# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 01:12:08 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: N-(4-bromo-2-{[(3R,5S)-3,5-dimethylpiperidin-1-yl]carbonyl}phenyl)-4-morpholin-4-yl-4-oxobutanamide
#   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)N3CCOCC3
#
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
 SX6  SX6  N-(4-bromo-2-{[(3R,5S)-3,5-dimethylpiperidin-1-yl]carbonyl}phenyl)-4-morpholin-4-yl-4-oxobutanamide  ligand  60  30  .  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_SX6
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
 SX6  O3    O   O     0  -0.500  -3.4768  -2.3177  -0.7934
 SX6  C18   C   C     0   0.587  -3.9707  -1.2030  -0.6825
 SX6  N3    N   NT    0  -0.475  -5.3067  -1.0086  -0.6845
 SX6  C22   C   CH2   0  -0.333  -5.9856   0.2697  -0.5771
 SX6  C21   C   CH2   0  -0.175  -6.9717   0.2297   0.5787
 SX6  O4    O   O2    0  -0.483  -7.8799  -0.8403   0.4498
 SX6  C20   C   CH2   0  -0.182  -7.2097  -2.0800   0.3775
 SX6  C19   C   CH2   0  -0.328  -6.2328  -2.1229  -0.7846
 SX6  C17   C   CH2   0  -0.602  -3.0942   0.0271  -0.5282
 SX6  C16   C   CH2   0  -0.610  -1.6197  -0.3305  -0.5572
 SX6  C15   C   C     0   0.581  -0.7268   0.8855  -0.4365
 SX6  O2    O   O     0  -0.455  -1.0787   2.0063  -0.7449
 SX6  N2    N   NH1   0  -0.765   0.5208   0.5759   0.0213
 SX6  C14   C   CR6   0   0.383   1.6350   1.3951   0.2003
 SX6  C13   C   CR16  0  -0.306   1.7235   2.6913  -0.3088
 SX6  C12   C   CR16  0  -0.218   2.8642   3.4517  -0.1093
 SX6  C11   C   CR6   0  -0.123   3.9275   2.9322   0.6100
 SX6  BR1   BR  BR    0  -0.040   5.4769   3.9714   0.8843
 SX6  C10   C   CR16  0  -0.233   3.8562   1.6537   1.1355
 SX6  C9    C   CR6   0  -0.146   2.7257   0.8793   0.9194
 SX6  C8    C   C     0   0.491   2.6679  -0.4656   1.5894
 SX6  O1    O   O     0  -0.455   2.6783  -0.5242   2.8079
 SX6  N1    N   NT    0  -0.477   2.5481  -1.5470   0.7848
 SX6  C6    C   CH2   0  -0.289   2.9915  -1.5669  -0.6059
 SX6  C4    C   CH1   0  -0.256   2.0217  -2.3338  -1.4972
 SX6  C5    C   CH3   0  -0.654   2.5582  -2.4060  -2.9193
 SX6  C3    C   CH2   0  -0.401   1.7603  -3.7191  -0.9162
 SX6  C7    C   CH2   0  -0.273   2.3484  -2.8691   1.3621
 SX6  C2    C   CH1   0  -0.258   1.3287  -3.6575   0.5459
 SX6  C1    C   CH3   0  -0.656   1.1331  -5.0454   1.1375
 SX6  H22   H   HCH2  0   0.277  -5.2837   1.0839  -0.4209
 SX6  H22A  H   HCH2  0   0.251  -6.5150   0.4746  -1.5137
 SX6  H21   H   HCH2  0   0.208  -6.4153   0.1556   1.5240
 SX6  H21A  H   HCH2  0   0.245  -7.5527   1.1526   0.6006
 SX6  H20   H   HCH2  0   0.208  -6.6701  -2.2815   1.3137
 SX6  H20A  H   HCH2  0   0.244  -7.9679  -2.8540   0.2529
 SX6  H19   H   HCH2  0   0.246  -6.7755  -2.0579  -1.7338
 SX6  H19A  H   HCH2  0   0.269  -5.6868  -3.0628  -0.7769
