# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 15:44:04 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: N-(1-benzylpiperidin-4-yl)-4-iodobenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Ic1ccc(cc1)C(=O)NC2CCN(CC2)Cc3ccccc3
#
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
 61V  61V  N-(1-benzylpiperidin-4-yl)-4-iodobenzamide  ligand  44  23  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_61V
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
 61V  CAA  C  CH2   0  -0.438  -2.9637   0.1235   0.7689
 61V  CAB  C  CH2   0  -0.282  -4.4233  -0.2765   0.9145
 61V  CAD  C  CH2   0  -0.286  -4.2039  -1.9846  -0.7482
 61V  CAE  C  CH2   0  -0.432  -2.7347  -1.6549  -0.9620
 61V  CAF  C  CH1   0  -0.078  -2.1306  -1.0662   0.3093
 61V  CAJ  C  CR6   0  -0.037   1.6531  -0.8436   0.2458
 61V  CAK  C  CR16  0  -0.260   2.7316  -1.7127   0.1066
 61V  CAL  C  CR16  0  -0.212   4.0108  -1.2289  -0.1169
 61V  CAM  C  CR6   0  -0.223   4.2136   0.1429  -0.1809
 61V  CAN  C  CR16  0  -0.210   3.1578   1.0286  -0.0254
 61V  CAO  C  CR16  0  -0.282   1.8810   0.5284   0.1854
 61V  CAR  C  CR6   0   0.088  -7.1962   0.1604  -0.0988
 61V  CAS  C  CR16  0  -0.314  -8.2024   0.2514   0.8561
 61V  CAT  C  CR16  0  -0.242  -8.9915   1.3923   0.9532
 61V  CAU  C  CR16  0  -0.271  -8.7768   2.4610   0.0950
 61V  CAV  C  CR16  0  -0.243  -7.7687   2.3813  -0.8599
 61V  CAW  C  CR16  0  -0.283  -6.9859   1.2404  -0.9550
 61V  NAC  N  NT    0  -0.413  -4.9494  -0.8114  -0.3280
 61V  NAG  N  NH1   0  -0.653  -0.7464  -0.6792   0.1264
 61V  OAI  O  O     0  -0.488   0.1889  -2.5295   1.0309
 61V  IAP  I  I     0   0.069   6.1499   0.8893  -0.5092
 61V  H1   H  HCH2  0   0.225  -2.8846   0.9373   0.0406
 61V  H2   H  HCH2  0   0.245  -2.5910   0.4997   1.7238
 61V  H3   H  HCH2  0   0.192  -4.5221  -1.0095   1.7362
 61V  H4   H  HCH2  0   0.247  -5.0083   0.5983   1.2041
 61V  H5   H  HCH2  0   0.241  -4.6336  -2.3576  -1.6807
 61V  H6   H  HCH2  0   0.191  -4.2863  -2.8034  -0.0105
 61V  H7   H  HCH2  0   0.243  -2.1954  -2.5593  -1.2520
 61V  H8   H  HCH2  0   0.223  -2.6355  -0.9347  -1.7803
 61V  H9   H  HCH1  0   0.245  -2.1522  -1.8283   1.0917
 61V  H10  H  HCR6  0   0.271   2.5770  -2.7817   0.1649
 61V  H11  H  HCR6  0   0.285   4.8312  -1.9233  -0.2340
 61V  H12  H  HCR6  0   0.286   3.3118   2.0982  -0.0583
 61V  H13  H  HCR6  0   0.269   1.0748   1.2371   0.3258
 61V  H14  H  HCH2  0   0.211  -6.6002  -1.7790   0.5961
 61V  H15  H  HCH2  0   0.250  -6.6673  -1.6091  -1.1506
 61V  H16  H  HCR6  0   0.247  -8.3708  -0.5759   1.5361
 61V  H17  H  HCR6  0   0.253  -9.7691   1.4458   1.7043
 61V  H18  H  HCR6  0   0.253  -9.3868   3.3520   0.1701
 61V  H19  H  HCR6  0   0.252  -7.5931   3.2117  -1.5322
