# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:16:28 2022
#   Inital geometry file: a 106 line input string
#   Ligand name: 2-[5-[(1~{R},5~{S})-3,7-diazabicyclo[3.3.1]nonan-3-yl]pyridin-3-yl]oxy-~{N},~{N}-dimethyl-ethanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CCOc1cncc(c1)N2C[C@H]3CNC[C@H](C3)C2
#
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
 6S7  6S7  2-[5-[(1~{R},5~{S})-3,7-diazabicyclo[3.3.1]nonan-3-yl]pyridin-3-yl]oxy-~{N},~{N}-dimethyl-ethanamine  ligand  47  21  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6S7
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
 6S7  C17  C  CH3   0  -0.528   5.6608  -0.7110  -1.3962
 6S7  N16  N  NT    0  -0.400   5.0860  -1.1968  -0.1607
 6S7  C21  C  CH2   0  -0.312  -3.4264  -2.2883   0.4222
 6S7  C14  C  CH2   0  -0.216   3.8707   0.8886   0.4385
 6S7  C12  C  CR16  0  -0.178  -0.7503   2.4125  -0.3302
 6S7  N11  N  N     0  -0.376   0.3985   3.0524  -0.2028
 6S7  C10  C  CR16  0  -0.226   1.5258   2.3768  -0.0348
 6S7  C9   C  CR6   0   0.344   1.5344   0.9817   0.0172
 6S7  C8   C  CR16  0  -0.363   0.3318   0.3017  -0.1231
 6S7  C3   C  CH1   0  -0.269  -4.5253   0.3310  -0.0258
 6S7  C7   C  CR6   0   0.328  -0.8595   1.0098  -0.2941
 6S7  C4   C  CH2   0  -0.299  -3.2841   1.1726  -0.3082
 6S7  C2   C  CH2   0  -0.441  -4.6582  -0.7465  -1.0941
 6S7  C18  C  CH3   0  -0.519   5.8776  -2.2783   0.3846
 6S7  C15  C  CH2   0  -0.292   4.9004  -0.1505   0.8225
 6S7  O13  O  O2    0  -0.465   2.6325   0.2334   0.2137
 6S7  N5   N  NT    0  -0.531  -2.0790   0.3610  -0.3796
 6S7  C6   C  CH2   0  -0.294  -2.1776  -0.8108  -1.2469
 6S7  C19  C  CH2   0  -0.310  -4.4994  -0.3326   1.3581
 6S7  N20  N  NH1   0  -0.578  -3.4789  -1.3550   1.5370
 6S7  C1   C  CH1   0  -0.271  -3.4284  -1.6386  -0.9677
 6S7  H1   H  HCH3  0   0.236   5.7545  -1.5339  -2.1058
 6S7  H2   H  HCH3  0   0.237   5.0218   0.0402  -1.8605
 6S7  H3   H  HCH3  0   0.192   6.6608  -0.2671  -1.2653
 6S7  H6   H  HCH2  0   0.222  -4.2961  -2.9527   0.4830
 6S7  H7   H  HCH2  0   0.241   3.7864   1.6078   1.2604
 6S7  H8   H  HCH2  0   0.231   4.1730   1.4484  -0.4526
 6S7  H9   H  HCR6  0   0.263  -1.6233   3.0362  -0.4727
 6S7  H10  H  HCR6  0   0.268   2.4323   2.9627   0.0549
 6S7  H11  H  HCR6  0   0.274   0.3395  -0.7794  -0.0606
 6S7  H12  H  HCH1  0   0.242  -5.3827   1.0099  -0.0600
 6S7  H13  H  HCH2  0   0.221  -3.4429   1.7425  -1.2376
 6S7  H14  H  HCH2  0   0.248  -3.1610   1.9054   0.4927
 6S7  H15  H  HCH2  0   0.235  -5.5737  -1.3279  -0.9494
 6S7  H16  H  HCH2  0   0.231  -4.7152  -0.3009  -2.0920
 6S7  H17  H  HCH3  0   0.191   6.9028  -1.9772   0.6522
