# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 23:32:53 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: ~{N}-methyl-1-(4-piperidin-1-ylphenyl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCc1ccc(cc1)N2CCCCC2
#
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
 5TT  5TT  ~{N}-methyl-1-(4-piperidin-1-ylphenyl)methanamine  ligand  35  15  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5TT
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
 5TT  CAI  C  CH2   0  -0.298  -2.6217  -1.1233  -0.3976
 5TT  CAG  C  CH2   0  -0.438  -3.9875  -1.2475   0.2576
 5TT  CAF  C  CH2   0  -0.440  -4.8092   0.0144   0.0360
 5TT  CAH  C  CH2   0  -0.433  -4.0209   1.2284   0.5059
 5TT  CAJ  C  CH2   0  -0.303  -2.6465   1.2873  -0.1470
 5TT  NAO  N  NT    0  -0.509  -1.9084   0.0583   0.0784
 5TT  CAN  C  CR6   0   0.346  -0.5270   0.0850  -0.1205
 5TT  CAE  C  CR16  0  -0.315   0.2635  -1.0062   0.2799
 5TT  CAC  C  CR16  0  -0.276   1.6364  -0.9932   0.1310
 5TT  CAD  C  CR16  0  -0.346   0.1395   1.1826  -0.6729
 5TT  CAB  C  CR16  0  -0.306   1.5247   1.1881  -0.8023
 5TT  CAM  C  CR6   0   0.066   2.3005   0.1058  -0.4171
 5TT  CAK  C  CH2   0  -0.323   3.7955   0.1091  -0.5799
 5TT  NAL  N  NH1   0  -0.584   4.4684  -0.2239   0.6608
 5TT  CAA  C  CH3   0  -0.520   5.9101  -0.2405   0.5247
 5TT  H1   H  HCH2  0   0.250  -2.0363  -2.0160  -0.1878
 5TT  H2   H  HCH2  0   0.207  -2.7460  -1.0761  -1.4913
 5TT  H3   H  HCH2  0   0.234  -4.4967  -2.1224  -0.1524
 5TT  H4   H  HCH2  0   0.219  -3.8575  -1.4239   1.3293
 5TT  H5   H  HCH2  0   0.213  -5.0367   0.1175  -1.0304
 5TT  H6   H  HCH2  0   0.233  -5.7660  -0.0493   0.5582
 5TT  H7   H  HCH2  0   0.234  -4.5548   2.1532   0.2769
 5TT  H8   H  HCH2  0   0.218  -3.8980   1.1907   1.5923
 5TT  H9   H  HCH2  0   0.203  -2.7629   1.4977  -1.2227
 5TT  H10  H  HCH2  0   0.246  -2.0892   2.1207   0.2822
 5TT  H11  H  HCR6  0   0.254  -0.1998  -1.8705   0.7380
 5TT  H12  H  HCR6  0   0.241   2.2072  -1.8510   0.4658
 5TT  H13  H  HCR6  0   0.260  -0.4079   2.0494  -1.0160
 5TT  H14  H  HCR6  0   0.244   2.0023   2.0638  -1.2274
 5TT  H15  H  HCH2  0   0.229   4.0866  -0.6404  -1.3245
 5TT  H16  H  HCH2  0   0.206   4.1106   1.0803  -0.9944
 5TT  H17  H  HNH1  0   0.343   4.2086   0.4540   1.3667
 5TT  H19  H  HCH3  0   0.222   6.2057  -1.0258  -0.1742
 5TT  H20  H  HCH3  0   0.193   6.3419   0.7017   0.1586
 5TT  H21  H  HCH3  0   0.232   6.3703  -0.4669   1.4867

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
 5TT  CAH  CAF  single    1.522  0.020  1.522
 5TT  CAH  CAJ  single    1.523  0.020  1.523
 5TT  CAF  CAG  single    1.522  0.020  1.522
 5TT  CAJ  NAO  single    1.451  0.020  1.451
