# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 14:44:04 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 1-[3-[5-[(1~{R},2~{R})-2-methylcyclopropyl]furan-2-yl]propanoyl]piperidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1C[C@H]1c2oc(CCC(=O)N3CCC(CC3)C(N)=O)cc2
#
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
 8YT  8YT  1-[3-[5-[(1~{R},2~{R})-2-methylcyclopropyl]furan-2-yl]propanoyl]piperidine-4-carboxamide  ligand  46  22  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_8YT
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
 8YT  CAO  C  CH2   0  -0.318  -3.5387   1.5678   0.2112
 8YT  CAP  C  CH2   0  -0.419  -4.1993   0.3513   0.8463
 8YT  CAQ  C  CH1   0  -0.395  -4.2450  -0.8121  -0.1428
 8YT  CAT  C  C     0   0.538  -4.8233  -2.0617   0.4928
 8YT  OAU  O  O     0  -0.495  -4.4604  -2.4506   1.5950
 8YT  NAV  N  NH2   0  -0.801  -5.7309  -2.7140  -0.2475
 8YT  CAR  C  CH2   0  -0.414  -2.8358  -1.1018  -0.6722
 8YT  CAS  C  CH2   0  -0.323  -2.2216   0.1599  -1.2641
 8YT  NAN  N  NT    0  -0.457  -2.2153   1.2357  -0.2891
 8YT  CAL  C  C     0   0.581  -1.1096   1.8225   0.2185
 8YT  OAM  O  O     0  -0.506  -1.1690   2.6874   1.0843
 8YT  CAK  C  CH2   0  -0.610   0.2311   1.3762  -0.3377
 8YT  CAJ  C  CH2   0  -0.531   1.4028   2.1522   0.2632
 8YT  CAH  C  CR5   0   0.365   2.7014   1.7366  -0.3235
 8YT  OAI  O  O     0  -0.450   3.1481   0.4843  -0.0442
 8YT  CAG  C  CR15  0  -0.385   3.5791   2.3480  -1.1532
 8YT  CAF  C  CR15  0  -0.378   4.6325   1.4110  -1.3967
 8YT  CAE  C  CR5   0   0.413   4.3172   0.2931  -0.6958
 8YT  CAD  C  CH1   0  -0.409   5.0060  -0.9880  -0.5331
 8YT  CAC  C  CH2   0  -0.471   4.2509  -2.2737  -0.3044
 8YT  CAB  C  CH1   0  -0.226   5.0743  -1.6933   0.7973
 8YT  CAA  C  CH3   0  -0.665   6.3597  -2.3478   1.2254
 8YT  H1   H  HCH2  0   0.239  -4.1475   1.9267  -0.6258
 8YT  H2   H  HCH2  0   0.267  -3.4598   2.3797   0.9279
 8YT  H3   H  HCH2  0   0.235  -3.6433   0.0593   1.7402
 8YT  H4   H  HCH2  0   0.249  -5.2085   0.6221   1.1644
 8YT  H5   H  HCH1  0   0.253  -4.8673  -0.5143  -0.9952
 8YT  H6   H  HNH2  0   0.407  -6.0072  -2.3868  -1.1565
 8YT  H7   H  HNH2  0   0.399  -6.1270  -3.5828   0.0735
 8YT  H8   H  HCH2  0   0.238  -2.2013  -1.4696   0.1392
 8YT  H9   H  HCH2  0   0.252  -2.8673  -1.8761  -1.4419
 8YT  H10  H  HCH2  0   0.279  -1.2183  -0.0471  -1.6229
 8YT  H11  H  HCH2  0   0.246  -2.8056   0.4801  -2.1337
 8YT  H12  H  HCH2  0   0.275   0.3601   0.3064  -0.1522
 8YT  H13  H  HCH2  0   0.278   0.2388   1.4967  -1.4244
 8YT  H14  H  HCH2  0   0.260   1.2824   3.2193   0.0751
 8YT  H15  H  HCH2  0   0.255   1.4197   2.0250   1.3484
 8YT  H16  H  HCR5  0   0.254   3.4857   3.3472  -1.5483
