# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 16:49:26 2021
#   Inital geometry file: a 93 line input string
#   Ligand name: 1-(phenylmethyl)-4-pyrrolidin-1-yl-pyridin-1-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CCN(C1)c2cc[n+](Cc3ccccc3)cc2
#
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
 QTK  QTK  1-(phenylmethyl)-4-pyrrolidin-1-yl-pyridin-1-ium  ligand  37  18  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_QTK
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
 QTK  CAP  C  CH2   0  -0.291   6.9609  -26.7963  -28.1773
 QTK  CAN  C  CH2   0  -0.479   6.2768  -26.3899  -29.4753
 QTK  CAO  C  CH2   0  -0.482   7.1003  -25.1959  -29.9450
 QTK  CAQ  C  CH2   0  -0.290   8.5267  -25.5922  -29.5884
 QTK  NAW  N  NT    0  -0.503   8.3595  -26.4377  -28.4069
 QTK  CAV  C  CR6   0   0.544   9.3609  -26.8329  -27.6387
 QTK  CAK  C  CR16  0  -0.441   9.1479  -27.5918  -26.4556
 QTK  CAM  C  CR16  0   0.093  10.2025  -27.9768  -25.6918
 QTK  CAJ  C  CR16  0  -0.444  10.7115  -26.5253  -27.9474
 QTK  CAL  C  CR16  0   0.072  11.7144  -26.9526  -27.1336
 QTK  NAX  N  NR6   1  -0.448  11.4753  -27.6694  -26.0187
 QTK  CAR  C  CH2   0  -0.414  12.5690  -28.1007  -25.1400
 QTK  CAS  C  CR6   0   0.105  12.4947  -27.4401  -23.7903
 QTK  CAG  C  CR16  0  -0.303  12.4568  -28.2158  -22.6382
 QTK  CAI  C  CR16  0  -0.239  12.4044  -27.6152  -21.3860
 QTK  CAF  C  CR16  0  -0.281  12.4748  -26.0515  -23.6788
 QTK  CAH  C  CR16  0  -0.239  12.4168  -25.4515  -22.4306
 QTK  CAU  C  CR16  0  -0.260  12.3826  -26.2325  -21.2805
 QTK  H1   H  HCH2  0   0.260   6.5656  -26.2428  -27.3208
 QTK  H2   H  HCH2  0   0.267   6.8605  -27.8619  -27.9687
 QTK  H3   H  HCH2  0   0.262   5.2249  -26.1547  -29.3239
 QTK  H4   H  HCH2  0   0.249   6.3398  -27.2038  -30.1998
 QTK  H5   H  HCH2  0   0.249   6.8114  -24.2972  -29.3969
 QTK  H6   H  HCH2  0   0.263   6.9906  -24.9895  -31.0081
 QTK  H7   H  HCH2  0   0.259   9.0002  -26.1606  -30.3939
 QTK  H8   H  HCH2  0   0.267   9.1570  -24.7311  -29.3635
 QTK  H9   H  HCR6  0   0.314   8.1568  -27.8683  -26.1298
 QTK  H10  H  HCR6  0   0.334  10.0617  -28.5486  -24.7856
 QTK  H11  H  HCR6  0   0.314  10.9806  -25.9642  -28.8291
 QTK  H12  H  HCR6  0   0.339  12.7488  -26.7363  -27.3572
 QTK  H13  H  HCH2  0   0.308  12.5232  -29.1852  -25.0445
 QTK  H14  H  HCH2  0   0.306  13.5031  -27.8586  -25.6446
 QTK  H15  H  HCR6  0   0.262  12.4661  -29.2962  -22.7179
 QTK  H16  H  HCR6  0   0.262  12.3747  -28.2309  -20.4967
 QTK  H17  H  HCR6  0   0.258  12.5053  -25.4295  -24.5660
 QTK  H18  H  HCR6  0   0.262  12.4017  -24.3722  -22.3536
 QTK  H19  H  HCR6  0   0.262  12.3371  -25.7622  -20.3068

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
 QTK  CAO  CAQ  single    1.523  0.020  1.523
 QTK  CAO  CAN  single    1.525  0.020  1.525
 QTK  CAQ  NAW  single    1.462  0.020  1.462
 QTK  CAN  CAP  single    1.522  0.020  1.522
 QTK  NAW  CAP  single    1.462  0.020  1.462
 QTK  NAW  CAV  single    1.323  0.020  1.323
 QTK  CAJ  CAV  aromatic  1.419  0.020  1.419
 QTK  CAJ  CAL  aromatic  1.360  0.020  1.360
 QTK  CAV  CAK  aromatic  1.422  0.020  1.422
