# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 23:55:32 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: 3-cyclopentyl-1-pyrrolidin-1-yl-propan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CCC1CCCC1)N2CCCC2
#
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
 5TO  5TO  3-cyclopentyl-1-pyrrolidin-1-yl-propan-1-one  ligand  35  14  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5TO
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
 5TO  CAG  C  CH2   0  -0.433   3.8532  -0.8658  -0.2947
 5TO  CAB  C  CH2   0  -0.444   4.9705   0.1196   0.1140
 5TO  CAC  C  CH2   0  -0.447   4.2612   1.4538   0.4101
 5TO  CAH  C  CH2   0  -0.431   2.8019   1.0726   0.6443
 5TO  CAM  C  CH1   0  -0.231   2.5621  -0.0381  -0.3800
 5TO  CAI  C  CH2   0  -0.404   1.3036  -0.8673  -0.1694
 5TO  CAF  C  CH2   0  -0.601   0.0295  -0.0458  -0.2879
 5TO  CAL  C  C     0   0.571  -1.2380  -0.8675  -0.1635
 5TO  OAA  O  O     0  -0.516  -1.2242  -2.0942  -0.1303
 5TO  NAN  N  NT    0  -0.476  -2.3872  -0.1762  -0.0957
 5TO  CAJ  C  CH2   0  -0.269  -2.5151   1.2770  -0.1417
 5TO  CAD  C  CH2   0  -0.475  -4.0125   1.4912  -0.3310
 5TO  CAE  C  CH2   0  -0.483  -4.6262   0.2984   0.3956
 5TO  CAK  C  CH2   0  -0.258  -3.6764  -0.8428   0.0529
 5TO  H1   H  HCH2  0   0.228   4.0688  -1.3823  -1.2315
 5TO  H2   H  HCH2  0   0.216   3.7326  -1.6382   0.4703
 5TO  H3   H  HCH2  0   0.223   5.4967  -0.2444   0.9979
 5TO  H4   H  HCH2  0   0.225   5.7210   0.2334  -0.6691
 5TO  H5   H  HCH2  0   0.227   4.7046   1.9914   1.2497
 5TO  H6   H  HCH2  0   0.218   4.3240   2.1154  -0.4577
 5TO  H7   H  HCH2  0   0.209   2.6662   0.6745   1.6566
 5TO  H8   H  HCH2  0   0.229   2.1214   1.9194   0.5361
 5TO  H9   H  HCH1  0   0.213   2.5125   0.4294  -1.3725
 5TO  H10  H  HCH2  0   0.226   1.2839  -1.6818  -0.8980
 5TO  H11  H  HCH2  0   0.214   1.3476  -1.3406   0.8172
 5TO  H12  H  HCH2  0   0.264   0.0168   0.7467   0.4663
 5TO  H13  H  HCH2  0   0.263   0.0104   0.4760  -1.2522
 5TO  H14  H  HCH2  0   0.239  -2.1692   1.7293   0.7931
 5TO  H15  H  HCH2  0   0.252  -1.9277   1.7076  -0.9543
 5TO  H16  H  HCH2  0   0.252  -4.3412   2.4529   0.0605
 5TO  H17  H  HCH2  0   0.239  -4.2636   1.4592  -1.3934
 5TO  H18  H  HCH2  0   0.237  -4.6286   0.4767   1.4733
 5TO  H19  H  HCH2  0   0.251  -5.6503   0.0877   0.0906
 5TO  H20  H  HCH2  0   0.232  -3.9676  -1.3320  -0.8816
 5TO  H21  H  HCH2  0   0.244  -3.6355  -1.6088   0.8273

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
 5TO  OAA  CAL  double  1.227  0.020  1.227
