# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 22:01:33 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: (3R)-N-(4-chlorophenyl)-5,5-difluoro-1-[3-fluoro-5-(pyridin-4-yl)benzene-1-carbonyl]piperidine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cc(cc(c1)c2ccncc2)C(=O)N3C[C@@H](CC(F)(F)C3)C(=O)Nc4ccc(Cl)cc4
#
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
 K8M  K8M  (3R)-N-(4-chlorophenyl)-5,5-difluoro-1-[3-fluoro-5-(pyridin-4-yl)benzene-1-carbonyl]piperidine-3-carboxamide  ligand  52  33  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_K8M
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
 K8M  C10   C   CR16  0  -0.351  -5.2885   2.0452  -0.1229
 K8M  C17   C   CR16  0  -0.430   3.4448  -1.5475   1.8580
 K8M  C20   C   CR16  0  -0.471   5.5692  -0.6188   1.1625
 K8M  C21   C   CR6   0   0.130   4.9122   0.4511   0.5566
 K8M  C22   C   CR6   0   0.172   5.6852   1.4966  -0.1403
 K8M  C24   C   CR16  0  -0.059   6.0489   3.7731  -0.7920
 K8M  C26   C   CR16  0  -0.058   7.5371   2.2091  -1.4834
 K8M  C28   C   CR16  0  -0.345   3.5222   0.5202   0.6178
 K8M  C02   C   C     0   0.584  -3.0315  -0.8668  -0.1036
 K8M  C04   C   CR6   0   0.383  -4.9755   0.6847  -0.0719
 K8M  C05   C   CR16  0  -0.317  -6.0112  -0.2399   0.0655
 K8M  C06   C   CR16  0  -0.200  -7.3252   0.1983   0.1491
 K8M  C07   C   CR6   0  -0.057  -7.6156   1.5501   0.0963
 K8M  C09   C   CR16  0  -0.200  -6.5977   2.4811  -0.0402
 K8M  C11   C   CH1   0  -0.449  -1.5181  -0.8342  -0.2297
 K8M  C12   C   CH2   0  -0.305  -0.8893  -1.3284   1.0807
 K8M  C16   C   CR6   0  -0.041   2.7955  -0.4790   1.2503
 K8M  C18   C   CR6   0   0.577   4.8235  -1.5856   1.8041
 K8M  C23   C   CR16  0  -0.376   5.2853   2.8307  -0.1221
 K8M  C27   C   CR16  0  -0.374   6.8463   1.1909  -0.8462
 K8M  C29   C   CH2   0  -0.448   0.9873  -2.3351  -0.0639
 K8M  C30   C   CT    0   0.772   0.4276  -1.8824  -1.4029
 K8M  C33   C   CH2   0  -0.558  -1.0747  -1.7298  -1.3923
 K8M  F19   F   F     0  -0.307   5.4621  -2.5996   2.4016
 K8M  F31   F   F     0  -0.339   0.8074  -2.7660  -2.3685
 K8M  F32   F   F     0  -0.347   1.0155  -0.6880  -1.7310
 K8M  N03   N   NH1   0  -0.744  -3.6221   0.3495  -0.1702
 K8M  N13   N   NT    0  -0.463   0.5560  -1.3970   0.9525
 K8M  N25   N   N     0  -0.404   7.1567   3.4811  -1.4636
 K8M  O01   O   O     0  -0.460  -3.6297  -1.9154   0.0563
 K8M  O15   O   O     0  -0.458   0.8287   0.6764   1.8227
 K8M  CL08  CL  CL    0  -0.132  -9.2613   2.0843   0.2002
 K8M  H1    H   HCR6  0   0.283  -4.4981   2.7789  -0.2266
 K8M  H2    H   HCR6  0   0.296   2.8956  -2.3285   2.3685
 K8M  H3    H   HCR6  0   0.288   6.6494  -0.6912   1.1557
 K8M  H4    H   HCR6  0   0.268   5.7489   4.8149  -0.7785
 K8M  H5    H   HCR6  0   0.268   8.4395   1.9803  -2.0392
