# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 10:15:56 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 4-bromo-2-{[(3R,5S)-3,5-dimethylpiperidin-1-yl]carbonyl}aniline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1C[C@H](C)CN(C1)C(=O)c2cc(Br)ccc2N
#
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
 SX3  SX3  4-bromo-2-{[(3R,5S)-3,5-dimethylpiperidin-1-yl]carbonyl}aniline  ligand  37  18  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SX3
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
 SX3  BR1   BR  BR    0  -0.062   3.8804  -0.5260  -1.1055
 SX3  C11   C   CR6   0  -0.133   2.5116   0.4933  -0.2934
 SX3  C10   C   CR16  0  -0.228   1.2148   0.4073  -0.7679
 SX3  C12   C   CR16  0  -0.226   2.8070   1.3247   0.7785
 SX3  C13   C   CR16  0  -0.322   1.8018   2.0753   1.3575
 SX3  C14   C   CR6   0   0.300   0.4830   2.0257   0.8861
 SX3  N2    N   NH2   0  -0.859  -0.5038   2.7458   1.5108
 SX3  C9    C   CR6   0  -0.137   0.2020   1.1588  -0.1837
 SX3  C8    C   C     0   0.513  -1.1759   1.1138  -0.7674
 SX3  O1    O   O     0  -0.494  -1.6595   2.1378  -1.2418
 SX3  N1    N   NT    0  -0.437  -1.8101  -0.0731  -0.7749
 SX3  C6    C   CH2   0  -0.290  -1.4786  -1.1869   0.0995
 SX3  C4    C   CH1   0  -0.240  -2.4806  -1.2854   1.2494
 SX3  C5    C   CH3   0  -0.658  -2.1568  -2.4809   2.1332
 SX3  C3    C   CH2   0  -0.403  -3.9044  -1.3568   0.7007
 SX3  C7    C   CH2   0  -0.294  -3.1358  -0.1860  -1.3618
 SX3  C2    C   CH1   0  -0.247  -4.2145  -0.2300  -0.2832
 SX3  C1    C   CH3   0  -0.657  -5.5918  -0.3948  -0.9093
 SX3  H10   H   HCR6  0   0.283   0.9742  -0.2470  -1.5971
 SX3  H12   H   HCR6  0   0.279   3.8140   1.3999   1.1668
 SX3  H13   H   HCR6  0   0.272   2.0412   2.7221   2.1929
 SX3  HN2   H   HNH2  0   0.386  -0.1839   3.4933   2.1053
 SX3  HN2A  H   HNH2  0   0.384  -1.2885   3.0241   0.9440
 SX3  H6    H   HCH2  0   0.238  -1.4976  -2.1089  -0.4916
 SX3  H6A   H   HCH2  0   0.273  -0.4701  -1.0789   0.4904
 SX3  H4    H   HCH1  0   0.224  -2.3829  -0.3692   1.8454
 SX3  H5    H   HCH3  0   0.231  -1.1595  -2.3996   2.5687
 SX3  H5A   H   HCH3  0   0.233  -2.8711  -2.5657   2.9532
 SX3  H5B   H   HCH3  0   0.219  -2.1940  -3.4117   1.5625
 SX3  H3    H   HCH2  0   0.208  -4.0428  -2.3207   0.1932
 SX3  H3A   H   HCH2  0   0.236  -4.6213  -1.3384   1.5269
 SX3  H7    H   HCH2  0   0.262  -3.2993   0.6386  -2.0516
 SX3  H7A   H   HCH2  0   0.240  -3.1629  -1.1122  -1.9466
 SX3  H2    H   HCH1  0   0.227  -4.1854   0.7241   0.2573
 SX3  H1    H   HCH3  0   0.232  -6.3692  -0.4131  -0.1445
 SX3  H1A   H   HCH3  0   0.230  -5.8200   0.4212  -1.5972
 SX3  H1B   H   HCH3  0   0.218  -5.6562  -1.3306  -1.4698

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
 SX3  BR1  C11   single    1.890  0.020  1.890
 SX3  C11  C12   aromatic  1.388  0.020  1.388
 SX3  C11  C10   aromatic  1.384  0.020  1.384
 SX3  C10  C9    aromatic  1.390  0.020  1.390
