 AX6  HAD   H  HCR6  0   0.258   2.0551   0.4129   2.0526
 AX6  HAI   H  HCH2  0   0.291   0.0636   1.3638   0.9077
 AX6  HAIA  H  HCH2  0   0.291   0.0058   1.4437  -0.8548
 AX6  HNAC  H  HNH2  0   0.391  -5.1197   2.8237  -0.0446
 AX6  HNAA  H  HNH2  0   0.391  -3.4628   3.2451  -0.0953
 AX6  HNAB  H  HNH2  0   0.402  -5.3254  -2.7786  -0.0651
 AX6  HNAD  H  HNH2  0   0.393  -6.4480  -1.4830  -0.0157
 AX6  OAL   O  O2    0  -0.470   5.8601  -0.2884  -0.3412

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
 AX6  C4   C5    aromatic  1.382  0.020  1.382
 AX6  C4   N3    aromatic  1.326  0.020  1.326
 AX6  C4   SAM   single    1.758  0.020  1.758
 AX6  C5   C6    aromatic  1.404  0.020  1.404
 AX6  C6   N1    aromatic  1.335  0.020  1.335
 AX6  C6   NAB   single    1.344  0.020  1.344
 AX6  N1   C2    aromatic  1.330  0.020  1.330
 AX6  N3   C2    aromatic  1.338  0.020  1.338
 AX6  CAA  OAL   single    1.414  0.020  1.414
 AX6  OAL  CAP   single    1.346  0.020  1.346
 AX6  CAP  CAG   aromatic  1.397  0.020  1.397
 AX6  CAP  CAF   aromatic  1.393  0.020  1.393
 AX6  CAG  CAE   aromatic  1.382  0.020  1.382
 AX6  CAE  CAO   aromatic  1.395  0.020  1.395
 AX6  CAF  CAD   aromatic  1.390  0.020  1.390
 AX6  CAD  CAO   aromatic  1.388  0.020  1.388
 AX6  CAO  CAI   single    1.498  0.020  1.498
 AX6  CAI  SAM   single    1.823  0.020  1.823
 AX6  C2   NAC   single    1.351  0.020  1.351
 AX6  C5   H5    single    0.930  0.020  1.080
 AX6  CAA  HAA   single    0.970  0.020  1.090
 AX6  CAA  HAAA  single    0.970  0.020  1.090
 AX6  CAA  HAAB  single    0.970  0.020  1.090
 AX6  CAG  HAG   single    0.930  0.020  1.080
 AX6  CAE  HAE   single    0.930  0.020  1.080
 AX6  CAF  HAF   single    0.930  0.020  1.080
 AX6  CAD  HAD   single    0.930  0.020  1.080
 AX6  CAI  HAI   single    0.970  0.020  1.090
 AX6  CAI  HAIA  single    0.970  0.020  1.090
 AX6  NAC  HNAC  single    0.890  0.020  1.040
 AX6  NAC  HNAA  single    0.890  0.020  1.040
 AX6  NAB  HNAB  single    0.890  0.020  1.040
 AX6  NAB  HNAD  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
 AX6  SAM   C4   N3    118.37  3.000
 AX6  SAM   C4   C5    117.87  3.000
 AX6  N3    C4   C5    123.75  3.000
 AX6  H5    C5   C6    121.81  3.000
 AX6  H5    C5   C4    122.56  3.000
 AX6  C6    C5   C4    115.63  3.000
 AX6  NAB   C6   N1    117.08  3.000
 AX6  NAB   C6   C5    121.28  3.000
 AX6  N1    C6   C5    121.63  3.000
 AX6  C2    N1   C6    116.89  3.000
 AX6  C2    N3   C4    115.62  3.000
 AX6  HAAB  CAA  HAAA  108.77  3.000
 AX6  HAAB  CAA  HAA   108.76  3.000
 AX6  HAAA  CAA  HAA   108.85  3.000
 AX6  HAAB  CAA  OAL   106.51  3.000
 AX6  HAAA  CAA  OAL   111.95  3.000
 AX6  HAA   CAA  OAL   111.89  3.000
 AX6  CAF   CAP  CAG   119.27  3.000
 AX6  CAF   CAP  OAL   124.41  3.000
 AX6  CAG   CAP  OAL   116.32  3.000
 AX6  HAG   CAG  CAE   120.31  3.000
 AX6  HAG   CAG  CAP   119.49  3.000
 AX6  CAE   CAG  CAP   120.20  3.000
 AX6  HAE   CAE  CAO   119.69  3.000
 AX6  HAE   CAE  CAG   119.13  3.000
 AX6  CAO   CAE  CAG   121.18  3.000
 AX6  HAF   CAF  CAD   118.82  3.000
 AX6  HAF   CAF  CAP   121.51  3.000
 AX6  CAD   CAF  CAP   119.67  3.000
 AX6  HAD   CAD  CAO   119.65  3.000
 AX6  HAD   CAD  CAF   118.75  3.000
 AX6  CAO   CAD  CAF   121.60  3.000
 AX6  CAI   CAO  CAD   121.03  3.000
 AX6  CAI   CAO  CAE   120.87  3.000