 QTK  CAL  NAX  aromatic  1.347  0.020  1.347
 QTK  CAK  CAM  aromatic  1.358  0.020  1.358
 QTK  NAX  CAM  aromatic  1.350  0.020  1.350
 QTK  NAX  CAR  single    1.468  0.020  1.468
 QTK  CAR  CAS  single    1.505  0.020  1.505
 QTK  CAS  CAF  aromatic  1.393  0.020  1.393
 QTK  CAS  CAG  aromatic  1.389  0.020  1.389
 QTK  CAF  CAH  aromatic  1.386  0.020  1.386
 QTK  CAG  CAI  aromatic  1.390  0.020  1.390
 QTK  CAH  CAU  aromatic  1.391  0.020  1.391
 QTK  CAI  CAU  aromatic  1.387  0.020  1.387
 QTK  CAP  H1   single    0.970  0.020  1.090
 QTK  CAP  H2   single    0.970  0.020  1.090
 QTK  CAN  H3   single    0.970  0.020  1.090
 QTK  CAN  H4   single    0.970  0.020  1.090
 QTK  CAO  H5   single    0.970  0.020  1.090
 QTK  CAO  H6   single    0.970  0.020  1.090
 QTK  CAQ  H7   single    0.970  0.020  1.090
 QTK  CAQ  H8   single    0.970  0.020  1.090
 QTK  CAK  H9   single    0.930  0.020  1.080
 QTK  CAM  H10  single    0.930  0.020  1.080
 QTK  CAJ  H11  single    0.930  0.020  1.080
 QTK  CAL  H12  single    0.930  0.020  1.080
 QTK  CAR  H13  single    0.970  0.020  1.090
 QTK  CAR  H14  single    0.970  0.020  1.090
 QTK  CAG  H15  single    0.930  0.020  1.080
 QTK  CAI  H16  single    0.930  0.020  1.080
 QTK  CAF  H17  single    0.930  0.020  1.080
 QTK  CAH  H18  single    0.930  0.020  1.080
 QTK  CAU  H19  single    0.930  0.020  1.080

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
 QTK  H2   CAP  H1   108.15  3.000
 QTK  H2   CAP  NAW  110.96  3.000
 QTK  H1   CAP  NAW  110.16  3.000
 QTK  H2   CAP  CAN  112.50  3.000
 QTK  H1   CAP  CAN  111.73  3.000
 QTK  NAW  CAP  CAN  103.32  3.000
 QTK  H4   CAN  H3   108.01  3.000
 QTK  H4   CAN  CAO  110.38  3.000
 QTK  H3   CAN  CAO  113.30  3.000
 QTK  H4   CAN  CAP  109.94  3.000
 QTK  H3   CAN  CAP  111.92  3.000
 QTK  CAO  CAN  CAP  103.24  3.000
 QTK  H6   CAO  H5   107.92  3.000
 QTK  H6   CAO  CAQ  111.86  3.000
 QTK  H5   CAO  CAQ  110.16  3.000
 QTK  H6   CAO  CAN  113.26  3.000
 QTK  H5   CAO  CAN  110.31  3.000
 QTK  CAQ  CAO  CAN  103.30  3.000
 QTK  H8   CAQ  H7   108.18  3.000
 QTK  H8   CAQ  NAW  110.85  3.000
 QTK  H7   CAQ  NAW  110.12  3.000
 QTK  H8   CAQ  CAO  112.60  3.000
 QTK  H7   CAQ  CAO  111.61  3.000
 QTK  NAW  CAQ  CAO  103.45  3.000
 QTK  CAV  NAW  CAQ  123.74  3.000
 QTK  CAV  NAW  CAP  124.04  3.000
 QTK  CAQ  NAW  CAP  112.21  3.000
 QTK  CAJ  CAV  CAK  116.06  3.000
 QTK  CAK  CAV  NAW  121.97  3.000
 QTK  CAJ  CAV  NAW  121.97  3.000
 QTK  H9   CAK  CAM  118.08  3.000
 QTK  H9   CAK  CAV  121.71  3.000
 QTK  CAM  CAK  CAV  120.21  3.000
 QTK  H10  CAM  NAX  116.52  3.000
 QTK  H10  CAM  CAK  121.37  3.000
 QTK  NAX  CAM  CAK  122.12  3.000
 QTK  H11  CAJ  CAL  117.92  3.000
 QTK  H11  CAJ  CAV  121.85  3.000
 QTK  CAL  CAJ  CAV  120.23  3.000
 QTK  H12  CAL  NAX  116.61  3.000
 QTK  H12  CAL  CAJ  121.28  3.000
 QTK  NAX  CAL  CAJ  122.11  3.000
 QTK  CAR  NAX  CAL  121.31  3.000
 QTK  CAR  NAX  CAM  119.39  3.000
 QTK  CAL  NAX  CAM  119.28  3.000
 QTK  H14  CAR  H13  107.33  3.000
 QTK  H14  CAR  CAS  111.12  3.000
 QTK  H13  CAR  CAS  110.87  3.000
 QTK  H14  CAR  NAX  107.25  3.000
 QTK  H13  CAR  NAX  108.28  3.000
