# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 21:11:29 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: 6-[(4-aminobenzyl)amino]-2,3,4,5-tetrahydropyridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc(CNC2=[NH+]CCCC2)cc1
#
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
 TPM  TPM  6-[(4-aminobenzyl)amino]-2,3,4,5-tetrahydropyridinium  ligand  33  15  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_TPM
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
 TPM  C1    C  CR6   0   0.305   4.2101   0.2636   0.0409
 TPM  C2    C  CR16  0  -0.314   3.5211  -0.2067   1.1671
 TPM  C3    C  CR16  0  -0.274   2.2059  -0.6232   1.0660
 TPM  C5    C  CR16  0  -0.273   2.2110  -0.1193  -1.2673
 TPM  C6    C  CR16  0  -0.314   3.5264   0.3002  -1.1820
 TPM  C4    C  CR6   0   0.023   1.5271  -0.5896  -0.1494
 TPM  C7    C  CH2   0  -0.388   0.0892  -1.0004  -0.2399
 TPM  N1    N  NH2   0  -0.857   5.5327   0.6252   0.1210
 TPM  N2    N  NH1   0  -0.612  -0.7783   0.1512  -0.0017
 TPM  C8    C  C     0   0.687  -2.0927   0.1245   0.0126
 TPM  N3    N  NC1   1  -0.635  -2.7516  -0.9847  -0.2181
 TPM  C9    C  CH2   0  -0.553  -2.8184   1.3933   0.3348
 TPM  C10   C  CH2   0  -0.458  -4.2835   1.3542  -0.0710
 TPM  C11   C  CH2   0  -0.479  -4.9013   0.0462   0.3939
 TPM  C12   C  CH2   0  -0.268  -4.2056  -1.1200  -0.2753
 TPM  HC21  H  HCR6  0   0.258   4.0247  -0.2446   2.1259
 TPM  HC31  H  HCR6  0   0.253   1.6995  -0.9820   1.9546
 TPM  HC51  H  HCR6  0   0.253   1.7089  -0.0823  -2.2275
 TPM  HC61  H  HCR6  0   0.259   4.0352   0.6553  -2.0702
 TPM  HC71  H  HCH2  0   0.282  -0.1308  -1.4137  -1.2279
 TPM  HC72  H  HCH2  0   0.282  -0.1325  -1.7737   0.5006
 TPM  HN11  H  HNH2  0   0.382   5.8743   0.8708   1.0359
 TPM  HN12  H  HNH2  0   0.382   5.8675   1.2521  -0.5924
 TPM  HN21  H  HNH1  0   0.432  -0.3335   1.0360   0.1927
 TPM  HN31  H  HNC1  0   0.447  -2.2308  -1.8208  -0.4443
 TPM  HC91  H  HCH2  0   0.303  -2.7291   1.5403   1.4151
 TPM  HC92  H  HCH2  0   0.301  -2.2916   2.2239  -0.1364
 TPM  H101  H  HCH2  0   0.249  -4.3767   1.4499  -1.1556
 TPM  H102  H  HCH2  0   0.269  -4.7968   2.2075   0.3706
 TPM  H111  H  HCH2  0   0.269  -5.9625   0.0014   0.1504
 TPM  H112  H  HCH2  0   0.248  -4.8157  -0.0396   1.4803
 TPM  H121  H  HCH2  0   0.263  -4.4998  -1.1945  -1.3243
 TPM  H122  H  HCH2  0   0.277  -4.4618  -2.0625   0.2057

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
 TPM  C1   C2    aromatic  1.401  0.020  1.401
 TPM  C1   C6    aromatic  1.402  0.020  1.402
 TPM  C1   N1    single    1.374  0.020  1.374
 TPM  C2   C3    aromatic  1.383  0.020  1.383
 TPM  C2   HC21  single    0.930  0.020  1.080
 TPM  C3   C4    aromatic  1.392  0.020  1.392
 TPM  C3   HC31  single    0.930  0.020  1.080
 TPM  C5   C6    aromatic  1.383  0.020  1.383
