# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 14:03:09 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: N-[1-(1H-indol-3-ylmethyl)piperidin-4-yl]glycinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC(=O)NC1CCN(CC1)Cc2c[nH]c3ccccc23
#
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
 2PZ  2PZ  N-[1-(1H-indol-3-ylmethyl)piperidin-4-yl]glycinamide  ligand  43  21  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2PZ
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
 2PZ  CAD  C  CR16  0  -0.308   5.1237  -0.9090   1.0440
 2PZ  CAC  C  CR16  0  -0.284   4.6609  -2.1875   0.7979
 2PZ  CAB  C  CR16  0  -0.270   3.4660  -2.4073   0.0916
 2PZ  CAA  C  CR16  0  -0.365   2.7144  -1.3513  -0.3862
 2PZ  CAF  C  CR56  0   0.030   3.1647  -0.0443  -0.1635
 2PZ  CAE  C  CR56  0   0.349   4.3637   0.1547   0.5580
 2PZ  NAG  N  NR15  0  -0.687   4.5654   1.5007   0.6498
 2PZ  CAI  C  CR15  0  -0.087   3.5433   2.1539   0.0188
 2PZ  CAH  C  CR5   0  -0.012   2.6601   1.2537  -0.5047
 2PZ  CAJ  C  CH2   0  -0.346   1.4423   1.5609  -1.3102
 2PZ  NAK  N  NT    0  -0.405   0.2784   0.8145  -0.8699
 2PZ  CAP  C  CH2   0  -0.276  -0.1233   1.1492   0.4808
 2PZ  CAO  C  CH2   0  -0.444  -1.2444   0.2399   0.9584
 2PZ  CAL  C  CH2   0  -0.281  -0.8279   0.9554  -1.7956
 2PZ  CAM  C  CH2   0  -0.428  -1.9788   0.0374  -1.4150
 2PZ  CAN  C  CH1   0  -0.063  -2.4369   0.3155   0.0137
 2PZ  NAQ  N  NH1   0  -0.640  -3.4805  -0.5914   0.4445
 2PZ  C    C  C     0   0.529  -4.7939  -0.3675   0.2741
 2PZ  O    O  O     0  -0.503  -5.2430   0.6380  -0.2569
 2PZ  CA   C  CH2   0  -0.409  -5.6958  -1.4421   0.8588
 2PZ  N    N  NH2   0  -0.793  -7.0338  -1.3513   0.3173
 2PZ  H1   H  HCR6  0   0.256   6.0405  -0.7409   1.5952
 2PZ  H2   H  HCR6  0   0.247   5.2278  -3.0361   1.1591
 2PZ  H3   H  HCR6  0   0.242   3.1293  -3.4230  -0.0729
 2PZ  H4   H  HCR6  0   0.238   1.7837  -1.5217  -0.9108
 2PZ  H5   H  HNR5  0   0.407   5.3400   1.9485   1.1090
 2PZ  H6   H  HCR5  0   0.280   3.5203   3.2323  -0.0148
 2PZ  H7   H  HCH2  0   0.202   1.2681   2.6513  -1.3006
 2PZ  H8   H  HCH2  0   0.235   1.6189   1.2923  -2.3573
 2PZ  H10  H  HCH2  0   0.246   0.7349   1.0430   1.1460
 2PZ  H11  H  HCH2  0   0.185  -0.4501   2.2032   0.5559
 2PZ  H12  H  HCH2  0   0.224  -0.8721  -0.7889   1.0040
 2PZ  H13  H  HCH2  0   0.241  -1.5433   0.5263   1.9691
 2PZ  H14  H  HCH2  0   0.185  -1.1924   1.9984  -1.8381
 2PZ  H15  H  HCH2  0   0.236  -0.4800   0.7052  -2.8007
 2PZ  H16  H  HCH2  0   0.238  -2.8082   0.1797  -2.1114
 2PZ  H17  H  HCH2  0   0.219  -1.6553  -1.0045  -1.4984
 2PZ  H18  H  HCH1  0   0.235  -2.8432   1.3302   0.0546
