# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 01:59:48 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  44  24  .  2021-08-09  2021-08-09  
;
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  OH1   0  -0.594  -4.5354   0.4369  -2.4889
 E0D  CAV  C  C     0   0.571  -5.0230   0.4446  -1.2533
 E0D  OAX  O  O     0  -0.433  -6.2002   0.5359  -1.0122
 E0D  CAR  C  CH1   0  -0.397  -3.9296   0.3354  -0.2172
 E0D  CAQ  C  CH2   0  -0.303  -3.0917  -0.9358  -0.4328
 E0D  CAS  C  CH2   0  -0.434  -4.4818   0.3738   1.2048
 E0D  CAT  C  CH2   0  -0.434  -3.3650   0.1954   2.2287
 E0D  CAU  C  CH2   0  -0.335  -2.5473  -1.0534   1.9308
 E0D  NAO  N  NT    0  -0.453  -2.0435  -1.0017   0.5672
 E0D  C    C  C     0   0.550  -0.7603  -0.7924   0.2189
 E0D  O    O  O     0  -0.474  -0.3887  -0.6434  -0.9326
 E0D  CA   C  CH2   0  -0.485   0.2675  -0.7726   1.3545
 E0D  N    N  NR5   0  -0.514   1.5720  -0.4717   0.8413
 E0D  CAH  C  CR15  0  -0.009   2.4697  -1.3822   0.4139
 E0D  CAE  C  CR56  0   0.380   2.0299   0.7918   0.5380
 E0D  CAF  C  CR16  0  -0.299   1.4330   2.0259   0.7711
 E0D  CAA  C  CR16  0  -0.279   2.1336   3.1511   0.3773
 E0D  CAB  C  CR16  0  -0.258   3.3914   3.0442  -0.2313
 E0D  CAC  C  CR16  0  -0.364   3.9760   1.8126  -0.4634
 E0D  CAD  C  CR56  0   0.080   3.2880   0.6584  -0.0773
 E0D  CAG  C  CR5   0  -0.158   3.5593  -0.7554  -0.1510
 E0D  CAK  C  C     0   0.299   4.7374  -1.3924  -0.7091
 E0D  OAM  O  O     0  -0.433   5.6240  -0.7331  -1.2301
 E0D  CAL  C  CH3   0  -0.782   4.8686  -2.8920  -0.6076
 E0D  H1   H  HOH1  0   0.482  -5.2563   0.5097  -3.1324
 E0D  H2   H  HCH1  0   0.289  -3.2628   1.1934  -0.3703
 E0D  H3   H  HCH2  0   0.262  -3.7271  -1.8207  -0.3263
 E0D  H4   H  HCH2  0   0.281  -2.6465  -0.9620  -1.4223
 E0D  H5   H  HCH2  0   0.254  -5.0034   1.3149   1.3836
 E0D  H6   H  HCH2  0   0.233  -5.2167  -0.4264   1.3314
 E0D  H7   H  HCH2  0   0.230  -2.7064   1.0693   2.2265
 E0D  H8   H  HCH2  0   0.251  -3.7879   0.1193   3.2320
 E0D  H9   H  HCH2  0   0.283  -1.7376  -1.1726   2.6455
 E0D  H10  H  HCH2  0   0.257  -3.1767  -1.9434   2.0237
 E0D  H11  H  HCH2  0   0.305   0.0109  -0.0368   2.1186
 E0D  H12  H  HCH2  0   0.327   0.2999  -1.7415   1.8557
 E0D  H13  H  HCR5  0   0.308   2.2718  -2.4343   0.5479
 E0D  H14  H  HCR6  0   0.259   0.4623   2.1167   1.2423
 E0D  H15  H  HCR6  0   0.257   1.7024   4.1296   0.5422
 E0D  H16  H  HCR6  0   0.252   3.9131   3.9461  -0.5242
