# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 17 05:20:55 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: (3S,5R)-5-amino-N~3~-(4-chloro-3-fluorophenyl)-N~1~-propylpiperidine-1,3-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCNC(=O)N1C[C@H](N)C[C@@H](C1)C(=O)Nc2ccc(Cl)c(F)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
 MXJ  MXJ  (3S,5R)-5-amino-N~3~-(4-chloro-3-fluorophenyl)-N~1~-propylpiperidine-1,3-dicarboxamide  ligand  46  24  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MXJ
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
 MXJ  C01  C   CH3   0  -0.665   4.5940   4.8861   0.4510
 MXJ  C02  C   CH2   0  -0.464   3.7413   3.6789   0.0899
 MXJ  C03  C   CH2   0  -0.233   4.5686   2.4042   0.0280
 MXJ  C05  C   C     0   0.733   4.2046   0.0089  -0.2862
 MXJ  C07  C   CH2   0  -0.316   2.0063  -0.8215  -1.1048
 MXJ  C08  C   CH1   0  -0.425   1.1863  -1.3026   0.1053
 MXJ  C09  C   C     0   0.583  -0.2870  -1.1640  -0.2196
 MXJ  C12  C   CR6   0   0.406  -2.1986   0.3532   0.2580
 MXJ  C13  C   CR16  0  -0.494  -3.1605  -0.2496  -0.5522
 MXJ  C14  C   CR6   0   0.655  -4.4228   0.3057  -0.6110
 MXJ  C16  C   CR6   0  -0.259  -4.7720   1.4358   0.1046
 MXJ  C18  C   CR16  0  -0.197  -3.8130   2.0302   0.9103
 MXJ  C19  C   CR16  0  -0.366  -2.5418   1.4955   0.9869
 MXJ  C20  C   CH2   0  -0.426   1.5555  -2.7491   0.4331
 MXJ  C21  C   CH1   0  -0.078   3.0612  -2.9127   0.6153
 MXJ  C22  C   CH2   0  -0.312   3.7834  -2.3603  -0.6121
 MXJ  F15  F   F     0  -0.297  -5.3385  -0.2743  -1.3898
 MXJ  N04  N   NH1   0  -0.687   3.7384   1.2828  -0.3632
 MXJ  N06  N   NT    0  -0.493   3.4225  -0.9740  -0.8476
 MXJ  N11  N   NH1   0  -0.749  -0.8932  -0.1129   0.3937
 MXJ  N23  N   NH2   0  -0.803   3.3804  -4.3231   0.7586
 MXJ  O10  O   O     0  -0.458  -0.8506  -1.9131  -0.9960
 MXJ  O24  O   O     0  -0.541   5.2775  -0.2483   0.2501
 MXJ  CL1  CL  CL    0  -0.096  -6.3676   2.0740  -0.0134
 MXJ  H1   H   HCH3  0   0.234   3.9934   5.7947   0.4889
 MXJ  H2   H   HCH3  0   0.222   5.0656   4.7616   1.4272
 MXJ  H3   H   HCH3  0   0.222   5.3868   5.0443  -0.2820
 MXJ  H4   H   HCH2  0   0.229   2.9391   3.5542   0.8217
 MXJ  H5   H   HCH2  0   0.225   3.2597   3.8506  -0.8779
 MXJ  H6   H   HCH2  0   0.217   5.4038   2.5413  -0.6688
 MXJ  H7   H   HCH2  0   0.232   5.0028   2.2022   1.0080
 MXJ  H8   H   HCH2  0   0.264   1.7495  -1.4264  -1.9784
 MXJ  H9   H   HCH2  0   0.269   1.7440   0.2025  -1.3624
 MXJ  H10  H   HCH1  0   0.273   1.4408  -0.6634   0.9576
 MXJ  H11  H   HCR6  0   0.311  -2.9503  -1.1347  -1.1305
 MXJ  H12  H   HCR6  0   0.294  -4.0596   2.9157   1.4795
 MXJ  H13  H   HCR6  0   0.287  -1.8085   1.9733   1.6238
