# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 02:12:16 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: 2-(3-chlorophenoxy)-3-fluoro-4-{[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]methyl}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@H]2CCCN(C2)Cc3ccc(C(O)=O)c(Oc4cccc(Cl)c4)c3F)C(=O)NC1=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
 31Z  31Z  '2-(3-chlorophenoxy)-3-fluoro-4-{[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]methyl}benzoic acid'  ligand  56  34  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_31Z
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
 31Z  C1   C   CH3    0  -0.707   8.2070  -2.4897   0.7119
 31Z  C2   C   CR6    0  -0.180   7.4913  -1.2735   0.2232
 31Z  C3   C   CR16   0   0.055   6.2254  -0.9771   0.5680
 31Z  N4   N   NR6    0  -0.549   5.5360   0.1284   0.1424
 31Z  C5   C   CR6    0   0.737   6.1297   1.0339  -0.7037
 31Z  O6   O   O      0  -0.484   5.5794   2.0306  -1.1278
 31Z  N7   N   NR16   0  -0.731   7.4229   0.7295  -1.0494
 31Z  C8   C   CR6    0   0.554   8.1807  -0.3585  -0.6607
 31Z  O9   O   O      0  -0.460   9.3263  -0.4923  -1.0544
 31Z  C10  C   CH1    0  -0.090   4.1612   0.3290   0.6264
 31Z  C11  C   CH2    0  -0.440   3.9862   1.5789   1.4794
 31Z  C12  C   CH2    0  -0.448   2.5508   1.6226   1.9934
 31Z  C13  C   CH2    0  -0.291   1.5557   1.4781   0.8534
 31Z  N14  N   NT     0  -0.432   1.8017   0.2535   0.1093
 31Z  C15  C   CH2    0  -0.269   3.1230   0.2558  -0.4913
 31Z  C16  C   CH2    0  -0.291   0.7607  -0.0177  -0.8555
 31Z  C17  C   CR6    0  -0.161  -0.4907  -0.5604  -0.2091
 31Z  C18  C   CR16   0  -0.272  -0.4897  -1.1366   1.0569
 31Z  C19  C   CR16   0  -0.305  -1.6529  -1.6412   1.6141
 31Z  C20  C   CR6    0  -0.139  -2.8660  -1.6339   0.9298
 31Z  C21  C   CR6    0   0.148  -2.8704  -1.0703  -0.3451
 31Z  C22  C   CR6    0   0.486  -1.7037  -0.5338  -0.8734
 31Z  F23  F   F      0  -0.305  -1.7678   0.0234  -2.0945
 31Z  O24  O   O2     0  -0.500  -3.9784  -1.0087  -1.1418
 31Z  C25  C   C      0   0.403  -5.0205  -0.2233  -0.7761
 31Z  C26  C   C1     0  -0.333  -4.9223   0.7990   0.1601
 31Z  C27  C   C1     0  -0.253  -6.0399   1.5760   0.4315
 31Z  C28  C   C1     0  -0.239  -7.2478   1.3585  -0.2133
 31Z  C29  C   C      0  -0.031  -7.3114   0.3350  -1.1477
 31Z  C30  C   C1     0  -0.297  -6.2203  -0.4630  -1.4374
 31Z  CL   CL  CL     0  -0.130  -8.8064   0.0357  -1.9755
 31Z  C32  C   C      0   0.402  -4.0987  -2.2626   1.5785
 31Z  O33  O   O      0  -0.575  -4.9629  -2.7232   0.8151
 31Z  O34  O   OC    -1  -0.589  -4.1043  -2.2730   2.8231
 31Z  H1   H   HCH3   0   0.246   8.5314  -3.1205  -0.1170
 31Z  H2   H   HCH3   0   0.246   9.0988  -2.2242   1.2814
 31Z  H3   H   HCH3   0   0.246   7.5634  -3.0870   1.3555
