# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 02:38:32 2021
#   Inital geometry file: a 126 line input string
#   Ligand name: 7-(azetidin-1-yl)-~{N}-[4-(2-oxidanylpropan-2-yl)cyclohexyl]-1,6-naphthyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(O)[C@H]1CC[C@@H](CC1)NC(=O)c2cnc3cc(ncc3c2)N4CCC4
#
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
 SWS  SWS  7-(azetidin-1-yl)-~{N}-[4-(2-oxidanylpropan-2-yl)cyclohexyl]-1,6-naphthyridine-3-carboxamide  ligand  55  27  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SWS
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
 SWS  C10  C  CH2   0  -0.448  67.9451  -3.8348  80.0937
 SWS  C15  C  CR16  0  -0.072  63.0944  -7.1955  75.6330
 SWS  C17  C  CR66  0   0.330  60.8557  -6.8811  75.9595
 SWS  C21  C  CR16  0  -0.086  59.9908  -5.7307  77.9038
 SWS  C22  C  CR66  0  -0.030  61.1064  -6.1921  77.1737
 SWS  C26  C  C     0  -0.532  55.2734  -6.4721  75.3246
 SWS  C01  C  CH3   0  -0.678  71.0522  -3.8281  79.9352
 SWS  C02  C  CT    0   0.237  70.1654  -2.6721  79.4887
 SWS  C03  C  CH3   0  -0.675  70.0355  -1.6564  80.6254
 SWS  C05  C  CH1   0  -0.252  68.7706  -3.1383  79.0090
 SWS  C06  C  CH2   0  -0.426  68.8236  -4.0312  77.7671
 SWS  C07  C  CH2   0  -0.429  67.4235  -4.3655  77.2635
 SWS  C08  C  CH1   0  -0.050  66.5915  -5.0475  78.3477
 SWS  C09  C  CH2   0  -0.442  66.5437  -4.1859  79.6040
 SWS  C14  C  CR6   0  -0.145  63.4506  -6.4992  76.8165
 SWS  C18  C  CR16  0  -0.471  59.5329  -7.0507  75.5516
 SWS  C19  C  CR6   0   0.508  58.5151  -6.5458  76.3582
 SWS  C23  C  CR16  0  -0.215  62.4310  -6.0027  77.5894
 SWS  C25  C  C     0  -0.248  56.0492  -6.0168  76.5794
 SWS  C27  C  C     0  -0.257  56.5962  -7.0500  74.7807
 SWS  N11  N  NH1   0  -0.656  65.2376  -5.3227  77.9021
 SWS  N16  N  N     0  -0.446  61.8762  -7.3740  75.2064
 SWS  N20  N  N     0  -0.447  58.7563  -5.8938  77.5263
 SWS  N24  N  N     0  -0.481  57.2212  -6.6855  76.0392
 SWS  O04  O  OH1   0  -0.679  70.8553  -2.0592  78.4029
 SWS  O13  O  O     0  -0.493  65.6862  -7.2636  76.8284
 SWS  H1   H  HCH2  0   0.221  68.4537  -4.7518  80.4091
 SWS  H2   H  HCH2  0   0.241  67.8590  -3.2072  80.9822
 SWS  H4   H  HCR6  0   0.274  60.1546  -5.2019  78.8390
 SWS  H5   H  H     0   0.259  54.8448  -5.6681  74.7319
 SWS  H6   H  H     0   0.258  54.5077  -7.2201  75.5181
 SWS  H7   H  HCH3  0   0.227  70.6392  -4.3256  80.8123
 SWS  H8   H  HCH3  0   0.234  71.1755  -4.5789  79.1533
 SWS  H9   H  HCH3  0   0.234  72.0444  -3.4618  80.2055
 SWS  H10  H  HCH3  0   0.226  69.6173  -2.0976  81.5293
 SWS  H11  H  HCH3  0   0.234  71.0156  -1.2514  80.8826
