# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 00:44:59 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: [2-[4-(hydroxymethyl)piperidin-1-yl]phenyl]methylazanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+]Cc1ccccc1N2CCC(CO)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
 A7K  A7K  '[2-[4-(hydroxymethyl)piperidin-1-yl]phenyl]methylazanium'  ligand  37  16  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A7K
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
 A7K  C12  C  CH2   0  -0.306  -0.6462   0.4577  -1.4477
 A7K  C13  C  CH2   0  -0.127  -4.1657  -0.5926  -0.2803
 A7K  C11  C  CH2   0  -0.437  -2.0100  -0.2123  -1.4770
 A7K  C10  C  CH1   0  -0.281  -2.8412   0.1476  -0.2489
 A7K  C9   C  CH2   0  -0.423  -2.0387  -0.1399   1.0166
 A7K  C8   C  CH2   0  -0.313  -0.6721   0.5212   0.9657
 A7K  C7   C  CH2   0  -0.405   1.8602  -1.6593   1.1539
 A7K  C4   C  CR6   0   0.313   1.4449   0.4482  -0.1880
 A7K  C5   C  CR6   0   0.062   2.3341  -0.3934   0.4980
 A7K  C6   C  CR16  0  -0.305   3.6829  -0.0663   0.5557
 A7K  C3   C  CR16  0  -0.289   1.9412   1.5840  -0.8204
 A7K  C2   C  CR16  0  -0.258   3.2922   1.8971  -0.7577
 A7K  C1   C  CR16  0  -0.250   4.1671   1.0781  -0.0617
 A7K  N1   N  NT3   1  -0.787   1.0695  -2.4731   0.1963
 A7K  N2   N  NT    0  -0.566   0.0684   0.0901  -0.2276
 A7K  O1   O  OH1   0  -0.674  -4.9495  -0.2084   0.8272
 A7K  H1   H  HCH2  0   0.260  -0.0549   0.1389  -2.3074
 A7K  H2   H  HCH2  0   0.221  -0.7796   1.5461  -1.5254
 A7K  H3   H  HCH2  0   0.200  -4.6764  -0.3683  -1.2268
 A7K  H4   H  HCH2  0   0.185  -3.9652  -1.6738  -0.2753
 A7K  H5   H  HCH2  0   0.246  -2.5265   0.0954  -2.3893
 A7K  H6   H  HCH2  0   0.224  -1.8797  -1.2987  -1.5374
 A7K  H7   H  HCH1  0   0.226  -3.0479   1.2252  -0.2880
 A7K  H8   H  HCH2  0   0.248  -2.5654   0.2189   1.9020
 A7K  H9   H  HCH2  0   0.214  -1.9151  -1.2227   1.1375
 A7K  H10  H  HCH2  0   0.231  -0.7835   1.6153   0.9649
 A7K  H11  H  HCH2  0   0.258  -0.1012   0.2683   1.8600
 A7K  H12  H  HCH2  0   0.319   2.6978  -2.2623   1.4953
 A7K  H13  H  HCH2  0   0.306   1.2171  -1.4756   2.0130
 A7K  H14  H  HCR6  0   0.263   4.3647  -0.7240   1.0810
 A7K  H15  H  HCR6  0   0.267   1.2737   2.2366  -1.3672
 A7K  H16  H  HCR6  0   0.264   3.6571   2.7872  -1.2531
 A7K  H17  H  HCR6  0   0.263   5.2208   1.3171  -0.0108
 A7K  H18  H  HNT3  0   0.459   0.3423  -1.8482  -0.1975
 A7K  H19  H  HNT3  0   0.468   1.6416  -2.8280  -0.5685
 A7K  H20  H  HNT3  0   0.473   0.6254  -3.2727   0.6441
 A7K  H21  H  HOH1  0   0.454  -5.7589  -0.7263   0.8149

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
 A7K  O1   C13  single    1.410  0.020  1.410
 A7K  C13  C10  single    1.518  0.020  1.518
 A7K  C9   C10  single    1.526  0.020  1.526
 A7K  C9   C8   single    1.519  0.020  1.519