 31Z  H4   H   HCR6   0   0.311   5.6690  -1.6290   1.2275
 31Z  H5   H   HNR6   0   0.423   7.8664   1.3933  -1.6725
 31Z  H6   H   HCH1   0   0.261   3.9692  -0.5298   1.2728
 31Z  H7   H   HCH2   0   0.247   4.6930   1.5621   2.3121
 31Z  H8   H   HCH2   0   0.240   4.1917   2.4754   0.8938
 31Z  H9   H   HCH2   0   0.227   2.3871   0.8163   2.7143
 31Z  H10  H   HCH2   0   0.241   2.3721   2.5630   2.5173
 31Z  H11  H   HCH2   0   0.246   0.5411   1.4511   1.2555
 31Z  H12  H   HCH2   0   0.203   1.6106   2.3615   0.1933
 31Z  H14  H   HCH2   0   0.217   3.2534   1.0861  -1.1990
 31Z  H15  H   HCH2   0   0.248   3.2599  -0.6752  -1.0469
 31Z  H16  H   HCH2   0   0.225   0.5207   0.8699  -1.4603
 31Z  H17  H   HCH2   0   0.265   1.1306  -0.7667  -1.5623
 31Z  H18  H   HCR6   0   0.257   0.4404  -1.1756   1.6087
 31Z  H19  H   HCR6   0   0.251  -1.6231  -2.0666   2.6079
 31Z  H20  H   H      0   0.281  -3.9931   0.9995   0.6766
 31Z  H21  H   H      0   0.271  -5.9645   2.3716   1.1605
 31Z  H22  H   H      0   0.276  -8.1123   1.9703   0.0029
 31Z  H23  H   H      0   0.286  -6.2896  -1.2606  -2.1648

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
 31Z  C12  C11  single    1.525  0.020  1.525
 31Z  C12  C13  single    1.520  0.020  1.520
 31Z  C11  C10  single    1.523  0.020  1.523
 31Z  C10  N4   single    1.471  0.020  1.471
 31Z  C10  C15  single    1.527  0.020  1.527
 31Z  O6   C5   double    1.215  0.020  1.215
 31Z  C5   N7   single    1.373  0.020  1.373
 31Z  C5   N4   single    1.374  0.020  1.374
 31Z  N7   C8   single    1.382  0.020  1.382
 31Z  N4   C3   single    1.371  0.020  1.371
 31Z  C8   O9   double    1.219  0.020  1.219
 31Z  C8   C2   single    1.447  0.020  1.447
 31Z  C3   C2   double    1.345  0.020  1.345
 31Z  C2   C1   single    1.493  0.020  1.493
 31Z  C13  N14  single    1.454  0.020  1.454
 31Z  N14  C15  single    1.451  0.020  1.451
 31Z  N14  C16  single    1.445  0.020  1.445
 31Z  C16  C17  single    1.509  0.020  1.509
 31Z  C18  C17  aromatic  1.391  0.020  1.391
 31Z  C18  C19  aromatic  1.385  0.020  1.385
 31Z  C17  C22  aromatic  1.383  0.020  1.383
 31Z  C27  C26  aromatic  1.388  0.020  1.388
 31Z  C27  C28  aromatic  1.386  0.020  1.386
 31Z  C19  C20  aromatic  1.393  0.020  1.393
 31Z  C22  F23  single    1.344  0.020  1.344
 31Z  C22  C21  aromatic  1.388  0.020  1.388
 31Z  C26  C25  aromatic  1.390  0.020  1.390
 31Z  C28  C29  aromatic  1.387  0.020  1.387
 31Z  C20  C21  aromatic  1.394  0.020  1.394
 31Z  C20  C32  single    1.528  0.020  1.528
 31Z  C21  O24  single    1.366  0.020  1.366
 31Z  C25  O24  single    1.355  0.020  1.355
 31Z  C25  C30  aromatic  1.391  0.020  1.391
 31Z  O33  C32  deloc     1.242  0.020  1.242
 31Z  C32  O34  deloc     1.245  0.020  1.245
 31Z  C29  C30  aromatic  1.382  0.020  1.382