 8YT  H17  H  HCR5  0   0.253   5.5083   1.5518  -2.0101
 8YT  H18  H  HCH1  0   0.269   5.8937  -1.0589  -1.1522
 8YT  H19  H  HCH2  0   0.254   3.1721  -2.2223  -0.2260
 8YT  H20  H  HCH2  0   0.253   4.6178  -3.1588  -0.8109
 8YT  H21  H  HCH1  0   0.254   4.5161  -1.2227   1.6006
 8YT  H22  H  HCH3  0   0.232   7.0274  -1.6300   1.7040
 8YT  H23  H  HCH3  0   0.231   6.1726  -3.1533   1.9373
 8YT  H24  H  HCH3  0   0.224   6.8901  -2.7767   0.3737

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
 8YT  CAA  CAB  single    1.505  0.020  1.505
 8YT  CAB  CAD  single    1.507  0.020  1.507
 8YT  CAB  CAC  single    1.493  0.020  1.493
 8YT  OAI  CAE  aromatic  1.352  0.020  1.352
 8YT  OAI  CAH  aromatic  1.359  0.020  1.359
 8YT  CAD  CAE  single    1.464  0.020  1.464
 8YT  CAD  CAC  single    1.509  0.020  1.509
 8YT  CAJ  CAH  single    1.484  0.020  1.484
 8YT  CAJ  CAK  single    1.528  0.020  1.528
 8YT  CAE  CAF  aromatic  1.357  0.020  1.357
 8YT  CAH  CAG  aromatic  1.354  0.020  1.354
 8YT  CAK  CAL  single    1.519  0.020  1.519
 8YT  CAO  CAP  single    1.523  0.020  1.523
 8YT  CAO  NAN  single    1.453  0.020  1.453
 8YT  CAF  CAG  aromatic  1.431  0.020  1.431
 8YT  CAP  CAQ  single    1.528  0.020  1.528
 8YT  CAL  NAN  single    1.351  0.020  1.351
 8YT  CAL  OAM  double    1.225  0.020  1.225
 8YT  NAN  CAS  single    1.452  0.020  1.452
 8YT  CAQ  CAT  single    1.516  0.020  1.516
 8YT  CAQ  CAR  single    1.533  0.020  1.533
 8YT  OAU  CAT  double    1.224  0.020  1.224
 8YT  CAT  NAV  single    1.341  0.020  1.341
 8YT  CAS  CAR  single    1.523  0.020  1.523
 8YT  CAO  H1   single    0.970  0.020  1.090
 8YT  CAO  H2   single    0.970  0.020  1.090
 8YT  CAP  H3   single    0.970  0.020  1.090
 8YT  CAP  H4   single    0.970  0.020  1.090
 8YT  CAQ  H5   single    0.970  0.020  1.090
 8YT  NAV  H6   single    0.860  0.020  1.020
 8YT  NAV  H7   single    0.860  0.020  1.020
 8YT  CAR  H8   single    0.970  0.020  1.090
 8YT  CAR  H9   single    0.970  0.020  1.090
 8YT  CAS  H10  single    0.970  0.020  1.090
 8YT  CAS  H11  single    0.970  0.020  1.090
 8YT  CAK  H12  single    0.970  0.020  1.090
 8YT  CAK  H13  single    0.970  0.020  1.090
 8YT  CAJ  H14  single    0.970  0.020  1.090
 8YT  CAJ  H15  single    0.970  0.020  1.090
 8YT  CAG  H16  single    0.930  0.020  1.080
 8YT  CAF  H17  single    0.930  0.020  1.080
 8YT  CAD  H18  single    0.970  0.020  1.090
 8YT  CAC  H19  single    0.970  0.020  1.090
 8YT  CAC  H20  single    0.970  0.020  1.090
 8YT  CAB  H21  single    0.970  0.020  1.090
 8YT  CAA  H22  single    0.970  0.020  1.090
 8YT  CAA  H23  single    0.970  0.020  1.090
 8YT  CAA  H24  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