 SWS  H12  H  HCH3  0   0.224  69.3894  -0.8231  80.3358
 SWS  H13  H  HCH1  0   0.210  68.2245  -2.2238  78.7280
 SWS  H14  H  HCH2  0   0.215  69.3491  -4.9631  78.0024
 SWS  H15  H  HCH2  0   0.233  69.3883  -3.5475  76.9692
 SWS  H16  H  HCH2  0   0.214  66.9123  -3.4481  76.9513
 SWS  H17  H  HCH2  0   0.238  67.4838  -5.0103  76.3842
 SWS  H18  H  HCH1  0   0.238  67.0574  -6.0046  78.5985
 SWS  H19  H  HCH2  0   0.221  65.9937  -3.2625  79.3871
 SWS  H20  H  HCH2  0   0.243  65.9918  -4.7067  80.3900
 SWS  H21  H  HCR6  0   0.269  59.3142  -7.5701  74.6277
 SWS  H22  H  HCR6  0   0.272  62.6199  -5.4876  78.5248
 SWS  H23  H  H     0   0.236  56.1666  -4.9353  76.6786
 SWS  H24  H  H     0   0.240  55.7014  -6.4199  77.5317
 SWS  H25  H  H     0   0.245  56.6031  -8.1210  74.5666
 SWS  H26  H  H     0   0.238  57.0096  -6.5186  73.9184
 SWS  H27  H  HNH1  0   0.401  64.5732  -4.5698  77.9917
 SWS  H28  H  HOH1  0   0.439  70.3222  -1.3209  78.0876
 SWS  C12  C  C     0   0.530  64.8918  -6.3985  77.1775
 SWS  H3   H  HCR6  0   0.269  63.8854  -7.6084  75.0151

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
 SWS  C26  C27  single    1.543  0.020  1.543
 SWS  C26  C25  single    1.544  0.020  1.544
 SWS  C27  N24  single    1.452  0.020  1.452
 SWS  N16  C15  aromatic  1.303  0.020  1.303
 SWS  N16  C17  aromatic  1.361  0.020  1.361
 SWS  C18  C17  aromatic  1.395  0.020  1.395
 SWS  C18  C19  aromatic  1.393  0.020  1.393
 SWS  N24  C25  single    1.453  0.020  1.453
 SWS  N24  C19  single    1.340  0.020  1.340
 SWS  C15  C14  aromatic  1.419  0.020  1.419
 SWS  C17  C22  aromatic  1.418  0.020  1.418
 SWS  C19  N20  aromatic  1.359  0.020  1.359
 SWS  C14  C12  single    1.489  0.020  1.489
 SWS  C14  C23  aromatic  1.372  0.020  1.372
 SWS  C07  C06  single    1.525  0.020  1.525
 SWS  C07  C08  single    1.527  0.020  1.527
 SWS  O13  C12  double    1.225  0.020  1.225
 SWS  C22  C23  aromatic  1.401  0.020  1.401
 SWS  C22  C21  aromatic  1.411  0.020  1.411
 SWS  N20  C21  aromatic  1.301  0.020  1.301
 SWS  C12  N11  single    1.342  0.020  1.342
 SWS  C06  C05  single    1.530  0.020  1.530
 SWS  N11  C08  single    1.452  0.020  1.452
 SWS  C08  C09  single    1.524  0.020  1.524
 SWS  O04  C02  single    1.425  0.020  1.425
 SWS  C01  C02  single    1.524  0.020  1.524
 SWS  C05  C02  single    1.547  0.020  1.547
 SWS  C05  C10  single    1.531  0.020  1.531
 SWS  C02  C03  single    1.530  0.020  1.530
 SWS  C09  C10  single    1.525  0.020  1.525
 SWS  C10  H1   single    0.970  0.020  1.090
 SWS  C10  H2   single    0.970  0.020  1.090
 SWS  C15  H3   single    0.930  0.020  1.080
 SWS  C21  H4   single    0.930  0.020  1.080
