# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 19 02:42:55 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 5-bromo-N~2~-[(3-methyl-1,2-oxazol-5-yl)methyl]-N~4~-[3-(2-phenylethyl)-1H-pyrazol-5-yl]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(CNc2ncc(Br)c(Nc3[nH]nc(CCc4ccccc4)c3)n2)on1
#
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
 0S9  0S9  5-bromo-N~2~-[(3-methyl-1,2-oxazol-5-yl)methyl]-N~4~-[3-(2-phenylethyl)-1H-pyrazol-5-yl]pyrimidine-2,4-diamine  ligand  49  29  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_0S9
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
 0S9  C26  C   CR16  0  -0.273   7.8658  -3.0035  -0.4213
 0S9  C25  C   CR16  0  -0.240   7.1728  -4.1352  -0.0104
 0S9  C27  C   CR16  0  -0.241   7.2104  -1.7800  -0.4702
 0S9  C24  C   CR16  0  -0.309   5.8346  -4.0416   0.3476
 0S9  C28  C   CR16  0  -0.310   5.8715  -1.6923  -0.1117
 0S9  C3   C   CR15  0  -0.516   0.6959   5.7153  -0.9999
 0S9  C17  C   CR15  0  -0.521   0.5942  -1.7375  -0.1981
 0S9  C11  C   CR16  0   0.004  -3.6705   1.5870   0.2137
 0S9  C23  C   CR6   0   0.129   5.1657  -2.8199   0.3025
 0S9  C12  C   CR6   0  -0.322  -3.4350   0.2765   0.5622
 0S9  C2   C   CR5   0   0.261   0.8803   6.2016   0.3227
 0S9  C18  C   CR5   0   0.267   1.3670  -2.9157  -0.2563
 0S9  C4   C   CR5   0   0.450  -0.2245   4.7354  -0.8593
 0S9  C16  C   CR5   0   0.626  -0.6533  -2.1700   0.2035
 0S9  C13  C   CR6   0   0.612  -2.1855  -0.2652   0.1845
 0S9  C9   C   CR6   0   0.632  -1.6538   1.7343  -0.7741
 0S9  C22  C   CH2   0  -0.509   3.7047  -2.7296   0.6413
 0S9  C21  C   CH2   0  -0.505   2.8193  -3.0232  -0.5800
 0S9  N10  N   N     0  -0.478  -2.7981   2.3337  -0.4478
 0S9  N6   N   N     0  -0.182   0.1293   5.5481   1.1618
 0S9  N14  N   N     0  -0.512  -1.3173   0.4773  -0.4756
 0S9  N20  N   NR15  0  -0.518  -0.5627  -3.5062   0.3507
 0S9  N19  N   N     0  -0.298   0.6580  -3.9759   0.0773
 0S9  N15  N   NH1   0  -0.773  -1.8515  -1.5438   0.4841
 0S9  N8   N   NH1   0  -0.653  -0.7457   2.4295  -1.4866
 0S9  O5   O   O     0  -0.340  -0.5678   4.6318   0.4260
 0S9  H1   H   HCR6  0   0.253   8.9102  -3.0747  -0.6969
 0S9  H2   H   HCR6  0   0.253   7.6760  -5.0930   0.0334
 0S9  H3   H   HCR6  0   0.253   7.7423  -0.8907  -0.7840
 0S9  H4   H   HCR6  0   0.246   5.3034  -4.9299   0.6701
 0S9  H5   H   HCR6  0   0.245   5.3676  -0.7328  -0.1480
 0S9  H6   H   HCR5  0   0.278   1.1835   6.0438  -1.9023
 0S9  H7   H   HCR5  0   0.269   0.9062  -0.7338  -0.4174
 0S9  H8   H   HCR6  0   0.285  -4.6078   2.0625   0.4832
 0S9  H9   H   HCH3  0   0.260   1.4953   8.2393   0.3198