 MXJ  H14  H   HCH2  0   0.254   1.0303  -3.0731   1.3360
 MXJ  H15  H   HCH2  0   0.233   1.2323  -3.4025  -0.3828
 MXJ  H16  H   HCH1  0   0.207   3.3740  -2.3137   1.4855
 MXJ  H17  H   HCH2  0   0.262   4.8624  -2.4499  -0.5059
 MXJ  H18  H   HCH2  0   0.239   3.4894  -2.9442  -1.4900
 MXJ  H19  H   HNH1  0   0.391   3.0203   1.4992  -1.0336
 MXJ  H20  H   HNH1  0   0.423  -0.3157   0.4221   1.0248
 MXJ  H21  H   HNH2  0   0.347   4.3619  -4.4272   0.9865
 MXJ  H22  H   HNH2  0   0.347   2.8759  -4.7042   1.5500

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
 MXJ  C01  C02  single    1.522  0.020  1.522
 MXJ  C02  C03  single    1.521  0.020  1.521
 MXJ  N23  C21  single    1.453  0.020  1.453
 MXJ  C21  C22  single    1.527  0.020  1.527
 MXJ  C21  C20  single    1.526  0.020  1.526
 MXJ  C22  N06  single    1.452  0.020  1.452
 MXJ  C03  N04  single    1.449  0.020  1.449
 MXJ  N04  C05  single    1.359  0.020  1.359
 MXJ  C20  C08  single    1.528  0.020  1.528
 MXJ  N06  C05  single    1.376  0.020  1.376
 MXJ  N06  C07  single    1.447  0.020  1.447
 MXJ  C05  O24  double    1.227  0.020  1.227
 MXJ  C08  C07  single    1.539  0.020  1.539
 MXJ  C08  C09  single    1.515  0.020  1.515
 MXJ  O10  C09  double    1.217  0.020  1.217
 MXJ  C09  N11  single    1.360  0.020  1.360
 MXJ  N11  C12  single    1.393  0.020  1.393
 MXJ  C12  C13  aromatic  1.395  0.020  1.395
 MXJ  C12  C19  aromatic  1.398  0.020  1.398
 MXJ  C13  C14  aromatic  1.380  0.020  1.380
 MXJ  C19  C18  aromatic  1.381  0.020  1.381
 MXJ  C14  F15  single    1.335  0.020  1.335
 MXJ  C14  C16  aromatic  1.382  0.020  1.382
 MXJ  C18  C16  aromatic  1.386  0.020  1.386
 MXJ  C16  CL1  single    1.723  0.020  1.723
 MXJ  C01  H1   single    0.970  0.020  1.090
 MXJ  C01  H2   single    0.970  0.020  1.090
 MXJ  C01  H3   single    0.970  0.020  1.090
 MXJ  C02  H4   single    0.970  0.020  1.090
 MXJ  C02  H5   single    0.970  0.020  1.090
 MXJ  C03  H6   single    0.970  0.020  1.090
 MXJ  C03  H7   single    0.970  0.020  1.090
 MXJ  C07  H8   single    0.970  0.020  1.090
 MXJ  C07  H9   single    0.970  0.020  1.090
 MXJ  C08  H10  single    0.970  0.020  1.090
 MXJ  C13  H11  single    0.930  0.020  1.080
 MXJ  C18  H12  single    0.930  0.020  1.080
 MXJ  C19  H13  single    0.930  0.020  1.080
 MXJ  C20  H14  single    0.970  0.020  1.090
 MXJ  C20  H15  single    0.970  0.020  1.090
 MXJ  C21  H16  single    0.970  0.020  1.090
 MXJ  C22  H17  single    0.970  0.020  1.090
 MXJ  C22  H18  single    0.970  0.020  1.090
 MXJ  N04  H19  single    0.890  0.020  1.040
 MXJ  N11  H20  single    0.860  0.020  1.020
 MXJ  N23  H21  single    0.890  0.020  1.040