 E0D  H17  H  HCR6  0   0.249   4.9452   1.7461  -0.9359
 E0D  H18  H  HCH3  0   0.248   3.9313  -3.4084  -0.4152
 E0D  H19  H  HCH3  0   0.263   5.3046  -3.2901  -1.5228
 E0D  H20  H  HCH3  0   0.270   5.5512  -3.1312   0.2109

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    1.455  0.020  1.455
 E0D  CAA  CAF  aromatic  1.383  0.020  1.383
 E0D  CAA  CAB  aromatic  1.401  0.020  1.401
 E0D  CAF  CAE  aromatic  1.391  0.020  1.391
 E0D  CAT  CAS  single    1.526  0.020  1.526
 E0D  NAO  CAQ  single    1.450  0.020  1.450
 E0D  NAO  C    single    1.346  0.020  1.346
 E0D  CAB  CAC  aromatic  1.383  0.020  1.383
 E0D  CA   C    single    1.532  0.020  1.532
 E0D  CA   N    single    1.434  0.020  1.434
 E0D  CAS  CAR  single    1.526  0.020  1.526
 E0D  CAQ  CAR  single    1.538  0.020  1.538
 E0D  CAE  N    aromatic  1.378  0.020  1.378
 E0D  CAE  CAD  aromatic  1.407  0.020  1.407
 E0D  C    O    double    1.219  0.020  1.219
 E0D  N    CAH  aromatic  1.348  0.020  1.348
 E0D  OAX  CAV  double    1.205  0.020  1.205
 E0D  CAR  CAV  single    1.510  0.020  1.510
 E0D  CAC  CAD  aromatic  1.398  0.020  1.398
 E0D  CAD  CAG  aromatic  1.441  0.020  1.441
 E0D  CAV  OAW  single    1.328  0.020  1.328
 E0D  CAH  CAG  aromatic  1.378  0.020  1.378
 E0D  CAG  CAK  single    1.451  0.020  1.451
 E0D  CAK  OAM  double    1.222  0.020  1.222
 E0D  CAK  CAL  single    1.509  0.020  1.509
 E0D  OAW  H1   single    0.850  0.020  0.980
 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  H1   OAW  CAV  110.13  3.000
 E0D  CAR  CAV  OAX  125.13  3.000
 E0D  CAR  CAV  OAW  111.84  3.000
 E0D  OAX  CAV  OAW  123.03  3.000
 E0D  H2   CAR  CAS  109.28  3.000
 E0D  H2   CAR  CAQ  107.20  3.000
 E0D  CAS  CAR  CAQ  110.40  3.000
 E0D  H2   CAR  CAV  106.72  3.000
 E0D  CAQ  CAR  CAV  110.98  3.000
 E0D  CAS  CAR  CAV  112.05  3.000
 E0D  H4   CAQ  H3   107.90  3.000
 E0D  H4   CAQ  NAO  109.33  3.000
 E0D  H3   CAQ  NAO  108.41  3.000
 E0D  H4   CAQ  CAR  111.79  3.000
 E0D  H3   CAQ  CAR  109.78  3.000
 E0D  NAO  CAQ  CAR  109.56  3.000
 E0D  H6   CAS  H5   106.92  3.000
 E0D  H6   CAS  CAT  109.18  3.000
 E0D  H5   CAS  CAT  109.93  3.000
 E0D  H6   CAS  CAR  109.42  3.000
 E0D  H5   CAS  CAR  110.34  3.000
 E0D  CAT  CAS  CAR  110.95  3.000
 E0D  H8   CAT  H7   106.91  3.000
 E0D  H8   CAT  CAU  109.32  3.000
 E0D  H7   CAT  CAU  109.36  3.000
 E0D  H8   CAT  CAS  109.96  3.000
 E0D  H7   CAT  CAS  110.23  3.000
 E0D  CAU  CAT  CAS  110.97  3.000