 2PZ  H19  H  HNH1  0   0.394  -3.1915  -1.4796   0.8247
 2PZ  H20  H  HCH2  0   0.249  -5.2829  -2.4263   0.6241
 2PZ  H21  H  HCH2  0   0.239  -5.6362  -1.3441   1.9535
 2PZ  H22  H  HNH2  0   0.353  -7.6081  -2.0662   0.7437
 2PZ  H23  H  HNH2  0   0.344  -7.4484  -0.4668   0.5798

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
 2PZ  O    C    double    1.223  0.020  1.223
 2PZ  CA   C    single    1.520  0.020  1.520
 2PZ  CA   N    single    1.446  0.020  1.446
 2PZ  C    NAQ  single    1.343  0.020  1.343
 2PZ  CAO  CAP  single    1.521  0.020  1.521
 2PZ  CAO  CAN  single    1.523  0.020  1.523
 2PZ  CAP  NAK  single    1.448  0.020  1.448
 2PZ  NAQ  CAN  single    1.448  0.020  1.448
 2PZ  CAN  CAM  single    1.526  0.020  1.526
 2PZ  NAK  CAJ  single    1.451  0.020  1.451
 2PZ  NAK  CAL  single    1.449  0.020  1.449
 2PZ  CAJ  CAH  single    1.492  0.020  1.492
 2PZ  CAM  CAL  single    1.520  0.020  1.520
 2PZ  CAI  CAH  aromatic  1.365  0.020  1.365
 2PZ  CAI  NAG  aromatic  1.367  0.020  1.367
 2PZ  CAH  CAF  aromatic  1.434  0.020  1.434
 2PZ  NAG  CAE  aromatic  1.364  0.020  1.364
 2PZ  CAF  CAE  aromatic  1.413  0.020  1.413
 2PZ  CAF  CAA  aromatic  1.400  0.020  1.400
 2PZ  CAE  CAD  aromatic  1.395  0.020  1.395
 2PZ  CAA  CAB  aromatic  1.381  0.020  1.381
 2PZ  CAD  CAC  aromatic  1.382  0.020  1.382
 2PZ  CAB  CAC  aromatic  1.405  0.020  1.405
 2PZ  CAD  H1   single    0.930  0.020  1.080
 2PZ  CAC  H2   single    0.930  0.020  1.080
 2PZ  CAB  H3   single    0.930  0.020  1.080
 2PZ  CAA  H4   single    0.930  0.020  1.080
 2PZ  NAG  H5   single    0.860  0.020  1.020
 2PZ  CAI  H6   single    0.930  0.020  1.080
 2PZ  CAJ  H7   single    0.970  0.020  1.090
 2PZ  CAJ  H8   single    0.970  0.020  1.090
 2PZ  CAP  H10  single    0.970  0.020  1.090
 2PZ  CAP  H11  single    0.970  0.020  1.090
 2PZ  CAO  H12  single    0.970  0.020  1.090
 2PZ  CAO  H13  single    0.970  0.020  1.090
 2PZ  CAL  H14  single    0.970  0.020  1.090
 2PZ  CAL  H15  single    0.970  0.020  1.090
 2PZ  CAM  H16  single    0.970  0.020  1.090
 2PZ  CAM  H17  single    0.970  0.020  1.090
 2PZ  CAN  H18  single    0.970  0.020  1.090
 2PZ  NAQ  H19  single    0.860  0.020  1.020
 2PZ  CA   H20  single    0.970  0.020  1.090
 2PZ  CA   H21  single    0.970  0.020  1.090
 2PZ  N    H22  single    0.890  0.020  1.040
 2PZ  N    H23  single    0.890  0.020  1.040

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
 2PZ  H1   CAD  CAE  121.36  3.000
 2PZ  H1   CAD  CAC  121.19  3.000
 2PZ  CAE  CAD  CAC  117.45  3.000
 2PZ  H2   CAC  CAB  119.36  3.000
 2PZ  H2   CAC  CAD  119.37  3.000
 2PZ  CAB  CAC  CAD  121.27  3.000
