# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 16:36:25 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: (3~{S})-1-[2-(3-ethanoylindol-1-yl)ethanoyl]piperidine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)c1cn(CC(=O)N2CCC[C@@H](C2)C(O)=O)c3ccccc13
#
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
 E0D  E0D  '(3~{S})-1-[2-(3-ethanoylindol-1-yl)ethanoyl]piperidine-3-carboxylic acid'  ligand  43  24  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E0D
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
 E0D  OAW  O  OC    -1  -0.604  -5.0142  -0.3263  -2.3193
 E0D  CAV  C  C      0   0.438  -5.1884   0.3400  -1.2790
 E0D  OAX  O  O      0  -0.611  -6.1758   1.0553  -1.0183
 E0D  CAR  C  CH1    0  -0.396  -4.0698   0.2990  -0.2166
 E0D  CAQ  C  CH2    0  -0.285  -3.0657  -0.8192  -0.4773
 E0D  CAS  C  CH2    0  -0.432  -4.6240   0.1831   1.2031
 E0D  CAT  C  CH2    0  -0.427  -3.5034   0.1121   2.2333
 E0D  CAU  C  CH2    0  -0.321  -2.5184  -0.9977   1.8924
 E0D  NAO  N  NT     0  -0.452  -2.0187  -0.8286   0.5376
 E0D  C    C  C      0   0.544  -0.7369  -0.6232   0.2035
 E0D  O    O  O      0  -0.488  -0.3488  -0.4490  -0.9421
 E0D  CA   C  CH2    0  -0.485   0.2874  -0.6299   1.3450
 E0D  N    N  NR5    0  -0.513   1.6058  -0.3868   0.8343
 E0D  CAH  C  CR15   0  -0.009   2.4578  -1.3399   0.4076
 E0D  CAE  C  CR56   0   0.377   2.1218   0.8520   0.5242
 E0D  CAF  C  CR16   0  -0.301   1.5849   2.1145   0.7517
 E0D  CAA  C  CR16   0  -0.279   2.3371   3.2029   0.3502
 E0D  CAB  C  CR16   0  -0.259   3.5876   3.0339  -0.2598
 E0D  CAC  C  CR16   0  -0.364   4.1124   1.7747  -0.4864
 E0D  CAD  C  CR56   0   0.079   3.3711   0.6569  -0.0931
 E0D  CAG  C  CR5    0  -0.158   3.5752  -0.7680  -0.1620
 E0D  CAK  C  C      0   0.298   4.7209  -1.4614  -0.7190
 E0D  OAM  O  O      0  -0.433   5.6371  -0.8464  -1.2437
 E0D  CAL  C  CH3    0  -0.782   4.7814  -2.9654  -0.6126
 E0D  H2   H  HCH1   0   0.231  -3.5244   1.2519  -0.2844
 E0D  H3   H  HCH2   0   0.229  -3.5723  -1.7906  -0.4516
 E0D  H4   H  HCH2   0   0.255  -2.6088  -0.7179  -1.4555
 E0D  H5   H  HCH2   0   0.233  -5.2852   1.0230   1.4159
 E0D  H6   H  HCH2   0   0.209  -5.2369  -0.7232   1.2765
 E0D  H7   H  HCH2   0   0.221  -2.9661   1.0650   2.2698
 E0D  H8   H  HCH2   0   0.238  -3.9076  -0.0662   3.2322
 E0D  H9   H  HCH2   0   0.273  -1.7048  -1.0212   2.6123
 E0D  H10  H  HCH2   0   0.244  -3.0176  -1.9704   1.9549
 E0D  H11  H  HCH2   0   0.305   0.0545   0.1244   2.0986
 E0D  H12  H  HCH2   0   0.319   0.2861  -1.5923   1.8590
 E0D  H13  H  HCR5   0   0.307   2.2096  -2.3810   0.5440
 E0D  H14  H  HCR6   0   0.262   0.6198   2.2542   1.2221
 E0D  H15  H  HCR6   0   0.256   1.9520   4.2014   0.5093
