# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 21:58:45 2022
#   Inital geometry file: a 119 line input string
#   Ligand name: ~{N}-[3-[(3~{R},6~{R})-5-azanyl-3,6-dimethyl-6-(trifluoromethyl)-2~{H}-1,4-oxazin-3-yl]phenyl]-5-bromanyl-pyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]1(CO[C@](C)(C(=N1)N)C(F)(F)F)c2cccc(NC(=O)c3ccc(Br)cn3)c2
#
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
 SL8  SL8  ~{N}-[3-[(3~{R},6~{R})-5-azanyl-3,6-dimethyl-6-(trifluoromethyl)-2~{H}-1,4-oxazin-3-yl]phenyl]-5-bromanyl-pyridine-2-carboxamide  ligand  47  29  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SL8
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
 SL8  C2   C   CR6   0  -0.184  26.1633  79.4460  16.8993
 SL8  C3   C   CR16  0  -0.031  26.2417  78.1084  17.2740
 SL8  C44  C   CH3   0  -0.636  29.0041  71.7057  22.7960
 SL8  C11  C   C     0   0.536  29.0836  77.9937  19.5559
 SL8  C15  C   CR6   0   0.424  29.6857  75.8261  20.6124
 SL8  C16  C   CR16  0  -0.449  29.3129  74.4774  20.5999
 SL8  C18  C   CR6   0   0.186  29.9496  73.5399  21.3959
 SL8  C19  C   CR16  0  -0.322  30.9835  73.9712  22.2289
 SL8  C21  C   CR16  0  -0.230  31.3600  75.3025  22.2387
 SL8  C23  C   CR16  0  -0.333  30.7250  76.2444  21.4391
 SL8  C25  C   CT    0  -0.057  29.5211  72.0734  21.4024
 SL8  C27  C   C     0   0.412  28.6573  71.3668  19.3163
 SL8  C28  C   CT    0  -0.056  30.0524  71.0867  18.7499
 SL8  C30  C   CH2   0  -0.189  30.6925  71.1685  21.0510
 SL8  BR1  BR  BR    0   0.001  24.8149  79.9999  15.7196
 SL8  N5   N   N     0  -0.435  27.1695  77.6766  18.1064
 SL8  C6   C   CR6   0   0.129  28.0554  78.5334  18.6005
 SL8  C7   C   CR16  0  -0.285  28.0532  79.8811  18.2744
 SL8  C9   C   CR16  0  -0.114  27.0837  80.3502  17.4023
 SL8  O12  O   O     0  -0.448  29.9230  78.7248  20.0508
 SL8  N13  N   NH1   0  -0.763  28.9516  76.6710  19.7775
 SL8  N26  N   N     0  -0.415  28.4351  71.8567  20.4686
 SL8  O29  O   O2    0  -0.487  31.0500  71.3511  19.6951
 SL8  C33  C   CT    0   1.030  30.1904  69.6062  18.3277
 SL8  F34  F   F     0  -0.301  29.7486  68.7673  19.2735
 SL8  F35  F   F     0  -0.303  29.5124  69.3195  17.2106
 SL8  F36  F   F     0  -0.301  31.4670  69.2981  18.0938
 SL8  C37  C   CH3   0  -0.676  30.3308  72.0102  17.5619
 SL8  N41  N   NH2   0  -0.818  27.6131  71.0513  18.5028
 SL8  H1   H   HCR6  0   0.293  25.5391  77.3761  16.8940
 SL8  H2   H   HCH3  0   0.230  29.7727  71.8309  23.5589
 SL8  H3   H   HCH3  0   0.238  28.1553  72.3354  23.0624
 SL8  H4   H   HCH3  0   0.235  28.6751  70.6657  22.8138
 SL8  H5   H   HCR6  0   0.269  28.4966  74.1681  19.9589
 SL8  H6   H   HCR6  0   0.251  31.4993  73.2735  22.8767
 SL8  H7   H   HCR6  0   0.255  32.1659  75.6247  22.8856
 SL8  H8   H   HCR6  0   0.275  31.0390  77.2745  21.4723
 SL8  H9   H   HCH2  0   0.232  30.4272  70.1282  21.2685
 SL8  H10  H   HCH2  0   0.254  31.5830  71.4049  21.6324