 SX3  C10  H10   single    0.930  0.020  1.080
 SX3  C12  C13   aromatic  1.382  0.020  1.382
 SX3  C12  H12   single    0.930  0.020  1.080
 SX3  C13  C14   aromatic  1.401  0.020  1.401
 SX3  C13  H13   single    0.930  0.020  1.080
 SX3  C9   C14   aromatic  1.405  0.020  1.405
 SX3  C14  N2    single    1.372  0.020  1.372
 SX3  N2   HN2   single    0.890  0.020  1.040
 SX3  N2   HN2A  single    0.890  0.020  1.040
 SX3  C9   C8    single    1.497  0.020  1.497
 SX3  C8   N1    single    1.346  0.020  1.346
 SX3  C8   O1    double    1.228  0.020  1.228
 SX3  C6   N1    single    1.454  0.020  1.454
 SX3  N1   C7    single    1.454  0.020  1.454
 SX3  C4   C6    single    1.528  0.020  1.528
 SX3  C6   H6    single    0.970  0.020  1.090
 SX3  C6   H6A   single    0.970  0.020  1.090
 SX3  C5   C4    single    1.522  0.020  1.522
 SX3  C4   C3    single    1.527  0.020  1.527
 SX3  C4   H4    single    0.970  0.020  1.090
 SX3  C5   H5    single    0.970  0.020  1.090
 SX3  C5   H5A   single    0.970  0.020  1.090
 SX3  C5   H5B   single    0.970  0.020  1.090
 SX3  C3   C2    single    1.528  0.020  1.528
 SX3  C3   H3    single    0.970  0.020  1.090
 SX3  C3   H3A   single    0.970  0.020  1.090
 SX3  C2   C7    single    1.526  0.020  1.526
 SX3  C7   H7    single    0.970  0.020  1.090
 SX3  C7   H7A   single    0.970  0.020  1.090
 SX3  C2   C1    single    1.522  0.020  1.522
 SX3  C2   H2    single    0.970  0.020  1.090
 SX3  C1   H1    single    0.970  0.020  1.090
 SX3  C1   H1A   single    0.970  0.020  1.090
 SX3  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
 SX3  C12   C11  C10  120.09  3.000
 SX3  C10   C11  BR1  119.86  3.000
 SX3  C12   C11  BR1  120.04  3.000
 SX3  H10   C10  C9   119.11  3.000
 SX3  H10   C10  C11  120.54  3.000
 SX3  C9    C10  C11  120.35  3.000
 SX3  H12   C12  C13  119.28  3.000
 SX3  H12   C12  C11  121.12  3.000
 SX3  C13   C12  C11  119.61  3.000
 SX3  H13   C13  C14  119.24  3.000
 SX3  H13   C13  C12  119.13  3.000
 SX3  C14   C13  C12  121.63  3.000
 SX3  C9    C14  N2   121.77  3.000
 SX3  N2    C14  C13  120.34  3.000
 SX3  C9    C14  C13  117.78  3.000
 SX3  HN2A  N2   HN2  112.00  3.000
 SX3  HN2A  N2   C14  116.69  3.000
 SX3  HN2   N2   C14  115.45  3.000
 SX3  C8    C9   C14  119.96  3.000
 SX3  C8    C9   C10  119.38  3.000
 SX3  C14   C9   C10  120.52  3.000
 SX3  N1    C8   O1   123.22  3.000
 SX3  O1    C8   C9   119.21  3.000
 SX3  N1    C8   C9   117.54  3.000
 SX3  C7    N1   C6   113.02  3.000
 SX3  C7    N1   C8   120.02  3.000
 SX3  C6    N1   C8   124.38  3.000
 SX3  H6A   C6   H6   107.08  3.000
 SX3  H6A   C6   C4   110.13  3.000
 SX3  H6    C6   C4   109.90  3.000
 SX3  H6A   C6   N1   110.58  3.000
 SX3  H6    C6   N1   108.43  3.000
 SX3  C4    C6   N1   110.63  3.000
 SX3  H4    C4   C3   108.49  3.000
 SX3  H4    C4   C5   108.76  3.000
 SX3  C3    C4   C5   111.74  3.000
 SX3  H4    C4   C6   107.24  3.000