 E0D  H16  H  HCR6   0   0.252   4.1505   3.9085  -0.5593
 E0D  H17  H  HCR6   0   0.248   5.0757   1.6580  -0.9611
 E0D  H18  H  HCH3   0   0.248   3.8217  -3.4359  -0.4130
 E0D  H19  H  HCH3   0   0.263   5.1928  -3.3875  -1.5284
 E0D  H20  H  HCH3   0   0.270   5.4559  -3.2338   0.2035

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
 E0D  CAU  CAT  single    1.522  0.020  1.522
 E0D  CAU  NAO  single    1.454  0.020  1.454
 E0D  CAA  CAF  aromatic  1.383  0.020  1.383
 E0D  CAA  CAB  aromatic  1.402  0.020  1.402
 E0D  CAF  CAE  aromatic  1.391  0.020  1.391
 E0D  CAT  CAS  single    1.524  0.020  1.524
 E0D  NAO  CAQ  single    1.458  0.020  1.458
 E0D  NAO  C    single    1.341  0.020  1.341
 E0D  CAB  CAC  aromatic  1.383  0.020  1.383
 E0D  CA   C    single    1.534  0.020  1.534
 E0D  CA   N    single    1.435  0.020  1.435
 E0D  CAS  CAR  single    1.528  0.020  1.528
 E0D  CAQ  CAR  single    1.525  0.020  1.525
 E0D  CAE  N    aromatic  1.377  0.020  1.377
 E0D  CAE  CAD  aromatic  1.407  0.020  1.407
 E0D  C    O    double    1.222  0.020  1.222
 E0D  N    CAH  aromatic  1.348  0.020  1.348
 E0D  OAX  CAV  deloc     1.247  0.020  1.247
 E0D  CAR  CAV  single    1.543  0.020  1.543
 E0D  CAC  CAD  aromatic  1.398  0.020  1.398
 E0D  CAD  CAG  aromatic  1.441  0.020  1.441
 E0D  CAV  OAW  deloc     1.248  0.020  1.248
 E0D  CAH  CAG  aromatic  1.378  0.020  1.378
 E0D  CAG  CAK  single    1.450  0.020  1.450
 E0D  CAK  OAM  double    1.222  0.020  1.222
 E0D  CAK  CAL  single    1.509  0.020  1.509
 E0D  CAR  H2   single    0.970  0.020  1.090
 E0D  CAQ  H3   single    0.970  0.020  1.090
 E0D  CAQ  H4   single    0.970  0.020  1.090
 E0D  CAS  H5   single    0.970  0.020  1.090
 E0D  CAS  H6   single    0.970  0.020  1.090
 E0D  CAT  H7   single    0.970  0.020  1.090
 E0D  CAT  H8   single    0.970  0.020  1.090
 E0D  CAU  H9   single    0.970  0.020  1.090
 E0D  CAU  H10  single    0.970  0.020  1.090
 E0D  CA   H11  single    0.970  0.020  1.090
 E0D  CA   H12  single    0.970  0.020  1.090
 E0D  CAH  H13  single    0.930  0.020  1.080
 E0D  CAF  H14  single    0.930  0.020  1.080
 E0D  CAA  H15  single    0.930  0.020  1.080
 E0D  CAB  H16  single    0.930  0.020  1.080
 E0D  CAC  H17  single    0.930  0.020  1.080
 E0D  CAL  H18  single    0.970  0.020  1.090
 E0D  CAL  H19  single    0.970  0.020  1.090
 E0D  CAL  H20  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
 E0D  CAR  CAV  OAX  116.44  3.000
 E0D  CAR  CAV  OAW  117.30  3.000
 E0D  OAX  CAV  OAW  126.25  3.000
 E0D  H2   CAR  CAS  107.62  3.000
 E0D  H2   CAR  CAQ  107.34  3.000
 E0D  CAS  CAR  CAQ  109.99  3.000
 E0D  H2   CAR  CAV  107.09  3.000
 E0D  CAQ  CAR  CAV  112.27  3.000
 E0D  CAS  CAR  CAV  112.25  3.000
 E0D  H4   CAQ  H3   107.38  3.000
