# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 12:08:05 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 2-[4-(phenylmethyl)piperidin-1-yl]ethanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCN1CCC(CC1)Cc2ccccc2
#
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
 5NR  5NR  2-[4-(phenylmethyl)piperidin-1-yl]ethanamine  ligand  38  16  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5NR
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
 5NR  C4   C  CR16  0  -0.240   4.4912   0.4341  -0.8296
 5NR  C14  C  CH2   0  -0.282  -3.4113  -0.1740   0.2466
 5NR  C5   C  CR16  0  -0.276   4.8255  -0.8903  -0.5726
 5NR  C6   C  CR16  0  -0.241   4.0224  -1.6448   0.2716
 5NR  C7   C  CH2   0  -0.499   1.3108   0.8598   1.1998
 5NR  C8   C  CH1   0  -0.226   0.1619   1.0221   0.1989
 5NR  C9   C  CH2   0  -0.430  -1.0117   1.7706   0.8284
 5NR  C10  C  CH2   0  -0.325  -2.1689   1.8871  -0.1628
 5NR  C12  C  CH2   0  -0.322  -1.5228  -0.1138  -1.2913
 5NR  C13  C  CH2   0  -0.425  -0.3285  -0.3129  -0.3563
 5NR  C3   C  CR16  0  -0.310   3.3627   0.9937  -0.2474
 5NR  C1   C  CR16  0  -0.317   2.8937  -1.0784   0.8520
 5NR  C2   C  CR6   0   0.144   2.5452   0.2463   0.6005
 5NR  N11  N  NT    0  -0.408  -2.6303   0.6149  -0.6908
 5NR  C15  C  CH2   0  -0.283  -4.4117  -1.0722  -0.4696
 5NR  N16  N  NH2   0  -0.802  -5.1762  -1.8480   0.4959
 5NR  H1   H  HCR6  0   0.251   5.1127   1.0334  -1.4827
 5NR  H2   H  HCH2  0   0.198  -2.7972  -0.7870   0.9226
 5NR  H3   H  HCH2  0   0.223  -3.9685   0.5170   0.8870
 5NR  H4   H  HCR6  0   0.251   5.7060  -1.3283  -1.0245
 5NR  H5   H  HCR6  0   0.251   4.2737  -2.6768   0.4813
 5NR  H6   H  HCH2  0   0.241   1.5568   1.8442   1.6101
 5NR  H7   H  HCH2  0   0.233   0.9662   0.2503   2.0411
 5NR  H8   H  HCH1  0   0.215   0.5269   1.6257  -0.6440
 5NR  H9   H  HCH2  0   0.215  -1.3371   1.2448   1.7335
 5NR  H10  H  HCH2  0   0.227  -0.6980   2.7700   1.1444
 5NR  H11  H  HCH2  0   0.234  -3.0130   2.4097   0.2931
 5NR  H12  H  HCH2  0   0.221  -1.8417   2.5034  -1.0089
 5NR  H13  H  HCH2  0   0.223  -1.1910   0.4420  -2.1758
 5NR  H14  H  HCH2  0   0.234  -1.8786  -1.0797  -1.6561
 5NR  H15  H  HCH2  0   0.233   0.4703  -0.8254  -0.8985
 5NR  H16  H  HCH2  0   0.211  -0.6079  -0.9716   0.4744
 5NR  H17  H  HCR6  0   0.244   3.1150   2.0294  -0.4514
 5NR  H18  H  HCR6  0   0.244   2.2752  -1.6755   1.5119
 5NR  H20  H  HCH2  0   0.190  -5.0272  -0.4434  -1.1271
 5NR  H21  H  HCH2  0   0.214  -3.8822  -1.7734  -1.1199
 5NR  H22  H  HNH2  0   0.338  -5.7824  -1.2279   1.0188
 5NR  H23  H  HNH2  0   0.348  -5.7953  -2.4800   0.0049

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
 5NR  C5   C4   aromatic  1.390  0.020  1.390
 5NR  C5   C6   aromatic  1.388  0.020  1.388
 5NR  C4   C3   aromatic  1.388  0.020  1.388
 5NR  C6   C1   aromatic  1.390  0.020  1.390