 E0D  H10  CAU  H9   106.48  3.000
 E0D  H10  CAU  NAO  107.93  3.000
 E0D  H9   CAU  NAO  111.25  3.000
 E0D  H10  CAU  CAT  109.98  3.000
 E0D  H9   CAU  CAT  111.19  3.000
 E0D  NAO  CAU  CAT  109.90  3.000
 E0D  C    NAO  CAU  125.33  3.000
 E0D  C    NAO  CAQ  120.24  3.000
 E0D  CAU  NAO  CAQ  113.43  3.000
 E0D  CA   C    O    119.61  3.000
 E0D  O    C    NAO  123.64  3.000
 E0D  CA   C    NAO  116.74  3.000
 E0D  H12  CA   H11  106.49  3.000
 E0D  H12  CA   N    108.89  3.000
 E0D  H11  CA   N    108.86  3.000
 E0D  H12  CA   C    110.42  3.000
 E0D  H11  CA   C    111.71  3.000
 E0D  N    CA   C    110.36  3.000
 E0D  CAE  N    CAH  109.17  3.000
 E0D  CAH  N    CA   125.28  3.000
 E0D  CAE  N    CA   125.00  3.000
 E0D  H13  CAH  CAG  129.75  3.000
 E0D  H13  CAH  N    119.81  3.000
 E0D  CAG  CAH  N    110.44  3.000
 E0D  CAD  CAE  CAF  122.77  3.000
 E0D  CAD  CAE  N    107.85  3.000
 E0D  CAF  CAE  N    129.37  3.000
 E0D  H14  CAF  CAA  120.66  3.000
 E0D  H14  CAF  CAE  122.15  3.000
 E0D  CAA  CAF  CAE  117.19  3.000
 E0D  H15  CAA  CAB  119.53  3.000
 E0D  H15  CAA  CAF  119.38  3.000
 E0D  CAB  CAA  CAF  121.09  3.000
 E0D  H16  CAB  CAC  119.53  3.000
 E0D  H16  CAB  CAA  119.11  3.000
 E0D  CAC  CAB  CAA  121.35  3.000
 E0D  H17  CAC  CAD  120.76  3.000
 E0D  H17  CAC  CAB  120.50  3.000
 E0D  CAD  CAC  CAB  118.74  3.000
 E0D  CAG  CAD  CAC  134.67  3.000
 E0D  CAG  CAD  CAE  106.48  3.000
 E0D  CAC  CAD  CAE  118.86  3.000
 E0D  CAK  CAG  CAD  127.09  3.000
 E0D  CAK  CAG  CAH  126.87  3.000
 E0D  CAD  CAG  CAH  106.04  3.000
 E0D  CAL  CAK  OAM  120.14  3.000
 E0D  CAL  CAK  CAG  118.76  3.000
 E0D  OAM  CAK  CAG  121.09  3.000
 E0D  H20  CAL  H19  107.43  3.000
 E0D  H20  CAL  H18  107.58  3.000
 E0D  H19  CAL  H18  108.67  3.000
 E0D  H20  CAL  CAK  108.81  3.000
 E0D  H19  CAL  CAK  109.97  3.000
 E0D  H18  CAL  CAK  114.14  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  CONST_33  H1   OAW  CAV  CAR   180.00   0.0  0
 E0D  Var_01    CAU  CAT  CAS  CAR   -52.95  30.0  1
 E0D  Var_02    CAU  NAO  CAQ  CAR    60.65  30.0  1
 E0D  Var_03    CAT  CAU  NAO  CAQ   -60.42  30.0  1
 E0D  Var_04    NAO  CAU  CAT  CAS    55.16  30.0  1
 E0D  Var_05    N    CA   C    NAO  -177.00  30.0  1
 E0D  Var_06    CAE  N    CA   C      80.42  30.0  2
 E0D  Var_07    OAM  CAK  CAG  CAH   177.28  30.0  2
 E0D  Var_08    H18  CAL  CAK  CAG    19.03  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
 E0D  plan-4  H1   0.020