 61V  H20  H  HCR6  0   0.244  -6.1944   1.1855  -1.6920
 61V  H22  H  HNH1  0   0.403  -0.5777   0.1447  -0.4296
 61V  CAH  C  C     0   0.536   0.2997  -1.4307   0.5032
 61V  CAQ  C  CH2   0  -0.321  -6.3674  -1.0907  -0.2345

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
 61V  CAT  CAS  aromatic  1.391  0.020  1.391
 61V  CAT  CAU  aromatic  1.387  0.020  1.387
 61V  CAS  CAR  aromatic  1.390  0.020  1.390
 61V  CAU  CAV  aromatic  1.391  0.020  1.391
 61V  CAR  CAQ  single    1.507  0.020  1.507
 61V  CAR  CAW  aromatic  1.394  0.020  1.394
 61V  CAQ  NAC  single    1.448  0.020  1.448
 61V  CAV  CAW  aromatic  1.387  0.020  1.387
 61V  CAD  NAC  single    1.452  0.020  1.452
 61V  CAD  CAE  single    1.521  0.020  1.521
 61V  NAC  CAB  single    1.451  0.020  1.451
 61V  CAE  CAF  single    1.526  0.020  1.526
 61V  CAB  CAA  single    1.520  0.020  1.520
 61V  CAA  CAF  single    1.523  0.020  1.523
 61V  CAF  NAG  single    1.449  0.020  1.449
 61V  OAI  CAH  double    1.224  0.020  1.224
 61V  NAG  CAH  single    1.342  0.020  1.342
 61V  CAH  CAJ  single    1.498  0.020  1.498
 61V  CAJ  CAK  aromatic  1.392  0.020  1.392
 61V  CAJ  CAO  aromatic  1.392  0.020  1.392
 61V  CAK  CAL  aromatic  1.386  0.020  1.386
 61V  CAO  CAN  aromatic  1.387  0.020  1.387
 61V  CAL  CAM  aromatic  1.388  0.020  1.388
 61V  CAN  CAM  aromatic  1.387  0.020  1.387
 61V  CAM  IAP  single    2.101  0.020  2.101
 61V  CAA  H1   single    0.970  0.020  1.090
 61V  CAA  H2   single    0.970  0.020  1.090
 61V  CAB  H3   single    0.970  0.020  1.090
 61V  CAB  H4   single    0.970  0.020  1.090
 61V  CAD  H5   single    0.970  0.020  1.090
 61V  CAD  H6   single    0.970  0.020  1.090
 61V  CAE  H7   single    0.970  0.020  1.090
 61V  CAE  H8   single    0.970  0.020  1.090
 61V  CAF  H9   single    0.970  0.020  1.090
 61V  CAK  H10  single    0.930  0.020  1.080
 61V  CAL  H11  single    0.930  0.020  1.080
 61V  CAN  H12  single    0.930  0.020  1.080
 61V  CAO  H13  single    0.930  0.020  1.080
 61V  CAQ  H14  single    0.970  0.020  1.090
 61V  CAQ  H15  single    0.970  0.020  1.090
 61V  CAS  H16  single    0.930  0.020  1.080
 61V  CAT  H17  single    0.930  0.020  1.080
 61V  CAU  H18  single    0.930  0.020  1.080
 61V  CAV  H19  single    0.930  0.020  1.080
 61V  CAW  H20  single    0.930  0.020  1.080
 61V  NAG  H22  single    0.860  0.020  1.020

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
 61V  H2   CAA  H1   107.51  3.000
 61V  H2   CAA  CAF  110.26  3.000
 61V  H1   CAA  CAF  109.89  3.000
 61V  H2   CAA  CAB  109.55  3.000
 61V  H1   CAA  CAB  109.18  3.000
 61V  CAF  CAA  CAB  110.40  3.000
 61V  H4   CAB  H3   106.64  3.000