 5NR  C3   C2   aromatic  1.395  0.020  1.395
 5NR  C1   C2   aromatic  1.393  0.020  1.393
 5NR  C2   C7   single    1.503  0.020  1.503
 5NR  C7   C8   single    1.532  0.020  1.532
 5NR  C8   C9   single    1.528  0.020  1.528
 5NR  C8   C13  single    1.527  0.020  1.527
 5NR  C9   C10  single    1.528  0.020  1.528
 5NR  C10  N11  single    1.453  0.020  1.453
 5NR  C15  N16  single    1.456  0.020  1.456
 5NR  C15  C14  single    1.523  0.020  1.523
 5NR  C13  C12  single    1.530  0.020  1.530
 5NR  C12  N11  single    1.455  0.020  1.455
 5NR  N11  C14  single    1.453  0.020  1.453
 5NR  C4   H1   single    0.930  0.020  1.080
 5NR  C14  H2   single    0.970  0.020  1.090
 5NR  C14  H3   single    0.970  0.020  1.090
 5NR  C5   H4   single    0.930  0.020  1.080
 5NR  C6   H5   single    0.930  0.020  1.080
 5NR  C7   H6   single    0.970  0.020  1.090
 5NR  C7   H7   single    0.970  0.020  1.090
 5NR  C8   H8   single    0.970  0.020  1.090
 5NR  C9   H9   single    0.970  0.020  1.090
 5NR  C9   H10  single    0.970  0.020  1.090
 5NR  C10  H11  single    0.970  0.020  1.090
 5NR  C10  H12  single    0.970  0.020  1.090
 5NR  C12  H13  single    0.970  0.020  1.090
 5NR  C12  H14  single    0.970  0.020  1.090
 5NR  C13  H15  single    0.970  0.020  1.090
 5NR  C13  H16  single    0.970  0.020  1.090
 5NR  C3   H17  single    0.930  0.020  1.080
 5NR  C1   H18  single    0.930  0.020  1.080
 5NR  C15  H20  single    0.970  0.020  1.090
 5NR  C15  H21  single    0.970  0.020  1.090
 5NR  N16  H22  single    0.890  0.020  1.040
 5NR  N16  H23  single    0.890  0.020  1.040

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
 5NR  H1   C4   C3   119.79  3.000
 5NR  H1   C4   C5   120.06  3.000
 5NR  C3   C4   C5   120.15  3.000
 5NR  H3   C14  H2   106.05  3.000
 5NR  H3   C14  C15  108.24  3.000
 5NR  H2   C14  C15  109.09  3.000
 5NR  H3   C14  N11  107.96  3.000
 5NR  H2   C14  N11  113.52  3.000
 5NR  C15  C14  N11  111.70  3.000
 5NR  H4   C5   C6   120.31  3.000
 5NR  H4   C5   C4   120.27  3.000
 5NR  C6   C5   C4   119.42  3.000
 5NR  H5   C6   C1   119.74  3.000
 5NR  H5   C6   C5   120.11  3.000
 5NR  C1   C6   C5   120.15  3.000
 5NR  H7   C7   H6   106.47  3.000
 5NR  H7   C7   C2   109.74  3.000
 5NR  H6   C7   C2   109.39  3.000
 5NR  H7   C7   C8   108.97  3.000
 5NR  H6   C7   C8   108.55  3.000
 5NR  C2   C7   C8   113.48  3.000
 5NR  H8   C8   C13  107.94  3.000
 5NR  H8   C8   C9   107.58  3.000
 5NR  C13  C8   C9   109.36  3.000
 5NR  H8   C8   C7   108.07  3.000
 5NR  C13  C8   C7   112.69  3.000
 5NR  C9   C8   C7   111.02  3.000
 5NR  H10  C9   H9   106.54  3.000
 5NR  H10  C9   C10  109.56  3.000
 5NR  H9   C9   C10  110.33  3.000
 5NR  H10  C9   C8   110.26  3.000
 5NR  H9   C9   C8   109.46  3.000
 5NR  C10  C9   C8   110.60  3.000
 5NR  H12  C10  H11  106.47  3.000
 5NR  H12  C10  N11  107.85  3.000