 5TT  CAG  CAI  single    1.520  0.020  1.520
 5TT  NAO  CAI  single    1.460  0.020  1.460
 5TT  NAO  CAN  single    1.396  0.020  1.396
 5TT  CAD  CAN  aromatic  1.398  0.020  1.398
 5TT  CAD  CAB  aromatic  1.391  0.020  1.391
 5TT  CAN  CAE  aromatic  1.406  0.020  1.406
 5TT  CAB  CAM  aromatic  1.386  0.020  1.386
 5TT  CAE  CAC  aromatic  1.381  0.020  1.381
 5TT  CAM  CAC  aromatic  1.396  0.020  1.396
 5TT  CAM  CAK  single    1.504  0.020  1.504
 5TT  CAK  NAL  single    1.450  0.020  1.450
 5TT  NAL  CAA  single    1.448  0.020  1.448
 5TT  CAI  H1   single    0.970  0.020  1.090
 5TT  CAI  H2   single    0.970  0.020  1.090
 5TT  CAG  H3   single    0.970  0.020  1.090
 5TT  CAG  H4   single    0.970  0.020  1.090
 5TT  CAF  H5   single    0.970  0.020  1.090
 5TT  CAF  H6   single    0.970  0.020  1.090
 5TT  CAH  H7   single    0.970  0.020  1.090
 5TT  CAH  H8   single    0.970  0.020  1.090
 5TT  CAJ  H9   single    0.970  0.020  1.090
 5TT  CAJ  H10  single    0.970  0.020  1.090
 5TT  CAE  H11  single    0.930  0.020  1.080
 5TT  CAC  H12  single    0.930  0.020  1.080
 5TT  CAD  H13  single    0.930  0.020  1.080
 5TT  CAB  H14  single    0.930  0.020  1.080
 5TT  CAK  H15  single    0.970  0.020  1.090
 5TT  CAK  H16  single    0.970  0.020  1.090
 5TT  NAL  H17  single    0.890  0.020  1.040
 5TT  CAA  H19  single    0.970  0.020  1.090
 5TT  CAA  H20  single    0.970  0.020  1.090
 5TT  CAA  H21  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
 5TT  H2   CAI  H1   106.70  3.000
 5TT  H2   CAI  NAO  110.13  3.000
 5TT  H1   CAI  NAO  109.77  3.000
 5TT  H2   CAI  CAG  109.27  3.000
 5TT  H1   CAI  CAG  109.47  3.000
 5TT  NAO  CAI  CAG  111.38  3.000
 5TT  H4   CAG  H3   107.10  3.000
 5TT  H4   CAG  CAF  109.91  3.000
 5TT  H3   CAG  CAF  110.96  3.000
 5TT  H4   CAG  CAI  109.19  3.000
 5TT  H3   CAG  CAI  108.82  3.000
 5TT  CAF  CAG  CAI  110.77  3.000
 5TT  H6   CAF  H5   106.80  3.000
 5TT  H6   CAF  CAH  110.65  3.000
 5TT  H5   CAF  CAH  109.46  3.000
 5TT  H6   CAF  CAG  110.80  3.000
 5TT  H5   CAF  CAG  109.39  3.000
 5TT  CAH  CAF  CAG  109.68  3.000
 5TT  H8   CAH  H7   107.00  3.000
 5TT  H8   CAH  CAJ  109.01  3.000
 5TT  H7   CAH  CAJ  108.58  3.000
 5TT  H8   CAH  CAF  109.71  3.000
 5TT  H7   CAH  CAF  110.95  3.000
 5TT  CAJ  CAH  CAF  111.46  3.000
 5TT  H10  CAJ  H9   106.99  3.000
 5TT  H10  CAJ  NAO  109.03  3.000
 5TT  H9   CAJ  NAO  111.53  3.000
 5TT  H10  CAJ  CAH  108.79  3.000
 5TT  H9   CAJ  CAH  109.30  3.000
 5TT  NAO  CAJ  CAH  111.08  3.000
 5TT  CAN  NAO  CAJ  117.71  3.000
 5TT  CAN  NAO  CAI  116.90  3.000
 5TT  CAJ  NAO  CAI  112.72  3.000
 5TT  CAD  CAN  CAE  117.00  3.000
 5TT  CAE  CAN  NAO  120.07  3.000