 0S9  H10  H   HCH3  0   0.257   1.7463   7.4079   1.8586
 0S9  H11  H   HCH3  0   0.259   2.8110   7.0870   0.4835
 0S9  H12  H   HCH2  0   0.249   3.4583  -3.4387   1.4352
 0S9  H13  H   HCH2  0   0.249   3.4716  -1.7323   1.0217
 0S9  H14  H   HCH2  0   0.248   3.0384  -4.0275  -0.9490
 0S9  H15  H   HCH2  0   0.250   3.0714  -2.3261  -1.3826
 0S9  H16  H   HCH2  0   0.287  -1.9341   4.0640  -1.9338
 0S9  H17  H   HCH2  0   0.294  -0.4192   3.9825  -2.8133
 0S9  H18  H   HNR5  0   0.419  -1.2993  -4.1435   0.6107
 0S9  H19  H   HNH1  0   0.419  -2.5356  -2.1022   0.9722
 0S9  H20  H   HNH1  0   0.404   0.1319   1.9724  -1.6736
 0S9  BR1  BR  BR    0  -0.024  -4.7315  -0.7080   1.5022
 0S9  C7   C   CH2   0  -0.401  -0.8765   3.8169  -1.8384
 0S9  C1   C   CH3   0  -0.733   1.7820   7.2923   0.7773

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
 0S9  BR1  C12  single    1.880  0.020  1.880
 0S9  C12  C11  aromatic  1.376  0.020  1.376
 0S9  C12  C13  aromatic  1.413  0.020  1.413
 0S9  C11  N10  aromatic  1.325  0.020  1.325
 0S9  N20  C16  aromatic  1.347  0.020  1.347
 0S9  N20  N19  aromatic  1.336  0.020  1.336
 0S9  N15  C13  single    1.355  0.020  1.355
 0S9  N15  C16  single    1.381  0.020  1.381
 0S9  C13  N14  aromatic  1.319  0.020  1.319
 0S9  C16  C17  aromatic  1.380  0.020  1.380
 0S9  N19  C18  aromatic  1.318  0.020  1.318
 0S9  N10  C9   aromatic  1.332  0.020  1.332
 0S9  N14  C9   aromatic  1.335  0.020  1.335
 0S9  C9   N8   single    1.347  0.020  1.347
 0S9  C17  C18  aromatic  1.410  0.020  1.410
 0S9  C18  C21  single    1.492  0.020  1.492
 0S9  N8   C7   single    1.437  0.020  1.437
 0S9  C21  C22  single    1.537  0.020  1.537
 0S9  C7   C4   single    1.492  0.020  1.492
 0S9  C28  C27  aromatic  1.389  0.020  1.389
 0S9  C28  C23  aromatic  1.393  0.020  1.393
 0S9  C22  C23  single    1.502  0.020  1.502
 0S9  C27  C26  aromatic  1.389  0.020  1.389
 0S9  C23  C24  aromatic  1.394  0.020  1.394
 0S9  C4   O5   aromatic  1.334  0.020  1.334
 0S9  C4   C3   aromatic  1.352  0.020  1.352
 0S9  O5   N6   aromatic  1.366  0.020  1.366
 0S9  C26  C25  aromatic  1.389  0.020  1.389
 0S9  C3   C2   aromatic  1.421  0.020  1.421
 0S9  C24  C25  aromatic  1.388  0.020  1.388
 0S9  N6   C2   aromatic  1.302  0.020  1.302
 0S9  C2   C1   single    1.486  0.020  1.486
 0S9  C26  H1   single    0.930  0.020  1.080
 0S9  C25  H2   single    0.930  0.020  1.080
 0S9  C27  H3   single    0.930  0.020  1.080
 0S9  C24  H4   single    0.930  0.020  1.080
 0S9  C28  H5   single    0.930  0.020  1.080
 0S9  C3   H6   single    0.930  0.020  1.080
