# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 09:00:30 2021
#   Inital geometry file: a 144 line input string
#   Ligand name: (2~{S},3~{R},4~{S},5~{R})-~{N}-[5-(1-adamantylmethoxy)pentyl]-5-(hydroxymethyl)-3,4-bis(oxidanyl)pyrrolidine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1N[C@@H]([C@@H](O)[C@H]1O)C(=O)NCCCCCOCC23CC4CC(CC(C4)C2)C3
#
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
 KFE  KFE  (2~{S},3~{R},4~{S},5~{R})-~{N}-[5-(1-adamantylmethoxy)pentyl]-5-(hydroxymethyl)-3,4-bis(oxidanyl)pyrrolidine-2-carboxamide  ligand  67  29  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_KFE
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
 KFE  N1   N  NH1   0  -0.624  50.0132  -14.4906   -5.4161
 KFE  C2   C  CH2   0  -0.276  51.2432  -15.0223   -4.8695
 KFE  O2   O  O2    0  -0.491  53.8865  -19.7551   -7.1012
 KFE  C4   C  CH2   0  -0.442  52.9348  -16.8949   -4.8571
 KFE  O4   O  OH1   0  -0.673  45.7188  -13.4645   -7.8060
 KFE  C5   C  CH2   0  -0.468  53.2987  -18.3127   -5.2909
 KFE  C7   C  CH2   0  -0.094  53.9785  -19.9795   -8.4848
 KFE  C6   C  CH2   0  -0.122  53.5278  -18.4323   -6.7851
 KFE  O1   O  O     0  -0.493  50.9268  -13.5755   -7.2685
 KFE  C1   C  C     0   0.513  49.9448  -13.8496   -6.5904
 KFE  C3   C  CH2   0  -0.437  51.6266  -16.3798   -5.4477
 KFE  C8   C  CR6   0  -0.147  54.2842  -21.4384   -8.7843
 KFE  C9   C  C     0  -0.398  53.2117  -22.3679   -8.1996
 KFE  C10  C  C     0  -0.247  53.5105  -23.8229   -8.5702
 KFE  C11  C  C     0  -0.417  53.5233  -23.9706  -10.0931
 KFE  C12  C  CR16  0  -0.244  54.6045  -23.0631  -10.6844
 KFE  C13  C  C     0  -0.417  55.9710  -23.4606  -10.1218
 KFE  C14  C  C     0  -0.248  55.9572  -23.3107   -8.5994
 KFE  C15  C  C     0  -0.417  54.8777  -24.2204   -8.0086
 KFE  C16  C  C     0  -0.398  55.6548  -21.8547   -8.2329
 KFE  C17  C  CH2   0  -0.406  54.3031  -21.6112  -10.3101
 KFE  C18  C  CH1   0  -0.173  48.5327  -13.4851   -7.0271
 KFE  N2   N  NH1   0  -0.635  48.5099  -12.6272   -8.1951
 KFE  C19  C  CH1   0  -0.114  47.6461  -13.2215   -9.2210
 KFE  C20  C  CH2   0  -0.145  46.9345  -12.1321   -9.9987
 KFE  O3   O  OH1   0  -0.676  46.1424  -12.7349  -10.9958
 KFE  C21  C  CH1   0   0.001  46.7451  -14.1761   -8.4487
 KFE  C22  C  CH1   0  -0.017  47.7315  -14.7383   -7.4222
 KFE  O5   O  OH1   0  -0.660  47.1262  -15.3130   -6.2947
 KFE  H1   H  HNH1  0   0.398  49.1501  -14.7428   -4.9603
 KFE  H2   H  HCH2  0   0.247  51.1128  -15.0988   -3.7892
 KFE  H3   H  HCH2  0   0.238  52.0445  -14.3016   -5.0408
 KFE  H4   H  HCH2  0   0.220  53.7474  -16.2089   -5.1191
 KFE  H5   H  HCH2  0   0.230  52.8657  -16.8757   -3.7655
 KFE  H6   H  HOH1  0   0.445  45.4184  -13.9975   -7.0605