 5TO  CAJ  CAD  single  1.524  0.020  1.524
 5TO  CAJ  NAN  single  1.460  0.020  1.460
 5TO  CAD  CAE  single  1.526  0.020  1.526
 5TO  CAL  NAN  single  1.343  0.020  1.343
 5TO  CAL  CAF  single  1.516  0.020  1.516
 5TO  NAN  CAK  single  1.459  0.020  1.459
 5TO  CAI  CAF  single  1.521  0.020  1.521
 5TO  CAI  CAM  single  1.522  0.020  1.522
 5TO  CAG  CAM  single  1.536  0.020  1.536
 5TO  CAG  CAB  single  1.545  0.020  1.545
 5TO  CAE  CAK  single  1.524  0.020  1.524
 5TO  CAM  CAH  single  1.530  0.020  1.530
 5TO  CAB  CAC  single  1.540  0.020  1.540
 5TO  CAH  CAC  single  1.526  0.020  1.526
 5TO  CAG  H1   single  0.970  0.020  1.090
 5TO  CAG  H2   single  0.970  0.020  1.090
 5TO  CAB  H3   single  0.970  0.020  1.090
 5TO  CAB  H4   single  0.970  0.020  1.090
 5TO  CAC  H5   single  0.970  0.020  1.090
 5TO  CAC  H6   single  0.970  0.020  1.090
 5TO  CAH  H7   single  0.970  0.020  1.090
 5TO  CAH  H8   single  0.970  0.020  1.090
 5TO  CAM  H9   single  0.970  0.020  1.090
 5TO  CAI  H10  single  0.970  0.020  1.090
 5TO  CAI  H11  single  0.970  0.020  1.090
 5TO  CAF  H12  single  0.970  0.020  1.090
 5TO  CAF  H13  single  0.970  0.020  1.090
 5TO  CAJ  H14  single  0.970  0.020  1.090
 5TO  CAJ  H15  single  0.970  0.020  1.090
 5TO  CAD  H16  single  0.970  0.020  1.090
 5TO  CAD  H17  single  0.970  0.020  1.090
 5TO  CAE  H18  single  0.970  0.020  1.090
 5TO  CAE  H19  single  0.970  0.020  1.090
 5TO  CAK  H20  single  0.970  0.020  1.090
 5TO  CAK  H21  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
 5TO  H2   CAG  H1   106.74  3.000
 5TO  H2   CAG  CAM  109.07  3.000
 5TO  H1   CAG  CAM  111.93  3.000
 5TO  H2   CAG  CAB  110.20  3.000
 5TO  H1   CAG  CAB  112.71  3.000
 5TO  CAM  CAG  CAB  106.19  3.000
 5TO  H4   CAB  H3   106.53  3.000
 5TO  H4   CAB  CAC  111.39  3.000
 5TO  H3   CAB  CAC  110.82  3.000
 5TO  H4   CAB  CAG  111.98  3.000
 5TO  H3   CAB  CAG  110.50  3.000
 5TO  CAC  CAB  CAG  105.69  3.000
 5TO  H6   CAC  H5   106.82  3.000
 5TO  H6   CAC  CAH  109.14  3.000
 5TO  H5   CAC  CAH  113.17  3.000
 5TO  H6   CAC  CAB  110.20  3.000
 5TO  H5   CAC  CAB  112.81  3.000
 5TO  CAH  CAC  CAB  104.69  3.000
 5TO  H8   CAH  H7   107.21  3.000
 5TO  H8   CAH  CAM  113.52  3.000
 5TO  H7   CAH  CAM  109.59  3.000
 5TO  H8   CAH  CAC  112.77  3.000
 5TO  H7   CAH  CAC  110.54  3.000
 5TO  CAM  CAH  CAC  103.21  3.000
 5TO  H9   CAM  CAI  108.65  3.000
 5TO  H9   CAM  CAH  107.65  3.000
 5TO  CAI  CAM  CAH  115.64  3.000
 5TO  H9   CAM  CAG  108.51  3.000
 5TO  CAH  CAM  CAG  102.84  3.000