 SL8  H11  H   HCR6  0   0.289  28.7888  80.5550  18.6894
 SL8  H12  H   HCR6  0   0.302  27.0543  81.3966  17.1295
 SL8  H13  H   HNH1  0   0.423  28.1950  76.2381  19.2609
 SL8  H14  H   HCH3  0   0.267  30.2277  73.0439  17.8893
 SL8  H15  H   HCH3  0   0.266  31.3497  71.8698  17.2017
 SL8  H16  H   HCH3  0   0.250  29.6536  71.8527  16.7259
 SL8  H17  H   HNH2  0   0.388  26.7134  71.3837  18.8146
 SL8  H18  H   HNH2  0   0.397  27.7276  71.0726  17.5033

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
 SL8  BR1  C2   single    1.875  0.020  1.875
 SL8  C2   C9   aromatic  1.385  0.020  1.385
 SL8  C2   C3   aromatic  1.391  0.020  1.391
 SL8  C9   C7   aromatic  1.386  0.020  1.386
 SL8  F35  C33  single    1.338  0.020  1.338
 SL8  C3   N5   aromatic  1.319  0.020  1.319
 SL8  C37  C28  single    1.530  0.020  1.530
 SL8  F36  C33  single    1.334  0.020  1.334
 SL8  C7   C6   aromatic  1.387  0.020  1.387
 SL8  C33  C28  single    1.546  0.020  1.546
 SL8  C33  F34  single    1.339  0.020  1.339
 SL8  N5   C6   aromatic  1.328  0.020  1.328
 SL8  C6   C11  single    1.504  0.020  1.504
 SL8  N41  C27  single    1.361  0.020  1.361
 SL8  C28  C27  single    1.532  0.020  1.532
 SL8  C28  O29  single    1.399  0.020  1.399
 SL8  C27  N26  double    1.272  0.020  1.272
 SL8  O29  C30  single    1.414  0.020  1.414
 SL8  C11  N13  single    1.348  0.020  1.348
 SL8  C11  O12  double    1.218  0.020  1.218
 SL8  N13  C15  single    1.396  0.020  1.396
 SL8  N26  C25  single    1.449  0.020  1.449
 SL8  C16  C15  aromatic  1.399  0.020  1.399
 SL8  C16  C18  aromatic  1.385  0.020  1.385
 SL8  C15  C23  aromatic  1.392  0.020  1.392
 SL8  C30  C25  single    1.521  0.020  1.521
 SL8  C25  C18  single    1.528  0.020  1.528
 SL8  C25  C44  single    1.531  0.020  1.531
 SL8  C18  C19  aromatic  1.396  0.020  1.396
 SL8  C23  C21  aromatic  1.389  0.020  1.389
 SL8  C19  C21  aromatic  1.384  0.020  1.384
 SL8  C3   H1   single    0.930  0.020  1.080
 SL8  C44  H2   single    0.970  0.020  1.090
 SL8  C44  H3   single    0.970  0.020  1.090
 SL8  C44  H4   single    0.970  0.020  1.090
 SL8  C16  H5   single    0.930  0.020  1.080
 SL8  C19  H6   single    0.930  0.020  1.080
 SL8  C21  H7   single    0.930  0.020  1.080
 SL8  C23  H8   single    0.930  0.020  1.080
 SL8  C30  H9   single    0.970  0.020  1.090
 SL8  C30  H10  single    0.970  0.020  1.090
 SL8  C7   H11  single    0.930  0.020  1.080
 SL8  C9   H12  single    0.930  0.020  1.080
 SL8  N13  H13  single    0.860  0.020  1.020
 SL8  C37  H14  single    0.970  0.020  1.090
 SL8  C37  H15  single    0.970  0.020  1.090
 SL8  C37  H16  single    0.970  0.020  1.090
 SL8  N41  H17  single    0.890  0.020  1.040
 SL8  N41  H18  single    0.890  0.020  1.040

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
 SL8  C9   C2   BR1  120.90  3.000
 SL8  C9   C2   C3   119.51  3.000
 SL8  BR1  C2   C3   119.60  3.000
