# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 22:34:43 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 6-[(2~{R})-butan-2-yl]oxy-2-(3-chlorophenyl)sulfanyl-pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](C)Oc1cc(N)nc(Sc2cccc(Cl)c2)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
 RDS  RDS  6-[(2~{R})-butan-2-yl]oxy-2-(3-chlorophenyl)sulfanyl-pyrimidin-4-amine  ligand  36  20  .  2021-08-23  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RDS
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
 RDS  CL   CL  CL    0  -0.122  -5.5278  -0.0475   1.6429
 RDS  C13  C   CR6   0  -0.028  -4.3710   0.3728   0.4232
 RDS  C12  C   CR16  0  -0.198  -3.0778   0.6995   0.8044
 RDS  C8   C   CR6   0  -0.129  -2.1562   1.0378  -0.1774
 RDS  C9   C   CR16  0  -0.202  -2.5228   1.0513  -1.5184
 RDS  C10  C   CR16  0  -0.256  -3.8170   0.7101  -1.8768
 RDS  C11  C   CR16  0  -0.212  -4.7529   0.3706  -0.9084
 RDS  S    S   S2    0   0.073  -0.5298   1.5370   0.3089
 RDS  C7   C   CR6   0   0.228   0.4538   0.1309  -0.1251
 RDS  N1   N   N     0  -0.499   1.7417   0.3484   0.0822
 RDS  C2   C   CR6   0   0.570   2.5473  -0.6584  -0.2435
 RDS  C1   C   CR16  0  -0.509   2.0767  -1.8573  -0.7572
 RDS  C    C   CR6   0   0.516   0.6918  -1.9629  -0.9154
 RDS  N    N   NH2   0  -0.831   0.1091  -3.0738  -1.3820
 RDS  N2   N   N     0  -0.449  -0.1269  -0.9430  -0.5923
 RDS  O    O   O2    0  -0.477   3.8545  -0.5316  -0.0796
 RDS  C3   C   CH1   0   0.025   4.4172   0.6903   0.4356
 RDS  C4   C   CH3   0  -0.682   4.4892   1.7400  -0.6579
 RDS  C5   C   CH2   0  -0.436   5.7884   0.3267   0.9803
 RDS  C6   C   CH3   0  -0.666   5.7567  -0.6886   2.1139
 RDS  H1   H   HCR6  0   0.293  -2.7914   0.6911   1.8474
 RDS  H2   H   HCR6  0   0.275  -1.8001   1.3245  -2.2754
 RDS  H3   H   HCR6  0   0.275  -4.1072   0.7127  -2.9189
 RDS  H4   H   HCR6  0   0.286  -5.7642   0.1105  -1.1896
 RDS  H5   H   HCR6  0   0.275   2.7458  -2.6652  -1.0185
 RDS  H6   H   HNH2  0   0.407   0.6525  -3.8540  -1.7049
 RDS  H7   H   HNH2  0   0.399  -0.8833  -3.0910  -1.5379
 RDS  H8   H   HCH1  0   0.232   3.7899   1.0524   1.2555
 RDS  H9   H   HCH3  0   0.228   5.0923   1.3893  -1.4973
 RDS  H10  H   HCH3  0   0.245   3.4995   2.0055  -1.0260
 RDS  H11  H   HCH3  0   0.236   4.9533   2.6467  -0.2690
 RDS  H12  H   HCH2  0   0.225   6.4209  -0.0336   0.1628
 RDS  H13  H   HCH2  0   0.232   6.2479   1.2527   1.3344
 RDS  H14  H   HCH3  0   0.220   5.1442  -0.3332   2.9447
 RDS  H15  H   HCH3  0   0.226   5.3555  -1.6485   1.7903
 RDS  H16  H   HCH3  0   0.232   6.7605  -0.8652   2.5005

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
 RDS  N    C    single    1.338  0.020  1.338
 RDS  CL   C13  single    1.733  0.020  1.733
 RDS  C    C1   aromatic  1.398  0.020  1.398
 RDS  C    N2   aromatic  1.347  0.020  1.347
 RDS  C1   C2   aromatic  1.387  0.020  1.387
 RDS  N2   C7   aromatic  1.307  0.020  1.307
 RDS  C13  C12  aromatic  1.387  0.020  1.387