 K8M  H6    H   HCR6  0   0.272   2.9999   1.3410   0.1440
 K8M  H7    H   HCR6  0   0.291  -5.8160  -1.2982   0.1074
 K8M  H8    H   HCR6  0   0.283  -8.1188  -0.5289   0.2536
 K8M  H9    H   HCR6  0   0.284  -6.8151   3.5396  -0.0814
 K8M  H10   H   HCH1  0   0.294  -1.1794   0.1896  -0.4109
 K8M  H11   H   HCH2  0   0.292  -1.1530  -0.6784   1.9112
 K8M  H12   H   HCH2  0   0.276  -1.2510  -2.3332   1.3107
 K8M  H13   H   HCR6  0   0.274   4.4036   3.1484   0.4182
 K8M  H14   H   HCR6  0   0.273   7.2062   0.1737  -0.9233
 K8M  H15   H   HCH2  0   0.292   0.6030  -3.3292   0.1738
 K8M  H16   H   HCH2  0   0.312   2.0717  -2.4031  -0.1199
 K8M  H17   H   HCH2  0   0.275  -1.5095  -2.7246  -1.2726
 K8M  H18   H   HCH2  0   0.295  -1.4173  -1.3287  -2.3485
 K8M  H19   H   HNH1  0   0.423  -3.0030   1.1346  -0.3026
 K8M  C14   C   C     0   0.534   1.3088  -0.3383   1.3493

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
 K8M  CL08  C07  single    1.733  0.020  1.733
 K8M  C07   C06  aromatic  1.384  0.020  1.384
 K8M  C07   C09  aromatic  1.386  0.020  1.386
 K8M  C06   C05  aromatic  1.388  0.020  1.388
 K8M  C09   C10  aromatic  1.382  0.020  1.382
 K8M  C05   C04  aromatic  1.395  0.020  1.395
 K8M  C10   C04  aromatic  1.397  0.020  1.397
 K8M  C04   N03  single    1.398  0.020  1.398
 K8M  N03   C02  single    1.354  0.020  1.354
 K8M  C02   O01  double    1.218  0.020  1.218
 K8M  C02   C11  single    1.519  0.020  1.519
 K8M  O15   C14  double    1.218  0.020  1.218
 K8M  C12   C11  single    1.535  0.020  1.535
 K8M  C12   N13  single    1.453  0.020  1.453
 K8M  C11   C33  single    1.533  0.020  1.533
 K8M  C14   N13  single    1.358  0.020  1.358
 K8M  C14   C16  single    1.497  0.020  1.497
 K8M  N13   C29  single    1.449  0.020  1.449
 K8M  C16   C17  aromatic  1.390  0.020  1.390
 K8M  C16   C28  aromatic  1.388  0.020  1.388
 K8M  C17   C18  aromatic  1.380  0.020  1.380
 K8M  C28   C21  aromatic  1.393  0.020  1.393
 K8M  C33   C30  single    1.510  0.020  1.510
 K8M  C29   C30  single    1.520  0.020  1.520
 K8M  C18   F19  single    1.339  0.020  1.339
 K8M  C18   C20  aromatic  1.379  0.020  1.379
 K8M  C21   C20  aromatic  1.394  0.020  1.394
 K8M  C21   C22  single    1.475  0.020  1.475
 K8M  C30   F31  single    1.363  0.020  1.363
 K8M  C30   F32  single    1.371  0.020  1.371
 K8M  C23   C22  aromatic  1.393  0.020  1.393
 K8M  C23   C24  aromatic  1.386  0.020  1.386
 K8M  C22   C27  aromatic  1.393  0.020  1.393
 K8M  C24   N25  aromatic  1.328  0.020  1.328
 K8M  C27   C26  aromatic  1.386  0.020  1.386
 K8M  N25   C26  aromatic  1.328  0.020  1.328
 K8M  C10   H1   single    0.930  0.020  1.080
 K8M  C17   H2   single    0.930  0.020  1.080
 K8M  C20   H3   single    0.930  0.020  1.080