 KFE  H7   H  HCH2  0   0.221  52.5025  -19.0010   -4.9902
 KFE  H8   H  HCH2  0   0.232  54.2034  -18.6277   -4.7634
 KFE  H9   H  HCH2  0   0.193  54.7626  -19.3432   -8.9266
 KFE  H10  H  HCH2  0   0.193  53.0329  -19.7007   -8.9776
 KFE  H11  H  HCH2  0   0.189  54.3140  -17.7291   -7.1010
 KFE  H12  H  HCH2  0   0.194  52.6196  -18.1479   -7.3347
 KFE  H13  H  HCH2  0   0.230  51.7077  -16.2869   -6.5331
 KFE  H14  H  HCH2  0   0.220  50.8237  -17.0983   -5.2525
 KFE  H15  H  H     0   0.214  52.2249  -22.0783   -8.5798
 KFE  H16  H  H     0   0.224  53.1730  -22.2615   -7.1118
 KFE  H17  H  H     0   0.220  52.7359  -24.4688   -8.1454
 KFE  H18  H  H     0   0.220  53.7083  -25.0131  -10.3726
 KFE  H19  H  H     0   0.219  52.5442  -23.7033  -10.5047
 KFE  H20  H  HCR6  0   0.221  54.6128  -23.1615  -11.7742
 KFE  H21  H  H     0   0.220  56.2077  -24.4931  -10.3987
 KFE  H22  H  H     0   0.219  56.7553  -22.8312  -10.5551
 KFE  H23  H  H     0   0.220  56.9341  -23.5895   -8.1928
 KFE  H24  H  H     0   0.219  54.8759  -24.1408   -6.9164
 KFE  H25  H  H     0   0.219  55.0933  -25.2671   -8.2475
 KFE  H26  H  H     0   0.214  56.4308  -21.1993   -8.6463
 KFE  H27  H  H     0   0.223  55.6779  -21.7311   -7.1459
 KFE  H28  H  HCH2  0   0.220  55.0579  -20.9468  -10.7471
 KFE  H29  H  HCH2  0   0.221  53.3367  -21.3110  -10.7316
 KFE  H30  H  HCH1  0   0.254  48.0273  -13.0072   -6.1767
 KFE  H31  H  HNH1  0   0.355  49.4482  -12.4896   -8.5467
 KFE  H33  H  HCH1  0   0.229  48.2239  -13.8292   -9.9328
 KFE  H34  H  HCH2  0   0.201  47.6944  -11.4699  -10.4365
 KFE  H35  H  HCH2  0   0.194  46.3437  -11.5212   -9.3075
 KFE  H36  H  HOH1  0   0.456  45.6862  -12.0408  -11.4791
 KFE  H37  H  HCH1  0   0.232  46.3415  -14.9660   -9.0957
 KFE  H38  H  HCH1  0   0.241  48.3931  -15.4539   -7.9291
 KFE  H39  H  HOH1  0   0.466  46.9093  -16.2301   -6.4902

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
 KFE  C11  C10  single  1.530  0.020  1.530
 KFE  C11  C12  single  1.530  0.020  1.530
 KFE  C10  C9   single  1.531  0.020  1.531
 KFE  C10  C15  single  1.531  0.020  1.531
 KFE  C9   C8   single  1.535  0.020  1.535
 KFE  C12  C17  single  1.529  0.020  1.529
 KFE  C12  C13  single  1.530  0.020  1.530
 KFE  C17  C8   single  1.536  0.020  1.536
 KFE  C15  C14  single  1.530  0.020  1.530
 KFE  C20  O3   single  1.409  0.020  1.409
 KFE  C20  C19  single  1.516  0.020  1.516
 KFE  C8   C7   single  1.520  0.020  1.520
 KFE  C8   C16  single  1.535  0.020  1.535
 KFE  C7   O2   single  1.405  0.020  1.405
 KFE  C13  C14  single  1.530  0.020  1.530
 KFE  O1   C1   double  1.224  0.020  1.224
 KFE  N2   C19  single  1.467  0.020  1.467
 KFE  N2   C18  single  1.449  0.020  1.449
 KFE  C19  C21  single  1.523  0.020  1.523