 2PZ  H3   CAB  CAA  119.70  3.000
 2PZ  H3   CAB  CAC  119.18  3.000
 2PZ  CAA  CAB  CAC  121.12  3.000
 2PZ  H4   CAA  CAF  120.05  3.000
 2PZ  H4   CAA  CAB  121.02  3.000
 2PZ  CAF  CAA  CAB  118.92  3.000
 2PZ  CAH  CAF  CAE  107.01  3.000
 2PZ  CAE  CAF  CAA  119.04  3.000
 2PZ  CAH  CAF  CAA  133.95  3.000
 2PZ  NAG  CAE  CAF  107.38  3.000
 2PZ  CAF  CAE  CAD  122.19  3.000
 2PZ  NAG  CAE  CAD  130.43  3.000
 2PZ  H5   NAG  CAI  125.01  3.000
 2PZ  H5   NAG  CAE  125.73  3.000
 2PZ  CAI  NAG  CAE  109.26  3.000
 2PZ  H6   CAI  CAH  129.28  3.000
 2PZ  H6   CAI  NAG  120.51  3.000
 2PZ  CAH  CAI  NAG  110.21  3.000
 2PZ  CAJ  CAH  CAI  126.81  3.000
 2PZ  CAI  CAH  CAF  106.14  3.000
 2PZ  CAJ  CAH  CAF  127.02  3.000
 2PZ  H8   CAJ  H7   106.01  3.000
 2PZ  H8   CAJ  NAK  107.06  3.000
 2PZ  H7   CAJ  NAK  112.25  3.000
 2PZ  H8   CAJ  CAH  109.51  3.000
 2PZ  H7   CAJ  CAH  109.11  3.000
 2PZ  NAK  CAJ  CAH  112.65  3.000
 2PZ  CAL  NAK  CAP  111.19  3.000
 2PZ  CAL  NAK  CAJ  111.62  3.000
 2PZ  CAP  NAK  CAJ  112.74  3.000
 2PZ  H11  CAP  H10  106.49  3.000
 2PZ  H11  CAP  CAO  109.31  3.000
 2PZ  H10  CAP  CAO  109.29  3.000
 2PZ  H11  CAP  NAK  111.44  3.000
 2PZ  H10  CAP  NAK  109.14  3.000
 2PZ  CAO  CAP  NAK  111.05  3.000
 2PZ  H13  CAO  H12  107.51  3.000
 2PZ  H13  CAO  CAN  110.28  3.000
 2PZ  H12  CAO  CAN  109.80  3.000
 2PZ  H13  CAO  CAP  109.61  3.000
 2PZ  H12  CAO  CAP  108.92  3.000
 2PZ  CAN  CAO  CAP  110.65  3.000
 2PZ  H15  CAL  H14  106.59  3.000
 2PZ  H15  CAL  CAM  109.46  3.000
 2PZ  H14  CAL  CAM  109.24  3.000
 2PZ  H15  CAL  NAK  108.80  3.000
 2PZ  H14  CAL  NAK  111.59  3.000
 2PZ  CAM  CAL  NAK  111.05  3.000
 2PZ  H17  CAM  H16  107.45  3.000
 2PZ  H17  CAM  CAN  109.49  3.000
 2PZ  H16  CAM  CAN  110.20  3.000
 2PZ  H17  CAM  CAL  109.39  3.000
 2PZ  H16  CAM  CAL  109.67  3.000
 2PZ  CAN  CAM  CAL  110.58  3.000
 2PZ  H18  CAN  NAQ  107.59  3.000
 2PZ  H18  CAN  CAM  108.40  3.000
 2PZ  NAQ  CAN  CAM  112.38  3.000
 2PZ  H18  CAN  CAO  108.28  3.000
 2PZ  CAM  CAN  CAO  109.67  3.000
 2PZ  NAQ  CAN  CAO  110.40  3.000
 2PZ  H19  NAQ  C    118.35  3.000
 2PZ  H19  NAQ  CAN  117.21  3.000
 2PZ  C    NAQ  CAN  124.23  3.000
 2PZ  CA   C    O    122.05  3.000
 2PZ  CA   C    NAQ  114.43  3.000
 2PZ  O    C    NAQ  123.46  3.000
 2PZ  H21  CA   H20  105.86  3.000
 2PZ  H21  CA   N    114.63  3.000
 2PZ  H20  CA   N    109.01  3.000
 2PZ  H21  CA   C    106.71  3.000
 2PZ  H20  CA   C    109.27  3.000
 2PZ  N    CA   C    111.13  3.000
 2PZ  H23  N    H22  106.02  3.000
 2PZ  H23  N    CA   109.69  3.000
 2PZ  H22  N    CA   108.85  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