 MXJ  N23  H22  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
 MXJ  H3   C01  H2   107.66  3.000
 MXJ  H3   C01  H1   107.63  3.000
 MXJ  H2   C01  H1   107.59  3.000
 MXJ  H3   C01  C02  111.27  3.000
 MXJ  H2   C01  C02  111.35  3.000
 MXJ  H1   C01  C02  111.16  3.000
 MXJ  H5   C02  H4   106.68  3.000
 MXJ  H5   C02  C03  109.56  3.000
 MXJ  H4   C02  C03  109.32  3.000
 MXJ  H5   C02  C01  109.39  3.000
 MXJ  H4   C02  C01  110.05  3.000
 MXJ  C03  C02  C01  111.70  3.000
 MXJ  H7   C03  H6   106.91  3.000
 MXJ  H7   C03  N04  109.11  3.000
 MXJ  H6   C03  N04  111.20  3.000
 MXJ  H7   C03  C02  109.59  3.000
 MXJ  H6   C03  C02  109.60  3.000
 MXJ  N04  C03  C02  110.36  3.000
 MXJ  O24  C05  N06  121.72  3.000
 MXJ  O24  C05  N04  121.43  3.000
 MXJ  N06  C05  N04  116.85  3.000
 MXJ  H9   C07  H8   105.96  3.000
 MXJ  H9   C07  N06  112.15  3.000
 MXJ  H8   C07  N06  108.27  3.000
 MXJ  H9   C07  C08  110.61  3.000
 MXJ  H8   C07  C08  109.29  3.000
 MXJ  N06  C07  C08  110.41  3.000
 MXJ  H10  C08  C20  109.22  3.000
 MXJ  H10  C08  C09  109.84  3.000
 MXJ  C20  C08  C09  111.56  3.000
 MXJ  H10  C08  C07  107.80  3.000
 MXJ  C09  C08  C07  108.72  3.000
 MXJ  C20  C08  C07  109.62  3.000
 MXJ  O10  C09  N11  123.86  3.000
 MXJ  N11  C09  C08  114.05  3.000
 MXJ  O10  C09  C08  122.05  3.000
 MXJ  N11  C12  C19  116.92  3.000
 MXJ  C19  C12  C13  119.13  3.000
 MXJ  N11  C12  C13  123.95  3.000
 MXJ  H11  C13  C14  119.06  3.000
 MXJ  H11  C13  C12  122.14  3.000
 MXJ  C14  C13  C12  118.79  3.000
 MXJ  F15  C14  C16  118.95  3.000
 MXJ  C16  C14  C13  122.53  3.000
 MXJ  F15  C14  C13  118.52  3.000
 MXJ  CL1  C16  C18  121.45  3.000
 MXJ  CL1  C16  C14  120.09  3.000
 MXJ  C18  C16  C14  118.46  3.000
 MXJ  H12  C18  C19  119.85  3.000
 MXJ  H12  C18  C16  119.96  3.000
 MXJ  C19  C18  C16  120.19  3.000
 MXJ  H13  C19  C18  119.03  3.000
 MXJ  H13  C19  C12  120.08  3.000
 MXJ  C18  C19  C12  120.89  3.000
 MXJ  H15  C20  H14  107.27  3.000
 MXJ  H15  C20  C21  108.46  3.000
 MXJ  H14  C20  C21  110.10  3.000
 MXJ  H15  C20  C08  109.51  3.000
 MXJ  H14  C20  C08  109.96  3.000
 MXJ  C21  C20  C08  111.44  3.000
 MXJ  H16  C21  N23  112.80  3.000
 MXJ  H16  C21  C22  107.69  3.000
 MXJ  N23  C21  C22  109.05  3.000
 MXJ  H16  C21  C20  108.43  3.000
 MXJ  C22  C21  C20  109.38  3.000
 MXJ  N23  C21  C20  109.43  3.000
 MXJ  H18  C22  H17  107.51  3.000
 MXJ  H18  C22  N06  108.21  3.000
 MXJ  H17  C22  N06  109.94  3.000
 MXJ  H18  C22  C21  108.94  3.000
 MXJ  H17  C22  C21  111.14  3.000
 MXJ  N06  C22  C21  110.98  3.000
 MXJ  H19  N04  C05  118.98  3.000
 MXJ  H19  N04  C03  114.99  3.000
 MXJ  C05  N04  C03  120.91  3.000
 MXJ  C22  N06  C07  111.88  3.000