 SWS  C26  H5   single    0.970  0.020  1.090
 SWS  C26  H6   single    0.970  0.020  1.090
 SWS  C01  H7   single    0.970  0.020  1.090
 SWS  C01  H8   single    0.970  0.020  1.090
 SWS  C01  H9   single    0.970  0.020  1.090
 SWS  C03  H10  single    0.970  0.020  1.090
 SWS  C03  H11  single    0.970  0.020  1.090
 SWS  C03  H12  single    0.970  0.020  1.090
 SWS  C05  H13  single    0.970  0.020  1.090
 SWS  C06  H14  single    0.970  0.020  1.090
 SWS  C06  H15  single    0.970  0.020  1.090
 SWS  C07  H16  single    0.970  0.020  1.090
 SWS  C07  H17  single    0.970  0.020  1.090
 SWS  C08  H18  single    0.970  0.020  1.090
 SWS  C09  H19  single    0.970  0.020  1.090
 SWS  C09  H20  single    0.970  0.020  1.090
 SWS  C18  H21  single    0.930  0.020  1.080
 SWS  C23  H22  single    0.930  0.020  1.080
 SWS  C25  H23  single    0.970  0.020  1.090
 SWS  C25  H24  single    0.970  0.020  1.090
 SWS  C27  H25  single    0.970  0.020  1.090
 SWS  C27  H26  single    0.970  0.020  1.090
 SWS  N11  H27  single    0.860  0.020  1.020
 SWS  O04  H28  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
 SWS  H2   C10  H1   106.48  3.000
 SWS  H2   C10  C09  108.74  3.000
 SWS  H1   C10  C09  109.05  3.000
 SWS  H2   C10  C05  110.97  3.000
 SWS  H1   C10  C05  109.55  3.000
 SWS  C09  C10  C05  111.88  3.000
 SWS  H3   C15  N16  116.29  3.000
 SWS  H3   C15  C14  118.60  3.000
 SWS  N16  C15  C14  125.11  3.000
 SWS  N16  C17  C18  120.36  3.000
 SWS  C18  C17  C22  118.50  3.000
 SWS  N16  C17  C22  121.15  3.000
 SWS  H4   C21  N20  116.97  3.000
 SWS  H4   C21  C22  119.03  3.000
 SWS  N20  C21  C22  124.00  3.000
 SWS  C23  C22  C21  123.35  3.000
 SWS  C21  C22  C17  117.52  3.000
 SWS  C23  C22  C17  119.13  3.000
 SWS  H6   C26  H5   109.15  3.000
 SWS  H6   C26  C27  114.13  3.000
 SWS  H5   C26  C27  115.02  3.000
 SWS  H6   C26  C25  114.33  3.000
 SWS  H5   C26  C25  115.03  3.000
 SWS  C27  C26  C25   88.06  3.000
 SWS  H9   C01  H8   107.80  3.000
 SWS  H9   C01  H7   107.37  3.000
 SWS  H8   C01  H7   107.79  3.000
 SWS  H9   C01  C02  110.30  3.000
 SWS  H8   C01  C02  112.20  3.000
 SWS  H7   C01  C02  111.20  3.000
 SWS  O04  C02  C05  109.26  3.000
 SWS  C05  C02  C03  110.73  3.000
 SWS  O04  C02  C03  108.77  3.000
 SWS  C03  C02  C01  109.59  3.000
 SWS  C05  C02  C01  112.76  3.000
 SWS  O04  C02  C01  105.53  3.000
 SWS  H12  C03  H11  108.08  3.000
 SWS  H12  C03  H10  107.55  3.000
 SWS  H11  C03  H10  107.43  3.000
 SWS  H12  C03  C02  111.05  3.000
 SWS  H11  C03  C02  110.20  3.000
 SWS  H10  C03  C02  112.35  3.000
 SWS  H13  C05  C06  107.13  3.000
 SWS  H13  C05  C02  106.01  3.000
 SWS  C06  C05  C02  113.35  3.000