 E0D  H4   CAQ  NAO  109.02  3.000
 E0D  H3   CAQ  NAO  108.05  3.000
 E0D  H4   CAQ  CAR  111.29  3.000
 E0D  H3   CAQ  CAR  109.97  3.000
 E0D  NAO  CAQ  CAR  111.00  3.000
 E0D  H6   CAS  H5   106.55  3.000
 E0D  H6   CAS  CAT  109.10  3.000
 E0D  H5   CAS  CAT  110.49  3.000
 E0D  H6   CAS  CAR  109.12  3.000
 E0D  H5   CAS  CAR  110.06  3.000
 E0D  CAT  CAS  CAR  111.40  3.000
 E0D  H8   CAT  H7   107.05  3.000
 E0D  H8   CAT  CAU  108.98  3.000
 E0D  H7   CAT  CAU  108.93  3.000
 E0D  H8   CAT  CAS  110.72  3.000
 E0D  H7   CAT  CAS  110.06  3.000
 E0D  CAU  CAT  CAS  111.00  3.000
 E0D  H10  CAU  H9   106.52  3.000
 E0D  H10  CAU  NAO  108.25  3.000
 E0D  H9   CAU  NAO  111.26  3.000
 E0D  H10  CAU  CAT  109.86  3.000
 E0D  H9   CAU  CAT  110.60  3.000
 E0D  NAO  CAU  CAT  110.25  3.000
 E0D  C    NAO  CAU  125.36  3.000
 E0D  C    NAO  CAQ  120.80  3.000
 E0D  CAU  NAO  CAQ  113.74  3.000
 E0D  CA   C    O    119.10  3.000
 E0D  O    C    NAO  124.00  3.000
 E0D  CA   C    NAO  116.90  3.000
 E0D  H12  CA   H11  106.51  3.000
 E0D  H12  CA   N    108.56  3.000
 E0D  H11  CA   N    108.95  3.000
 E0D  H12  CA   C    110.71  3.000
 E0D  H11  CA   C    111.62  3.000
 E0D  N    CA   C    110.36  3.000
 E0D  CAE  N    CAH  109.14  3.000
 E0D  CAH  N    CA   125.02  3.000
 E0D  CAE  N    CA   125.23  3.000
 E0D  H13  CAH  CAG  129.72  3.000
 E0D  H13  CAH  N    119.79  3.000
 E0D  CAG  CAH  N    110.48  3.000
 E0D  CAD  CAE  CAF  122.71  3.000
 E0D  CAD  CAE  N    107.86  3.000
 E0D  CAF  CAE  N    129.43  3.000
 E0D  H14  CAF  CAA  120.64  3.000
 E0D  H14  CAF  CAE  122.16  3.000
 E0D  CAA  CAF  CAE  117.20  3.000
 E0D  H15  CAA  CAB  119.53  3.000
 E0D  H15  CAA  CAF  119.35  3.000
 E0D  CAB  CAA  CAF  121.12  3.000
 E0D  H16  CAB  CAC  119.54  3.000
 E0D  H16  CAB  CAA  119.14  3.000
 E0D  CAC  CAB  CAA  121.31  3.000
 E0D  H17  CAC  CAD  120.67  3.000
 E0D  H17  CAC  CAB  120.59  3.000
 E0D  CAD  CAC  CAB  118.74  3.000
 E0D  CAG  CAD  CAC  134.60  3.000
 E0D  CAG  CAD  CAE  106.49  3.000
 E0D  CAC  CAD  CAE  118.91  3.000
 E0D  CAK  CAG  CAD  127.08  3.000
 E0D  CAK  CAG  CAH  126.92  3.000
 E0D  CAD  CAG  CAH  106.00  3.000
 E0D  CAL  CAK  OAM  120.12  3.000
 E0D  CAL  CAK  CAG  118.75  3.000
 E0D  OAM  CAK  CAG  121.11  3.000
 E0D  H20  CAL  H19  107.45  3.000
 E0D  H20  CAL  H18  107.55  3.000
 E0D  H19  CAL  H18  108.66  3.000
 E0D  H20  CAL  CAK  108.81  3.000
 E0D  H19  CAL  CAK  110.01  3.000
 E0D  H18  CAL  CAK  114.13  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
 E0D  CONST_01  CAA  CAF  CAE  N     180.00   0.0  0
 E0D  CONST_02  CAC  CAD  CAE  N     180.00   0.0  0
 E0D  CONST_03  CAG  CAD  CAE  N       0.00   0.0  0
 E0D  CONST_04  CAD  CAG  CAH  N       0.00   0.0  0