 RDS  C13  C11  aromatic  1.385  0.020  1.385
 RDS  C12  C8   aromatic  1.388  0.020  1.388
 RDS  C4   C3   single    1.518  0.020  1.518
 RDS  C2   O    single    1.324  0.020  1.324
 RDS  C2   N1   aromatic  1.330  0.020  1.330
 RDS  C3   O    single    1.440  0.020  1.440
 RDS  C3   C5   single    1.520  0.020  1.520
 RDS  C7   N1   aromatic  1.323  0.020  1.323
 RDS  C7   S    single    1.770  0.020  1.770
 RDS  C11  C10  aromatic  1.389  0.020  1.389
 RDS  C8   S    single    1.769  0.020  1.769
 RDS  C8   C9   aromatic  1.390  0.020  1.390
 RDS  C6   C5   single    1.522  0.020  1.522
 RDS  C10  C9   aromatic  1.386  0.020  1.386
 RDS  C12  H1   single    0.930  0.020  1.080
 RDS  C9   H2   single    0.930  0.020  1.080
 RDS  C10  H3   single    0.930  0.020  1.080
 RDS  C11  H4   single    0.930  0.020  1.080
 RDS  C1   H5   single    0.930  0.020  1.080
 RDS  N    H6   single    0.860  0.020  1.020
 RDS  N    H7   single    0.860  0.020  1.020
 RDS  C3   H8   single    0.970  0.020  1.090
 RDS  C4   H9   single    0.970  0.020  1.090
 RDS  C4   H10  single    0.970  0.020  1.090
 RDS  C4   H11  single    0.970  0.020  1.090
 RDS  C5   H12  single    0.970  0.020  1.090
 RDS  C5   H13  single    0.970  0.020  1.090
 RDS  C6   H14  single    0.970  0.020  1.090
 RDS  C6   H15  single    0.970  0.020  1.090
 RDS  C6   H16  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
 RDS  C11  C13  C12  121.44  3.000
 RDS  C11  C13  CL   119.49  3.000
 RDS  C12  C13  CL   119.08  3.000
 RDS  H1   C12  C8   120.53  3.000
 RDS  H1   C12  C13  120.66  3.000
 RDS  C8   C12  C13  118.81  3.000
 RDS  S    C8   C9   120.31  3.000
 RDS  C9   C8   C12  120.62  3.000
 RDS  S    C8   C12  118.98  3.000
 RDS  H2   C9   C10  120.35  3.000
 RDS  H2   C9   C8   120.09  3.000
 RDS  C10  C9   C8   119.56  3.000
 RDS  H3   C10  C11  119.44  3.000
 RDS  H3   C10  C9   119.95  3.000
 RDS  C11  C10  C9   120.61  3.000
 RDS  H4   C11  C10  120.51  3.000
 RDS  H4   C11  C13  120.54  3.000
 RDS  C10  C11  C13  118.95  3.000
 RDS  C7   S    C8   102.66  3.000
 RDS  N2   C7   N1   128.59  3.000
 RDS  N1   C7   S    111.84  3.000
 RDS  N2   C7   S    119.57  3.000
 RDS  C2   N1   C7   115.27  3.000
 RDS  O    C2   C1   117.64  3.000
 RDS  O    C2   N1   119.70  3.000
 RDS  C1   C2   N1   122.66  3.000
 RDS  H5   C1   C    121.96  3.000
 RDS  H5   C1   C2   121.72  3.000
 RDS  C    C1   C2   116.33  3.000
 RDS  N2   C    N    116.58  3.000
 RDS  N2   C    C1   121.18  3.000
 RDS  N    C    C1   122.24  3.000
 RDS  H7   N    H6   118.12  3.000
 RDS  H7   N    C    119.89  3.000
 RDS  H6   N    C    121.43  3.000
 RDS  C    N2   C7   115.96  3.000
 RDS  C3   O    C2   120.75  3.000
 RDS  H8   C3   C5   109.14  3.000
 RDS  H8   C3   C4   109.77  3.000
 RDS  C5   C3   C4   112.39  3.000
 RDS  H8   C3   O    108.96  3.000
 RDS  C5   C3   O    106.12  3.000
 RDS  C4   C3   O    110.34  3.000
 RDS  H11  C4   H10  107.74  3.000
 RDS  H11  C4   H9   107.84  3.000