 SL8  H1   C3   N5   117.13  3.000
 SL8  H1   C3   C2   121.25  3.000
 SL8  N5   C3   C2   121.62  3.000
 SL8  H4   C44  H3   108.18  3.000
 SL8  H4   C44  H2   108.10  3.000
 SL8  H3   C44  H2   108.16  3.000
 SL8  H4   C44  C25  110.22  3.000
 SL8  H3   C44  C25  110.28  3.000
 SL8  H2   C44  C25  111.79  3.000
 SL8  N13  C11  O12  126.14  3.000
 SL8  O12  C11  C6   120.92  3.000
 SL8  N13  C11  C6   112.94  3.000
 SL8  N13  C15  C23  124.45  3.000
 SL8  C23  C15  C16  119.58  3.000
 SL8  N13  C15  C16  115.97  3.000
 SL8  H5   C16  C18  119.56  3.000
 SL8  H5   C16  C15  118.77  3.000
 SL8  C18  C16  C15  121.66  3.000
 SL8  C25  C18  C19  120.11  3.000
 SL8  C19  C18  C16  118.31  3.000
 SL8  C25  C18  C16  121.56  3.000
 SL8  H6   C19  C21  119.09  3.000
 SL8  H6   C19  C18  120.71  3.000
 SL8  C21  C19  C18  120.20  3.000
 SL8  H7   C21  C23  118.85  3.000
 SL8  H7   C21  C19  119.55  3.000
 SL8  C23  C21  C19  121.60  3.000
 SL8  H8   C23  C21  119.82  3.000
 SL8  H8   C23  C15  121.53  3.000
 SL8  C21  C23  C15  118.64  3.000
 SL8  N26  C25  C30  109.84  3.000
 SL8  C30  C25  C18  110.73  3.000
 SL8  N26  C25  C18  110.55  3.000
 SL8  C18  C25  C44  109.21  3.000
 SL8  C30  C25  C44  109.11  3.000
 SL8  N26  C25  C44  107.31  3.000
 SL8  N41  C27  N26  119.80  3.000
 SL8  N26  C27  C28  124.38  3.000
 SL8  N41  C27  C28  115.82  3.000
 SL8  C37  C28  C33  110.47  3.000
 SL8  C33  C28  O29  107.57  3.000
 SL8  C37  C28  O29  106.30  3.000
 SL8  O29  C28  C27  111.40  3.000
 SL8  C33  C28  C27  110.94  3.000
 SL8  C37  C28  C27  110.03  3.000
 SL8  H10  C30  H9   107.35  3.000
 SL8  H10  C30  O29  106.08  3.000
 SL8  H9   C30  O29  111.98  3.000
 SL8  H10  C30  C25  112.15  3.000
 SL8  H9   C30  C25  109.42  3.000
 SL8  O29  C30  C25  109.83  3.000
 SL8  C6   N5   C3   119.53  3.000
 SL8  C7   C6   N5   122.59  3.000
 SL8  N5   C6   C11  117.45  3.000
 SL8  C7   C6   C11  119.95  3.000
 SL8  H11  C7   C9   120.45  3.000
 SL8  H11  C7   C6   120.99  3.000
 SL8  C9   C7   C6   118.56  3.000
 SL8  H12  C9   C7   120.34  3.000
 SL8  H12  C9   C2   121.47  3.000
 SL8  C7   C9   C2   118.20  3.000
 SL8  H13  N13  C15  116.03  3.000
 SL8  H13  N13  C11  114.12  3.000
 SL8  C15  N13  C11  129.84  3.000
 SL8  C27  N26  C25  120.71  3.000
 SL8  C30  O29  C28  116.30  3.000
 SL8  F36  C33  F35  106.80  3.000
 SL8  F36  C33  F34  107.15  3.000
 SL8  F35  C33  F34  106.76  3.000
 SL8  F34  C33  C28  112.19  3.000
 SL8  F36  C33  C28  110.76  3.000
 SL8  F35  C33  C28  112.84  3.000
 SL8  H16  C37  H15  108.03  3.000
 SL8  H16  C37  H14  108.03  3.000
 SL8  H15  C37  H14  108.07  3.000
 SL8  H16  C37  C28  113.34  3.000
 SL8  H15  C37  C28  110.43  3.000
 SL8  H14  C37  C28  108.79  3.000
 SL8  H18  N41  H17  113.69  3.000
 SL8  H18  N41  C27  120.10  3.000
 SL8  H17  N41  C27  115.05  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
 SL8  CONST_01  C6   C7   C9   C2     0.00   0.0  0