 K8M  C24   H4   single    0.930  0.020  1.080
 K8M  C26   H5   single    0.930  0.020  1.080
 K8M  C28   H6   single    0.930  0.020  1.080
 K8M  C05   H7   single    0.930  0.020  1.080
 K8M  C06   H8   single    0.930  0.020  1.080
 K8M  C09   H9   single    0.930  0.020  1.080
 K8M  C11   H10  single    0.970  0.020  1.090
 K8M  C12   H11  single    0.970  0.020  1.090
 K8M  C12   H12  single    0.970  0.020  1.090
 K8M  C23   H13  single    0.930  0.020  1.080
 K8M  C27   H14  single    0.930  0.020  1.080
 K8M  C29   H15  single    0.970  0.020  1.090
 K8M  C29   H16  single    0.970  0.020  1.090
 K8M  C33   H17  single    0.970  0.020  1.090
 K8M  C33   H18  single    0.970  0.020  1.090
 K8M  N03   H19  single    0.860  0.020  1.020

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
 K8M  H1    C10  C09  118.89  3.000
 K8M  H1    C10  C04  119.98  3.000
 K8M  C09   C10  C04  121.14  3.000
 K8M  H2    C17  C18  120.35  3.000
 K8M  H2    C17  C16  121.58  3.000
 K8M  C18   C17  C16  118.07  3.000
 K8M  H3    C20  C18  119.70  3.000
 K8M  H3    C20  C21  121.25  3.000
 K8M  C18   C20  C21  119.03  3.000
 K8M  C28   C21  C22  120.56  3.000
 K8M  C22   C21  C20  120.15  3.000
 K8M  C28   C21  C20  119.29  3.000
 K8M  C27   C22  C23  117.14  3.000
 K8M  C27   C22  C21  121.38  3.000
 K8M  C23   C22  C21  121.48  3.000
 K8M  H4    C24  N25  116.64  3.000
 K8M  H4    C24  C23  119.66  3.000
 K8M  N25   C24  C23  123.69  3.000
 K8M  H5    C26  N25  116.63  3.000
 K8M  H5    C26  C27  119.71  3.000
 K8M  N25   C26  C27  123.66  3.000
 K8M  H6    C28  C16  119.53  3.000
 K8M  H6    C28  C21  120.00  3.000
 K8M  C16   C28  C21  120.45  3.000
 K8M  O01   C02  N03  124.46  3.000
 K8M  O01   C02  C11  121.25  3.000
 K8M  N03   C02  C11  114.29  3.000
 K8M  N03   C04  C05  124.52  3.000
 K8M  N03   C04  C10  116.61  3.000
 K8M  C05   C04  C10  118.87  3.000
 K8M  H7    C05  C06  118.65  3.000
 K8M  H7    C05  C04  121.37  3.000
 K8M  C06   C05  C04  119.97  3.000
 K8M  H8    C06  C07  120.44  3.000
 K8M  H8    C06  C05  119.24  3.000
 K8M  C07   C06  C05  120.33  3.000
 K8M  CL08  C07  C09  119.74  3.000
 K8M  C09   C07  C06  120.39  3.000
 K8M  CL08  C07  C06  119.87  3.000
 K8M  H9    C09  C07  120.90  3.000
 K8M  H9    C09  C10  119.79  3.000
 K8M  C07   C09  C10  119.31  3.000
 K8M  H10   C11  C33  109.37  3.000
 K8M  H10   C11  C12  108.42  3.000
 K8M  C33   C11  C12  109.92  3.000
 K8M  H10   C11  C02  110.03  3.000
 K8M  C33   C11  C02  109.79  3.000
 K8M  C12   C11  C02  109.29  3.000
 K8M  H12   C12  H11  107.98  3.000
 K8M  H12   C12  N13  107.74  3.000
 K8M  H11   C12  N13  109.70  3.000
 K8M  H12   C12  C11  109.89  3.000
 K8M  H11   C12  C11  111.11  3.000
 K8M  N13   C12  C11  110.33  3.000
 K8M  C14   C16  C28  118.85  3.000
 K8M  C28   C16  C17  120.53  3.000