 5NR  H11  C10  N11  108.98  3.000
 5NR  H12  C10  C9   108.50  3.000
 5NR  H11  C10  C9   110.54  3.000
 5NR  N11  C10  C9   114.18  3.000
 5NR  H14  C12  H13  106.11  3.000
 5NR  H14  C12  N11  109.43  3.000
 5NR  H13  C12  N11  108.03  3.000
 5NR  H14  C12  C13  110.08  3.000
 5NR  H13  C12  C13  108.84  3.000
 5NR  N11  C12  C13  114.02  3.000
 5NR  H16  C13  H15  106.28  3.000
 5NR  H16  C13  C12  110.02  3.000
 5NR  H15  C13  C12  109.17  3.000
 5NR  H16  C13  C8   109.37  3.000
 5NR  H15  C13  C8   110.83  3.000
 5NR  C12  C13  C8   111.05  3.000
 5NR  H17  C3   C2   119.49  3.000
 5NR  H17  C3   C4   119.48  3.000
 5NR  C2   C3   C4   121.04  3.000
 5NR  H18  C1   C2   119.43  3.000
 5NR  H18  C1   C6   119.55  3.000
 5NR  C2   C1   C6   121.03  3.000
 5NR  C1   C2   C3   118.21  3.000
 5NR  C1   C2   C7   121.45  3.000
 5NR  C3   C2   C7   120.33  3.000
 5NR  C12  N11  C10  110.29  3.000
 5NR  C12  N11  C14  113.79  3.000
 5NR  C10  N11  C14  114.31  3.000
 5NR  H21  C15  H20  106.41  3.000
 5NR  H21  C15  N16  107.88  3.000
 5NR  H20  C15  N16  114.07  3.000
 5NR  H21  C15  C14  109.86  3.000
 5NR  H20  C15  C14  108.17  3.000
 5NR  N16  C15  C14  110.32  3.000
 5NR  H23  N16  H22  105.47  3.000
 5NR  H23  N16  C15  109.42  3.000
 5NR  H22  N16  C15  109.30  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
 5NR  CONST_01  C1   C6   C5   C4     0.00   0.0  0
 5NR  CONST_02  C1   C2   C3   C4     0.00   0.0  0
 5NR  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 5NR  CONST_04  C2   C1   C6   C5     0.00   0.0  0
 5NR  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 5NR  CONST_06  C3   C2   C1   C6     0.00   0.0  0
 5NR  CONST_07  C7   C2   C3   C4   180.00   0.0  0
 5NR  CONST_08  C7   C2   C1   C6   180.00   0.0  0
 5NR  CONST_09  H5   C6   C5   C4   180.00   0.0  0
 5NR  CONST_10  H17  C3   C4   C5   180.00   0.0  0
 5NR  CONST_11  H18  C1   C6   C5   180.00   0.0  0
 5NR  CONST_12  H1   C4   C5   C6   180.00   0.0  0
 5NR  CONST_13  H4   C5   C4   C3   180.00   0.0  0
 5NR  Var_01    N11  C10  C9   C8    55.88  30.0  1
 5NR  Var_02    N11  C12  C13  C8   -54.95  30.0  1
 5NR  Var_03    C12  N11  C10  C9   -55.16  30.0  1
 5NR  Var_04    C13  C12  N11  C10   54.52  30.0  1
 5NR  Var_05    C3   C2   C7   C8    74.19  30.0  1
 5NR  Var_06    C15  C14  N11  C10  151.43  30.0  3
 5NR  Var_07    N16  C15  C14  N11  179.97  30.0  1
 5NR  Var_08    H22  N16  C15  C14   68.42  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
 5NR  chir_01  C8  C7  C9  C13  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
 5NR  plan-1  C4   0.020
 5NR  plan-1  C5   0.020
 5NR  plan-1  C6   0.020
 5NR  plan-1  C7   0.020
 5NR  plan-1  C3   0.020
 5NR  plan-1  C1   0.020
 5NR  plan-1  C2   0.020
 5NR  plan-1  H1   0.020
 5NR  plan-1  H4   0.020
 5NR  plan-1  H5   0.020
 5NR  plan-1  H17  0.020
 5NR  plan-1  H18  0.020