 MXJ  C07  N06  C05  123.61  3.000
 MXJ  C22  N06  C05  118.34  3.000
 MXJ  H20  N11  C12  114.83  3.000
 MXJ  H20  N11  C09  115.91  3.000
 MXJ  C12  N11  C09  129.25  3.000
 MXJ  H22  N23  H21  105.55  3.000
 MXJ  H22  N23  C21  109.44  3.000
 MXJ  H21  N23  C21  109.55  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
 MXJ  CONST_01  C16  C14  C13  C12     0.00   0.0  0
 MXJ  CONST_02  C16  C18  C19  C12     0.00   0.0  0
 MXJ  CONST_03  C18  C19  C12  C13     0.00   0.0  0
 MXJ  CONST_04  C18  C16  C14  C13     0.00   0.0  0
 MXJ  CONST_05  C19  C12  C13  C14     0.00   0.0  0
 MXJ  CONST_06  C19  C18  C16  C14     0.00   0.0  0
 MXJ  CONST_07  F15  C14  C13  C12   180.00   0.0  0
 MXJ  CONST_08  CL1  C16  C14  C13   180.00   0.0  0
 MXJ  CONST_09  N11  C12  C13  C14   180.00   0.0  0
 MXJ  CONST_10  N11  C12  C19  C18   180.00   0.0  0
 MXJ  CONST_11  F15  C14  C16  C18   180.00   0.0  0
 MXJ  CONST_12  CL1  C16  C18  C19   180.00   0.0  0
 MXJ  CONST_13  H12  C18  C19  C12   180.00   0.0  0
 MXJ  CONST_14  H13  C19  C12  C13   180.00   0.0  0
 MXJ  CONST_15  H11  C13  C14  C16   180.00   0.0  0
 MXJ  CONST_17  C12  N11  C09  C08   180.00   0.0  0
 MXJ  CONST_18  O24  C05  N06  C22     0.00   0.0  0
 MXJ  CONST_19  C13  C12  N11  C09     0.00   0.0  0
 MXJ  CONST_20  C19  C12  N11  C09   180.00   0.0  0
 MXJ  CONST_22  N04  C05  N06  C22   180.00   0.0  0
 MXJ  CONST_23  H20  N11  C12  C13   180.00   0.0  0
 MXJ  CONST_24  O10  C09  N11  C12     0.00   0.0  0
 MXJ  CONST_25  N06  C05  N04  C03   180.00   0.0  0
 MXJ  CONST_27  O24  C05  N04  C03     0.00   0.0  0
 MXJ  Var_01    C21  C22  N06  C07   -61.37  30.0  1
 MXJ  Var_02    C22  N06  C07  C08    60.86  30.0  1
 MXJ  Var_03    N04  C03  C02  C01  -178.00  30.0  3
 MXJ  Var_04    C05  N04  C03  C02  -169.70  30.0  3
 MXJ  Var_05    H1   C01  C02  C03   179.77  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
 MXJ  chir_01  C08  C20  C07  C09  negativ
 MXJ  chir_02  C21  N23  C20  C22  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
 MXJ  plan-1  C12  0.020
 MXJ  plan-1  C13  0.020
 MXJ  plan-1  C14  0.020
 MXJ  plan-1  C16  0.020
 MXJ  plan-1  C18  0.020
 MXJ  plan-1  C19  0.020
 MXJ  plan-1  F15  0.020
 MXJ  plan-1  N11  0.020
 MXJ  plan-1  CL1  0.020
 MXJ  plan-1  H11  0.020
 MXJ  plan-1  H12  0.020
 MXJ  plan-1  H13  0.020
 MXJ  plan-2  C03  0.020
 MXJ  plan-2  C05  0.020
 MXJ  plan-2  C07  0.020
 MXJ  plan-2  C22  0.020
 MXJ  plan-2  N04  0.020
 MXJ  plan-2  N06  0.020
 MXJ  plan-2  O24  0.020
 MXJ  plan-2  H19  0.020
 MXJ  plan-3  C08  0.020
 MXJ  plan-3  C09  0.020
 MXJ  plan-3  C12  0.020
 MXJ  plan-3  N11  0.020
 MXJ  plan-3  O10  0.020
 MXJ  plan-3  H20  0.020