 KFE  C14  C16  single  1.532  0.020  1.532
 KFE  O2   C6   single  1.407  0.020  1.407
 KFE  C6   C5   single  1.516  0.020  1.516
 KFE  C1   C18  single  1.522  0.020  1.522
 KFE  C1   N1   single  1.340  0.020  1.340
 KFE  C18  C22  single  1.539  0.020  1.539
 KFE  O4   C21  single  1.405  0.020  1.405
 KFE  C3   C4   single  1.525  0.020  1.525
 KFE  C3   C2   single  1.525  0.020  1.525
 KFE  C21  C22  single  1.531  0.020  1.531
 KFE  C5   C4   single  1.527  0.020  1.527
 KFE  N1   C2   single  1.447  0.020  1.447
 KFE  C22  O5   single  1.403  0.020  1.403
 KFE  N1   H1   single  0.860  0.020  1.020
 KFE  C2   H2   single  0.970  0.020  1.090
 KFE  C2   H3   single  0.970  0.020  1.090
 KFE  C4   H4   single  0.970  0.020  1.090
 KFE  C4   H5   single  0.970  0.020  1.090
 KFE  O4   H6   single  0.850  0.020  0.980
 KFE  C5   H7   single  0.970  0.020  1.090
 KFE  C5   H8   single  0.970  0.020  1.090
 KFE  C7   H9   single  0.970  0.020  1.090
 KFE  C7   H10  single  0.970  0.020  1.090
 KFE  C6   H11  single  0.970  0.020  1.090
 KFE  C6   H12  single  0.970  0.020  1.090
 KFE  C3   H13  single  0.970  0.020  1.090
 KFE  C3   H14  single  0.970  0.020  1.090
 KFE  C9   H15  single  0.970  0.020  1.090
 KFE  C9   H16  single  0.970  0.020  1.090
 KFE  C10  H17  single  0.970  0.020  1.090
 KFE  C11  H18  single  0.970  0.020  1.090
 KFE  C11  H19  single  0.970  0.020  1.090
 KFE  C12  H20  single  0.970  0.020  1.090
 KFE  C13  H21  single  0.970  0.020  1.090
 KFE  C13  H22  single  0.970  0.020  1.090
 KFE  C14  H23  single  0.970  0.020  1.090
 KFE  C15  H24  single  0.970  0.020  1.090
 KFE  C15  H25  single  0.970  0.020  1.090
 KFE  C16  H26  single  0.970  0.020  1.090
 KFE  C16  H27  single  0.970  0.020  1.090
 KFE  C17  H28  single  0.970  0.020  1.090
 KFE  C17  H29  single  0.970  0.020  1.090
 KFE  C18  H30  single  0.970  0.020  1.090
 KFE  N2   H31  single  0.890  0.020  1.040
 KFE  C19  H33  single  0.970  0.020  1.090
 KFE  C20  H34  single  0.970  0.020  1.090
 KFE  C20  H35  single  0.970  0.020  1.090
 KFE  O3   H36  single  0.850  0.020  0.980
 KFE  C21  H37  single  0.970  0.020  1.090
 KFE  C22  H38  single  0.970  0.020  1.090
 KFE  O5   H39  single  0.850  0.020  0.980

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
 KFE  H1   N1   C1   118.18  3.000
 KFE  H1   N1   C2   117.71  3.000
 KFE  C1   N1   C2   123.38  3.000
 KFE  H3   C2   H2   106.83  3.000
 KFE  H3   C2   C3   110.11  3.000
 KFE  H2   C2   C3   110.07  3.000
 KFE  H3   C2   N1   108.79  3.000
 KFE  H2   C2   N1   107.35  3.000
 KFE  C3   C2   N1   113.43  3.000
 KFE  C6   O2   C7   112.85  3.000
 KFE  H5   C4   H4   105.93  3.000
 KFE  H5   C4   C3   109.04  3.000
 KFE  H4   C4   C3   109.40  3.000