 5TO  CAI  CAM  CAG  113.19  3.000
 5TO  H11  CAI  H10  106.22  3.000
 5TO  H11  CAI  CAF  109.71  3.000
 5TO  H10  CAI  CAF  109.61  3.000
 5TO  H11  CAI  CAM  109.08  3.000
 5TO  H10  CAI  CAM  109.19  3.000
 5TO  CAF  CAI  CAM  112.81  3.000
 5TO  H13  CAF  H12  105.15  3.000
 5TO  H13  CAF  CAL  108.40  3.000
 5TO  H12  CAF  CAL  109.05  3.000
 5TO  H13  CAF  CAI  109.89  3.000
 5TO  H12  CAF  CAI  110.32  3.000
 5TO  CAL  CAF  CAI  113.67  3.000
 5TO  NAN  CAL  OAA  121.52  3.000
 5TO  NAN  CAL  CAF  116.15  3.000
 5TO  OAA  CAL  CAF  122.33  3.000
 5TO  CAK  NAN  CAJ  112.38  3.000
 5TO  CAK  NAN  CAL  121.75  3.000
 5TO  CAJ  NAN  CAL  125.87  3.000
 5TO  H15  CAJ  H14  107.63  3.000
 5TO  H15  CAJ  CAD  112.39  3.000
 5TO  H14  CAJ  CAD  111.00  3.000
 5TO  H15  CAJ  NAN  111.67  3.000
 5TO  H14  CAJ  NAN  110.90  3.000
 5TO  CAD  CAJ  NAN  103.29  3.000
 5TO  H17  CAD  H16  107.83  3.000
 5TO  H17  CAD  CAE  110.36  3.000
 5TO  H16  CAD  CAE  113.44  3.000
 5TO  H17  CAD  CAJ  110.03  3.000
 5TO  H16  CAD  CAJ  112.08  3.000
 5TO  CAE  CAD  CAJ  103.07  3.000
 5TO  H19  CAE  H18  107.80  3.000
 5TO  H19  CAE  CAK  112.23  3.000
 5TO  H18  CAE  CAK  110.22  3.000
 5TO  H19  CAE  CAD  113.33  3.000
 5TO  H18  CAE  CAD  110.07  3.000
 5TO  CAK  CAE  CAD  103.16  3.000
 5TO  H21  CAK  H20  107.61  3.000
 5TO  H21  CAK  CAE  112.95  3.000
 5TO  H20  CAK  CAE  111.16  3.000
 5TO  H21  CAK  NAN  111.12  3.000
 5TO  H20  CAK  NAN  110.63  3.000
 5TO  CAE  CAK  NAN  103.39  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
 5TO  CONST_01  CAJ  NAN  CAL  CAF    0.00   0.0  0
 5TO  CONST_02  CAK  NAN  CAL  CAF  180.00   0.0  0
 5TO  CONST_03  CAJ  NAN  CAL  OAA  180.00   0.0  0
 5TO  CONST_04  CAK  NAN  CAL  OAA    0.00   0.0  0
 5TO  Var_01    CAH  CAC  CAB  CAG   19.33  30.0  1
 5TO  Var_02    CAM  CAH  CAC  CAB  -37.86  30.0  1
 5TO  Var_03    CAM  CAG  CAB  CAC    6.35  30.0  1
 5TO  Var_04    CAE  CAD  CAJ  NAN   31.28  30.0  1
 5TO  Var_05    CAD  CAE  CAK  NAN   30.77  30.0  1
 5TO  Var_06    CAK  CAE  CAD  CAJ  -38.62  30.0  1
 5TO  Var_07    CAE  CAK  NAN  CAJ  -11.55  30.0  1
 5TO  Var_08    CAK  NAN  CAJ  CAD  -12.49  30.0  1
 5TO  Var_09    CAL  CAF  CAI  CAM  176.56  30.0  3
 5TO  Var_10    NAN  CAL  CAF  CAI  172.11  30.0  1

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
 5TO  chir_01  CAM  CAI  CAG  CAH  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
 5TO  plan-1  CAF  0.020
 5TO  plan-1  CAL  0.020
 5TO  plan-1  OAA  0.020
 5TO  plan-1  NAN  0.020
 5TO  plan-1  CAJ  0.020
 5TO  plan-1  CAK  0.020