 0S9  C17  H7   single    0.930  0.020  1.080
 0S9  C11  H8   single    0.930  0.020  1.080
 0S9  C1   H9   single    0.970  0.020  1.090
 0S9  C1   H10  single    0.970  0.020  1.090
 0S9  C1   H11  single    0.970  0.020  1.090
 0S9  C22  H12  single    0.970  0.020  1.090
 0S9  C22  H13  single    0.970  0.020  1.090
 0S9  C21  H14  single    0.970  0.020  1.090
 0S9  C21  H15  single    0.970  0.020  1.090
 0S9  C7   H16  single    0.970  0.020  1.090
 0S9  C7   H17  single    0.970  0.020  1.090
 0S9  N20  H18  single    0.860  0.020  1.020
 0S9  N15  H19  single    0.860  0.020  1.020
 0S9  N8   H20  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
 0S9  H1   C26  C27  120.29  3.000
 0S9  H1   C26  C25  120.19  3.000
 0S9  C27  C26  C25  119.51  3.000
 0S9  H2   C25  C24  119.81  3.000
 0S9  H2   C25  C26  120.05  3.000
 0S9  C24  C25  C26  120.14  3.000
 0S9  H3   C27  C28  119.77  3.000
 0S9  H3   C27  C26  120.12  3.000
 0S9  C28  C27  C26  120.10  3.000
 0S9  H4   C24  C23  119.52  3.000
 0S9  H4   C24  C25  119.59  3.000
 0S9  C23  C24  C25  120.89  3.000
 0S9  H5   C28  C23  119.39  3.000
 0S9  H5   C28  C27  119.68  3.000
 0S9  C23  C28  C27  120.93  3.000
 0S9  H6   C3   C4   128.06  3.000
 0S9  H6   C3   C2   128.07  3.000
 0S9  C4   C3   C2   103.86  3.000
 0S9  H7   C17  C16  127.96  3.000
 0S9  H7   C17  C18  127.83  3.000
 0S9  C16  C17  C18  104.21  3.000
 0S9  H8   C11  N10  116.47  3.000
 0S9  H8   C11  C12  120.15  3.000
 0S9  N10  C11  C12  123.38  3.000
 0S9  C22  C23  C28  120.73  3.000
 0S9  C22  C23  C24  120.80  3.000
 0S9  C28  C23  C24  118.43  3.000
 0S9  BR1  C12  C13  122.86  3.000
 0S9  C13  C12  C11  116.66  3.000
 0S9  BR1  C12  C11  120.48  3.000
 0S9  N6   C2   C1   121.41  3.000
 0S9  C1   C2   C3   127.91  3.000
 0S9  N6   C2   C3   110.68  3.000
 0S9  N19  C18  C21  121.37  3.000
 0S9  C21  C18  C17  127.06  3.000
 0S9  N19  C18  C17  111.51  3.000
 0S9  O5   C4   C7   118.15  3.000
 0S9  O5   C4   C3   109.37  3.000
 0S9  C7   C4   C3   132.48  3.000
 0S9  N15  C16  N20  119.07  3.000
 0S9  N15  C16  C17  134.54  3.000
 0S9  N20  C16  C17  106.37  3.000
 0S9  N15  C13  N14  118.65  3.000
 0S9  N14  C13  C12  119.98  3.000
 0S9  N15  C13  C12  121.37  3.000
 0S9  N8   C9   N14  115.73  3.000
 0S9  N8   C9   N10  118.44  3.000
 0S9  N14  C9   N10  125.82  3.000
 0S9  H13  C22  H12  106.94  3.000
 0S9  H13  C22  C21  109.15  3.000
 0S9  H12  C22  C21  108.88  3.000
 0S9  H13  C22  C23  109.93  3.000
 0S9  H12  C22  C23  110.13  3.000
 0S9  C21  C22  C23  111.69  3.000
 0S9  H15  C21  H14  107.00  3.000
 0S9  H15  C21  C22  109.20  3.000
 0S9  H14  C21  C22  109.18  3.000