 6S7  H18  H  HCH3  0   0.233   5.4027  -2.6758   1.2829
 6S7  H19  H  HCH3  0   0.233   5.9504  -3.0895  -0.3411
 6S7  H20  H  HCH2  0   0.241   4.5873  -0.6141   1.7618
 6S7  H21  H  HCH2  0   0.204   5.8374   0.3910   1.0426
 6S7  H22  H  HCH2  0   0.228  -2.1873  -0.4985  -2.3023
 6S7  H23  H  HCH2  0   0.252  -1.2973  -1.4391  -1.1158
 6S7  H24  H  HCH2  0   0.232  -4.3662   0.4231   2.1364
 6S7  H25  H  HCH2  0   0.222  -5.4821  -0.7862   1.5332
 6S7  H26  H  HNH1  0   0.346  -2.5812  -0.8946   1.6053
 6S7  H28  H  HCH1  0   0.242  -3.4561  -2.4357  -1.7169
 6S7  H5   H  HCH2  0   0.232  -2.5433  -2.9211   0.5438

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
 6S7  C2   C3   single    1.523  0.020  1.523
 6S7  C2   C1   single    1.524  0.020  1.524
 6S7  C3   C19  single    1.535  0.020  1.535
 6S7  C3   C4   single    1.526  0.020  1.526
 6S7  C19  N20  single    1.456  0.020  1.456
 6S7  C1   C21  single    1.534  0.020  1.534
 6S7  C1   C6   single    1.526  0.020  1.526
 6S7  C21  N20  single    1.455  0.020  1.455
 6S7  C4   N5   single    1.455  0.020  1.455
 6S7  C6   N5   single    1.461  0.020  1.461
 6S7  N5   C7   single    1.384  0.020  1.384
 6S7  C7   C12  aromatic  1.407  0.020  1.407
 6S7  C7   C8   aromatic  1.396  0.020  1.396
 6S7  C12  N11  aromatic  1.321  0.020  1.321
 6S7  C8   C9   aromatic  1.389  0.020  1.389
 6S7  N11  C10  aromatic  1.325  0.020  1.325
 6S7  C9   C10  aromatic  1.396  0.020  1.396
 6S7  C9   O13  single    1.343  0.020  1.343
 6S7  C14  O13  single    1.419  0.020  1.419
 6S7  C14  C15  single    1.512  0.020  1.512
 6S7  C18  N16  single    1.447  0.020  1.447
 6S7  C15  N16  single    1.448  0.020  1.448
 6S7  N16  C17  single    1.447  0.020  1.447
 6S7  C17  H1   single    0.970  0.020  1.090
 6S7  C17  H2   single    0.970  0.020  1.090
 6S7  C17  H3   single    0.970  0.020  1.090
 6S7  C21  H5   single    0.970  0.020  1.090
 6S7  C21  H6   single    0.970  0.020  1.090
 6S7  C14  H7   single    0.970  0.020  1.090
 6S7  C14  H8   single    0.970  0.020  1.090
 6S7  C12  H9   single    0.930  0.020  1.080
 6S7  C10  H10  single    0.930  0.020  1.080
 6S7  C8   H11  single    0.930  0.020  1.080
 6S7  C3   H12  single    0.970  0.020  1.090
 6S7  C4   H13  single    0.970  0.020  1.090
 6S7  C4   H14  single    0.970  0.020  1.090
 6S7  C2   H15  single    0.970  0.020  1.090
 6S7  C2   H16  single    0.970  0.020  1.090
 6S7  C18  H17  single    0.970  0.020  1.090
 6S7  C18  H18  single    0.970  0.020  1.090
 6S7  C18  H19  single    0.970  0.020  1.090
 6S7  C15  H20  single    0.970  0.020  1.090
