# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 28 09:44:02 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 4-[(4-bromo-2-{[(3R,5S)-3,5-dimethylpiperidin-1-yl]carbonyl}phenyl)amino]-4-oxobutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1C[C@H](C)CN(C1)C(=O)c2cc(Br)ccc2NC(=O)CCC(O)=O
#
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
 SX5  SX5  '4-[(4-bromo-2-{[(3R,5S)-3,5-dimethylpiperidin-1-yl]carbonyl}phenyl)amino]-4-oxobutanoic acid'  ligand  48  25  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SX5
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
 SX5  O3    O   O     0  -0.443  -5.9831  -0.7895   0.0576
 SX5  C18   C   C     0   0.557  -5.8260   0.2352   0.6735
 SX5  O4    O   OH1   0  -0.595  -6.8156   0.8700   1.2920
 SX5  C17   C   CH2   0  -0.579  -4.5152   0.9495   0.8509
 SX5  C16   C   CH2   0  -0.600  -3.3884   0.2995   0.0717
 SX5  C15   C   C     0   0.561  -2.0558   0.9670   0.3294
 SX5  O2    O   O     0  -0.458  -1.8138   1.6095   1.3319
 SX5  N2    N   NH1   0  -0.767  -1.1393   0.7417  -0.6512
 SX5  C14   C   CR6   0   0.343   0.2072   1.1335  -0.6182
 SX5  C13   C   CR16  0  -0.271   0.5926   2.4053  -0.2042
 SX5  C12   C   CR16  0  -0.232   1.9289   2.7707  -0.2045
 SX5  C11   C   CR6   0  -0.112   2.8874   1.8618  -0.6264
 SX5  BR1   BR  BR    0  -0.036   4.7061   2.3603  -0.6436
 SX5  C10   C   CR16  0  -0.234   2.5250   0.5902  -1.0377
 SX5  C9    C   CR6   0  -0.131   1.1859   0.2234  -1.0212
 SX5  C8    C   C     0   0.511   0.7813  -1.1295  -1.5309
 SX5  O1    O   O     0  -0.486   0.2283  -1.2060  -2.6226
 SX5  N1    N   NT    0  -0.429   1.0704  -2.1876  -0.7595
 SX5  C6    C   CH2   0  -0.290   1.4206  -2.0996   0.6503
 SX5  C4    C   CH1   0  -0.242   0.2356  -2.5054   1.5260
 SX5  C5    C   CH3   0  -0.658   0.6161  -2.4516   2.9982
 SX5  C3    C   CH2   0  -0.403  -0.2614  -3.8888   1.1151
 SX5  C7    C   CH2   0  -0.297   0.6664  -3.5231  -1.1711
 SX5  C2    C   CH1   0  -0.246  -0.5555  -3.9871  -0.3806
 SX5  C1    C   CH3   0  -0.658  -0.9499  -5.3996  -0.7852
 SX5  HO4   H   HOH1  0   0.480  -7.6453   0.3839   1.1744
 SX5  H17   H   HCH2  0   0.290  -4.6449   1.9928   0.5524
 SX5  H17A  H   HCH2  0   0.292  -4.2870   0.9716   1.9194
 SX5  H16   H   HCH2  0   0.289  -3.2852  -0.7524   0.3576
 SX5  H16A  H   HCH2  0   0.278  -3.6047   0.3019  -0.9985
 SX5  HN2   H   HNH1  0   0.415  -1.4259   0.1722  -1.4340
 SX5  H13   H   HCR6  0   0.283  -0.1471   3.1302   0.1009
 SX5  H12   H   HCR6  0   0.287   2.2061   3.7655   0.1162
 SX5  H10   H   HCR6  0   0.289   3.2710  -0.1272  -1.3552
 SX5  H6    H   HCH2  0   0.245   2.2650  -2.7712   0.8366
 SX5  H6A   H   HCH2  0   0.273   1.7502  -1.0930   0.8982
 SX5  H4    H   HCH1  0   0.218  -0.5685  -1.7794   1.3492