 31Z  C29  CL   single    1.735  0.020  1.735
 31Z  C1   H1   single    0.970  0.020  1.090
 31Z  C1   H2   single    0.970  0.020  1.090
 31Z  C1   H3   single    0.970  0.020  1.090
 31Z  C3   H4   single    0.930  0.020  1.080
 31Z  N7   H5   single    0.860  0.020  1.020
 31Z  C10  H6   single    0.970  0.020  1.090
 31Z  C11  H7   single    0.970  0.020  1.090
 31Z  C11  H8   single    0.970  0.020  1.090
 31Z  C12  H9   single    0.970  0.020  1.090
 31Z  C12  H10  single    0.970  0.020  1.090
 31Z  C13  H11  single    0.970  0.020  1.090
 31Z  C13  H12  single    0.970  0.020  1.090
 31Z  C15  H14  single    0.970  0.020  1.090
 31Z  C15  H15  single    0.970  0.020  1.090
 31Z  C16  H16  single    0.970  0.020  1.090
 31Z  C16  H17  single    0.970  0.020  1.090
 31Z  C18  H18  single    0.930  0.020  1.080
 31Z  C19  H19  single    0.930  0.020  1.080
 31Z  C26  H20  single    0.930  0.020  1.080
 31Z  C27  H21  single    0.930  0.020  1.080
 31Z  C28  H22  single    0.930  0.020  1.080
 31Z  C30  H23  single    0.930  0.020  1.080

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
 31Z  H3   C1   H2   107.95  3.000
 31Z  H3   C1   H1   107.92  3.000
 31Z  H2   C1   H1   107.11  3.000
 31Z  H3   C1   C2   110.91  3.000
 31Z  H2   C1   C2   111.37  3.000
 31Z  H1   C1   C2   111.39  3.000
 31Z  C8   C2   C3   117.76  3.000
 31Z  C3   C2   C1   123.13  3.000
 31Z  C8   C2   C1   119.11  3.000
 31Z  H4   C3   N4   114.63  3.000
 31Z  H4   C3   C2   120.51  3.000
 31Z  N4   C3   C2   124.85  3.000
 31Z  C10  N4   C5   121.09  3.000
 31Z  C5   N4   C3   120.36  3.000
 31Z  C10  N4   C3   118.54  3.000
 31Z  N7   C5   O6   121.38  3.000
 31Z  N7   C5   N4   114.58  3.000
 31Z  O6   C5   N4   124.05  3.000
 31Z  H5   N7   C8   116.68  3.000
 31Z  H5   N7   C5   114.97  3.000
 31Z  C8   N7   C5   128.35  3.000
 31Z  O9   C8   N7   120.74  3.000
 31Z  O9   C8   C2   125.15  3.000
 31Z  N7   C8   C2   114.11  3.000
 31Z  H6   C10  C15  106.03  3.000
 31Z  H6   C10  C11  107.08  3.000
 31Z  C15  C10  C11  111.78  3.000
 31Z  H6   C10  N4   104.58  3.000
 31Z  C15  C10  N4   112.83  3.000
 31Z  C11  C10  N4   113.79  3.000
 31Z  H8   C11  H7   107.47  3.000
 31Z  H8   C11  C12  109.56  3.000
 31Z  H7   C11  C12  110.64  3.000
 31Z  H8   C11  C10  110.63  3.000
 31Z  H7   C11  C10  109.87  3.000
 31Z  C12  C11  C10  108.68  3.000
 31Z  H10  C12  H9   107.11  3.000
 31Z  H10  C12  C13  109.56  3.000
 31Z  H9   C12  C13  109.04  3.000
 31Z  H10  C12  C11  109.91  3.000
 31Z  H9   C12  C11  109.99  3.000
 31Z  C13  C12  C11  111.14  3.000
 31Z  H12  C13  H11  106.63  3.000
 31Z  H12  C13  N14  111.07  3.000
 31Z  H11  C13  N14  108.96  3.000
 31Z  H12  C13  C12  109.86  3.000
 31Z  H11  C13  C12  109.55  3.000
 31Z  N14  C13  C12  110.68  3.000
 31Z  C16  N14  C15  112.32  3.000