 TPM  C5   C4    aromatic  1.392  0.020  1.392
 TPM  C5   HC51  single    0.930  0.020  1.080
 TPM  C6   HC61  single    0.930  0.020  1.080
 TPM  C4   C7    single    1.498  0.020  1.498
 TPM  C7   N2    single    1.461  0.020  1.461
 TPM  C7   HC71  single    0.970  0.020  1.090
 TPM  C7   HC72  single    0.970  0.020  1.090
 TPM  N1   HN11  single    0.890  0.020  1.040
 TPM  N1   HN12  single    0.890  0.020  1.040
 TPM  N2   C8    single    1.315  0.020  1.315
 TPM  N2   HN21  single    0.860  0.020  1.020
 TPM  C8   N3    double    1.311  0.020  1.311
 TPM  C8   C9    single    1.497  0.020  1.497
 TPM  N3   C12   single    1.461  0.020  1.461
 TPM  N3   HN31  single    0.860  0.020  1.020
 TPM  C9   C10   single    1.521  0.020  1.521
 TPM  C9   HC91  single    0.970  0.020  1.090
 TPM  C9   HC92  single    0.970  0.020  1.090
 TPM  C10  C11   single    1.519  0.020  1.519
 TPM  C10  H101  single    0.970  0.020  1.090
 TPM  C10  H102  single    0.970  0.020  1.090
 TPM  C11  C12   single    1.514  0.020  1.514
 TPM  C11  H111  single    0.970  0.020  1.090
 TPM  C11  H112  single    0.970  0.020  1.090
 TPM  C12  H121  single    0.970  0.020  1.090
 TPM  C12  H122  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
 TPM  N1    C1   C6    120.92  3.000
 TPM  N1    C1   C2    120.99  3.000
 TPM  C6    C1   C2    118.04  3.000
 TPM  HC21  C2   C3    119.73  3.000
 TPM  HC21  C2   C1    119.62  3.000
 TPM  C3    C2   C1    120.65  3.000
 TPM  HC31  C3   C4    119.72  3.000
 TPM  HC31  C3   C2    118.94  3.000
 TPM  C4    C3   C2    121.33  3.000
 TPM  HC51  C5   C4    119.68  3.000
 TPM  HC51  C5   C6    118.99  3.000
 TPM  C4    C5   C6    121.33  3.000
 TPM  HC61  C6   C5    119.70  3.000
 TPM  HC61  C6   C1    119.65  3.000
 TPM  C5    C6   C1    120.65  3.000
 TPM  C7    C4   C5    121.03  3.000
 TPM  C7    C4   C3    120.93  3.000
 TPM  C5    C4   C3    118.00  3.000
 TPM  HC72  C7   HC71  107.69  3.000
 TPM  HC72  C7   N2    109.06  3.000
 TPM  HC71  C7   N2    109.01  3.000
 TPM  HC72  C7   C4    110.34  3.000
 TPM  HC71  C7   C4    110.57  3.000
 TPM  N2    C7   C4    110.11  3.000
 TPM  HN12  N1   HN11  112.27  3.000
 TPM  HN12  N1   C1    116.28  3.000
 TPM  HN11  N1   C1    116.34  3.000
 TPM  HN21  N2   C8    117.15  3.000
 TPM  HN21  N2   C7    117.43  3.000
 TPM  C8    N2   C7    125.40  3.000
 TPM  C9    C8   N3    120.77  3.000
 TPM  C9    C8   N2    118.02  3.000
 TPM  N3    C8   N2    121.19  3.000
 TPM  HN31  N3   C12   115.30  3.000
 TPM  HN31  N3   C8    118.72  3.000
 TPM  C12   N3   C8    125.83  3.000
 TPM  HC92  C9   HC91  106.55  3.000
 TPM  HC92  C9   C10   111.69  3.000
 TPM  HC91  C9   C10   110.21  3.000
 TPM  HC92  C9   C8    108.57  3.000
 TPM  HC91  C9   C8    106.67  3.000
 TPM  C10   C9   C8    112.82  3.000
 TPM  H102  C10  H101  107.07  3.000
