# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 13:26:07 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: (2R,3R)-3-{[2-({4-[(R)-amino(cyclopropyl)hydroxy-lambda~4~-sulfanyl]phenyl}amino)-5-(trifluoromethyl)pyrimidin-4-yl]oxy}butan-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@@H](C)Oc1nc(Nc2ccc(cc2)[S@](N)(O)C3CC3)ncc1C(F)(F)F
#
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
 R0N  R0N  (2R,3R)-3-{[2-({4-[(R)-amino(cyclopropyl)hydroxy-lambda~4~-sulfanyl]phenyl}amino)-5-(trifluoromethyl)pyrimidin-4-yl]oxy}butan-2-ol  ligand  52  29  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_R0N
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
 R0N  C5   C  CR6   0  -0.485  -3.3495   1.4234  -0.1992
 R0N  C6   C  CR6   0   0.624  -3.2224   0.0213  -0.0962
 R0N  C8   C  CR6   0   0.636  -0.9688   0.2234   0.0028
 R0N  C10  C  CR16  0   0.019  -2.1631   2.1237  -0.1845
 R0N  C13  C  CR16  0  -0.344   2.4966  -1.0316   0.1115
 R0N  C15  C  CR6   0  -0.049   4.2395   0.6085   0.0346
 R0N  C17  C  CR16  0  -0.305   1.9351   1.3054   0.0435
 R0N  C21  C  CH1   0  -0.359   6.9104  -0.3122   0.5943
 R0N  C22  C  CH2   0  -0.487   8.3407  -0.4305   0.1709
 R0N  C26  C  CH1   0   0.011  -5.6238  -2.5275   0.6495
 R0N  C28  C  CH3   0  -0.690  -5.8399  -1.9042   2.0214
 R0N  C23  C  CH2   0  -0.472   7.3659  -1.5052  -0.1809
 R0N  S18  S  S     0   0.602   5.9538   1.0696  -0.0792
 R0N  N19  N  NH2   0  -0.956   5.9679   0.5947  -1.8063
 R0N  O20  O  OH1   0  -0.898   5.7216   1.6286   1.7608
 R0N  C16  C  CR16  0  -0.234   3.2860   1.6126   0.0297
 R0N  C14  C  CR16  0  -0.243   3.8438  -0.7179   0.0813
 R0N  C12  C  CR6   0   0.369   1.5228  -0.0292   0.0827
 R0N  N11  N  NH1   0  -0.764   0.1986  -0.4568   0.0974
 R0N  N7   N  N     0  -0.516  -2.0547  -0.5595   0.0047
 R0N  N9   N  N     0  -0.487  -0.9723   1.5470  -0.0861
 R0N  C2   C  CT    0   1.081  -4.6768   2.0828  -0.3004
 R0N  F3   F  F     0  -0.312  -5.3815   1.6589  -1.3590
 R0N  F4   F  F     0  -0.312  -5.4424   1.8605   0.7793
 R0N  F1   F  F     0  -0.306  -4.5583   3.4105  -0.4216
 R0N  O24  O  O2    0  -0.473  -4.3259  -0.6904  -0.1007
 R0N  C25  C  CH1   0  -0.003  -4.2840  -2.1265   0.0344
 R0N  C29  C  CH3   0  -0.678  -4.0210  -2.7708  -1.3109
 R0N  H1   H  HCR6  0   0.289  -2.1552   3.2047  -0.2537
 R0N  H2   H  HCR6  0   0.277   2.1993  -2.0728   0.1527
 R0N  H3   H  HCR6  0   0.295   1.2102   2.1013   0.0276
 R0N  H4   H  HCH1  0   0.315   6.6841  -0.4563   1.6393
 R0N  H5   H  HCH2  0   0.262   8.6834   0.2018  -0.6396
 R0N  H6   H  HCH2  0   0.275   9.0775  -0.6006   0.9444
 R0N  H7   H  HCH1  0   0.240  -5.5776  -3.6144   0.7664
 R0N  H8   H  HCH3  0   0.242  -6.7421  -2.3057   2.4829
 R0N  H9   H  HCH3  0   0.232  -5.0009  -2.1212   2.6837
 R0N  H10  H  HCH3  0   0.228  -5.9456  -0.8195   1.9622
 R0N  H11  H  HCH2  0   0.275   7.3915  -2.4342   0.3744
 R0N  H12  H  HCH2  0   0.257   7.0998  -1.6205  -1.2220
 R0N  H13  H  HNH2  0   0.363   6.8597   0.8365  -2.2251