 KFE  H5   C4   C5   108.36  3.000
 KFE  H4   C4   C5   109.69  3.000
 KFE  C3   C4   C5   114.09  3.000
 KFE  H6   O4   C21  107.54  3.000
 KFE  H8   C5   H7   106.74  3.000
 KFE  H8   C5   C6   109.12  3.000
 KFE  H7   C5   C6   109.33  3.000
 KFE  H8   C5   C4   109.13  3.000
 KFE  H7   C5   C4   109.43  3.000
 KFE  C6   C5   C4   112.91  3.000
 KFE  H10  C7   H9   106.57  3.000
 KFE  H10  C7   C8   109.09  3.000
 KFE  H9   C7   C8   109.38  3.000
 KFE  H10  C7   O2   110.11  3.000
 KFE  H9   C7   O2   110.44  3.000
 KFE  C8   C7   O2   111.13  3.000
 KFE  H12  C6   H11  106.34  3.000
 KFE  H12  C6   C5   110.34  3.000
 KFE  H11  C6   C5   109.89  3.000
 KFE  H12  C6   O2   109.98  3.000
 KFE  H11  C6   O2   110.73  3.000
 KFE  C5   C6   O2   109.52  3.000
 KFE  C18  C1   O1   122.11  3.000
 KFE  C18  C1   N1   114.41  3.000
 KFE  O1   C1   N1   123.48  3.000
 KFE  H14  C3   H13  106.70  3.000
 KFE  H14  C3   C4   109.78  3.000
 KFE  H13  C3   C4   110.47  3.000
 KFE  H14  C3   C2   109.41  3.000
 KFE  H13  C3   C2   108.65  3.000
 KFE  C4   C3   C2   111.69  3.000
 KFE  C17  C8   C16  108.38  3.000
 KFE  C16  C8   C9   108.84  3.000
 KFE  C17  C8   C9   108.60  3.000
 KFE  C16  C8   C7   111.65  3.000
 KFE  C17  C8   C7   107.83  3.000
 KFE  C9   C8   C7   111.44  3.000
 KFE  H16  C9   H15  106.70  3.000
 KFE  H16  C9   C10  109.89  3.000
 KFE  H15  C9   C10  110.04  3.000
 KFE  H16  C9   C8   110.16  3.000
 KFE  H15  C9   C8   109.68  3.000
 KFE  C10  C9   C8   110.30  3.000
 KFE  H17  C10  C15  109.66  3.000
 KFE  H17  C10  C11  109.59  3.000
 KFE  C15  C10  C11  109.43  3.000
 KFE  H17  C10  C9   109.20  3.000
 KFE  C15  C10  C9   109.41  3.000
 KFE  C11  C10  C9   109.53  3.000
 KFE  H19  C11  H18  106.71  3.000
 KFE  H19  C11  C12  109.98  3.000
 KFE  H18  C11  C12  110.28  3.000
 KFE  H19  C11  C10  110.06  3.000
 KFE  H18  C11  C10  110.32  3.000
 KFE  C12  C11  C10  109.46  3.000
 KFE  H20  C12  C17  109.30  3.000
 KFE  H20  C12  C13  109.63  3.000
 KFE  C17  C12  C13  109.43  3.000
 KFE  H20  C12  C11  109.68  3.000
 KFE  C13  C12  C11  109.56  3.000
 KFE  C17  C12  C11  109.22  3.000
 KFE  H22  C13  H21  106.69  3.000
 KFE  H22  C13  C14  110.12  3.000
 KFE  H21  C13  C14  110.24  3.000
 KFE  H22  C13  C12  110.17  3.000
 KFE  H21  C13  C12  110.19  3.000
 KFE  C14  C13  C12  109.41  3.000
 KFE  H23  C14  C16  109.24  3.000
 KFE  H23  C14  C15  109.56  3.000
 KFE  C16  C14  C15  109.48  3.000
 KFE  H23  C14  C13  109.68  3.000
 KFE  C16  C14  C13  109.45  3.000
 KFE  C15  C14  C13  109.41  3.000
 KFE  H25  C15  H24  106.70  3.000
 KFE  H25  C15  C14  110.19  3.000
 KFE  H24  C15  C14  110.06  3.000
 KFE  H25  C15  C10  110.13  3.000
 KFE  H24  C15  C10  110.22  3.000
 KFE  C14  C15  C10  109.51  3.000