 AX6  CAD   CAO  CAE   118.08  3.000
 AX6  HAIA  CAI  HAI   108.34  3.000
 AX6  HAIA  CAI  SAM   108.92  3.000
 AX6  HAI   CAI  SAM   108.94  3.000
 AX6  HAIA  CAI  CAO   111.74  3.000
 AX6  HAI   CAI  CAO   111.75  3.000
 AX6  SAM   CAI  CAO   107.09  3.000
 AX6  CAI   SAM  C4    103.08  3.000
 AX6  NAC   C2   N3    116.47  3.000
 AX6  NAC   C2   N1    117.04  3.000
 AX6  N3    C2   N1    126.47  3.000
 AX6  HNAA  NAC  HNAC  116.56  3.000
 AX6  HNAA  NAC  C2    118.06  3.000
 AX6  HNAC  NAC  C2    118.19  3.000
 AX6  HNAD  NAB  HNAB  117.14  3.000
 AX6  HNAD  NAB  C6    119.14  3.000
 AX6  HNAB  NAB  C6    120.40  3.000
 AX6  CAP   OAL  CAA   118.50  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
 AX6  CONST_01  N1    C6   C5   C4      0.00   0.0  0
 AX6  CONST_02  N1    C2   N3   C4      0.00   0.0  0
 AX6  CONST_03  C2    N3   C4   C5      0.00   0.0  0
 AX6  CONST_04  C2    N1   C6   C5      0.00   0.0  0
 AX6  CONST_05  N3    C4   C5   C6      0.00   0.0  0
 AX6  CONST_06  N3    C2   N1   C6      0.00   0.0  0
 AX6  CONST_07  CAO   CAE  CAG  CAP     0.00   0.0  0
 AX6  CONST_08  CAO   CAD  CAF  CAP     0.00   0.0  0
 AX6  CONST_09  CAD   CAF  CAP  CAG     0.00   0.0  0
 AX6  CONST_10  CAD   CAO  CAE  CAG     0.00   0.0  0
 AX6  CONST_11  CAF   CAP  CAG  CAE     0.00   0.0  0
 AX6  CONST_12  CAF   CAD  CAO  CAE     0.00   0.0  0
 AX6  CONST_13  NAB   C6   C5   C4    180.00   0.0  0
 AX6  CONST_14  NAC   C2   N3   C4    180.00   0.0  0
 AX6  CONST_15  SAM   C4   C5   C6    180.00   0.0  0
 AX6  CONST_16  NAC   C2   N1   C6    180.00   0.0  0
 AX6  CONST_17  CAE   CAG  CAP  OAL   180.00   0.0  0
 AX6  CONST_18  CAD   CAF  CAP  OAL   180.00   0.0  0
 AX6  CONST_19  CAI   CAO  CAE  CAG   180.00   0.0  0
 AX6  CONST_20  CAI   CAO  CAD  CAF   180.00   0.0  0
 AX6  CONST_21  C2    N3   C4   SAM   180.00   0.0  0
 AX6  CONST_22  NAB   C6   N1   C2    180.00   0.0  0
 AX6  CONST_23  H5    C5   C6   N1    180.00   0.0  0
 AX6  CONST_24  HAE   CAE  CAG  CAP   180.00   0.0  0
 AX6  CONST_25  HAD   CAD  CAF  CAP   180.00   0.0  0
 AX6  CONST_26  HAF   CAF  CAP  CAG   180.00   0.0  0
 AX6  CONST_27  HAG   CAG  CAP  CAF   180.00   0.0  0
 AX6  CONST_28  HNAB  NAB  C6   C5      0.00   0.0  0
 AX6  CONST_29  HNAD  NAB  C6   C5    180.00   0.0  0
 AX6  CONST_31  HNAA  NAC  C2   N1    180.00   0.0  0
 AX6  Var_01    CAO   CAI  SAM  C4   -179.50  30.0  1
 AX6  Var_02    CAG   CAP  OAL  CAA   179.40  30.0  2
 AX6  Var_03    SAM   CAI  CAO  CAE    89.36  30.0  2
 AX6  Var_04    HAA   CAA  OAL  CAP   -60.28  30.0  3

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
 AX6  plan-1  C4    0.020
 AX6  plan-1  C5    0.020
 AX6  plan-1  C6    0.020
 AX6  plan-1  N1    0.020
 AX6  plan-1  N3    0.020
 AX6  plan-1  SAM   0.020
 AX6  plan-1  C2    0.020
 AX6  plan-1  NAC   0.020
 AX6  plan-1  NAB   0.020
 AX6  plan-1  H5    0.020
 AX6  plan-2  CAP   0.020
 AX6  plan-2  CAG   0.020
 AX6  plan-2  CAE   0.020
 AX6  plan-2  CAF   0.020
 AX6  plan-2  CAD   0.020
 AX6  plan-2  CAO   0.020
 AX6  plan-2  CAI   0.020
 AX6  plan-2  HAG   0.020
 AX6  plan-2  HAE   0.020
 AX6  plan-2  HAF   0.020
 AX6  plan-2  HAD   0.020
 AX6  plan-2  OAL   0.020
 AX6  plan-3  C2    0.020
 AX6  plan-3  NAC   0.020
 AX6  plan-3  HNAC  0.020
 AX6  plan-3  HNAA  0.020
 AX6  plan-4  C6    0.020
 AX6  plan-4  NAB   0.020
 AX6  plan-4  HNAB  0.020
 AX6  plan-4  HNAD  0.020

