# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 16:22:15 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: N-ethyl-6-(methylsulfanyl)-N'-(propan-2-yl)-1,3,5-triazine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNc1nc(NC(C)C)nc(SC)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
 RYN  RYN  N-ethyl-6-(methylsulfanyl)-N'-(propan-2-yl)-1,3,5-triazine-2,4-diamine  ligand  32  15  .  2021-08-23  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_RYN
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
 RYN  N1    N  N     0  -0.473  -1.3912   0.3748   0.0251
 RYN  C2    C  CR6   0   0.241  -0.2999   1.1072   0.0680
 RYN  N3    N  N     0  -0.497   0.9505   0.6829   0.1140
 RYN  C4    C  CR6   0   0.605   1.0724  -0.6538   0.1043
 RYN  N5    N  N     0  -0.523   0.0505  -1.5112   0.0564
 RYN  C6    C  CR6   0   0.604  -1.1567  -0.9496   0.0229
 RYN  N7    N  NH1   0  -0.647   2.3030  -1.1731   0.1596
 RYN  C8    C  CH1   0  -0.081   3.5372  -0.4060   0.1314
 RYN  C9    C  CH3   0  -0.673   4.6512  -1.2522   0.7291
 RYN  C10   C  CH3   0  -0.650   3.8802   0.0615  -1.2786
 RYN  N11   N  NH1   0  -0.647  -2.2189  -1.7569  -0.0196
 RYN  C12   C  CH2   0  -0.253  -3.5929  -1.2965  -0.0155
 RYN  C13   C  CH3   0  -0.701  -4.5404  -2.4752  -0.1303
 RYN  S21   S  S2    0   0.041  -0.4487   2.8532   0.0641
 RYN  C22   C  CH3   0  -0.760  -2.2340   3.0923  -0.0253
 RYN  HN7   H  HNH1  0   0.390   2.3655  -2.1771   0.0902
 RYN  H9    H  HCH3  0   0.226   4.8374  -2.1454   0.1285
 RYN  H9A   H  HCH3  0   0.240   5.5781  -0.6807   0.7657
 RYN  H10   H  HCH3  0   0.235   3.0785   0.6713  -1.6941
 RYN  H10A  H  HCH3  0   0.226   4.7899   0.6637  -1.2701
 RYN  H10B  H  HCH3  0   0.219   4.0462  -0.7889  -1.9425
 RYN  HN11  H  HNH1  0   0.395  -2.0389  -2.7476   0.0116
 RYN  H12   H  HCH2  0   0.230  -3.8014  -0.7405   0.9021
 RYN  H12A  H  HCH2  0   0.234  -3.7519  -0.6032  -0.8434
 RYN  H13   H  HCH3  0   0.234  -4.4237  -3.1632   0.7080
 RYN  H13A  H  HCH3  0   0.246  -5.5703  -2.1218  -0.1299
 RYN  H13B  H  HCH3  0   0.234  -4.3782  -3.0304  -1.0548
 RYN  H22   H  HCH3  0   0.274  -2.6434   2.6506  -0.9301
 RYN  H22A  H  HCH3  0   0.274  -2.7329   2.6728   0.8442
 RYN  H22B  H  HCH3  0   0.277  -2.3917   4.1688  -0.0463
 RYN  H16   H  HCH1  0   0.241   3.3931   0.4714   0.7644
 RYN  H17   H  HCH3  0   0.240   4.4094  -1.5673   1.7446

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
 RYN  N1   C6    aromatic  1.345  0.020  1.345
 RYN  C2   N1    aromatic  1.315  0.020  1.315
 RYN  C2   N3    aromatic  1.321  0.020  1.321
 RYN  N3   C4    aromatic  1.342  0.020  1.342
 RYN  C4   N7    single    1.337  0.020  1.337
 RYN  C4   N5    aromatic  1.335  0.020  1.335
 RYN  C6   N5    aromatic  1.332  0.020  1.332
 RYN  C6   N11   single    1.335  0.020  1.335
 RYN  N7   C8    single    1.453  0.020  1.453
 RYN  N7   HN7   single    0.860  0.020  1.020
 RYN  C8   C10   single    1.525  0.020  1.525
 RYN  C9   C8    single    1.521  0.020  1.521
 RYN  C9   H9    single    0.970  0.020  1.090
 RYN  C9   H9A   single    0.970  0.020  1.090
 RYN  C10  H10   single    0.970  0.020  1.090
 RYN  C10  H10A  single    0.970  0.020  1.090
 RYN  C10  H10B  single    0.970  0.020  1.090
 RYN  N11  C12   single    1.449  0.020  1.449
 RYN  N11  HN11  single    0.860  0.020  1.020
 RYN  C12  H12   single    0.970  0.020  1.090
 RYN  C12  H12A  single    0.970  0.020  1.090
 RYN  C13  C12   single    1.517  0.020  1.517
 RYN  C13  H13   single    0.970  0.020  1.090
 RYN  C13  H13A  single    0.970  0.020  1.090
 RYN  C13  H13B  single    0.970  0.020  1.090
 RYN  S21  C2    single    1.752  0.020  1.752
 RYN  C22  S21   single    1.803  0.020  1.803
 RYN  C22  H22   single    0.970  0.020  1.090
 RYN  C22  H22A  single    0.970  0.020  1.090
 RYN  C22  H22B  single    0.970  0.020  1.090
 RYN  C8   H16   single    0.970  0.020  1.090
 RYN  C9   H17   single    0.970  0.020  1.090