 SX3  C3    C4   C6   110.11  3.000
 SX3  C5    C4   C6   110.37  3.000
 SX3  H5B   C5   H5A  107.71  3.000
 SX3  H5B   C5   H5   107.65  3.000
 SX3  H5A   C5   H5   107.72  3.000
 SX3  H5B   C5   C4   111.02  3.000
 SX3  H5A   C5   C4   111.00  3.000
 SX3  H5    C5   C4   111.58  3.000
 SX3  H3A   C3   H3   106.33  3.000
 SX3  H3A   C3   C2   109.93  3.000
 SX3  H3    C3   C2   108.92  3.000
 SX3  H3A   C3   C4   109.80  3.000
 SX3  H3    C3   C4   108.93  3.000
 SX3  C2    C3   C4   112.72  3.000
 SX3  H7A   C7   H7   107.38  3.000
 SX3  H7A   C7   C2   109.59  3.000
 SX3  H7    C7   C2   111.34  3.000
 SX3  H7A   C7   N1   107.67  3.000
 SX3  H7    C7   N1   109.53  3.000
 SX3  C2    C7   N1   111.19  3.000
 SX3  H2    C2   C1   108.72  3.000
 SX3  H2    C2   C7   107.72  3.000
 SX3  C1    C2   C7   110.61  3.000
 SX3  H2    C2   C3   108.59  3.000
 SX3  C1    C2   C3   111.64  3.000
 SX3  C7    C2   C3   109.45  3.000
 SX3  H1B   C1   H1A  107.74  3.000
 SX3  H1B   C1   H1   107.66  3.000
 SX3  H1A   C1   H1   107.78  3.000
 SX3  H1B   C1   C2   110.92  3.000
 SX3  H1A   C1   C2   111.57  3.000
 SX3  H1    C1   C2   111.00  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
 SX3  CONST_01  C14  C13  C12  C11    0.00   0.0  0
 SX3  CONST_02  C14  C9   C10  C11    0.00   0.0  0
 SX3  CONST_03  C13  C12  C11  C10    0.00   0.0  0
 SX3  CONST_04  C13  C14  C9   C10    0.00   0.0  0
 SX3  CONST_05  C9   C10  C11  C12    0.00   0.0  0
 SX3  CONST_06  C9   C14  C13  C12    0.00   0.0  0
 SX3  CONST_07  C13  C12  C11  BR1  180.00   0.0  0
 SX3  CONST_08  C9   C10  C11  BR1  180.00   0.0  0
 SX3  CONST_09  C8   C9   C10  C11  180.00   0.0  0
 SX3  CONST_10  N2   C14  C9   C10  180.00   0.0  0
 SX3  CONST_11  N2   C14  C13  C12  180.00   0.0  0
 SX3  CONST_12  C8   C9   C14  C13  180.00   0.0  0
 SX3  CONST_14  C7   N1   C8   C9   180.00   0.0  0
 SX3  CONST_15  H13  C13  C12  C11  180.00   0.0  0
 SX3  CONST_16  H12  C12  C11  C10  180.00   0.0  0
 SX3  CONST_17  H10  C10  C11  C12  180.00   0.0  0
 SX3  CONST_19  C7   N1   C8   O1     0.00   0.0  0
 SX3  Var_01    C2   C7   N1   C6    60.14  30.0  1
 SX3  Var_02    C7   N1   C6   C4   -59.53  30.0  1
 SX3  Var_03    N1   C8   C9   C10   62.00  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
 SX3  chir_01  C4  C6  C5  C3  positiv
 SX3  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
 SX3  plan-1  BR1   0.020
 SX3  plan-1  C11   0.020
 SX3  plan-1  C10   0.020
 SX3  plan-1  C12   0.020
 SX3  plan-1  C13   0.020
 SX3  plan-1  C14   0.020
 SX3  plan-1  N2    0.020
 SX3  plan-1  C9    0.020
 SX3  plan-1  C8    0.020
 SX3  plan-1  H10   0.020
 SX3  plan-1  H12   0.020
 SX3  plan-1  H13   0.020
 SX3  plan-2  C9    0.020
 SX3  plan-2  C8    0.020
 SX3  plan-2  O1    0.020
 SX3  plan-2  N1    0.020
 SX3  plan-2  C6    0.020
 SX3  plan-2  C7    0.020
 SX3  plan-3  C14   0.020
 SX3  plan-3  N2    0.020
 SX3  plan-3  HN2   0.020
 SX3  plan-3  HN2A  0.020