 QTK  CAS  CAR  NAX  111.80  3.000
 QTK  CAF  CAS  CAG  119.32  3.000
 QTK  CAG  CAS  CAR  120.00  3.000
 QTK  CAF  CAS  CAR  120.67  3.000
 QTK  H15  CAG  CAI  119.84  3.000
 QTK  H15  CAG  CAS  119.71  3.000
 QTK  CAI  CAG  CAS  120.46  3.000
 QTK  H16  CAI  CAU  120.29  3.000
 QTK  H16  CAI  CAG  119.71  3.000
 QTK  CAU  CAI  CAG  119.99  3.000
 QTK  H17  CAF  CAH  119.33  3.000
 QTK  H17  CAF  CAS  120.40  3.000
 QTK  CAH  CAF  CAS  120.27  3.000
 QTK  H18  CAH  CAU  120.07  3.000
 QTK  H18  CAH  CAF  119.76  3.000
 QTK  CAU  CAH  CAF  120.17  3.000
 QTK  H19  CAU  CAH  120.07  3.000
 QTK  H19  CAU  CAI  120.15  3.000
 QTK  CAH  CAU  CAI  119.78  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
 QTK  CONST_01  NAX  CAL  CAJ  CAV    0.00   0.0  0
 QTK  CONST_02  NAX  CAM  CAK  CAV    0.00   0.0  0
 QTK  CONST_03  CAL  CAJ  CAV  CAK    0.00   0.0  0
 QTK  CONST_04  CAL  NAX  CAM  CAK    0.00   0.0  0
 QTK  CONST_05  CAJ  CAV  CAK  CAM    0.00   0.0  0
 QTK  CONST_06  CAJ  CAL  NAX  CAM    0.00   0.0  0
 QTK  CONST_07  CAU  CAH  CAF  CAS    0.00   0.0  0
 QTK  CONST_08  CAU  CAI  CAG  CAS    0.00   0.0  0
 QTK  CONST_09  CAH  CAF  CAS  CAG    0.00   0.0  0
 QTK  CONST_10  CAH  CAU  CAI  CAG    0.00   0.0  0
 QTK  CONST_11  CAF  CAS  CAG  CAI    0.00   0.0  0
 QTK  CONST_12  CAF  CAH  CAU  CAI    0.00   0.0  0
 QTK  CONST_13  CAL  CAJ  CAV  NAW  180.00   0.0  0
 QTK  CONST_14  CAM  CAK  CAV  NAW  180.00   0.0  0
 QTK  CONST_15  CAR  NAX  CAM  CAK  180.00   0.0  0
 QTK  CONST_16  CAR  NAX  CAL  CAJ  180.00   0.0  0
 QTK  CONST_17  CAH  CAF  CAS  CAR  180.00   0.0  0
 QTK  CONST_18  CAI  CAG  CAS  CAR  180.00   0.0  0
 QTK  CONST_19  H11  CAJ  CAV  NAW    0.00   0.0  0
 QTK  CONST_20  H9   CAK  CAV  NAW    0.00   0.0  0
 QTK  CONST_21  H12  CAL  CAJ  CAV  180.00   0.0  0
 QTK  CONST_22  H10  CAM  CAK  CAV  180.00   0.0  0
 QTK  CONST_23  H18  CAH  CAF  CAS  180.00   0.0  0
 QTK  CONST_24  H16  CAI  CAG  CAS  180.00   0.0  0
 QTK  CONST_25  H17  CAF  CAS  CAG  180.00   0.0  0
 QTK  CONST_26  H19  CAU  CAI  CAG  180.00   0.0  0
 QTK  CONST_27  H15  CAG  CAS  CAF  180.00   0.0  0
 QTK  Var_01    CAQ  CAO  CAN  CAP   38.38  30.0  1
 QTK  Var_02    CAO  CAQ  NAW  CAP   11.15  30.0  1
 QTK  Var_03    CAJ  CAV  NAW  CAP  176.14  30.0  2
 QTK  Var_04    NAW  CAQ  CAO  CAN  -30.34  30.0  1
 QTK  Var_05    CAQ  NAW  CAP  CAN   12.69  30.0  1
 QTK  Var_06    NAW  CAP  CAN  CAO  -31.23  30.0  1
 QTK  Var_07    CAS  CAR  NAX  CAM  -64.68  30.0  2
 QTK  Var_08    CAF  CAS  CAR  NAX  -56.13  30.0  2

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
 QTK  plan-1  NAW  0.020
 QTK  plan-1  CAV  0.020
 QTK  plan-1  CAK  0.020
 QTK  plan-1  CAM  0.020
 QTK  plan-1  CAJ  0.020
 QTK  plan-1  CAL  0.020
 QTK  plan-1  NAX  0.020
 QTK  plan-1  CAR  0.020
 QTK  plan-1  H9   0.020
 QTK  plan-1  H10  0.020
 QTK  plan-1  H11  0.020
 QTK  plan-1  H12  0.020
 QTK  plan-2  CAR  0.020
 QTK  plan-2  CAS  0.020
 QTK  plan-2  CAG  0.020
 QTK  plan-2  CAI  0.020
 QTK  plan-2  CAF  0.020
 QTK  plan-2  CAH  0.020
 QTK  plan-2  CAU  0.020
 QTK  plan-2  H15  0.020
 QTK  plan-2  H16  0.020
 QTK  plan-2  H17  0.020
 QTK  plan-2  H18  0.020
 QTK  plan-2  H19  0.020