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
 RYN  C6    N1   C2    113.82  3.000
 RYN  S21   C2   N3    113.61  3.000
 RYN  S21   C2   N1    118.97  3.000
 RYN  N3    C2   N1    127.42  3.000
 RYN  C4    N3   C2    113.92  3.000
 RYN  N7    C4   N5    117.17  3.000
 RYN  N5    C4   N3    124.78  3.000
 RYN  N7    C4   N3    118.05  3.000
 RYN  C6    N5   C4    115.09  3.000
 RYN  N11   C6   N5    117.84  3.000
 RYN  N11   C6   N1    117.19  3.000
 RYN  N5    C6   N1    124.97  3.000
 RYN  HN7   N7   C8    118.14  3.000
 RYN  HN7   N7   C4    116.17  3.000
 RYN  C8    N7   C4    125.16  3.000
 RYN  H16   C8   C10   108.64  3.000
 RYN  H16   C8   C9    108.42  3.000
 RYN  C10   C8   C9    111.66  3.000
 RYN  H16   C8   N7    107.51  3.000
 RYN  C9    C8   N7    108.70  3.000
 RYN  C10   C8   N7    111.77  3.000
 RYN  H17   C9   H9A   107.99  3.000
 RYN  H17   C9   H9    108.28  3.000
 RYN  H9A   C9   H9    107.60  3.000
 RYN  H17   C9   C8    111.36  3.000
 RYN  H9A   C9   C8    110.15  3.000
 RYN  H9    C9   C8    111.32  3.000
 RYN  H10B  C10  H10A  107.94  3.000
 RYN  H10B  C10  H10   108.42  3.000
 RYN  H10A  C10  H10   107.91  3.000
 RYN  H10B  C10  C8    110.97  3.000
 RYN  H10A  C10  C8    110.47  3.000
 RYN  H10   C10  C8    111.02  3.000
 RYN  HN11  N11  C12   118.80  3.000
 RYN  HN11  N11  C6    116.85  3.000
 RYN  C12   N11  C6    124.21  3.000
 RYN  H12A  C12  H12   106.62  3.000
 RYN  H12A  C12  C13   110.20  3.000
 RYN  H12   C12  C13   109.86  3.000
 RYN  C13   C12  N11   110.20  3.000
 RYN  H12A  C12  N11   109.74  3.000
 RYN  H12   C12  N11   110.17  3.000
 RYN  H13B  C13  H13A  107.83  3.000
 RYN  H13B  C13  H13   108.33  3.000
 RYN  H13A  C13  H13   107.79  3.000
 RYN  H13B  C13  C12   111.53  3.000
 RYN  H13A  C13  C12   109.80  3.000
 RYN  H13   C13  C12   111.42  3.000
 RYN  C22   S21  C2    102.49  3.000
 RYN  H22B  C22  H22A  109.31  3.000
 RYN  H22B  C22  H22   109.35  3.000
 RYN  H22A  C22  H22   109.65  3.000
 RYN  H22B  C22  S21   106.00  3.000
 RYN  H22A  C22  S21   111.32  3.000
 RYN  H22   C22  S21   111.11  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
 RYN  CONST_01  C4    N5   C6   N1     0.00   0.0  0
 RYN  CONST_02  C4    N3   C2   N1     0.00   0.0  0
 RYN  CONST_03  N5    C6   N1   C2     0.00   0.0  0
 RYN  CONST_04  N5    C4   N3   C2     0.00   0.0  0
 RYN  CONST_05  C6    N1   C2   N3     0.00   0.0  0
 RYN  CONST_06  C6    N5   C4   N3     0.00   0.0  0
 RYN  CONST_07  N11   C6   N1   C2   180.00   0.0  0
 RYN  CONST_08  N7    C4   N3   C2   180.00   0.0  0
 RYN  CONST_09  S21   C2   N3   C4   180.00   0.0  0
 RYN  CONST_10  N11   C6   N5   C4   180.00   0.0  0
 RYN  CONST_11  S21   C2   N1   C6   180.00   0.0  0
 RYN  CONST_12  N7    C4   N5   C6   180.00   0.0  0
 RYN  CONST_13  C12   N11  C6   N1     0.00   0.0  0
 RYN  CONST_14  C8    N7   C4   N3     0.00   0.0  0
 RYN  CONST_15  C8    N7   C4   N5   180.00   0.0  0
 RYN  CONST_16  C12   N11  C6   N5   180.00   0.0  0
 RYN  CONST_17  HN11  N11  C6   N1   180.00   0.0  0
 RYN  CONST_18  HN7   N7   C4   N3   180.00   0.0  0
 RYN  Var_01    C10   C8   N7   C4   -77.54  30.0  3
 RYN  Var_02    C13   C12  N11  C6   177.63  30.0  3
 RYN  Var_03    H22   C22  S21  C2   -60.46  30.0  3
 RYN  Var_04    H10   C10  C8   N7    58.34  30.0  3
 RYN  Var_05    H9    C9   C8   N7    63.57  30.0  3
 RYN  Var_06    H13   C13  C12  N11   60.84  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
 RYN  plan-1  N1    0.020
 RYN  plan-1  C2    0.020
 RYN  plan-1  N3    0.020
 RYN  plan-1  C4    0.020
 RYN  plan-1  N5    0.020
 RYN  plan-1  C6    0.020
 RYN  plan-1  N7    0.020
 RYN  plan-1  N11   0.020
 RYN  plan-1  S21   0.020
 RYN  plan-2  C4    0.020
 RYN  plan-2  N7    0.020
 RYN  plan-2  C8    0.020
 RYN  plan-2  HN7   0.020
 RYN  plan-3  C6    0.020
 RYN  plan-3  N11   0.020
 RYN  plan-3  C12   0.020
 RYN  plan-3  HN11  0.020