 KFE  H27  C16  H26  106.98  3.000
 KFE  H27  C16  C14  109.93  3.000
 KFE  H26  C16  C14  109.77  3.000
 KFE  H27  C16  C8   110.19  3.000
 KFE  H26  C16  C8   109.54  3.000
 KFE  C14  C16  C8   110.37  3.000
 KFE  H29  C17  H28  106.72  3.000
 KFE  H29  C17  C12  109.86  3.000
 KFE  H28  C17  C12  110.01  3.000
 KFE  H29  C17  C8   109.89  3.000
 KFE  H28  C17  C8   109.65  3.000
 KFE  C12  C17  C8   110.64  3.000
 KFE  H30  C18  C22  108.27  3.000
 KFE  H30  C18  N2   111.04  3.000
 KFE  C22  C18  N2   105.48  3.000
 KFE  H30  C18  C1   107.99  3.000
 KFE  C22  C18  C1   111.20  3.000
 KFE  N2   C18  C1   112.80  3.000
 KFE  H31  N2   C19  110.99  3.000
 KFE  H31  N2   C18  110.25  3.000
 KFE  C19  N2   C18  109.45  3.000
 KFE  H33  C19  C21  107.02  3.000
 KFE  H33  C19  C20  108.16  3.000
 KFE  C21  C19  C20  115.65  3.000
 KFE  H33  C19  N2   111.54  3.000
 KFE  C21  C19  N2   104.34  3.000
 KFE  C20  C19  N2   110.12  3.000
 KFE  H35  C20  H34  106.75  3.000
 KFE  H35  C20  O3   112.45  3.000
 KFE  H34  C20  O3   111.39  3.000
 KFE  H35  C20  C19  109.28  3.000
 KFE  H34  C20  C19  108.23  3.000
 KFE  O3   C20  C19  108.63  3.000
 KFE  H36  O3   C20  108.29  3.000
 KFE  H37  C21  C22  111.58  3.000
 KFE  H37  C21  C19  111.69  3.000
 KFE  C22  C21  C19  100.90  3.000
 KFE  H37  C21  O4   111.44  3.000
 KFE  C22  C21  O4   110.49  3.000
 KFE  C19  C21  O4   110.29  3.000
 KFE  H38  C22  O5   111.34  3.000
 KFE  H38  C22  C21  108.54  3.000
 KFE  O5   C22  C21  114.30  3.000
 KFE  H38  C22  C18  109.59  3.000
 KFE  O5   C22  C18  110.60  3.000
 KFE  C21  C22  C18  102.04  3.000
 KFE  H39  O5   C22  108.92  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
 KFE  CONST_01  C18  C1  N1  C2    180.00   0.0  0
 KFE  CONST_02  H1   N1  C1  C18     0.00   0.0  0
 KFE  CONST_03  O1   C1  N1  C2      0.00   0.0  0
 KFE  Var_01    C8   C7  O2  C6   -176.53  30.0  1
 KFE  Var_02    C4   C3  C2  N1    179.34  30.0  2
 KFE  Var_03    C5   C4  C3  C2    174.12  30.0  3
 KFE  Var_04    C4   C5  C6  O2    178.69  30.0  3
 KFE  Var_05    C3   C4  C5  C6     62.82  30.0  3
 KFE  Var_06    C3   C2  N1  C1    -81.57  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
 KFE  chir_01  C8   C9   C7   C16  negativ
 KFE  chir_02  C10  C15  C9   C11  negativ
 KFE  chir_03  C12  C11  C17  C13  negativ
 KFE  chir_04  C14  C15  C13  C16  negativ
 KFE  chir_05  C18  N2   C1   C22  positiv
 KFE  chir_06  C19  N2   C21  C20  negativ
 KFE  chir_07  C21  O4   C19  C22  negativ
 KFE  chir_08  C22  O5   C21  C18  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
 KFE  plan-1  N1   0.020
 KFE  plan-1  C2   0.020
 KFE  plan-1  O1   0.020
 KFE  plan-1  C1   0.020
 KFE  plan-1  C18  0.020
 KFE  plan-1  H1   0.020