 RDS  H10  C4   H9   108.70  3.000
 RDS  H11  C4   C3   109.78  3.000
 RDS  H10  C4   C3   111.67  3.000
 RDS  H9   C4   C3   110.99  3.000
 RDS  H13  C5   H12  106.14  3.000
 RDS  H13  C5   C6   109.43  3.000
 RDS  H12  C5   C6   110.41  3.000
 RDS  H13  C5   C3   107.03  3.000
 RDS  H12  C5   C3   109.42  3.000
 RDS  C6   C5   C3   114.06  3.000
 RDS  H16  C6   H15  107.56  3.000
 RDS  H16  C6   H14  107.43  3.000
 RDS  H15  C6   H14  107.84  3.000
 RDS  H16  C6   C5   110.67  3.000
 RDS  H15  C6   C5   111.97  3.000
 RDS  H14  C6   C5   111.18  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
 RDS  CONST_01  C9   C8   C12  C13    0.00   0.0  0
 RDS  CONST_02  C9   C10  C11  C13    0.00   0.0  0
 RDS  CONST_03  C10  C11  C13  C12    0.00   0.0  0
 RDS  CONST_04  C10  C9   C8   C12    0.00   0.0  0
 RDS  CONST_05  C11  C13  C12  C8     0.00   0.0  0
 RDS  CONST_06  C11  C10  C9   C8     0.00   0.0  0
 RDS  CONST_07  C1   C    N2   C7     0.00   0.0  0
 RDS  CONST_08  C1   C2   N1   C7     0.00   0.0  0
 RDS  CONST_09  C    C1   C2   N1     0.00   0.0  0
 RDS  CONST_10  C    N2   C7   N1     0.00   0.0  0
 RDS  CONST_11  N2   C    C1   C2     0.00   0.0  0
 RDS  CONST_12  N2   C7   N1   C2     0.00   0.0  0
 RDS  CONST_13  C8   C12  C13  CL   180.00   0.0  0
 RDS  CONST_14  C10  C11  C13  CL   180.00   0.0  0
 RDS  CONST_15  S    C8   C12  C13  180.00   0.0  0
 RDS  CONST_16  S    C8   C9   C10  180.00   0.0  0
 RDS  CONST_17  C    N2   C7   S    180.00   0.0  0
 RDS  CONST_18  C2   N1   C7   S    180.00   0.0  0
 RDS  CONST_19  N    C    N2   C7   180.00   0.0  0
 RDS  CONST_20  O    C2   N1   C7   180.00   0.0  0
 RDS  CONST_21  N    C    C1   C2   180.00   0.0  0
 RDS  CONST_22  O    C2   C1   C    180.00   0.0  0
 RDS  CONST_23  H3   C10  C11  C13  180.00   0.0  0
 RDS  CONST_24  H4   C11  C13  C12  180.00   0.0  0
 RDS  CONST_25  H2   C9   C8   C12  180.00   0.0  0
 RDS  CONST_26  H1   C12  C8   C9   180.00   0.0  0
 RDS  CONST_27  H5   C1   C2   N1   180.00   0.0  0
 RDS  CONST_28  H6   N    C    C1     0.00   0.0  0
 RDS  CONST_29  H7   N    C    C1   180.00   0.0  0
 RDS  Var_01    N2   C7   S    C8    -4.05  30.0  1
 RDS  Var_02    H14  C6   C5   C3   -57.40  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 RDS  chir_01  C3  C4  O  C5  negativ

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
 RDS  plan-1  CL   0.020
 RDS  plan-1  C13  0.020
 RDS  plan-1  C12  0.020
 RDS  plan-1  C8   0.020
 RDS  plan-1  C9   0.020
 RDS  plan-1  C10  0.020
 RDS  plan-1  C11  0.020
 RDS  plan-1  S    0.020
 RDS  plan-1  H1   0.020
 RDS  plan-1  H2   0.020
 RDS  plan-1  H3   0.020
 RDS  plan-1  H4   0.020
 RDS  plan-2  S    0.020
 RDS  plan-2  C7   0.020
 RDS  plan-2  N1   0.020
 RDS  plan-2  C2   0.020
 RDS  plan-2  C1   0.020
 RDS  plan-2  C    0.020
 RDS  plan-2  N    0.020
 RDS  plan-2  N2   0.020
 RDS  plan-2  O    0.020
 RDS  plan-2  H5   0.020
 RDS  plan-3  C    0.020
 RDS  plan-3  N    0.020
 RDS  plan-3  H6   0.020
 RDS  plan-3  H7   0.020