 6S7  C15  H21  single    0.970  0.020  1.090
 6S7  C6   H22  single    0.970  0.020  1.090
 6S7  C6   H23  single    0.970  0.020  1.090
 6S7  C19  H24  single    0.970  0.020  1.090
 6S7  C19  H25  single    0.970  0.020  1.090
 6S7  N20  H26  single    0.890  0.020  1.040
 6S7  C1   H28  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
 6S7  H3   C17  H2   107.76  3.000
 6S7  H3   C17  H1   107.66  3.000
 6S7  H2   C17  H1   107.05  3.000
 6S7  H3   C17  N16  113.22  3.000
 6S7  H2   C17  N16  111.24  3.000
 6S7  H1   C17  N16  109.66  3.000
 6S7  C15  N16  C18  110.75  3.000
 6S7  C15  N16  C17  112.85  3.000
 6S7  C18  N16  C17  110.83  3.000
 6S7  H6   C21  H5   106.49  3.000
 6S7  H6   C21  C1   107.81  3.000
 6S7  H5   C21  C1   110.31  3.000
 6S7  H6   C21  N20  108.52  3.000
 6S7  H5   C21  N20  108.38  3.000
 6S7  C1   C21  N20  114.99  3.000
 6S7  H8   C14  H7   107.23  3.000
 6S7  H8   C14  O13  110.38  3.000
 6S7  H7   C14  O13  110.79  3.000
 6S7  H8   C14  C15  111.71  3.000
 6S7  H7   C14  C15  108.23  3.000
 6S7  O13  C14  C15  108.49  3.000
 6S7  H9   C12  C7   121.01  3.000
 6S7  H9   C12  N11  115.78  3.000
 6S7  C7   C12  N11  123.21  3.000
 6S7  C10  N11  C12  120.33  3.000
 6S7  H10  C10  C9   122.16  3.000
 6S7  H10  C10  N11  116.54  3.000
 6S7  C9   C10  N11  121.30  3.000
 6S7  O13  C9   C8   116.75  3.000
 6S7  O13  C9   C10  124.56  3.000
 6S7  C8   C9   C10  118.69  3.000
 6S7  H11  C8   C7   121.29  3.000
 6S7  H11  C8   C9   118.47  3.000
 6S7  C7   C8   C9   120.20  3.000
 6S7  H12  C3   C19  108.04  3.000
 6S7  H12  C3   C2   110.40  3.000
 6S7  C19  C3   C2   109.15  3.000
 6S7  H12  C3   C4   106.83  3.000
 6S7  C19  C3   C4   113.05  3.000
 6S7  C2   C3   C4   109.35  3.000
 6S7  N5   C7   C8   121.44  3.000
 6S7  C8   C7   C12  116.25  3.000
 6S7  N5   C7   C12  122.28  3.000
 6S7  H14  C4   H13  106.72  3.000
 6S7  H14  C4   N5   108.47  3.000
 6S7  H13  C4   N5   111.51  3.000
 6S7  H14  C4   C3   109.02  3.000
 6S7  H13  C4   C3   108.91  3.000
 6S7  N5   C4   C3   112.04  3.000
 6S7  H16  C2   H15  107.06  3.000
 6S7  H16  C2   C1   110.85  3.000
 6S7  H15  C2   C1   110.68  3.000
 6S7  H16  C2   C3   110.85  3.000
 6S7  H15  C2   C3   110.86  3.000
 6S7  C1   C2   C3   106.58  3.000
 6S7  H19  C18  H18  107.81  3.000
 6S7  H19  C18  H17  107.62  3.000
 6S7  H18  C18  H17  107.73  3.000
 6S7  H19  C18  N16  109.98  3.000
 6S7  H18  C18  N16  110.15  3.000
 6S7  H17  C18  N16  113.35  3.000
 6S7  H21  C15  H20  106.25  3.000
 6S7  H21  C15  C14  106.94  3.000
 6S7  H20  C15  C14  108.33  3.000
 6S7  H21  C15  N16  112.39  3.000
 6S7  H20  C15  N16  108.29  3.000