 K8M  C14   C16  C17  120.48  3.000
 K8M  F19   C18  C20  118.72  3.000
 K8M  C20   C18  C17  122.61  3.000
 K8M  F19   C18  C17  118.68  3.000
 K8M  H13   C23  C24  119.40  3.000
 K8M  H13   C23  C22  121.45  3.000
 K8M  C24   C23  C22  119.13  3.000
 K8M  H14   C27  C26  119.49  3.000
 K8M  H14   C27  C22  121.32  3.000
 K8M  C26   C27  C22  119.17  3.000
 K8M  H16   C29  H15  107.76  3.000
 K8M  H16   C29  N13  111.92  3.000
 K8M  H15   C29  N13  109.39  3.000
 K8M  H16   C29  C30  109.89  3.000
 K8M  H15   C29  C30  109.47  3.000
 K8M  N13   C29  C30  108.39  3.000
 K8M  F32   C30  F31  106.01  3.000
 K8M  F32   C30  C33  109.89  3.000
 K8M  F31   C30  C33  110.35  3.000
 K8M  F32   C30  C29  108.20  3.000
 K8M  F31   C30  C29  109.17  3.000
 K8M  C33   C30  C29  112.96  3.000
 K8M  H18   C33  H17  107.79  3.000
 K8M  H18   C33  C30  110.07  3.000
 K8M  H17   C33  C30  107.74  3.000
 K8M  H18   C33  C11  111.02  3.000
 K8M  H17   C33  C11  109.50  3.000
 K8M  C30   C33  C11  110.62  3.000
 K8M  H19   N03  C04  114.64  3.000
 K8M  H19   N03  C02  115.98  3.000
 K8M  C04   N03  C02  129.38  3.000
 K8M  C29   N13  C14  123.00  3.000
 K8M  C29   N13  C12  112.87  3.000
 K8M  C14   N13  C12  119.27  3.000
 K8M  C26   N25  C24  117.20  3.000
 K8M  O15   C14  N13  122.98  3.000
 K8M  N13   C14  C16  117.26  3.000
 K8M  O15   C14  C16  119.70  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
 K8M  CONST_01  C06   C07  C09  C10    0.00   0.0  0
 K8M  CONST_02  C06   C05  C04  C10    0.00   0.0  0
 K8M  CONST_03  C21   C28  C16  C17    0.00   0.0  0
 K8M  CONST_04  C21   C20  C18  C17    0.00   0.0  0
 K8M  CONST_05  C16   C17  C18  C20    0.00   0.0  0
 K8M  CONST_06  C16   C28  C21  C20    0.00   0.0  0
 K8M  CONST_09  C24   C23  C22  C21  180.00   0.0  0
 K8M  CONST_10  C26   C27  C22  C21  180.00   0.0  0
 K8M  CONST_11  C16   C28  C21  C22  180.00   0.0  0
 K8M  CONST_12  C18   C20  C21  C22  180.00   0.0  0
 K8M  CONST_13  N25   C24  C23  C22    0.00   0.0  0
 K8M  CONST_14  N25   C26  C27  C22    0.00   0.0  0
 K8M  CONST_15  C27   C22  C23  C24    0.00   0.0  0
 K8M  CONST_16  C27   C26  N25  C24    0.00   0.0  0
 K8M  CONST_17  C23   C22  C27  C26    0.00   0.0  0
 K8M  CONST_18  C23   C24  N25  C26    0.00   0.0  0
 K8M  CONST_19  C18   C17  C16  C28    0.00   0.0  0
 K8M  CONST_20  C18   C20  C21  C28    0.00   0.0  0
 K8M  CONST_23  C07   C06  C05  C04    0.00   0.0  0
 K8M  CONST_24  C07   C09  C10  C04    0.00   0.0  0
 K8M  CONST_25  C09   C07  C06  C05    0.00   0.0  0
 K8M  CONST_26  C09   C10  C04  C05    0.00   0.0  0
 K8M  CONST_27  CL08  C07  C09  C10  180.00   0.0  0
 K8M  CONST_28  C14   C16  C28  C21  180.00   0.0  0
 K8M  CONST_29  F19   C18  C20  C21  180.00   0.0  0
 K8M  CONST_30  CL08  C07  C06  C05  180.00   0.0  0