 SL8  CONST_02  C6   N5   C3   C2     0.00   0.0  0
 SL8  CONST_03  C7   C9   C2   C3     0.00   0.0  0
 SL8  CONST_04  C7   C6   N5   C3     0.00   0.0  0
 SL8  CONST_05  C19  C18  C16  C15    0.00   0.0  0
 SL8  CONST_06  C19  C21  C23  C15    0.00   0.0  0
 SL8  CONST_07  C21  C23  C15  C16    0.00   0.0  0
 SL8  CONST_08  C21  C19  C18  C16    0.00   0.0  0
 SL8  CONST_09  C23  C15  C16  C18    0.00   0.0  0
 SL8  CONST_10  C23  C21  C19  C18    0.00   0.0  0
 SL8  CONST_11  C9   C2   C3   N5     0.00   0.0  0
 SL8  CONST_12  C9   C7   C6   N5     0.00   0.0  0
 SL8  CONST_13  C25  C18  C16  C15  180.00   0.0  0
 SL8  CONST_14  C25  C18  C19  C21  180.00   0.0  0
 SL8  CONST_15  C28  C27  N26  C25    0.00   0.0  0
 SL8  CONST_16  C11  C6   N5   C3   180.00   0.0  0
 SL8  CONST_17  C9   C7   C6   C11  180.00   0.0  0
 SL8  CONST_18  N13  C15  C16  C18  180.00   0.0  0
 SL8  CONST_19  N13  C15  C23  C21  180.00   0.0  0
 SL8  CONST_20  C7   C9   C2   BR1  180.00   0.0  0
 SL8  CONST_21  N5   C3   C2   BR1  180.00   0.0  0
 SL8  CONST_22  N41  C27  N26  C25  180.00   0.0  0
 SL8  CONST_23  H11  C7   C9   C2   180.00   0.0  0
 SL8  CONST_24  H12  C9   C2   C3   180.00   0.0  0
 SL8  CONST_25  H7   C21  C23  C15  180.00   0.0  0
 SL8  CONST_26  H8   C23  C15  C16  180.00   0.0  0
 SL8  CONST_27  H6   C19  C18  C16  180.00   0.0  0
 SL8  CONST_28  H5   C16  C18  C19  180.00   0.0  0
 SL8  CONST_29  H1   C3   N5   C6   180.00   0.0  0
 SL8  CONST_30  C6   C11  N13  C15  180.00   0.0  0
 SL8  CONST_31  C16  C15  N13  C11  180.00   0.0  0
 SL8  CONST_32  C23  C15  N13  C11    0.00   0.0  0
 SL8  CONST_33  H13  N13  C15  C16    0.00   0.0  0
 SL8  CONST_34  H17  N41  C27  C28  180.00   0.0  0
 SL8  CONST_36  O12  C11  N13  C15    0.00   0.0  0
 SL8  Var_01    H9   C30  O29  C28   62.51  30.0  1
 SL8  Var_02    N13  C11  C6   N5     0.08  30.0  2

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
 SL8  chir_01  C25  C30  C18  N26  negativ
 SL8  chir_02  C28  O29  C33  C27  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
 SL8  plan-1  C2   0.020
 SL8  plan-1  C3   0.020
 SL8  plan-1  C11  0.020
 SL8  plan-1  BR1  0.020
 SL8  plan-1  N5   0.020
 SL8  plan-1  C6   0.020
 SL8  plan-1  C7   0.020
 SL8  plan-1  C9   0.020
 SL8  plan-1  H1   0.020
 SL8  plan-1  H11  0.020
 SL8  plan-1  H12  0.020
 SL8  plan-2  C15  0.020
 SL8  plan-2  C16  0.020
 SL8  plan-2  C18  0.020
 SL8  plan-2  C19  0.020
 SL8  plan-2  C21  0.020
 SL8  plan-2  C23  0.020
 SL8  plan-2  C25  0.020
 SL8  plan-2  N13  0.020
 SL8  plan-2  H5   0.020
 SL8  plan-2  H6   0.020
 SL8  plan-2  H7   0.020
 SL8  plan-2  H8   0.020
 SL8  plan-3  C11  0.020
 SL8  plan-3  C15  0.020
 SL8  plan-3  C6   0.020
 SL8  plan-3  O12  0.020
 SL8  plan-3  N13  0.020
 SL8  plan-3  H13  0.020
 SL8  plan-4  C25  0.020
 SL8  plan-4  C27  0.020
 SL8  plan-4  C28  0.020
 SL8  plan-4  N26  0.020
 SL8  plan-4  N41  0.020
 SL8  plan-4  H17  0.020
 SL8  plan-4  H18  0.020