 61V  H4   CAB  NAC  109.16  3.000
 61V  H3   CAB  NAC  111.07  3.000
 61V  H4   CAB  CAA  109.21  3.000
 61V  H3   CAB  CAA  109.35  3.000
 61V  NAC  CAB  CAA  111.28  3.000
 61V  H6   CAD  H5   106.70  3.000
 61V  H6   CAD  NAC  111.54  3.000
 61V  H5   CAD  NAC  108.72  3.000
 61V  H6   CAD  CAE  109.05  3.000
 61V  H5   CAD  CAE  109.51  3.000
 61V  NAC  CAD  CAE  111.19  3.000
 61V  H8   CAE  H7   107.55  3.000
 61V  H8   CAE  CAF  109.46  3.000
 61V  H7   CAE  CAF  110.20  3.000
 61V  H8   CAE  CAD  109.59  3.000
 61V  H7   CAE  CAD  109.57  3.000
 61V  CAF  CAE  CAD  110.43  3.000
 61V  H9   CAF  NAG  107.20  3.000
 61V  H9   CAF  CAE  108.65  3.000
 61V  NAG  CAF  CAE  112.10  3.000
 61V  H9   CAF  CAA  108.53  3.000
 61V  NAG  CAF  CAA  110.61  3.000
 61V  CAE  CAF  CAA  109.65  3.000
 61V  CAO  CAJ  CAK  118.95  3.000
 61V  CAO  CAJ  CAH  122.81  3.000
 61V  CAK  CAJ  CAH  118.20  3.000
 61V  H10  CAK  CAL  119.05  3.000
 61V  H10  CAK  CAJ  120.06  3.000
 61V  CAL  CAK  CAJ  120.88  3.000
 61V  H11  CAL  CAM  121.25  3.000
 61V  H11  CAL  CAK  119.58  3.000
 61V  CAM  CAL  CAK  119.16  3.000
 61V  IAP  CAM  CAN  119.49  3.000
 61V  IAP  CAM  CAL  119.53  3.000
 61V  CAN  CAM  CAL  120.98  3.000
 61V  H12  CAN  CAO  119.50  3.000
 61V  H12  CAN  CAM  121.33  3.000
 61V  CAO  CAN  CAM  119.16  3.000
 61V  H13  CAO  CAN  117.97  3.000
 61V  H13  CAO  CAJ  121.17  3.000
 61V  CAN  CAO  CAJ  120.84  3.000
 61V  CAW  CAR  CAS  118.71  3.000
 61V  CAW  CAR  CAQ  120.32  3.000
 61V  CAS  CAR  CAQ  120.95  3.000
 61V  H16  CAS  CAT  119.62  3.000
 61V  H16  CAS  CAR  119.56  3.000
 61V  CAT  CAS  CAR  120.82  3.000
 61V  H17  CAT  CAU  120.15  3.000
 61V  H17  CAT  CAS  119.78  3.000
 61V  CAU  CAT  CAS  120.07  3.000
 61V  H18  CAU  CAV  120.22  3.000
 61V  H18  CAU  CAT  120.27  3.000
 61V  CAV  CAU  CAT  119.52  3.000
 61V  H19  CAV  CAW  119.79  3.000
 61V  H19  CAV  CAU  119.99  3.000
 61V  CAW  CAV  CAU  120.22  3.000
 61V  H20  CAW  CAV  120.07  3.000
 61V  H20  CAW  CAR  119.27  3.000
 61V  CAV  CAW  CAR  120.66  3.000
 61V  CAQ  NAC  CAD  111.44  3.000
 61V  CAD  NAC  CAB  111.06  3.000
 61V  CAQ  NAC  CAB  111.76  3.000
 61V  H22  NAG  CAH  118.82  3.000
 61V  H22  NAG  CAF  116.60  3.000
 61V  CAH  NAG  CAF  124.04  3.000
 61V  OAI  CAH  NAG  123.58  3.000
 61V  NAG  CAH  CAJ  115.89  3.000
 61V  OAI  CAH  CAJ  120.52  3.000
 61V  H15  CAQ  H14  106.07  3.000
 61V  H15  CAQ  NAC  107.79  3.000
 61V  H14  CAQ  NAC  112.04  3.000
 61V  H15  CAQ  CAR  108.54  3.000
 61V  H14  CAQ  CAR  109.52  3.000
 61V  NAC  CAQ  CAR  112.60  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
 61V  CONST_01  CAM  CAL  CAK  CAJ     0.00   0.0  0
 61V  CONST_02  CAM  CAN  CAO  CAJ     0.00   0.0  0