 E0D  CONST_05  CAF  CAE  N    CAH   180.00   0.0  0
 E0D  CONST_06  CAD  CAE  N    CAH     0.00   0.0  0
 E0D  CONST_07  CAE  CAD  CAG  CAH     0.00   0.0  0
 E0D  CONST_08  CAC  CAD  CAG  CAH   180.00   0.0  0
 E0D  CONST_09  CAB  CAA  CAF  CAE     0.00   0.0  0
 E0D  CONST_10  CAG  CAH  N    CAE     0.00   0.0  0
 E0D  CONST_11  CAB  CAC  CAD  CAE     0.00   0.0  0
 E0D  CONST_12  CAC  CAB  CAA  CAF     0.00   0.0  0
 E0D  CONST_13  CAC  CAD  CAE  CAF     0.00   0.0  0
 E0D  CONST_14  CAG  CAD  CAE  CAF   180.00   0.0  0
 E0D  CONST_15  CAD  CAE  CAF  CAA     0.00   0.0  0
 E0D  CONST_16  CAD  CAC  CAB  CAA     0.00   0.0  0
 E0D  CONST_17  CAG  CAD  CAC  CAB   180.00   0.0  0
 E0D  CONST_18  CAF  CAE  N    CA      0.00   0.0  0
 E0D  CONST_19  CAD  CAE  N    CA    180.00   0.0  0
 E0D  CONST_20  CAG  CAH  N    CA    180.00   0.0  0
 E0D  CONST_21  CAK  CAG  CAH  N     180.00   0.0  0
 E0D  CONST_22  CAK  CAG  CAD  CAE   180.00   0.0  0
 E0D  CONST_23  CAK  CAG  CAD  CAC     0.00   0.0  0
 E0D  CONST_24  H14  CAF  CAE  N       0.00   0.0  0
 E0D  CONST_25  H15  CAA  CAF  CAE   180.00   0.0  0
 E0D  CONST_26  H13  CAH  N    CAE   180.00   0.0  0
 E0D  CONST_27  H17  CAC  CAD  CAE   180.00   0.0  0
 E0D  CONST_28  H16  CAB  CAA  CAF   180.00   0.0  0
 E0D  CONST_29  CA   C    NAO  CAQ   180.00   0.0  0
 E0D  CONST_30  O    C    NAO  CAQ     0.00   0.0  0
 E0D  CONST_31  CA   C    NAO  CAU     0.00   0.0  0
 E0D  CONST_32  O    C    NAO  CAU   180.00   0.0  0
 E0D  Var_01    CAU  CAT  CAS  CAR   -53.42  30.0  1
 E0D  Var_02    CAU  NAO  CAQ  CAR    58.65  30.0  1
 E0D  Var_03    CAT  CAU  NAO  CAQ   -58.18  30.0  1
 E0D  Var_04    NAO  CAU  CAT  CAS    54.65  30.0  1
 E0D  Var_05    N    CA   C    NAO  -179.51  30.0  1
 E0D  Var_06    CAE  N    CA   C      80.83  30.0  2
 E0D  Var_07    OAM  CAK  CAG  CAH   177.33  30.0  2
 E0D  Var_08    H18  CAL  CAK  CAG    18.77  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
 E0D  chir_01  CAR  CAS  CAQ  CAV  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
 E0D  plan-1  CA   0.020
 E0D  plan-1  N    0.020
 E0D  plan-1  CAH  0.020
 E0D  plan-1  CAE  0.020
 E0D  plan-1  CAF  0.020
 E0D  plan-1  CAA  0.020
 E0D  plan-1  CAB  0.020
 E0D  plan-1  CAC  0.020
 E0D  plan-1  CAD  0.020
 E0D  plan-1  CAG  0.020
 E0D  plan-1  CAK  0.020
 E0D  plan-1  H13  0.020
 E0D  plan-1  H14  0.020
 E0D  plan-1  H15  0.020
 E0D  plan-1  H16  0.020
 E0D  plan-1  H17  0.020
 E0D  plan-2  CAQ  0.020
 E0D  plan-2  CAU  0.020
 E0D  plan-2  NAO  0.020
 E0D  plan-2  C    0.020
 E0D  plan-2  O    0.020
 E0D  plan-2  CA   0.020
 E0D  plan-3  CAG  0.020
 E0D  plan-3  CAK  0.020
 E0D  plan-3  OAM  0.020
 E0D  plan-3  CAL  0.020
 E0D  plan-4  OAW  0.020
 E0D  plan-4  CAV  0.020
 E0D  plan-4  OAX  0.020
 E0D  plan-4  CAR  0.020