 SX5  H5    H   HCH3  0   0.232   0.9466  -1.4529   3.2884
 SX5  H5A   H   HCH3  0   0.235  -0.2333  -2.7175   3.6285
 SX5  H5B   H   HCH3  0   0.221   1.4248  -3.1505   3.2227
 SX5  H3    H   HCH2  0   0.211   0.5054  -4.6310   1.3733
 SX5  H3A   H   HCH2  0   0.238  -1.1539  -4.1530   1.6893
 SX5  H7    H   HCH2  0   0.266   0.4727  -3.5329  -2.2412
 SX5  H7A   H   HCH2  0   0.244   1.5059  -4.2011  -0.9826
 SX5  H2    H   HCH1  0   0.225  -1.3841  -3.3097  -0.6217
 SX5  H1    H   HCH3  0   0.234  -1.8123  -5.7421  -0.2122
 SX5  H1A   H   HCH3  0   0.232  -1.2099  -5.4555  -1.8434
 SX5  H1B   H   HCH3  0   0.219  -0.1328  -6.1017  -0.6043

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
 SX5  O3   C18   double    1.206  0.020  1.206
 SX5  C18  O4    single    1.328  0.020  1.328
 SX5  C18  C17   single    1.503  0.020  1.503
 SX5  O4   HO4   single    0.850  0.020  0.980
 SX5  C16  C17   single    1.516  0.020  1.516
 SX5  C17  H17   single    0.970  0.020  1.090
 SX5  C17  H17A  single    0.970  0.020  1.090
 SX5  C15  C16   single    1.513  0.020  1.513
 SX5  C16  H16   single    0.970  0.020  1.090
 SX5  C16  H16A  single    0.970  0.020  1.090
 SX5  O2   C15   double    1.215  0.020  1.215
 SX5  N2   C15   single    1.361  0.020  1.361
 SX5  C14  N2    single    1.403  0.020  1.403
 SX5  N2   HN2   single    0.860  0.020  1.020
 SX5  C13  C14   aromatic  1.392  0.020  1.392
 SX5  C9   C14   aromatic  1.396  0.020  1.396
 SX5  C12  C13   aromatic  1.385  0.020  1.385
 SX5  C13  H13   single    0.930  0.020  1.080
 SX5  C11  C12   aromatic  1.387  0.020  1.387
 SX5  C12  H12   single    0.930  0.020  1.080
 SX5  BR1  C11   single    1.886  0.020  1.886
 SX5  C11  C10   aromatic  1.385  0.020  1.385
 SX5  C10  C9    aromatic  1.389  0.020  1.389
 SX5  C10  H10   single    0.930  0.020  1.080
 SX5  C9   C8    single    1.501  0.020  1.501
 SX5  C8   N1    single    1.341  0.020  1.341
 SX5  C8   O1    double    1.226  0.020  1.226
 SX5  C6   N1    single    1.455  0.020  1.455
 SX5  N1   C7    single    1.455  0.020  1.455
 SX5  C4   C6    single    1.528  0.020  1.528
 SX5  C6   H6    single    0.970  0.020  1.090
 SX5  C6   H6A   single    0.970  0.020  1.090
 SX5  C5   C4    single    1.522  0.020  1.522
 SX5  C4   C3    single    1.526  0.020  1.526
 SX5  C4   H4    single    0.970  0.020  1.090
 SX5  C5   H5    single    0.970  0.020  1.090
 SX5  C5   H5A   single    0.970  0.020  1.090
 SX5  C5   H5B   single    0.970  0.020  1.090
 SX5  C3   C2    single    1.528  0.020  1.528
 SX5  C3   H3    single    0.970  0.020  1.090
 SX5  C3   H3A   single    0.970  0.020  1.090
 SX5  C2   C7    single    1.527  0.020  1.527
 SX5  C7   H7    single    0.970  0.020  1.090
 SX5  C7   H7A   single    0.970  0.020  1.090
 SX5  C2   C1    single    1.521  0.020  1.521