 A7K  C10  C11  single    1.526  0.020  1.526
 A7K  N1   C7   single    1.485  0.020  1.485
 A7K  C8   N2   single    1.469  0.020  1.469
 A7K  C11  C12  single    1.520  0.020  1.520
 A7K  C7   C5   single    1.502  0.020  1.502
 A7K  N2   C12  single    1.461  0.020  1.461
 A7K  N2   C4   single    1.423  0.020  1.423
 A7K  C5   C4   aromatic  1.403  0.020  1.403
 A7K  C5   C6   aromatic  1.389  0.020  1.389
 A7K  C4   C3   aromatic  1.392  0.020  1.392
 A7K  C6   C1   aromatic  1.388  0.020  1.388
 A7K  C3   C2   aromatic  1.388  0.020  1.388
 A7K  C1   C2   aromatic  1.386  0.020  1.386
 A7K  C12  H1   single    0.970  0.020  1.090
 A7K  C12  H2   single    0.970  0.020  1.090
 A7K  C13  H3   single    0.970  0.020  1.090
 A7K  C13  H4   single    0.970  0.020  1.090
 A7K  C11  H5   single    0.970  0.020  1.090
 A7K  C11  H6   single    0.970  0.020  1.090
 A7K  C10  H7   single    0.970  0.020  1.090
 A7K  C9   H8   single    0.970  0.020  1.090
 A7K  C9   H9   single    0.970  0.020  1.090
 A7K  C8   H10  single    0.970  0.020  1.090
 A7K  C8   H11  single    0.970  0.020  1.090
 A7K  C7   H12  single    0.970  0.020  1.090
 A7K  C7   H13  single    0.970  0.020  1.090
 A7K  C6   H14  single    0.930  0.020  1.080
 A7K  C3   H15  single    0.930  0.020  1.080
 A7K  C2   H16  single    0.930  0.020  1.080
 A7K  C1   H17  single    0.930  0.020  1.080
 A7K  N1   H18  single    0.890  0.020  1.040
 A7K  N1   H19  single    0.890  0.020  1.040
 A7K  N1   H20  single    0.890  0.020  1.040
 A7K  O1   H21  single    0.850  0.020  0.980

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
 A7K  H2   C12  H1   107.42  3.000
 A7K  H2   C12  N2   111.56  3.000
 A7K  H1   C12  N2   108.63  3.000
 A7K  H2   C12  C11  109.04  3.000
 A7K  H1   C12  C11  110.02  3.000
 A7K  N2   C12  C11  110.12  3.000
 A7K  H4   C13  H3   106.82  3.000
 A7K  H4   C13  O1   111.45  3.000
 A7K  H3   C13  O1   111.26  3.000
 A7K  H4   C13  C10  108.68  3.000
 A7K  H3   C13  C10  108.91  3.000
 A7K  O1   C13  C10  109.63  3.000
 A7K  H6   C11  H5   106.82  3.000
 A7K  H6   C11  C10  110.05  3.000
 A7K  H5   C11  C10  110.37  3.000
 A7K  H6   C11  C12  109.36  3.000
 A7K  H5   C11  C12  108.43  3.000
 A7K  C10  C11  C12  111.67  3.000
 A7K  H7   C10  C9   108.27  3.000
 A7K  H7   C10  C11  107.78  3.000
 A7K  C9   C10  C11  109.67  3.000
 A7K  H7   C10  C13  108.27  3.000
 A7K  C11  C10  C13  110.10  3.000
 A7K  C9   C10  C13  112.60  3.000
 A7K  H9   C9   H8   106.84  3.000
 A7K  H9   C9   C8   109.39  3.000
 A7K  H8   C9   C8   108.56  3.000
 A7K  H9   C9   C10  109.68  3.000
 A7K  H8   C9   C10  110.94  3.000
 A7K  C8   C9   C10  111.31  3.000
 A7K  H11  C8   H10  106.52  3.000
 A7K  H11  C8   N2   109.52  3.000
 A7K  H10  C8   N2   110.03  3.000
 A7K  H11  C8   C9   110.03  3.000
 A7K  H10  C8   C9   109.99  3.000
 A7K  N2   C8   C9   110.67  3.000