 SX6  H17   H   HCH2  0   0.283  -3.3201   0.7463  -1.3181
 SX6  H17A  H   HCH2  0   0.281  -3.3375   0.5258   0.4137
 SX6  H16   H   HCH2  0   0.272  -1.3899  -1.0524   0.2293
 SX6  H16A  H   HCH2  0   0.292  -1.3680  -0.8204  -1.5032
 SX6  HN2   H   HNH1  0   0.404   0.6497  -0.3886   0.2892
 SX6  H13   H   HCR6  0   0.294   0.9092   3.1210  -0.8675
 SX6  H12   H   HCR6  0   0.286   2.9056   4.4495  -0.5246
 SX6  H10   H   HCR6  0   0.289   4.6780   1.2406   1.7060
 SX6  H6    H   HCH2  0   0.276   3.1266  -0.5505  -0.9727
 SX6  H6A   H   HCH2  0   0.254   3.9778  -2.0462  -0.6438
 SX6  H4    H   HCH1  0   0.215   1.0731  -1.7832  -1.5179
 SX6  H5    H   HCH3  0   0.222   3.5081  -2.9441  -2.9517
 SX6  H5A   H   HCH3  0   0.236   1.8574  -2.9299  -3.5702
 SX6  H5B   H   HCH3  0   0.233   2.7217  -1.4116  -3.3381
 SX6  H3    H   HCH2  0   0.240   1.0013  -4.2338  -1.5120
 SX6  H3A   H   HCH2  0   0.214   2.6759  -4.3190  -0.9915
 SX6  H7    H   HCH2  0   0.236   3.3050  -3.4062   1.3819
 SX6  H7A   H   HCH2  0   0.266   2.0117  -2.7615   2.3907
 SX6  H2    H   HCH1  0   0.221   0.3728  -3.1207   0.6036
 SX6  H1    H   HCH3  0   0.221   2.0595  -5.6228   1.1042
 SX6  H1A   H   HCH3  0   0.232   0.8080  -4.9949   2.1778
 SX6  H1B   H   HCH3  0   0.235   0.3778  -5.6003   0.5796

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
 SX6  O3   C18   double    1.224  0.020  1.224
 SX6  N3   C18   single    1.350  0.020  1.350
 SX6  C18  C17   single    1.518  0.020  1.518
 SX6  C22  N3    single    1.451  0.020  1.451
 SX6  N3   C19   single    1.452  0.020  1.452
 SX6  C21  C22   single    1.520  0.020  1.520
 SX6  C22  H22   single    0.970  0.020  1.090
 SX6  C22  H22A  single    0.970  0.020  1.090
 SX6  C21  O4    single    1.409  0.020  1.409
 SX6  C21  H21   single    0.970  0.020  1.090
 SX6  C21  H21A  single    0.970  0.020  1.090
 SX6  O4   C20   single    1.411  0.020  1.411
 SX6  C20  C19   single    1.519  0.020  1.519
 SX6  C20  H20   single    0.970  0.020  1.090
 SX6  C20  H20A  single    0.970  0.020  1.090
 SX6  C19  H19   single    0.970  0.020  1.090
 SX6  C19  H19A  single    0.970  0.020  1.090
 SX6  C17  C16   single    1.517  0.020  1.517
 SX6  C17  H17   single    0.970  0.020  1.090
 SX6  C17  H17A  single    0.970  0.020  1.090
 SX6  C16  C15   single    1.513  0.020  1.513
 SX6  C16  H16   single    0.970  0.020  1.090
 SX6  C16  H16A  single    0.970  0.020  1.090
 SX6  N2   C15   single    1.364  0.020  1.364
 SX6  C15  O2    double    1.215  0.020  1.215
 SX6  N2   C14   single    1.395  0.020  1.395
 SX6  N2   HN2   single    0.860  0.020  1.020
 SX6  C14  C9    aromatic  1.405  0.020  1.405
 SX6  C14  C13   aromatic  1.395  0.020  1.395
 SX6  C13  C12   aromatic  1.385  0.020  1.385
 SX6  C13  H13   single    0.930  0.020  1.080