 6S7  C14  C15  N16  114.29  3.000
 6S7  C9   O13  C14  118.64  3.000
 6S7  C6   N5   C4   114.88  3.000
 6S7  C6   N5   C7   118.17  3.000
 6S7  C4   N5   C7   117.74  3.000
 6S7  H23  C6   H22  106.63  3.000
 6S7  H23  C6   C1   109.12  3.000
 6S7  H22  C6   C1   108.80  3.000
 6S7  H23  C6   N5   109.67  3.000
 6S7  H22  C6   N5   110.01  3.000
 6S7  C1   C6   N5   112.44  3.000
 6S7  H25  C19  H24  106.35  3.000
 6S7  H25  C19  N20  108.55  3.000
 6S7  H24  C19  N20  108.22  3.000
 6S7  H25  C19  C3   107.93  3.000
 6S7  H24  C19  C3   110.19  3.000
 6S7  N20  C19  C3   115.23  3.000
 6S7  H26  N20  C19  108.11  3.000
 6S7  H26  N20  C21  108.17  3.000
 6S7  C19  N20  C21  112.45  3.000
 6S7  H28  C1   C6   106.89  3.000
 6S7  H28  C1   C2   110.43  3.000
 6S7  C6   C1   C2   109.19  3.000
 6S7  H28  C1   C21  108.17  3.000
 6S7  C6   C1   C21  113.23  3.000
 6S7  C2   C1   C21  108.91  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
 6S7  CONST_01  C9   C8   C7   C12     0.00   0.0  0
 6S7  CONST_02  C9   C10  N11  C12     0.00   0.0  0
 6S7  CONST_03  C8   C7   C12  N11     0.00   0.0  0
 6S7  CONST_04  C8   C9   C10  N11     0.00   0.0  0
 6S7  CONST_05  C7   C12  N11  C10     0.00   0.0  0
 6S7  CONST_06  C7   C8   C9   C10     0.00   0.0  0
 6S7  CONST_07  N5   C7   C12  N11   180.00   0.0  0
 6S7  CONST_08  N5   C7   C8   C9    180.00   0.0  0
 6S7  CONST_09  O13  C9   C10  N11   180.00   0.0  0
 6S7  CONST_10  O13  C9   C8   C7    180.00   0.0  0
 6S7  CONST_11  H11  C8   C7   C12   180.00   0.0  0
 6S7  CONST_12  H10  C10  N11  C12   180.00   0.0  0
 6S7  CONST_13  H9   C12  N11  C10   180.00   0.0  0
 6S7  Var_01    C3   C19  N20  C21   -46.49  30.0  1
 6S7  Var_02    C4   N5   C7   C12    -9.03  30.0  1
 6S7  Var_03    C1   C6   N5   C7    164.52  30.0  3
 6S7  Var_04    C1   C21  N20  C19    47.03  30.0  1
 6S7  Var_05    C8   C9   O13  C14  -176.45  30.0  2
 6S7  Var_06    C15  C14  O13  C9    172.09  30.0  2
 6S7  Var_07    C14  C15  N16  C17    66.36  30.0  1
 6S7  Var_08    O13  C14  C15  N16    57.86  30.0  1
 6S7  Var_09    H17  C18  N16  C17    62.59  30.0  3
 6S7  Var_10    H1   C17  N16  C18    56.53  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
 6S7  chir_01  C3  C2  C19  C4  negativ
 6S7  chir_02  C1  C2  C21  C6  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
 6S7  plan-1  C12  0.020
 6S7  plan-1  N11  0.020
 6S7  plan-1  C10  0.020
 6S7  plan-1  C9   0.020
 6S7  plan-1  C8   0.020
 6S7  plan-1  C7   0.020
 6S7  plan-1  O13  0.020
 6S7  plan-1  N5   0.020
 6S7  plan-1  H9   0.020
 6S7  plan-1  H10  0.020
 6S7  plan-1  H11  0.020