 31Z  C16  N14  C13  112.21  3.000
 31Z  C15  N14  C13  111.37  3.000
 31Z  H15  C15  H14  107.54  3.000
 31Z  H15  C15  N14  108.85  3.000
 31Z  H14  C15  N14  112.08  3.000
 31Z  H15  C15  C10  109.13  3.000
 31Z  H14  C15  C10  110.76  3.000
 31Z  N14  C15  C10  108.43  3.000
 31Z  H17  C16  H16  105.71  3.000
 31Z  H17  C16  C17  108.10  3.000
 31Z  H16  C16  C17  110.15  3.000
 31Z  H17  C16  N14  108.43  3.000
 31Z  H16  C16  N14  111.88  3.000
 31Z  C17  C16  N14  112.26  3.000
 31Z  C22  C17  C18  116.47  3.000
 31Z  C22  C17  C16  120.96  3.000
 31Z  C18  C17  C16  122.56  3.000
 31Z  H18  C18  C19  120.24  3.000
 31Z  H18  C18  C17  118.66  3.000
 31Z  C19  C18  C17  121.10  3.000
 31Z  H19  C19  C20  118.53  3.000
 31Z  H19  C19  C18  119.33  3.000
 31Z  C20  C19  C18  122.14  3.000
 31Z  C32  C20  C21  123.51  3.000
 31Z  C32  C20  C19  119.46  3.000
 31Z  C21  C20  C19  117.01  3.000
 31Z  O24  C21  C22  116.24  3.000
 31Z  O24  C21  C20  123.65  3.000
 31Z  C22  C21  C20  120.11  3.000
 31Z  F23  C22  C21  117.77  3.000
 31Z  C21  C22  C17  123.14  3.000
 31Z  F23  C22  C17  119.09  3.000
 31Z  C25  O24  C21  119.51  3.000
 31Z  C30  C25  C26  120.54  3.000
 31Z  C30  C25  O24  115.80  3.000
 31Z  C26  C25  O24  123.62  3.000
 31Z  H20  C26  C27  119.64  3.000
 31Z  H20  C26  C25  121.24  3.000
 31Z  C27  C26  C25  119.11  3.000
 31Z  H21  C27  C28  119.31  3.000
 31Z  H21  C27  C26  119.16  3.000
 31Z  C28  C27  C26  121.52  3.000
 31Z  H22  C28  C29  121.04  3.000
 31Z  H22  C28  C27  120.99  3.000
 31Z  C29  C28  C27  117.96  3.000
 31Z  CL   C29  C30  118.72  3.000
 31Z  CL   C29  C28  119.22  3.000
 31Z  C30  C29  C28  122.06  3.000
 31Z  H23  C30  C29  121.07  3.000
 31Z  H23  C30  C25  120.13  3.000
 31Z  C29  C30  C25  118.80  3.000
 31Z  O34  C32  O33  127.48  3.000
 31Z  O34  C32  C20  115.57  3.000
 31Z  O33  C32  C20  116.94  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
 31Z  CONST_01  C20  C19  C18  C17     0.00   0.0  0
 31Z  CONST_02  C20  C21  C22  C17     0.00   0.0  0
 31Z  CONST_03  C21  C22  C17  C18     0.00   0.0  0
 31Z  CONST_04  C21  C20  C19  C18     0.00   0.0  0
 31Z  CONST_05  C22  C17  C18  C19     0.00   0.0  0
 31Z  CONST_06  C22  C21  C20  C19     0.00   0.0  0
 31Z  CONST_07  C28  C27  C26  C25     0.00   0.0  0
 31Z  CONST_08  C28  C29  C30  C25     0.00   0.0  0
 31Z  CONST_09  C29  C28  C27  C26     0.00   0.0  0
 31Z  CONST_10  C29  C30  C25  C26     0.00   0.0  0
 31Z  CONST_11  C30  C25  C26  C27     0.00   0.0  0
 31Z  CONST_12  C30  C29  C28  C27     0.00   0.0  0
 31Z  CONST_13  C5   N7   C8   C2      0.00   0.0  0
 31Z  CONST_14  N7   C5   N4   C3      0.00   0.0  0
 31Z  CONST_15  C8   N7   C5   N4      0.00   0.0  0
 31Z  CONST_16  C10  N4   C5   N7    180.00   0.0  0