 0S9  H15  C21  C18  109.76  3.000
 0S9  H14  C21  C18  109.57  3.000
 0S9  C22  C21  C18  112.00  3.000
 0S9  C9   N10  C11  115.74  3.000
 0S9  O5   N6   C2   106.49  3.000
 0S9  C9   N14  C13  118.42  3.000
 0S9  H18  N20  N19  119.87  3.000
 0S9  H18  N20  C16  127.30  3.000
 0S9  N19  N20  C16  112.81  3.000
 0S9  N20  N19  C18  105.09  3.000
 0S9  H19  N15  C13  117.52  3.000
 0S9  H19  N15  C16  115.83  3.000
 0S9  C13  N15  C16  126.65  3.000
 0S9  H20  N8   C7   118.16  3.000
 0S9  H20  N8   C9   116.83  3.000
 0S9  C7   N8   C9   124.48  3.000
 0S9  N6   O5   C4   109.59  3.000
 0S9  H17  C7   H16  107.13  3.000
 0S9  H17  C7   N8   109.12  3.000
 0S9  H16  C7   N8   109.17  3.000
 0S9  H17  C7   C4   108.07  3.000
 0S9  H16  C7   C4   109.98  3.000
 0S9  N8   C7   C4   113.19  3.000
 0S9  H11  C1   H10  108.59  3.000
 0S9  H11  C1   H9   107.39  3.000
 0S9  H10  C1   H9   108.43  3.000
 0S9  H11  C1   C2   110.62  3.000
 0S9  H10  C1   C2   111.22  3.000
 0S9  H9   C1   C2   110.47  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
 0S9  CONST_01  C23  C28  C27  C26     0.00   0.0  0
 0S9  CONST_02  C23  C24  C25  C26     0.00   0.0  0
 0S9  CONST_03  C28  C27  C26  C25     0.00   0.0  0
 0S9  CONST_04  C28  C23  C24  C25     0.00   0.0  0
 0S9  CONST_05  C24  C23  C28  C27     0.00   0.0  0
 0S9  CONST_06  C24  C25  C26  C27     0.00   0.0  0
 0S9  CONST_07  N6   O5   C4   C3      0.00   0.0  0
 0S9  CONST_08  O5   N6   C2   C3      0.00   0.0  0
 0S9  CONST_09  N19  N20  C16  C17     0.00   0.0  0
 0S9  CONST_10  N20  N19  C18  C17     0.00   0.0  0
 0S9  CONST_11  N14  C13  C12  C11     0.00   0.0  0
 0S9  CONST_12  N14  C9   N10  C11     0.00   0.0  0
 0S9  CONST_13  C9   N10  C11  C12     0.00   0.0  0
 0S9  CONST_14  C9   N14  C13  C12     0.00   0.0  0
 0S9  CONST_15  O5   C4   C3   C2      0.00   0.0  0
 0S9  CONST_16  C4   O5   N6   C2      0.00   0.0  0
 0S9  CONST_17  C16  N20  N19  C18     0.00   0.0  0
 0S9  CONST_18  N20  C16  C17  C18     0.00   0.0  0
 0S9  CONST_19  N6   C2   C3   C4      0.00   0.0  0
 0S9  CONST_20  N19  C18  C17  C16     0.00   0.0  0
 0S9  CONST_21  N10  C11  C12  C13     0.00   0.0  0
 0S9  CONST_22  N10  C9   N14  C13     0.00   0.0  0
 0S9  CONST_23  C22  C23  C24  C25   180.00   0.0  0
 0S9  CONST_24  C22  C23  C28  C27   180.00   0.0  0
 0S9  CONST_25  N15  C13  C12  C11   180.00   0.0  0
 0S9  CONST_26  N8   C9   N10  C11   180.00   0.0  0
 0S9  CONST_27  C7   C4   C3   C2    180.00   0.0  0
 0S9  CONST_28  N15  C16  C17  C18   180.00   0.0  0
 0S9  CONST_29  C1   C2   C3   C4    180.00   0.0  0