 SX6  C12  C11   aromatic  1.385  0.020  1.385
 SX6  C12  H12   single    0.930  0.020  1.080
 SX6  C10  C11   aromatic  1.384  0.020  1.384
 SX6  C11  BR1   single    1.886  0.020  1.886
 SX6  C9   C10   aromatic  1.387  0.020  1.387
 SX6  C10  H10   single    0.930  0.020  1.080
 SX6  C8   C9    single    1.504  0.020  1.504
 SX6  O1   C8    double    1.220  0.020  1.220
 SX6  C8   N1    single    1.353  0.020  1.353
 SX6  C6   N1    single    1.460  0.020  1.460
 SX6  N1   C7    single    1.456  0.020  1.456
 SX6  C6   C4    single    1.524  0.020  1.524
 SX6  C6   H6    single    0.970  0.020  1.090
 SX6  C6   H6A   single    0.970  0.020  1.090
 SX6  C5   C4    single    1.522  0.020  1.522
 SX6  C4   C3    single    1.525  0.020  1.525
 SX6  C4   H4    single    0.970  0.020  1.090
 SX6  C5   H5    single    0.970  0.020  1.090
 SX6  C5   H5A   single    0.970  0.020  1.090
 SX6  C5   H5B   single    0.970  0.020  1.090
 SX6  C3   C2    single    1.526  0.020  1.526
 SX6  C3   H3    single    0.970  0.020  1.090
 SX6  C3   H3A   single    0.970  0.020  1.090
 SX6  C7   C2    single    1.526  0.020  1.526
 SX6  C7   H7    single    0.970  0.020  1.090
 SX6  C7   H7A   single    0.970  0.020  1.090
 SX6  C2   C1    single    1.521  0.020  1.521
 SX6  C2   H2    single    0.970  0.020  1.090
 SX6  C1   H1    single    0.970  0.020  1.090
 SX6  C1   H1A   single    0.970  0.020  1.090
 SX6  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
 SX6  C17   C18  N3   117.05  3.000
 SX6  C17   C18  O3   120.94  3.000
 SX6  N3    C18  O3   122.01  3.000
 SX6  C19   N3   C22  112.50  3.000
 SX6  C19   N3   C18  121.37  3.000
 SX6  C22   N3   C18  126.13  3.000
 SX6  H22A  C22  H22  107.16  3.000
 SX6  H22A  C22  C21  109.98  3.000
 SX6  H22   C22  C21  109.24  3.000
 SX6  H22A  C22  N3   109.12  3.000
 SX6  H22   C22  N3   111.63  3.000
 SX6  C21   C22  N3   109.67  3.000
 SX6  H21A  C21  H21  108.02  3.000
 SX6  H21A  C21  O4   107.51  3.000
 SX6  H21   C21  O4   110.70  3.000
 SX6  H21A  C21  C22  109.79  3.000
 SX6  H21   C21  C22  109.11  3.000
 SX6  O4    C21  C22  111.62  3.000
 SX6  C20   O4   C21  111.44  3.000
 SX6  H20A  C20  H20  107.97  3.000
 SX6  H20A  C20  C19  109.85  3.000
 SX6  H20   C20  C19  109.32  3.000
 SX6  H20A  C20  O4   107.40  3.000
 SX6  H20   C20  O4   110.53  3.000
 SX6  C19   C20  O4   111.69  3.000
 SX6  H19A  C19  H19  107.84  3.000
 SX6  H19A  C19  C20  110.01  3.000
 SX6  H19   C19  C20  110.05  3.000
 SX6  H19A  C19  N3   110.04  3.000
 SX6  H19   C19  N3   109.27  3.000
 SX6  C20   C19  N3   109.62  3.000
 SX6  H17A  C17  H17  106.07  3.000
 SX6  H17A  C17  C16  109.90  3.000
 SX6  H17   C17  C16  110.03  3.000
 SX6  H17A  C17  C18  109.19  3.000
 SX6  H17   C17  C18  109.92  3.000
 SX6  C16   C17  C18  111.59  3.000