 SX5  C2   H2    single    0.970  0.020  1.090
 SX5  C1   H1    single    0.970  0.020  1.090
 SX5  C1   H1A   single    0.970  0.020  1.090
 SX5  C1   H1B   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
 SX5  C17   C18  O4   111.56  3.000
 SX5  C17   C18  O3   125.29  3.000
 SX5  O4    C18  O3   123.15  3.000
 SX5  HO4   O4   C18  109.98  3.000
 SX5  H17A  C17  H17  105.81  3.000
 SX5  H17A  C17  C16  110.85  3.000
 SX5  H17   C17  C16  110.92  3.000
 SX5  H17A  C17  C18  107.89  3.000
 SX5  H17   C17  C18  108.54  3.000
 SX5  C16   C17  C18  112.56  3.000
 SX5  H16A  C16  H16  106.06  3.000
 SX5  H16A  C16  C15  109.91  3.000
 SX5  H16   C16  C15  107.24  3.000
 SX5  H16A  C16  C17  110.82  3.000
 SX5  H16   C16  C17  110.35  3.000
 SX5  C15   C16  C17  112.21  3.000
 SX5  N2    C15  O2   123.22  3.000
 SX5  N2    C15  C16  113.42  3.000
 SX5  O2    C15  C16  123.33  3.000
 SX5  HN2   N2   C14  116.64  3.000
 SX5  HN2   N2   C15  117.44  3.000
 SX5  C14   N2   C15  125.67  3.000
 SX5  C9    C14  C13  119.17  3.000
 SX5  C9    C14  N2   118.95  3.000
 SX5  C13   C14  N2   121.87  3.000
 SX5  H13   C13  C12  118.94  3.000
 SX5  H13   C13  C14  120.52  3.000
 SX5  C12   C13  C14  120.53  3.000
 SX5  H12   C12  C11  121.06  3.000
 SX5  H12   C12  C13  119.33  3.000
 SX5  C11   C12  C13  119.60  3.000
 SX5  C10   C11  BR1  119.50  3.000
 SX5  C10   C11  C12  120.75  3.000
 SX5  BR1   C11  C12  119.75  3.000
 SX5  H10   C10  C9   119.54  3.000
 SX5  H10   C10  C11  121.02  3.000
 SX5  C9    C10  C11  119.44  3.000
 SX5  C8    C9   C10  119.60  3.000
 SX5  C8    C9   C14  119.78  3.000
 SX5  C10   C9   C14  120.49  3.000
 SX5  N1    C8   O1   124.07  3.000
 SX5  O1    C8   C9   118.69  3.000
 SX5  N1    C8   C9   117.23  3.000
 SX5  C7    N1   C6   113.35  3.000
 SX5  C7    N1   C8   120.11  3.000
 SX5  C6    N1   C8   124.16  3.000
 SX5  H6A   C6   H6   107.16  3.000
 SX5  H6A   C6   C4   110.49  3.000
 SX5  H6    C6   C4   109.73  3.000
 SX5  H6A   C6   N1   110.46  3.000
 SX5  H6    C6   N1   108.26  3.000
 SX5  C4    C6   N1   110.64  3.000
 SX5  H4    C4   C3   108.52  3.000
 SX5  H4    C4   C5   108.40  3.000
 SX5  C3    C4   C5   111.96  3.000
 SX5  H4    C4   C6   107.47  3.000
 SX5  C3    C4   C6   109.81  3.000
 SX5  C5    C4   C6   110.56  3.000
 SX5  H5B   C5   H5A  107.56  3.000
 SX5  H5B   C5   H5   107.86  3.000
 SX5  H5A   C5   H5   107.78  3.000
 SX5  H5B   C5   C4   111.19  3.000
 SX5  H5A   C5   C4   110.85  3.000
 SX5  H5    C5   C4   111.44  3.000
 SX5  H3A   C3   H3   106.45  3.000
 SX5  H3A   C3   C2   109.96  3.000
 SX5  H3    C3   C2   108.74  3.000
 SX5  H3A   C3   C4   110.08  3.000
 SX5  H3    C3   C4   108.78  3.000
 SX5  C2    C3   C4   112.62  3.000
 SX5  H7A   C7   H7   107.47  3.000
 SX5  H7A   C7   C2   109.63  3.000