 R0N  H14  H  HNH2  0   0.360   5.7541  -0.3698  -2.0346
 R0N  H15  H  HOH1  0   0.397   6.4740   2.2139   1.9053
 R0N  H16  H  HCR6  0   0.267   3.5838   2.6524   0.0028
 R0N  H17  H  HCR6  0   0.286   4.5703  -1.5196   0.0957
 R0N  H18  H  HNH1  0   0.417   0.0717  -1.4572   0.1461
 R0N  H19  H  HCH1  0   0.253  -3.4934  -2.3961   0.7389
 R0N  H20  H  HCH3  0   0.236  -4.7804  -2.4947  -2.0414
 R0N  H21  H  HCH3  0   0.245  -3.0430  -2.4923  -1.7017
 R0N  H22  H  HCH3  0   0.239  -4.0348  -3.8558  -1.2023
 R0N  H23  H  HOH1  0   0.441  -6.8425  -1.3304  -0.2795
 R0N  O27  O  OH1   0  -0.661  -6.7080  -2.2822  -0.2192

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
 R0N  F3   C2   single    1.340  0.020  1.340
 R0N  C10  N9   aromatic  1.327  0.020  1.327
 R0N  C10  C5   aromatic  1.378  0.020  1.378
 R0N  C2   F1   single    1.338  0.020  1.338
 R0N  C2   C5   single    1.486  0.020  1.486
 R0N  C2   F4   single    1.342  0.020  1.342
 R0N  N9   C8   aromatic  1.327  0.020  1.327
 R0N  C5   C6   aromatic  1.412  0.020  1.412
 R0N  C8   N11  single    1.354  0.020  1.354
 R0N  C8   N7   aromatic  1.339  0.020  1.339
 R0N  C6   N7   aromatic  1.308  0.020  1.308
 R0N  C6   O24  single    1.313  0.020  1.313
 R0N  N11  C12  single    1.392  0.020  1.392
 R0N  C28  C26  single    1.522  0.020  1.522
 R0N  O24  C25  single    1.443  0.020  1.443
 R0N  C12  C17  aromatic  1.397  0.020  1.397
 R0N  C12  C13  aromatic  1.398  0.020  1.398
 R0N  C17  C16  aromatic  1.385  0.020  1.385
 R0N  C25  C26  single    1.528  0.020  1.528
 R0N  C25  C29  single    1.515  0.020  1.515
 R0N  C26  O27  single    1.411  0.020  1.411
 R0N  C13  C14  aromatic  1.384  0.020  1.384
 R0N  C16  C15  aromatic  1.385  0.020  1.385
 R0N  C14  C15  aromatic  1.385  0.020  1.385
 R0N  C15  S18  single    1.779  0.020  1.779
 R0N  O20  S18  single    1.937  0.020  1.937
 R0N  S18  C21  single    1.810  0.020  1.810
 R0N  S18  N19  single    1.791  0.020  1.791
 R0N  C21  C22  single    1.496  0.020  1.496
 R0N  C21  C23  single    1.494  0.020  1.494
 R0N  C22  C23  single    1.493  0.020  1.493
 R0N  C10  H1   single    0.930  0.020  1.080
 R0N  C13  H2   single    0.930  0.020  1.080
 R0N  C17  H3   single    0.930  0.020  1.080
 R0N  C21  H4   single    0.970  0.020  1.090
 R0N  C22  H5   single    0.970  0.020  1.090
 R0N  C22  H6   single    0.970  0.020  1.090
 R0N  C26  H7   single    0.970  0.020  1.090
 R0N  C28  H8   single    0.970  0.020  1.090
 R0N  C28  H9   single    0.970  0.020  1.090
 R0N  C28  H10  single    0.970  0.020  1.090
 R0N  C23  H11  single    0.970  0.020  1.090
 R0N  C23  H12  single    0.970  0.020  1.090
 R0N  N19  H13  single    0.890  0.020  1.040
 R0N  N19  H14  single    0.890  0.020  1.040
 R0N  O20  H15  single    0.850  0.020  0.980
 R0N  C16  H16  single    0.930  0.020  1.080
 R0N  C14  H17  single    0.930  0.020  1.080
 R0N  N11  H18  single    0.860  0.020  1.020
 R0N  C25  H19  single    0.970  0.020  1.090
 R0N  C29  H20  single    0.970  0.020  1.090