 8YT  H2   CAO  H1   107.44  3.000
 8YT  H2   CAO  NAN  109.38  3.000
 8YT  H1   CAO  NAN  108.53  3.000
 8YT  H2   CAO  CAP  110.71  3.000
 8YT  H1   CAO  CAP  109.83  3.000
 8YT  NAN  CAO  CAP  110.86  3.000
 8YT  H4   CAP  H3   107.35  3.000
 8YT  H4   CAP  CAQ  110.47  3.000
 8YT  H3   CAP  CAQ  109.96  3.000
 8YT  H4   CAP  CAO  108.92  3.000
 8YT  H3   CAP  CAO  109.51  3.000
 8YT  CAQ  CAP  CAO  110.57  3.000
 8YT  H5   CAQ  CAR  107.73  3.000
 8YT  H5   CAQ  CAT  109.46  3.000
 8YT  CAR  CAQ  CAT  109.85  3.000
 8YT  H5   CAQ  CAP  108.26  3.000
 8YT  CAR  CAQ  CAP  109.88  3.000
 8YT  CAT  CAQ  CAP  111.57  3.000
 8YT  NAV  CAT  OAU  122.91  3.000
 8YT  NAV  CAT  CAQ  115.32  3.000
 8YT  OAU  CAT  CAQ  121.75  3.000
 8YT  H7   NAV  H6   117.45  3.000
 8YT  H7   NAV  CAT  120.66  3.000
 8YT  H6   NAV  CAT  121.82  3.000
 8YT  H9   CAR  H8   107.53  3.000
 8YT  H9   CAR  CAS  108.97  3.000
 8YT  H8   CAR  CAS  109.45  3.000
 8YT  H9   CAR  CAQ  110.53  3.000
 8YT  H8   CAR  CAQ  109.91  3.000
 8YT  CAS  CAR  CAQ  110.39  3.000
 8YT  H11  CAS  H10  106.63  3.000
 8YT  H11  CAS  NAN  108.59  3.000
 8YT  H10  CAS  NAN  111.05  3.000
 8YT  H11  CAS  CAR  109.62  3.000
 8YT  H10  CAS  CAR  110.07  3.000
 8YT  NAN  CAS  CAR  110.77  3.000
 8YT  CAL  NAN  CAS  125.29  3.000
 8YT  CAS  NAN  CAO  113.36  3.000
 8YT  CAL  NAN  CAO  121.12  3.000
 8YT  CAK  CAL  OAM  120.60  3.000
 8YT  OAM  CAL  NAN  122.17  3.000
 8YT  CAK  CAL  NAN  117.22  3.000
 8YT  H13  CAK  H12  105.99  3.000
 8YT  H13  CAK  CAJ  109.23  3.000
 8YT  H12  CAK  CAJ  109.85  3.000
 8YT  H13  CAK  CAL  109.74  3.000
 8YT  H12  CAK  CAL  109.24  3.000
 8YT  CAJ  CAK  CAL  112.56  3.000
 8YT  H15  CAJ  H14  106.68  3.000
 8YT  H15  CAJ  CAH  110.26  3.000
 8YT  H14  CAJ  CAH  107.61  3.000
 8YT  H15  CAJ  CAK  110.07  3.000
 8YT  H14  CAJ  CAK  110.15  3.000
 8YT  CAH  CAJ  CAK  111.91  3.000
 8YT  CAG  CAH  OAI  109.22  3.000
 8YT  CAG  CAH  CAJ  133.08  3.000
 8YT  OAI  CAH  CAJ  117.68  3.000
 8YT  CAE  OAI  CAH  108.40  3.000
 8YT  H16  CAG  CAF  127.46  3.000
 8YT  H16  CAG  CAH  125.93  3.000
 8YT  CAF  CAG  CAH  106.61  3.000
 8YT  H17  CAF  CAE  126.18  3.000
 8YT  H17  CAF  CAG  127.53  3.000
 8YT  CAE  CAF  CAG  106.29  3.000
 8YT  CAD  CAE  CAF  132.01  3.000
 8YT  CAF  CAE  OAI  109.48  3.000
 8YT  CAD  CAE  OAI  118.50  3.000
 8YT  H18  CAD  CAB  115.86  3.000
 8YT  H18  CAD  CAC  116.14  3.000
 8YT  CAB  CAD  CAC   59.34  3.000
 8YT  H18  CAD  CAE  112.27  3.000
 8YT  CAC  CAD  CAE  121.82  3.000
 8YT  CAB  CAD  CAE  121.94  3.000
 8YT  H20  CAC  H19  114.20  3.000
 8YT  H20  CAC  CAB  118.40  3.000
 8YT  H19  CAC  CAB  118.53  3.000
 8YT  H20  CAC  CAD  117.11  3.000
