# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 19:20:13 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 6-(benzylsulfanyl)pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cc(SCc2ccccc2)nc(N)n1
#
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
 AX5  AX5  6-(benzylsulfanyl)pyrimidine-2,4-diamine  ligand  28  16  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AX5
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
 AX5  C4    C  CR6   0   0.127  -1.4049  -0.3261  -0.0239
 AX5  C5    C  CR16  0  -0.434  -2.3771  -1.3074  -0.0273
 AX5  C6    C  CR6   0   0.509  -3.7042  -0.8470  -0.0130
 AX5  N1    N  N     0  -0.517  -3.9930   0.4559   0.0064
 AX5  N3    N  N     0  -0.501  -1.6684   0.9732  -0.0062
 AX5  CAF   C  CR16  0  -0.286   3.3268   0.2838  -1.2011
 AX5  CAD   C  CR16  0  -0.241   4.6733  -0.0526  -1.2227
 AX5  CAC   C  CR16  0  -0.265   5.3532  -0.2818  -0.0334
 AX5  CAE   C  CR16  0  -0.241   4.6801  -0.1725   1.1767
 AX5  CAG   C  CR16  0  -0.285   3.3334   0.1639   1.1956
 AX5  CAN   C  CR6   0   0.098   2.6460   0.3999   0.0079
 AX5  CAI   C  CH2   0  -0.617   1.1850   0.7386   0.0287
 AX5  SAL   S  S2    0   0.049   0.2765  -0.8383  -0.0504
 AX5  C2    C  CR6   0   0.538  -2.9654   1.2997   0.0089
 AX5  NAB   N  NH2   0  -0.821  -3.2536   2.6184   0.0641
 AX5  NAA   N  NH2   0  -0.831  -4.7389  -1.7027  -0.0410
 AX5  H5    H  HCR6  0   0.270  -2.1405  -2.3621  -0.0427
 AX5  HAD   H  HCR6  0   0.258   5.1925  -0.1358  -2.1689
 AX5  HAC   H  HCR6  0   0.258   6.4036  -0.5415  -0.0497
 AX5  HAE   H  HCR6  0   0.258   5.2039  -0.3487   2.1075
 AX5  HAG   H  HCR6  0   0.255   2.8124   0.2512   2.1418
 AX5  HAI   H  HCH2  0   0.293   0.9065   1.2626   0.9416
 AX5  HAIA  H  HCH2  0   0.293   0.9037   1.3561  -0.8224
 AX5  HNAB  H  HNH2  0   0.391  -4.1940   2.9090  -0.1402
 AX5  HNAA  H  HNH2  0   0.391  -2.5228   3.2715  -0.1597
 AX5  HNAC  H  HNH2  0   0.403  -4.5915  -2.6902   0.0682
 AX5  HNAD  H  HNH2  0   0.394  -5.6727  -1.3554   0.0921
 AX5  HAF   H  HCR6  0   0.255   2.8010   0.4637  -2.1314

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
 AX5  C4   C5    aromatic  1.381  0.020  1.381
 AX5  C4   N3    aromatic  1.326  0.020  1.326
 AX5  C4   SAL   single    1.758  0.020  1.758
 AX5  C5   C6    aromatic  1.405  0.020  1.405
 AX5  C6   N1    aromatic  1.335  0.020  1.335
 AX5  C6   NAA   single    1.343  0.020  1.343
 AX5  N1   C2    aromatic  1.330  0.020  1.330
 AX5  N3   C2    aromatic  1.338  0.020  1.338
 AX5  CAF  CAD   aromatic  1.388  0.020  1.388
 AX5  CAF  CAN   aromatic  1.392  0.020  1.392