 SX6  H16A  C16  H16  106.16  3.000
 SX6  H16A  C16  C15  107.02  3.000
 SX6  H16   C16  C15  110.46  3.000
 SX6  H16A  C16  C17  110.21  3.000
 SX6  H16   C16  C17  110.27  3.000
 SX6  C15   C16  C17  112.48  3.000
 SX6  N2    C15  O2   124.02  3.000
 SX6  O2    C15  C16  123.38  3.000
 SX6  N2    C15  C16  112.58  3.000
 SX6  HN2   N2   C14  115.17  3.000
 SX6  HN2   N2   C15  115.00  3.000
 SX6  C14   N2   C15  129.81  3.000
 SX6  C9    C14  C13  118.60  3.000
 SX6  C13   C14  N2   123.34  3.000
 SX6  C9    C14  N2   118.06  3.000
 SX6  H13   C13  C12  118.57  3.000
 SX6  H13   C13  C14  120.80  3.000
 SX6  C12   C13  C14  120.63  3.000
 SX6  H12   C12  C11  121.07  3.000
 SX6  H12   C12  C13  118.86  3.000
 SX6  C11   C12  C13  120.08  3.000
 SX6  C10   C11  BR1  119.75  3.000
 SX6  BR1   C11  C12  119.98  3.000
 SX6  C10   C11  C12  120.27  3.000
 SX6  H10   C10  C9   119.19  3.000
 SX6  H10   C10  C11  120.90  3.000
 SX6  C9    C10  C11  119.90  3.000
 SX6  C8    C9   C10  117.47  3.000
 SX6  C8    C9   C14  121.78  3.000
 SX6  C10   C9   C14  120.50  3.000
 SX6  N1    C8   O1   123.80  3.000
 SX6  N1    C8   C9   116.95  3.000
 SX6  O1    C8   C9   119.19  3.000
 SX6  C7    N1   C6   114.01  3.000
 SX6  C7    N1   C8   120.12  3.000
 SX6  C6    N1   C8   123.40  3.000
 SX6  H6A   C6   H6   106.53  3.000
 SX6  H6A   C6   C4   109.39  3.000
 SX6  H6    C6   C4   110.59  3.000
 SX6  H6A   C6   N1   108.17  3.000
 SX6  H6    C6   N1   110.24  3.000
 SX6  C4    C6   N1   111.76  3.000
 SX6  H4    C4   C3   108.35  3.000
 SX6  H4    C4   C5   108.12  3.000
 SX6  C3    C4   C5   111.93  3.000
 SX6  H4    C4   C6   107.98  3.000
 SX6  C3    C4   C6   110.09  3.000
 SX6  C5    C4   C6   110.25  3.000
 SX6  H5B   C5   H5A  107.75  3.000
 SX6  H5B   C5   H5   107.89  3.000
 SX6  H5A   C5   H5   107.73  3.000
 SX6  H5B   C5   C4   111.61  3.000
 SX6  H5A   C5   C4   110.74  3.000
 SX6  H5    C5   C4   110.96  3.000
 SX6  H3A   C3   H3   106.52  3.000
 SX6  H3A   C3   C2   108.89  3.000
 SX6  H3    C3   C2   110.17  3.000
 SX6  H3A   C3   C4   109.12  3.000
 SX6  H3    C3   C4   109.82  3.000
 SX6  C2    C3   C4   112.15  3.000
 SX6  H7A   C7   H7   107.54  3.000
 SX6  H7A   C7   C2   110.50  3.000
 SX6  H7    C7   C2   109.84  3.000
 SX6  H7A   C7   N1   109.12  3.000
 SX6  H7    C7   N1   109.39  3.000
 SX6  C2    C7   N1   110.41  3.000
 SX6  H2    C2   C1   108.28  3.000
 SX6  H2    C2   C7   107.53  3.000
 SX6  C1    C2   C7   110.45  3.000
 SX6  H2    C2   C3   108.44  3.000
 SX6  C1    C2   C3   111.85  3.000
 SX6  C7    C2   C3   110.15  3.000
 SX6  H1B   C1   H1A  107.75  3.000
 SX6  H1B   C1   H1   107.63  3.000
 SX6  H1A   C1   H1   107.84  3.000
 SX6  H1B   C1   C2   110.75  3.000
 SX6  H1A   C1   C2   111.52  3.000
 SX6  H1    C1   C2   111.19  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