 2PZ  CONST_01  CAI  NAG  CAE  CAD   180.00   0.0  0
 2PZ  CONST_02  CAH  CAF  CAE  CAD   180.00   0.0  0
 2PZ  CONST_03  CAA  CAF  CAE  CAD     0.00   0.0  0
 2PZ  CONST_04  CAA  CAB  CAC  CAD     0.00   0.0  0
 2PZ  CONST_05  NAG  CAE  CAD  CAC   180.00   0.0  0
 2PZ  CONST_06  CAF  CAE  CAD  CAC     0.00   0.0  0
 2PZ  CONST_07  CAF  CAA  CAB  CAC     0.00   0.0  0
 2PZ  CONST_08  CAH  CAF  CAA  CAB   180.00   0.0  0
 2PZ  CONST_09  CAE  CAF  CAA  CAB     0.00   0.0  0
 2PZ  CONST_10  CAE  CAD  CAC  CAB     0.00   0.0  0
 2PZ  CONST_11  CAI  CAH  CAF  CAA   180.00   0.0  0
 2PZ  CONST_12  NAG  CAE  CAF  CAA   180.00   0.0  0
 2PZ  CONST_13  NAG  CAI  CAH  CAF     0.00   0.0  0
 2PZ  CONST_14  CAI  NAG  CAE  CAF     0.00   0.0  0
 2PZ  CONST_15  CAH  CAI  NAG  CAE     0.00   0.0  0
 2PZ  CONST_16  CAI  CAH  CAF  CAE     0.00   0.0  0
 2PZ  CONST_17  CAH  CAF  CAE  NAG     0.00   0.0  0
 2PZ  CONST_18  CAJ  CAH  CAF  CAA     0.00   0.0  0
 2PZ  CONST_19  CAJ  CAH  CAF  CAE   180.00   0.0  0
 2PZ  CONST_20  CAJ  CAH  CAI  NAG   180.00   0.0  0
 2PZ  CONST_21  H5   NAG  CAE  CAD     0.00   0.0  0
 2PZ  CONST_22  H3   CAB  CAC  CAD   180.00   0.0  0
 2PZ  CONST_23  H4   CAA  CAB  CAC   180.00   0.0  0
 2PZ  CONST_24  H1   CAD  CAC  CAB   180.00   0.0  0
 2PZ  CONST_25  H2   CAC  CAB  CAA   180.00   0.0  0
 2PZ  CONST_26  H6   CAI  CAH  CAF   180.00   0.0  0
 2PZ  CONST_27  O    C    NAQ  CAN     0.00   0.0  0
 2PZ  CONST_28  CA   C    NAQ  CAN   180.00   0.0  0
 2PZ  CONST_29  H19  NAQ  C    O     180.00   0.0  0
 2PZ  Var_01    CAN  CAO  CAP  NAK   -56.93  30.0  1
 2PZ  Var_02    CAN  CAM  CAL  NAK    56.88  30.0  1
 2PZ  Var_03    CAM  CAL  NAK  CAP   -60.11  30.0  1
 2PZ  Var_04    CAL  NAK  CAP  CAO    60.09  30.0  1
 2PZ  Var_05    NAK  CAJ  CAH  CAF    48.59  30.0  2
 2PZ  Var_06    CAP  NAK  CAJ  CAH    63.61  30.0  1
 2PZ  Var_07    N    CA   C    NAQ  -163.31  30.0  1
 2PZ  Var_08    H22  N    CA   C    -178.74  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
 2PZ  chir_01  CAN  CAO  NAQ  CAM  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
 2PZ  plan-1  CAD  0.020
 2PZ  plan-1  CAC  0.020
 2PZ  plan-1  CAB  0.020
 2PZ  plan-1  CAA  0.020
 2PZ  plan-1  CAF  0.020
 2PZ  plan-1  CAE  0.020
 2PZ  plan-1  NAG  0.020
 2PZ  plan-1  CAI  0.020
 2PZ  plan-1  CAH  0.020
 2PZ  plan-1  CAJ  0.020
 2PZ  plan-1  H1   0.020
 2PZ  plan-1  H2   0.020
 2PZ  plan-1  H3   0.020
 2PZ  plan-1  H4   0.020
 2PZ  plan-1  H5   0.020
 2PZ  plan-1  H6   0.020
 2PZ  plan-2  CAN  0.020
 2PZ  plan-2  NAQ  0.020
 2PZ  plan-2  C    0.020
 2PZ  plan-2  O    0.020
 2PZ  plan-2  CA   0.020
 2PZ  plan-2  H19  0.020