 TPM  H102  C10  C11   111.02  3.000
 TPM  H101  C10  C11   110.15  3.000
 TPM  H102  C10  C9    109.01  3.000
 TPM  H101  C10  C9    110.16  3.000
 TPM  C11   C10  C9    109.40  3.000
 TPM  H112  C11  H111  107.16  3.000
 TPM  H112  C11  C12   110.05  3.000
 TPM  H111  C11  C12   108.49  3.000
 TPM  H112  C11  C10   109.87  3.000
 TPM  H111  C11  C10   111.28  3.000
 TPM  C12   C11  C10   109.94  3.000
 TPM  H122  C12  H121  107.58  3.000
 TPM  H122  C12  C11   111.31  3.000
 TPM  H121  C12  C11   110.70  3.000
 TPM  H122  C12  N3    107.28  3.000
 TPM  H121  C12  N3    108.17  3.000
 TPM  C11   C12  N3    111.63  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
 TPM  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 TPM  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 TPM  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 TPM  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 TPM  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 TPM  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 TPM  CONST_07  C12   N3   C8   C9     0.00   0.0  0
 TPM  CONST_08  C7    C4   C3   C2   180.00   0.0  0
 TPM  CONST_09  N1    C1   C2   C3   180.00   0.0  0
 TPM  CONST_10  N1    C1   C6   C5   180.00   0.0  0
 TPM  CONST_11  C7    C4   C5   C6   180.00   0.0  0
 TPM  CONST_12  C12   N3   C8   N2   180.00   0.0  0
 TPM  CONST_13  HC31  C3   C2   C1   180.00   0.0  0
 TPM  CONST_14  HC51  C5   C6   C1   180.00   0.0  0
 TPM  CONST_15  HC61  C6   C1   C2   180.00   0.0  0
 TPM  CONST_16  HC21  C2   C1   C6   180.00   0.0  0
 TPM  CONST_17  HN31  N3   C8   C9   180.00   0.0  0
 TPM  CONST_18  N3    C8   N2   C7     0.00   0.0  0
 TPM  CONST_19  C9    C8   N2   C7   180.00   0.0  0
 TPM  CONST_22  HN21  N2   C8   N3   180.00   0.0  0
 TPM  Var_01    C11   C12  N3   C8   -18.54  30.0  1
 TPM  Var_02    C11   C10  C9   C8    46.75  30.0  1
 TPM  Var_03    C10   C9   C8   N3   -18.39  30.0  1
 TPM  Var_04    C10   C11  C12  N3    46.82  30.0  1
 TPM  Var_05    C12   C11  C10  C9   -61.85  30.0  1
 TPM  Var_06    N2    C7   C4   C3    89.25  30.0  2
 TPM  Var_07    C8    N2   C7   C4  -178.74  30.0  3

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
 TPM  plan-1  C1    0.020
 TPM  plan-1  C2    0.020
 TPM  plan-1  C3    0.020
 TPM  plan-1  C5    0.020
 TPM  plan-1  C6    0.020
 TPM  plan-1  C4    0.020
 TPM  plan-1  C7    0.020
 TPM  plan-1  N1    0.020
 TPM  plan-1  HC21  0.020
 TPM  plan-1  HC31  0.020
 TPM  plan-1  HC51  0.020
 TPM  plan-1  HC61  0.020
 TPM  plan-2  C1    0.020
 TPM  plan-2  N1    0.020
 TPM  plan-2  HN11  0.020
 TPM  plan-2  HN12  0.020
 TPM  plan-3  C7    0.020
 TPM  plan-3  N2    0.020
 TPM  plan-3  C8    0.020
 TPM  plan-3  N3    0.020
 TPM  plan-3  C9    0.020
 TPM  plan-3  C12   0.020
 TPM  plan-3  HN21  0.020
 TPM  plan-3  HN31  0.020