 SX6  CONST_01  C11  C10  C9   C14     0.00   0.0  0
 SX6  CONST_02  C11  C12  C13  C14     0.00   0.0  0
 SX6  CONST_03  C10  C9   C14  C13     0.00   0.0  0
 SX6  CONST_04  C10  C11  C12  C13     0.00   0.0  0
 SX6  CONST_05  C9   C14  C13  C12     0.00   0.0  0
 SX6  CONST_06  C9   C10  C11  C12     0.00   0.0  0
 SX6  CONST_07  C10  C9   C14  N2    180.00   0.0  0
 SX6  CONST_08  C12  C13  C14  N2    180.00   0.0  0
 SX6  CONST_09  C8   C9   C14  C13   180.00   0.0  0
 SX6  CONST_10  BR1  C11  C12  C13   180.00   0.0  0
 SX6  CONST_11  C8   C9   C10  C11   180.00   0.0  0
 SX6  CONST_12  C9   C10  C11  BR1   180.00   0.0  0
 SX6  CONST_15  C7   N1   C8   C9    180.00   0.0  0
 SX6  CONST_16  H10  C10  C9   C14   180.00   0.0  0
 SX6  CONST_17  H12  C12  C13  C14   180.00   0.0  0
 SX6  CONST_18  H13  C13  C12  C11   180.00   0.0  0
 SX6  CONST_19  C22  N3   C18  O3    180.00   0.0  0
 SX6  CONST_20  C19  N3   C18  O3      0.00   0.0  0
 SX6  CONST_21  C17  C18  N3   C22     0.00   0.0  0
 SX6  CONST_22  C17  C18  N3   C19   180.00   0.0  0
 SX6  CONST_24  C7   N1   C8   O1      0.00   0.0  0
 SX6  CONST_25  C9   C14  N2   C15   180.00   0.0  0
 SX6  CONST_26  C13  C14  N2   C15     0.00   0.0  0
 SX6  CONST_27  HN2  N2   C14  C13   180.00   0.0  0
 SX6  CONST_28  C14  N2   C15  C16   180.00   0.0  0
 SX6  CONST_29  C14  N2   C15  O2      0.00   0.0  0
 SX6  Var_01    O4   C21  C22  N3    -55.32  30.0  1
 SX6  Var_02    O4   C20  C19  N3     55.26  30.0  1
 SX6  Var_03    C20  C19  N3   C22   -54.06  30.0  1
 SX6  Var_04    C19  N3   C22  C21    54.09  30.0  1
 SX6  Var_05    C19  C20  O4   C21   -58.02  30.0  1
 SX6  Var_06    C2   C7   N1   C6    -57.85  30.0  1
 SX6  Var_07    C7   N1   C6   C4     56.92  30.0  1
 SX6  Var_08    C16  C17  C18  N3   -179.39  30.0  3
 SX6  Var_09    C15  C16  C17  C18   178.69  30.0  3
 SX6  Var_10    N2   C15  C16  C17   157.57  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
 SX6  chir_01  C4  C6  C5  C3  negativ
 SX6  chir_02  C2  C3  C7  C1  positiv

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
 SX6  plan-1  C16  0.020
 SX6  plan-1  C15  0.020
 SX6  plan-1  O2   0.020
 SX6  plan-1  N2   0.020
 SX6  plan-1  C14  0.020
 SX6  plan-1  HN2  0.020
 SX6  plan-2  N2   0.020
 SX6  plan-2  C14  0.020
 SX6  plan-2  C13  0.020
 SX6  plan-2  C12  0.020
 SX6  plan-2  C11  0.020
 SX6  plan-2  BR1  0.020
 SX6  plan-2  C10  0.020
 SX6  plan-2  C9   0.020
 SX6  plan-2  C8   0.020
 SX6  plan-2  O1   0.020
 SX6  plan-2  N1   0.020
 SX6  plan-2  C6   0.020
 SX6  plan-2  C7   0.020
 SX6  plan-2  H13  0.020
 SX6  plan-2  H12  0.020
 SX6  plan-2  H10  0.020
 SX6  plan-3  O3   0.020
 SX6  plan-3  C18  0.020
 SX6  plan-3  N3   0.020
 SX6  plan-3  C22  0.020
 SX6  plan-3  C19  0.020
 SX6  plan-3  C17  0.020