 61V  CONST_03  CAN  CAO  CAJ  CAK     0.00   0.0  0
 61V  CONST_04  CAN  CAM  CAL  CAK     0.00   0.0  0
 61V  CONST_05  CAO  CAJ  CAK  CAL     0.00   0.0  0
 61V  CONST_06  CAO  CAN  CAM  CAL     0.00   0.0  0
 61V  CONST_07  CAU  CAT  CAS  CAR     0.00   0.0  0
 61V  CONST_08  CAU  CAV  CAW  CAR     0.00   0.0  0
 61V  CONST_09  CAV  CAU  CAT  CAS     0.00   0.0  0
 61V  CONST_10  CAV  CAW  CAR  CAS     0.00   0.0  0
 61V  CONST_11  CAW  CAR  CAS  CAT     0.00   0.0  0
 61V  CONST_12  CAW  CAV  CAU  CAT     0.00   0.0  0
 61V  CONST_13  CAL  CAK  CAJ  CAH   180.00   0.0  0
 61V  CONST_14  CAN  CAO  CAJ  CAH   180.00   0.0  0
 61V  CONST_15  IAP  CAM  CAL  CAK   180.00   0.0  0
 61V  CONST_16  IAP  CAM  CAN  CAO   180.00   0.0  0
 61V  CONST_17  CAT  CAS  CAR  CAQ   180.00   0.0  0
 61V  CONST_18  CAV  CAW  CAR  CAQ   180.00   0.0  0
 61V  CONST_19  H11  CAL  CAK  CAJ   180.00   0.0  0
 61V  CONST_20  H12  CAN  CAO  CAJ   180.00   0.0  0
 61V  CONST_21  H13  CAO  CAJ  CAK   180.00   0.0  0
 61V  CONST_22  H10  CAK  CAL  CAM   180.00   0.0  0
 61V  CONST_23  H17  CAT  CAS  CAR   180.00   0.0  0
 61V  CONST_24  H19  CAV  CAW  CAR   180.00   0.0  0
 61V  CONST_25  H18  CAU  CAT  CAS   180.00   0.0  0
 61V  CONST_26  H20  CAW  CAR  CAS   180.00   0.0  0
 61V  CONST_27  H16  CAS  CAT  CAU   180.00   0.0  0
 61V  CONST_28  CAJ  CAH  NAG  CAF   180.00   0.0  0
 61V  CONST_29  OAI  CAH  NAG  CAF     0.00   0.0  0
 61V  CONST_30  H22  NAG  CAH  CAJ     0.00   0.0  0
 61V  Var_01    CAD  NAC  CAB  CAA    59.72  30.0  1
 61V  Var_02    CAE  CAD  NAC  CAB   -59.65  30.0  1
 61V  Var_03    NAC  CAD  CAE  CAF    57.00  30.0  1
 61V  Var_04    NAC  CAB  CAA  CAF   -57.10  30.0  1
 61V  Var_05    CAR  CAQ  NAC  CAB    67.64  30.0  2
 61V  Var_06    NAC  CAQ  CAR  CAS  -133.28  30.0  2
 61V  Var_07    OAI  CAH  CAJ  CAK    25.14  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
 61V  chir_01  CAF  CAE  CAA  NAG  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
 61V  plan-1  CAJ  0.020
 61V  plan-1  CAK  0.020
 61V  plan-1  CAL  0.020
 61V  plan-1  CAM  0.020
 61V  plan-1  CAN  0.020
 61V  plan-1  CAO  0.020
 61V  plan-1  IAP  0.020
 61V  plan-1  H10  0.020
 61V  plan-1  H11  0.020
 61V  plan-1  H12  0.020
 61V  plan-1  H13  0.020
 61V  plan-1  CAH  0.020
 61V  plan-2  CAR  0.020
 61V  plan-2  CAS  0.020
 61V  plan-2  CAT  0.020
 61V  plan-2  CAU  0.020
 61V  plan-2  CAV  0.020
 61V  plan-2  CAW  0.020
 61V  plan-2  H16  0.020
 61V  plan-2  H17  0.020
 61V  plan-2  H18  0.020
 61V  plan-2  H19  0.020
 61V  plan-2  H20  0.020
 61V  plan-2  CAQ  0.020
 61V  plan-3  CAF  0.020
 61V  plan-3  CAJ  0.020
 61V  plan-3  NAG  0.020
 61V  plan-3  OAI  0.020
 61V  plan-3  H22  0.020
 61V  plan-3  CAH  0.020