 AX5  CAD  CAC   aromatic  1.389  0.020  1.389
 AX5  CAC  CAE   aromatic  1.389  0.020  1.389
 AX5  CAE  CAG   aromatic  1.388  0.020  1.388
 AX5  CAG  CAN   aromatic  1.392  0.020  1.392
 AX5  CAN  CAI   single    1.500  0.020  1.500
 AX5  CAI  SAL   single    1.822  0.020  1.822
 AX5  C2   NAB   single    1.351  0.020  1.351
 AX5  C5   H5    single    0.930  0.020  1.080
 AX5  CAF  HAF   single    0.930  0.020  1.080
 AX5  CAD  HAD   single    0.930  0.020  1.080
 AX5  CAC  HAC   single    0.930  0.020  1.080
 AX5  CAE  HAE   single    0.930  0.020  1.080
 AX5  CAG  HAG   single    0.930  0.020  1.080
 AX5  CAI  HAI   single    0.970  0.020  1.090
 AX5  CAI  HAIA  single    0.970  0.020  1.090
 AX5  NAB  HNAB  single    0.890  0.020  1.040
 AX5  NAB  HNAA  single    0.890  0.020  1.040
 AX5  NAA  HNAC  single    0.860  0.020  1.020
 AX5  NAA  HNAD  single    0.860  0.020  1.020

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
 AX5  SAL   C4   N3    118.41  3.000
 AX5  SAL   C4   C5    117.78  3.000
 AX5  N3    C4   C5    123.80  3.000
 AX5  H5    C5   C6    121.78  3.000
 AX5  H5    C5   C4    122.62  3.000
 AX5  C6    C5   C4    115.60  3.000
 AX5  NAA   C6   N1    117.11  3.000
 AX5  NAA   C6   C5    121.25  3.000
 AX5  N1    C6   C5    121.63  3.000
 AX5  C2    N1   C6    116.89  3.000
 AX5  C2    N3   C4    115.60  3.000
 AX5  HAF   CAF  CAN   119.63  3.000
 AX5  HAF   CAF  CAD   119.84  3.000
 AX5  CAN   CAF  CAD   120.53  3.000
 AX5  HAD   CAD  CAC   120.07  3.000
 AX5  HAD   CAD  CAF   119.84  3.000
 AX5  CAC   CAD  CAF   120.10  3.000
 AX5  HAC   CAC  CAE   120.16  3.000
 AX5  HAC   CAC  CAD   120.11  3.000
 AX5  CAE   CAC  CAD   119.73  3.000
 AX5  HAE   CAE  CAG   119.82  3.000
 AX5  HAE   CAE  CAC   120.12  3.000
 AX5  CAG   CAE  CAC   120.07  3.000
 AX5  HAG   CAG  CAN   119.59  3.000
 AX5  HAG   CAG  CAE   119.86  3.000
 AX5  CAN   CAG  CAE   120.56  3.000
 AX5  CAI   CAN  CAG   120.49  3.000
 AX5  CAI   CAN  CAF   120.47  3.000
 AX5  CAG   CAN  CAF   119.02  3.000
 AX5  HAIA  CAI  HAI   108.45  3.000
 AX5  HAIA  CAI  SAL   109.16  3.000
 AX5  HAI   CAI  SAL   108.99  3.000
 AX5  HAIA  CAI  CAN   111.65  3.000
 AX5  HAI   CAI  CAN   111.68  3.000
 AX5  SAL   CAI  CAN   106.84  3.000
 AX5  CAI   SAL  C4    102.95  3.000
 AX5  NAB   C2   N3    116.46  3.000
 AX5  NAB   C2   N1    117.04  3.000
 AX5  N3    C2   N1    126.48  3.000
 AX5  HNAA  NAB  HNAB  116.55  3.000
 AX5  HNAA  NAB  C2    118.03  3.000
 AX5  HNAB  NAB  C2    118.25  3.000
 AX5  HNAD  NAA  HNAC  117.49  3.000
 AX5  HNAD  NAA  C6    119.53  3.000