 R0N  C29  H21  single    0.970  0.020  1.090
 R0N  C29  H22  single    0.970  0.020  1.090
 R0N  O27  H23  single    0.850  0.020  0.980

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
 R0N  C2   C5   C10  122.99  3.000
 R0N  C2   C5   C6   121.76  3.000
 R0N  C10  C5   C6   115.25  3.000
 R0N  O24  C6   N7   120.66  3.000
 R0N  O24  C6   C5   117.54  3.000
 R0N  N7   C6   C5   121.80  3.000
 R0N  N9   C8   N7   125.55  3.000
 R0N  N7   C8   N11  113.92  3.000
 R0N  N9   C8   N11  120.53  3.000
 R0N  H1   C10  N9   115.59  3.000
 R0N  H1   C10  C5   120.85  3.000
 R0N  N9   C10  C5   123.56  3.000
 R0N  H2   C13  C12  119.92  3.000
 R0N  H2   C13  C14  119.06  3.000
 R0N  C12  C13  C14  121.02  3.000
 R0N  C14  C15  C16  119.86  3.000
 R0N  C14  C15  S18  121.72  3.000
 R0N  C16  C15  S18  118.39  3.000
 R0N  H3   C17  C12  120.51  3.000
 R0N  H3   C17  C16  119.50  3.000
 R0N  C12  C17  C16  119.99  3.000
 R0N  H4   C21  S18  110.57  3.000
 R0N  H4   C21  C23  117.38  3.000
 R0N  S18  C21  C23  125.28  3.000
 R0N  H4   C21  C22  117.64  3.000
 R0N  C23  C21  C22   59.90  3.000
 R0N  S18  C21  C22  117.40  3.000
 R0N  H6   C22  H5   114.28  3.000
 R0N  H6   C22  C23  120.00  3.000
 R0N  H5   C22  C23  116.76  3.000
 R0N  H6   C22  C21  117.46  3.000
 R0N  H5   C22  C21  117.89  3.000
 R0N  C23  C22  C21   59.96  3.000
 R0N  H7   C26  O27  105.72  3.000
 R0N  H7   C26  C25  105.46  3.000
 R0N  O27  C26  C25  112.36  3.000
 R0N  H7   C26  C28  108.45  3.000
 R0N  O27  C26  C28  112.00  3.000
 R0N  C25  C26  C28  112.33  3.000
 R0N  H10  C28  H9   107.77  3.000
 R0N  H10  C28  H8   107.99  3.000
 R0N  H9   C28  H8   107.84  3.000
 R0N  H10  C28  C26  111.83  3.000
 R0N  H9   C28  C26  110.89  3.000
 R0N  H8   C28  C26  110.38  3.000
 R0N  H12  C23  H11  114.10  3.000
 R0N  H12  C23  C22  117.68  3.000
 R0N  H11  C23  C22  118.78  3.000
 R0N  H12  C23  C21  120.67  3.000
 R0N  H11  C23  C21  115.24  3.000
 R0N  C22  C23  C21   60.13  3.000
 R0N  O20  S18  N19  173.39  3.000
 R0N  N19  S18  C21   98.76  3.000
 R0N  O20  S18  C21   86.00  3.000
 R0N  N19  S18  C15   90.03  3.000
 R0N  C21  S18  C15  106.71  3.000
 R0N  O20  S18  C15   84.17  3.000
 R0N  H14  N19  H13  108.61  3.000
 R0N  H14  N19  S18  117.87  3.000
 R0N  H13  N19  S18  109.98  3.000
 R0N  H15  O20  S18  102.94  3.000
 R0N  H16  C16  C17  118.80  3.000
 R0N  H16  C16  C15  120.49  3.000
 R0N  C17  C16  C15  120.70  3.000
 R0N  H17  C14  C15  121.21  3.000
 R0N  H17  C14  C13  119.05  3.000
 R0N  C15  C14  C13  119.74  3.000
 R0N  N11  C12  C17  125.07  3.000
 R0N  C17  C12  C13  118.68  3.000
 R0N  N11  C12  C13  116.26  3.000
 R0N  H18  N11  C12  115.12  3.000
 R0N  H18  N11  C8   113.12  3.000
 R0N  C12  N11  C8   131.69  3.000
 R0N  C8   N7   C6   117.67  3.000
 R0N  C10  N9   C8   116.17  3.000
 R0N  F1   C2   F4   106.72  3.000
 R0N  F4   C2   F3   106.44  3.000
 R0N  F1   C2   F3   106.78  3.000
 R0N  F4   C2   C5   112.41  3.000
 R0N  F1   C2   C5   111.55  3.000
 R0N  F3   C2   C5   112.53  3.000
 R0N  C25  O24  C6   120.97  3.000