 K8M  CONST_31  N03   C04  C05  C06  180.00   0.0  0
 K8M  CONST_32  N03   C04  C10  C09  180.00   0.0  0
 K8M  CONST_33  C18   C17  C16  C14  180.00   0.0  0
 K8M  CONST_34  F19   C18  C17  C16  180.00   0.0  0
 K8M  CONST_35  C16   C14  N13  C12  180.00   0.0  0
 K8M  CONST_37  H7    C05  C04  C10  180.00   0.0  0
 K8M  CONST_38  H6    C28  C16  C17  180.00   0.0  0
 K8M  CONST_39  H3    C20  C18  C17  180.00   0.0  0
 K8M  CONST_40  H2    C17  C18  C20  180.00   0.0  0
 K8M  CONST_41  H13   C23  C22  C21    0.00   0.0  0
 K8M  CONST_42  H14   C27  C22  C21    0.00   0.0  0
 K8M  CONST_43  H4    C24  C23  C22  180.00   0.0  0
 K8M  CONST_44  H5    C26  C27  C22  180.00   0.0  0
 K8M  CONST_45  H8    C06  C05  C04  180.00   0.0  0
 K8M  CONST_46  H9    C09  C10  C04  180.00   0.0  0
 K8M  CONST_47  H1    C10  C04  C05  180.00   0.0  0
 K8M  CONST_48  C11   C02  N03  C04  180.00   0.0  0
 K8M  CONST_49  O15   C14  N13  C12    0.00   0.0  0
 K8M  CONST_51  C02   N03  C04  C10  180.00   0.0  0
 K8M  CONST_52  C05   C04  N03  C02    0.00   0.0  0
 K8M  CONST_53  H19   N03  C04  C10    0.00   0.0  0
 K8M  CONST_54  O01   C02  N03  C04    0.00   0.0  0
 K8M  Var_01    C29   N13  C12  C11  -62.16  30.0  1
 K8M  Var_02    C29   C30  C33  C11   52.48  30.0  1
 K8M  Var_03    C30   C29  N13  C12   60.90  30.0  1
 K8M  Var_04    N13   C29  C30  C33  -55.92  30.0  1
 K8M  Var_05    N13   C14  C16  C17  -54.50  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
 K8M  chir_01  C11  C02  C12  C33  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
 K8M  plan-1  C10   0.020
 K8M  plan-1  C04   0.020
 K8M  plan-1  C05   0.020
 K8M  plan-1  C06   0.020
 K8M  plan-1  C07   0.020
 K8M  plan-1  C09   0.020
 K8M  plan-1  N03   0.020
 K8M  plan-1  CL08  0.020
 K8M  plan-1  H1    0.020
 K8M  plan-1  H7    0.020
 K8M  plan-1  H8    0.020
 K8M  plan-1  H9    0.020
 K8M  plan-2  C17   0.020
 K8M  plan-2  C20   0.020
 K8M  plan-2  C21   0.020
 K8M  plan-2  C22   0.020
 K8M  plan-2  C28   0.020
 K8M  plan-2  C16   0.020
 K8M  plan-2  C18   0.020
 K8M  plan-2  F19   0.020
 K8M  plan-2  H2    0.020
 K8M  plan-2  H3    0.020
 K8M  plan-2  H6    0.020
 K8M  plan-2  C14   0.020
 K8M  plan-3  C21   0.020
 K8M  plan-3  C22   0.020
 K8M  plan-3  C24   0.020
 K8M  plan-3  C26   0.020
 K8M  plan-3  C23   0.020
 K8M  plan-3  C27   0.020
 K8M  plan-3  N25   0.020
 K8M  plan-3  H4    0.020
 K8M  plan-3  H5    0.020
 K8M  plan-3  H13   0.020
 K8M  plan-3  H14   0.020
 K8M  plan-4  C12   0.020
 K8M  plan-4  C16   0.020
 K8M  plan-4  C29   0.020
 K8M  plan-4  N13   0.020
 K8M  plan-4  O15   0.020
 K8M  plan-4  C14   0.020
 K8M  plan-5  C02   0.020
 K8M  plan-5  C04   0.020
 K8M  plan-5  C11   0.020
 K8M  plan-5  N03   0.020
 K8M  plan-5  O01   0.020
 K8M  plan-5  H19   0.020