 31Z  CONST_17  C19  C18  C17  C16   180.00   0.0  0
 31Z  CONST_18  C21  C22  C17  C16   180.00   0.0  0
 31Z  CONST_19  O24  C21  C22  C17   180.00   0.0  0
 31Z  CONST_20  F23  C22  C17  C18   180.00   0.0  0
 31Z  CONST_21  C32  C20  C19  C18   180.00   0.0  0
 31Z  CONST_22  O24  C21  C20  C19   180.00   0.0  0
 31Z  CONST_23  F23  C22  C21  C20   180.00   0.0  0
 31Z  CONST_24  C32  C20  C21  C22   180.00   0.0  0
 31Z  CONST_25  C27  C26  C25  O24   180.00   0.0  0
 31Z  CONST_26  C29  C30  C25  O24   180.00   0.0  0
 31Z  CONST_27  CL   C29  C30  C25   180.00   0.0  0
 31Z  CONST_28  CL   C29  C28  C27   180.00   0.0  0
 31Z  CONST_29  O6   C5   N4   C3    180.00   0.0  0
 31Z  CONST_30  O9   C8   N7   C5    180.00   0.0  0
 31Z  CONST_31  C8   N7   C5   O6    180.00   0.0  0
 31Z  CONST_32  C10  N4   C5   O6      0.00   0.0  0
 31Z  CONST_33  H19  C19  C18  C17   180.00   0.0  0
 31Z  CONST_34  H18  C18  C19  C20   180.00   0.0  0
 31Z  CONST_35  H21  C27  C26  C25   180.00   0.0  0
 31Z  CONST_36  H22  C28  C27  C26   180.00   0.0  0
 31Z  CONST_37  H23  C30  C25  C26   180.00   0.0  0
 31Z  CONST_38  H20  C26  C27  C28   180.00   0.0  0
 31Z  CONST_39  H5   N7   C8   C2    180.00   0.0  0
 31Z  Var_01    C13  C12  C11  C10   -52.47  30.0  1
 31Z  Var_02    C13  N14  C15  C10    61.97  30.0  1
 31Z  Var_03    N14  C13  C12  C11    56.38  30.0  1
 31Z  Var_04    C15  N14  C13  C12   -61.59  30.0  1
 31Z  Var_05    C17  C16  N14  C13   -76.52  30.0  3
 31Z  Var_06    C18  C17  C16  N14   -19.72  30.0  2
 31Z  Var_07    C26  C25  O24  C21    17.87  30.0  2
 31Z  Var_08    O33  C32  C20  C19  -151.70  30.0  2
 31Z  Var_09    H1   C1   C2   C3    121.09  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
 31Z  chir_01  C10  C11  N4  C15  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
 31Z  plan-1  C1   0.020
 31Z  plan-1  C2   0.020
 31Z  plan-1  C3   0.020
 31Z  plan-1  N4   0.020
 31Z  plan-1  C5   0.020
 31Z  plan-1  O6   0.020
 31Z  plan-1  N7   0.020
 31Z  plan-1  C8   0.020
 31Z  plan-1  O9   0.020
 31Z  plan-1  C10  0.020
 31Z  plan-1  H4   0.020
 31Z  plan-1  H5   0.020
 31Z  plan-2  C16  0.020
 31Z  plan-2  C17  0.020
 31Z  plan-2  C18  0.020
 31Z  plan-2  C19  0.020
 31Z  plan-2  C20  0.020
 31Z  plan-2  C21  0.020
 31Z  plan-2  C22  0.020
 31Z  plan-2  F23  0.020
 31Z  plan-2  O24  0.020
 31Z  plan-2  C32  0.020
 31Z  plan-2  H18  0.020
 31Z  plan-2  H19  0.020
 31Z  plan-3  O24  0.020
 31Z  plan-3  C25  0.020
 31Z  plan-3  C26  0.020
 31Z  plan-3  C27  0.020
 31Z  plan-3  C28  0.020
 31Z  plan-3  C29  0.020
 31Z  plan-3  C30  0.020
 31Z  plan-3  CL   0.020
 31Z  plan-3  H20  0.020
 31Z  plan-3  H21  0.020
 31Z  plan-3  H22  0.020
 31Z  plan-3  H23  0.020
 31Z  plan-4  C20  0.020
 31Z  plan-4  C32  0.020
 31Z  plan-4  O33  0.020
 31Z  plan-4  O34  0.020