 5TT  CAD  CAN  NAO  122.91  3.000
 5TT  H11  CAE  CAC  118.60  3.000
 5TT  H11  CAE  CAN  119.98  3.000
 5TT  CAC  CAE  CAN  121.40  3.000
 5TT  H12  CAC  CAM  119.60  3.000
 5TT  H12  CAC  CAE  118.88  3.000
 5TT  CAM  CAC  CAE  121.51  3.000
 5TT  H13  CAD  CAB  118.13  3.000
 5TT  H13  CAD  CAN  120.90  3.000
 5TT  CAB  CAD  CAN  120.97  3.000
 5TT  H14  CAB  CAM  119.54  3.000
 5TT  H14  CAB  CAD  118.57  3.000
 5TT  CAM  CAB  CAD  121.89  3.000
 5TT  CAK  CAM  CAB  121.64  3.000
 5TT  CAK  CAM  CAC  121.14  3.000
 5TT  CAB  CAM  CAC  117.22  3.000
 5TT  H16  CAK  H15  105.73  3.000
 5TT  H16  CAK  NAL  113.05  3.000
 5TT  H15  CAK  NAL  107.52  3.000
 5TT  H16  CAK  CAM  109.08  3.000
 5TT  H15  CAK  CAM  109.64  3.000
 5TT  NAL  CAK  CAM  111.61  3.000
 5TT  H17  NAL  CAA  109.19  3.000
 5TT  H17  NAL  CAK  108.88  3.000
 5TT  CAA  NAL  CAK  112.59  3.000
 5TT  H21  CAA  H20  107.82  3.000
 5TT  H21  CAA  H19  107.53  3.000
 5TT  H20  CAA  H19  107.28  3.000
 5TT  H21  CAA  NAL  109.86  3.000
 5TT  H20  CAA  NAL  114.36  3.000
 5TT  H19  CAA  NAL  109.75  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
 5TT  CONST_01  CAM  CAB  CAD  CAN    0.00   0.0  0
 5TT  CONST_02  CAM  CAC  CAE  CAN    0.00   0.0  0
 5TT  CONST_03  CAB  CAD  CAN  CAE    0.00   0.0  0
 5TT  CONST_04  CAB  CAM  CAC  CAE    0.00   0.0  0
 5TT  CONST_05  CAD  CAN  CAE  CAC    0.00   0.0  0
 5TT  CONST_06  CAD  CAB  CAM  CAC    0.00   0.0  0
 5TT  CONST_07  CAB  CAD  CAN  NAO  180.00   0.0  0
 5TT  CONST_08  CAC  CAE  CAN  NAO  180.00   0.0  0
 5TT  CONST_09  CAK  CAM  CAC  CAE  180.00   0.0  0
 5TT  CONST_10  CAK  CAM  CAB  CAD  180.00   0.0  0
 5TT  CONST_11  H13  CAD  CAN  NAO    0.00   0.0  0
 5TT  CONST_12  H11  CAE  CAN  NAO    0.00   0.0  0
 5TT  CONST_13  H14  CAB  CAD  CAN  180.00   0.0  0
 5TT  CONST_14  H12  CAC  CAE  CAN  180.00   0.0  0
 5TT  Var_01    CAH  CAF  CAG  CAI  -54.04  30.0  1
 5TT  Var_02    CAH  CAJ  NAO  CAI   56.79  30.0  1
 5TT  Var_03    CAD  CAN  NAO  CAI  131.26  30.0  2
 5TT  Var_04    CAJ  CAH  CAF  CAG   53.92  30.0  1
 5TT  Var_05    CAJ  NAO  CAI  CAG  -57.48  30.0  1
 5TT  Var_06    NAO  CAJ  CAH  CAF  -55.18  30.0  1
 5TT  Var_07    NAO  CAI  CAG  CAF   55.83  30.0  1
 5TT  Var_08    NAL  CAK  CAM  CAC  -52.33  30.0  2
 5TT  Var_09    CAA  NAL  CAK  CAM  179.39  30.0  3
 5TT  Var_10    H19  CAA  NAL  CAK  -63.58  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
 5TT  plan-1  NAO  0.020
 5TT  plan-1  CAN  0.020
 5TT  plan-1  CAE  0.020
 5TT  plan-1  CAC  0.020
 5TT  plan-1  CAD  0.020
 5TT  plan-1  CAB  0.020
 5TT  plan-1  CAM  0.020
 5TT  plan-1  CAK  0.020
 5TT  plan-1  H11  0.020
 5TT  plan-1  H12  0.020
 5TT  plan-1  H13  0.020
 5TT  plan-1  H14  0.020