 R0N  H19  C25  C29  110.01  3.000
 R0N  H19  C25  O24  109.08  3.000
 R0N  C29  C25  O24  110.20  3.000
 R0N  H19  C25  C26  108.07  3.000
 R0N  C29  C25  C26  113.47  3.000
 R0N  O24  C25  C26  105.86  3.000
 R0N  H22  C29  H21  107.55  3.000
 R0N  H22  C29  H20  108.06  3.000
 R0N  H21  C29  H20  108.69  3.000
 R0N  H22  C29  C25  109.42  3.000
 R0N  H21  C29  C25  111.46  3.000
 R0N  H20  C29  C25  111.52  3.000
 R0N  H23  O27  C26  108.52  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
 R0N  CONST_01  C8   N9   C10  C5      0.00   0.0  0
 R0N  CONST_02  C8   N7   C6   C5      0.00   0.0  0
 R0N  CONST_03  N9   C10  C5   C6      0.00   0.0  0
 R0N  CONST_04  N9   C8   N7   C6      0.00   0.0  0
 R0N  CONST_05  N7   C8   N9   C10     0.00   0.0  0
 R0N  CONST_06  N7   C6   C5   C10     0.00   0.0  0
 R0N  CONST_07  C16  C17  C12  C13     0.00   0.0  0
 R0N  CONST_08  C16  C15  C14  C13     0.00   0.0  0
 R0N  CONST_09  C12  C17  C16  C15     0.00   0.0  0
 R0N  CONST_10  C12  C13  C14  C15     0.00   0.0  0
 R0N  CONST_11  C14  C13  C12  C17     0.00   0.0  0
 R0N  CONST_12  C14  C15  C16  C17     0.00   0.0  0
 R0N  CONST_13  N11  C8   N7   C6    180.00   0.0  0
 R0N  CONST_14  O24  C6   N7   C8    180.00   0.0  0
 R0N  CONST_15  N11  C8   N9   C10   180.00   0.0  0
 R0N  CONST_16  O24  C6   C5   C10   180.00   0.0  0
 R0N  CONST_17  S18  C15  C14  C13   180.00   0.0  0
 R0N  CONST_18  S18  C15  C16  C17   180.00   0.0  0
 R0N  CONST_19  N11  C12  C17  C16   180.00   0.0  0
 R0N  CONST_20  N11  C12  C13  C14   180.00   0.0  0
 R0N  CONST_21  C2   C5   C6   N7    180.00   0.0  0
 R0N  CONST_22  C2   C5   C10  N9    180.00   0.0  0
 R0N  CONST_23  H1   C10  C5   C6    180.00   0.0  0
 R0N  CONST_24  H3   C17  C12  C13   180.00   0.0  0
 R0N  CONST_25  H2   C13  C14  C15   180.00   0.0  0
 R0N  CONST_26  H17  C14  C15  C16   180.00   0.0  0
 R0N  CONST_27  H16  C16  C15  C14   180.00   0.0  0
 R0N  Var_01    C17  C12  N11  C8      4.37  30.0  2
 R0N  Var_02    S18  C21  C23  C22   103.97  30.0  1
 R0N  Var_03    N9   C8   N11  C12    -2.29  30.0  1
 R0N  Var_04    H11  C23  C22  C21  -104.21  30.0  1
 R0N  Var_05    F3   C2   C5   C6    -58.46  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
 R0N  chir_02  C26  C28  C25  O27  positiv
 R0N  chir_03  S18  C15  C21  N19  negativ
 R0N  chir_04  C25  O24  C26  C29  negativ
 R0N  chir_05  C21  S18  C22  C23  both

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
 R0N  plan-1  C5   0.020
 R0N  plan-1  C6   0.020
 R0N  plan-1  C8   0.020
 R0N  plan-1  C10  0.020
 R0N  plan-1  N11  0.020
 R0N  plan-1  N7   0.020
 R0N  plan-1  N9   0.020
 R0N  plan-1  C2   0.020
 R0N  plan-1  O24  0.020
 R0N  plan-1  H1   0.020
 R0N  plan-2  C13  0.020
 R0N  plan-2  C15  0.020
 R0N  plan-2  C17  0.020
 R0N  plan-2  S18  0.020
 R0N  plan-2  C16  0.020
 R0N  plan-2  C14  0.020
 R0N  plan-2  C12  0.020
 R0N  plan-2  N11  0.020
 R0N  plan-2  H2   0.020
 R0N  plan-2  H3   0.020
 R0N  plan-2  H16  0.020
 R0N  plan-2  H17  0.020