 0S9  CONST_30  C21  C18  C17  C16   180.00   0.0  0
 0S9  CONST_31  N8   C9   N14  C13   180.00   0.0  0
 0S9  CONST_32  N15  C13  N14  C9    180.00   0.0  0
 0S9  CONST_33  O5   N6   C2   C1    180.00   0.0  0
 0S9  CONST_34  N20  N19  C18  C21   180.00   0.0  0
 0S9  CONST_35  N6   O5   C4   C7    180.00   0.0  0
 0S9  CONST_36  BR1  C12  C11  N10   180.00   0.0  0
 0S9  CONST_37  BR1  C12  C13  N14   180.00   0.0  0
 0S9  CONST_38  N15  C16  N20  N19   180.00   0.0  0
 0S9  CONST_39  H5   C28  C27  C26   180.00   0.0  0
 0S9  CONST_40  H4   C24  C25  C26   180.00   0.0  0
 0S9  CONST_41  H3   C27  C26  C25   180.00   0.0  0
 0S9  CONST_42  H2   C25  C26  C27   180.00   0.0  0
 0S9  CONST_43  H1   C26  C25  C24   180.00   0.0  0
 0S9  CONST_44  H18  N20  C16  C17   180.00   0.0  0
 0S9  CONST_45  H8   C11  C12  C13   180.00   0.0  0
 0S9  CONST_46  H6   C3   C2   N6    180.00   0.0  0
 0S9  CONST_47  H7   C17  C16  N20   180.00   0.0  0
 0S9  CONST_48  N10  C9   N8   C7      0.00   0.0  0
 0S9  CONST_49  N14  C9   N8   C7    180.00   0.0  0
 0S9  CONST_50  H20  N8   C9   N10   180.00   0.0  0
 0S9  Var_01    C13  N15  C16  C17    13.56  30.0  3
 0S9  Var_02    C16  N15  C13  C12  -178.04  30.0  2
 0S9  Var_03    C21  C22  C23  C24   -86.09  30.0  2
 0S9  Var_04    N8   C7   C4   C3    125.89  30.0  2
 0S9  Var_05    C22  C21  C18  C17    82.04  30.0  2
 0S9  Var_06    C18  C21  C22  C23  -179.16  30.0  2
 0S9  Var_07    C9   N8   C7   C4     93.19  30.0  1
 0S9  Var_08    H9   C1   C2   C3     62.42  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
 0S9  plan-1  C3   0.020
 0S9  plan-1  C2   0.020
 0S9  plan-1  C4   0.020
 0S9  plan-1  N6   0.020
 0S9  plan-1  O5   0.020
 0S9  plan-1  H6   0.020
 0S9  plan-1  C7   0.020
 0S9  plan-1  C1   0.020
 0S9  plan-2  C17  0.020
 0S9  plan-2  C18  0.020
 0S9  plan-2  C16  0.020
 0S9  plan-2  C21  0.020
 0S9  plan-2  N20  0.020
 0S9  plan-2  N19  0.020
 0S9  plan-2  N15  0.020
 0S9  plan-2  H7   0.020
 0S9  plan-2  H18  0.020
 0S9  plan-3  C26  0.020
 0S9  plan-3  C25  0.020
 0S9  plan-3  C27  0.020
 0S9  plan-3  C24  0.020
 0S9  plan-3  C28  0.020
 0S9  plan-3  C23  0.020
 0S9  plan-3  C22  0.020
 0S9  plan-3  H1   0.020
 0S9  plan-3  H2   0.020
 0S9  plan-3  H3   0.020
 0S9  plan-3  H4   0.020
 0S9  plan-3  H5   0.020
 0S9  plan-4  C11  0.020
 0S9  plan-4  C12  0.020
 0S9  plan-4  C13  0.020
 0S9  plan-4  C9   0.020
 0S9  plan-4  N10  0.020
 0S9  plan-4  N14  0.020
 0S9  plan-4  N15  0.020
 0S9  plan-4  N8   0.020
 0S9  plan-4  H8   0.020
 0S9  plan-4  BR1  0.020
 0S9  plan-5  C9   0.020
 0S9  plan-5  N8   0.020
 0S9  plan-5  H20  0.020
 0S9  plan-5  C7   0.020