 A7K  H13  C7   H12  107.51  3.000
 A7K  H13  C7   N1   106.67  3.000
 A7K  H12  C7   N1   107.99  3.000
 A7K  H13  C7   C5   112.87  3.000
 A7K  H12  C7   C5   111.19  3.000
 A7K  N1   C7   C5   110.38  3.000
 A7K  N2   C4   C3   122.54  3.000
 A7K  C3   C4   C5   119.05  3.000
 A7K  N2   C4   C5   118.40  3.000
 A7K  C6   C5   C4   119.62  3.000
 A7K  C6   C5   C7   119.11  3.000
 A7K  C4   C5   C7   121.25  3.000
 A7K  H14  C6   C1   119.80  3.000
 A7K  H14  C6   C5   119.23  3.000
 A7K  C1   C6   C5   120.97  3.000
 A7K  H15  C3   C2   119.16  3.000
 A7K  H15  C3   C4   120.14  3.000
 A7K  C2   C3   C4   120.71  3.000
 A7K  H16  C2   C1   120.21  3.000
 A7K  H16  C2   C3   119.54  3.000
 A7K  C1   C2   C3   120.25  3.000
 A7K  H17  C1   C2   120.53  3.000
 A7K  H17  C1   C6   120.09  3.000
 A7K  C2   C1   C6   119.38  3.000
 A7K  H20  N1   H19  107.54  3.000
 A7K  H20  N1   H18  109.54  3.000
 A7K  H19  N1   H18  108.59  3.000
 A7K  H20  N1   C7   112.27  3.000
 A7K  H19  N1   C7   112.09  3.000
 A7K  H18  N1   C7   106.76  3.000
 A7K  C4   N2   C8   113.03  3.000
 A7K  C4   N2   C12  115.66  3.000
 A7K  C8   N2   C12  110.98  3.000
 A7K  H21  O1   C13  108.14  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
 A7K  CONST_01  C1   C6   C5   C4      0.00   0.0  0
 A7K  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 A7K  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 A7K  CONST_04  C2   C1   C6   C5      0.00   0.0  0
 A7K  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 A7K  CONST_06  C3   C2   C1   C6      0.00   0.0  0
 A7K  CONST_07  N2   C4   C5   C6    180.00   0.0  0
 A7K  CONST_08  N2   C4   C3   C2    180.00   0.0  0
 A7K  CONST_09  N2   C4   C5   C7      0.00   0.0  0
 A7K  CONST_10  C3   C4   C5   C7    180.00   0.0  0
 A7K  CONST_11  C1   C6   C5   C7    180.00   0.0  0
 A7K  CONST_12  H14  C6   C5   C4    180.00   0.0  0
 A7K  CONST_13  H16  C2   C3   C4    180.00   0.0  0
 A7K  CONST_14  H15  C3   C4   C5    180.00   0.0  0
 A7K  CONST_15  H17  C1   C6   C5    180.00   0.0  0
 A7K  Var_01    C9   C8   N2   C12    60.59  30.0  1
 A7K  Var_02    C5   C4   N2   C12  -146.75  30.0  2
 A7K  Var_03    C8   N2   C12  C11   -60.59  30.0  1
 A7K  Var_04    N2   C8   C9   C10   -56.46  30.0  1
 A7K  Var_05    N2   C12  C11  C10    57.14  30.0  1
 A7K  Var_06    N1   C7   C5   C4     50.97  30.0  2
 A7K  Var_07    H18  N1   C7   C5    -51.98  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
 A7K  chir_01  C10  C13  C9  C11  negativ

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
 A7K  plan-1  C7   0.020
 A7K  plan-1  C4   0.020
 A7K  plan-1  C5   0.020
 A7K  plan-1  C6   0.020
 A7K  plan-1  C3   0.020
 A7K  plan-1  C2   0.020
 A7K  plan-1  C1   0.020
 A7K  plan-1  N2   0.020
 A7K  plan-1  H14  0.020
 A7K  plan-1  H15  0.020
 A7K  plan-1  H16  0.020
 A7K  plan-1  H17  0.020