 SX5  H7    C7   C2   111.35  3.000
 SX5  H7A   C7   N1   107.86  3.000
 SX5  H7    C7   N1   109.64  3.000
 SX5  C2    C7   N1   110.77  3.000
 SX5  H2    C2   C1   108.60  3.000
 SX5  H2    C2   C7   107.63  3.000
 SX5  C1    C2   C7   110.60  3.000
 SX5  H2    C2   C3   108.71  3.000
 SX5  C1    C2   C3   111.72  3.000
 SX5  C7    C2   C3   109.46  3.000
 SX5  H1B   C1   H1A  107.82  3.000
 SX5  H1B   C1   H1   107.62  3.000
 SX5  H1A   C1   H1   107.76  3.000
 SX5  H1B   C1   C2   111.02  3.000
 SX5  H1A   C1   C2   111.54  3.000
 SX5  H1    C1   C2   110.91  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
 SX5  CONST_01  C11  C12  C13  C14     0.00   0.0  0
 SX5  CONST_02  C11  C10  C9   C14     0.00   0.0  0
 SX5  CONST_03  C10  C9   C14  C13     0.00   0.0  0
 SX5  CONST_04  C10  C11  C12  C13     0.00   0.0  0
 SX5  CONST_05  C9   C14  C13  C12     0.00   0.0  0
 SX5  CONST_06  C9   C10  C11  C12     0.00   0.0  0
 SX5  CONST_07  C12  C13  C14  N2    180.00   0.0  0
 SX5  CONST_08  C10  C9   C14  N2    180.00   0.0  0
 SX5  CONST_09  C8   C9   C14  C13   180.00   0.0  0
 SX5  CONST_10  BR1  C11  C12  C13   180.00   0.0  0
 SX5  CONST_11  C8   C9   C10  C11   180.00   0.0  0
 SX5  CONST_12  C9   C10  C11  BR1   180.00   0.0  0
 SX5  CONST_15  C7   N1   C8   C9    180.00   0.0  0
 SX5  CONST_16  H12  C12  C13  C14   180.00   0.0  0
 SX5  CONST_17  H10  C10  C9   C14   180.00   0.0  0
 SX5  CONST_18  H13  C13  C12  C11   180.00   0.0  0
 SX5  CONST_20  C7   N1   C8   O1      0.00   0.0  0
 SX5  CONST_24  C14  N2   C15  C16   180.00   0.0  0
 SX5  CONST_25  C14  N2   C15  O2      0.00   0.0  0
 SX5  CONST_26  HO4  O4   C18  O3      0.00   0.0  0
 SX5  Var_01    C2   C7   N1   C6     59.86  30.0  1
 SX5  Var_02    C7   N1   C6   C4    -59.45  30.0  1
 SX5  Var_03    C16  C17  C18  O3      4.47  30.0  3
 SX5  Var_04    C15  C16  C17  C18  -176.11  30.0  1
 SX5  Var_05    O2   C15  C16  C17    23.33  30.0  1

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
 SX5  chir_01  C4  C6  C5  C3  positiv
 SX5  chir_02  C2  C3  C7  C1  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
 SX5  plan-1  C16  0.020
 SX5  plan-1  C15  0.020
 SX5  plan-1  O2   0.020
 SX5  plan-1  N2   0.020
 SX5  plan-1  C14  0.020
 SX5  plan-1  HN2  0.020
 SX5  plan-2  N2   0.020
 SX5  plan-2  C14  0.020
 SX5  plan-2  C13  0.020
 SX5  plan-2  C12  0.020
 SX5  plan-2  C11  0.020
 SX5  plan-2  BR1  0.020
 SX5  plan-2  C10  0.020
 SX5  plan-2  C9   0.020
 SX5  plan-2  C8   0.020
 SX5  plan-2  O1   0.020
 SX5  plan-2  N1   0.020
 SX5  plan-2  C6   0.020
 SX5  plan-2  C7   0.020
 SX5  plan-2  H13  0.020
 SX5  plan-2  H12  0.020
 SX5  plan-2  H10  0.020
 SX5  plan-3  O3   0.020
 SX5  plan-3  C18  0.020
 SX5  plan-3  O4   0.020
 SX5  plan-3  C17  0.020
 SX5  plan-3  HO4  0.020