 AX5  HNAC  NAA  C6    120.74  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
 AX5  CONST_01  N1    C6   C5   C4      0.00   0.0  0
 AX5  CONST_02  N1    C2   N3   C4      0.00   0.0  0
 AX5  CONST_03  C2    N3   C4   C5      0.00   0.0  0
 AX5  CONST_04  C2    N1   C6   C5      0.00   0.0  0
 AX5  CONST_05  N3    C4   C5   C6      0.00   0.0  0
 AX5  CONST_06  N3    C2   N1   C6      0.00   0.0  0
 AX5  CONST_07  CAE   CAC  CAD  CAF     0.00   0.0  0
 AX5  CONST_08  CAE   CAG  CAN  CAF     0.00   0.0  0
 AX5  CONST_09  CAG   CAN  CAF  CAD     0.00   0.0  0
 AX5  CONST_10  CAG   CAE  CAC  CAD     0.00   0.0  0
 AX5  CONST_11  CAN   CAF  CAD  CAC     0.00   0.0  0
 AX5  CONST_12  CAN   CAG  CAE  CAC     0.00   0.0  0
 AX5  CONST_13  NAA   C6   C5   C4    180.00   0.0  0
 AX5  CONST_14  NAB   C2   N3   C4    180.00   0.0  0
 AX5  CONST_15  SAL   C4   C5   C6    180.00   0.0  0
 AX5  CONST_16  NAB   C2   N1   C6    180.00   0.0  0
 AX5  CONST_17  CAI   CAN  CAF  CAD   180.00   0.0  0
 AX5  CONST_18  CAI   CAN  CAG  CAE   180.00   0.0  0
 AX5  CONST_19  C2    N3   C4   SAL   180.00   0.0  0
 AX5  CONST_20  NAA   C6   N1   C2    180.00   0.0  0
 AX5  CONST_21  H5    C5   C6   N1    180.00   0.0  0
 AX5  CONST_22  HAC   CAC  CAD  CAF   180.00   0.0  0
 AX5  CONST_23  HAG   CAG  CAN  CAF   180.00   0.0  0
 AX5  CONST_24  HAE   CAE  CAC  CAD   180.00   0.0  0
 AX5  CONST_25  HAF   CAF  CAD  CAC   180.00   0.0  0
 AX5  CONST_26  HAD   CAD  CAC  CAE   180.00   0.0  0
 AX5  CONST_27  HNAC  NAA  C6   C5      0.00   0.0  0
 AX5  CONST_28  HNAD  NAA  C6   C5    180.00   0.0  0
 AX5  CONST_30  HNAA  NAB  C2   N1    180.00   0.0  0
 AX5  Var_01    CAN   CAI  SAL  C4   -179.87  30.0  1
 AX5  Var_02    SAL   CAI  CAN  CAF    89.10  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
 AX5  plan-1  C4    0.020
 AX5  plan-1  C5    0.020
 AX5  plan-1  C6    0.020
 AX5  plan-1  N1    0.020
 AX5  plan-1  N3    0.020
 AX5  plan-1  SAL   0.020
 AX5  plan-1  C2    0.020
 AX5  plan-1  NAB   0.020
 AX5  plan-1  NAA   0.020
 AX5  plan-1  H5    0.020
 AX5  plan-2  CAF   0.020
 AX5  plan-2  CAD   0.020
 AX5  plan-2  CAC   0.020
 AX5  plan-2  CAE   0.020
 AX5  plan-2  CAG   0.020
 AX5  plan-2  CAN   0.020
 AX5  plan-2  CAI   0.020
 AX5  plan-2  HAD   0.020
 AX5  plan-2  HAC   0.020
 AX5  plan-2  HAE   0.020
 AX5  plan-2  HAG   0.020
 AX5  plan-2  HAF   0.020
 AX5  plan-3  C2    0.020
 AX5  plan-3  NAB   0.020
 AX5  plan-3  HNAB  0.020
 AX5  plan-3  HNAA  0.020
 AX5  plan-4  C6    0.020
 AX5  plan-4  NAA   0.020
 AX5  plan-4  HNAC  0.020
 AX5  plan-4  HNAD  0.020