 8YT  H19  CAC  CAD  117.98  3.000
 8YT  CAB  CAC  CAD   60.29  3.000
 8YT  H21  CAB  CAA  114.67  3.000
 8YT  H21  CAB  CAC  115.53  3.000
 8YT  CAA  CAB  CAC  120.81  3.000
 8YT  H21  CAB  CAD  115.28  3.000
 8YT  CAC  CAB  CAD   60.37  3.000
 8YT  CAA  CAB  CAD  119.56  3.000
 8YT  H24  CAA  H23  107.60  3.000
 8YT  H24  CAA  H22  107.67  3.000
 8YT  H23  CAA  H22  107.73  3.000
 8YT  H24  CAA  CAB  111.35  3.000
 8YT  H23  CAA  CAB  111.12  3.000
 8YT  H22  CAA  CAB  111.19  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
 8YT  CONST_01  CAF  CAE  OAI  CAH     0.00   0.0  0
 8YT  CONST_02  CAE  CAF  CAG  CAH     0.00   0.0  0
 8YT  CONST_03  CAG  CAF  CAE  OAI     0.00   0.0  0
 8YT  CONST_04  CAF  CAG  CAH  OAI     0.00   0.0  0
 8YT  CONST_05  CAE  OAI  CAH  CAG     0.00   0.0  0
 8YT  CONST_06  CAD  CAE  OAI  CAH   180.00   0.0  0
 8YT  CONST_07  CAD  CAE  CAF  CAG   180.00   0.0  0
 8YT  CONST_08  CAE  OAI  CAH  CAJ   180.00   0.0  0
 8YT  CONST_09  CAF  CAG  CAH  CAJ   180.00   0.0  0
 8YT  CONST_10  H17  CAF  CAG  CAH   180.00   0.0  0
 8YT  CONST_11  H16  CAG  CAH  OAI   180.00   0.0  0
 8YT  CONST_12  CAK  CAL  NAN  CAO   180.00   0.0  0
 8YT  CONST_13  OAM  CAL  NAN  CAO     0.00   0.0  0
 8YT  CONST_14  CAK  CAL  NAN  CAS     0.00   0.0  0
 8YT  CONST_15  OAM  CAL  NAN  CAS   180.00   0.0  0
 8YT  CONST_16  H6   NAV  CAT  CAQ     0.00   0.0  0
 8YT  CONST_17  H7   NAV  CAT  CAQ   180.00   0.0  0
 8YT  Var_01    CAR  CAS  NAN  CAO   -58.19  30.0  1
 8YT  Var_02    CAS  NAN  CAO  CAP    57.98  30.0  1
 8YT  Var_03    NAN  CAO  CAP  CAQ   -55.57  30.0  1
 8YT  Var_04    NAN  CAS  CAR  CAQ    55.89  30.0  1
 8YT  Var_05    CAB  CAD  CAE  OAI   -39.86  30.0  1
 8YT  Var_06    CAC  CAB  CAD  CAE   110.65  30.0  1
 8YT  Var_07    OAI  CAH  CAJ  CAK   -67.95  30.0  2
 8YT  Var_08    H22  CAA  CAB  CAD    84.95  30.0  3
 8YT  Var_09    CAJ  CAK  CAL  NAN   177.35  30.0  1
 8YT  Var_10    CAH  CAJ  CAK  CAL  -178.07  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
 8YT  chir_01  CAQ  CAP  CAT  CAR  positiv
 8YT  chir_02  CAD  CAB  CAE  CAC  both
 8YT  chir_03  CAB  CAA  CAD  CAC  both

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
 8YT  plan-1  CAJ  0.020
 8YT  plan-1  CAH  0.020
 8YT  plan-1  OAI  0.020
 8YT  plan-1  CAG  0.020
 8YT  plan-1  CAF  0.020
 8YT  plan-1  CAE  0.020
 8YT  plan-1  CAD  0.020
 8YT  plan-1  H16  0.020
 8YT  plan-1  H17  0.020
 8YT  plan-2  CAO  0.020
 8YT  plan-2  CAS  0.020
 8YT  plan-2  NAN  0.020
 8YT  plan-2  CAL  0.020
 8YT  plan-2  OAM  0.020
 8YT  plan-2  CAK  0.020
 8YT  plan-3  CAQ  0.020
 8YT  plan-3  CAT  0.020
 8YT  plan-3  OAU  0.020
 8YT  plan-3  NAV  0.020
 8YT  plan-3  H6   0.020
 8YT  plan-3  H7   0.020