 SWS  H13  C05  C10  106.93  3.000
 SWS  C02  C05  C10  113.80  3.000
 SWS  C06  C05  C10  109.16  3.000
 SWS  H15  C06  H14  106.62  3.000
 SWS  H15  C06  C07  109.33  3.000
 SWS  H14  C06  C07  108.96  3.000
 SWS  H15  C06  C05  110.66  3.000
 SWS  H14  C06  C05  109.79  3.000
 SWS  C07  C06  C05  111.35  3.000
 SWS  H17  C07  H16  106.90  3.000
 SWS  H17  C07  C08  109.75  3.000
 SWS  H16  C07  C08  108.78  3.000
 SWS  H17  C07  C06  110.16  3.000
 SWS  H16  C07  C06  109.81  3.000
 SWS  C08  C07  C06  111.32  3.000
 SWS  H18  C08  N11  107.57  3.000
 SWS  H18  C08  C09  108.61  3.000
 SWS  N11  C08  C09  109.33  3.000
 SWS  H18  C08  C07  108.75  3.000
 SWS  C09  C08  C07  110.47  3.000
 SWS  N11  C08  C07  112.01  3.000
 SWS  H20  C09  H19  106.88  3.000
 SWS  H20  C09  C08  109.83  3.000
 SWS  H19  C09  C08  109.19  3.000
 SWS  H20  C09  C10  110.05  3.000
 SWS  H19  C09  C10  109.30  3.000
 SWS  C08  C09  C10  111.47  3.000
 SWS  C23  C14  C12  123.91  3.000
 SWS  C23  C14  C15  117.45  3.000
 SWS  C12  C14  C15  118.59  3.000
 SWS  H21  C18  C19  121.37  3.000
 SWS  H21  C18  C17  119.98  3.000
 SWS  C19  C18  C17  118.65  3.000
 SWS  N24  C19  N20  115.21  3.000
 SWS  N20  C19  C18  122.80  3.000
 SWS  N24  C19  C18  121.99  3.000
 SWS  H22  C23  C14  121.89  3.000
 SWS  H22  C23  C22  119.00  3.000
 SWS  C14  C23  C22  119.10  3.000
 SWS  H24  C25  H23  108.71  3.000
 SWS  H24  C25  N24  114.30  3.000
 SWS  H23  C25  N24  113.74  3.000
 SWS  H24  C25  C26  116.12  3.000
 SWS  H23  C25  C26  114.82  3.000
 SWS  N24  C25  C26   88.13  3.000
 SWS  H26  C27  H25  108.63  3.000
 SWS  H26  C27  N24  113.49  3.000
 SWS  H25  C27  N24  114.42  3.000
 SWS  H26  C27  C26  114.83  3.000
 SWS  H25  C27  C26  116.22  3.000
 SWS  N24  C27  C26   88.25  3.000
 SWS  H27  N11  C12  118.48  3.000
 SWS  H27  N11  C08  116.47  3.000
 SWS  C12  N11  C08  123.91  3.000
 SWS  C17  N16  C15  118.06  3.000
 SWS  C19  N20  C21  118.54  3.000
 SWS  C27  N24  C25   95.20  3.000
 SWS  C25  N24  C19  129.95  3.000
 SWS  C27  N24  C19  130.41  3.000
 SWS  H28  O04  C02  108.12  3.000
 SWS  O13  C12  N11  123.55  3.000
 SWS  N11  C12  C14  115.75  3.000
 SWS  O13  C12  C14  120.70  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
 SWS  CONST_01  C18  C17  N16  C15  180.00   0.0  0
 SWS  CONST_02  C22  C17  N16  C15    0.00   0.0  0
 SWS  CONST_03  C22  C23  C14  C15    0.00   0.0  0
 SWS  CONST_04  C14  C15  N16  C17    0.00   0.0  0
 SWS  CONST_05  N20  C19  C18  C17    0.00   0.0  0
 SWS  CONST_06  C14  C23  C22  C17    0.00   0.0  0
 SWS  CONST_07  N20  C21  C22  C17    0.00   0.0  0
 SWS  CONST_08  N16  C17  C22  C21  180.00   0.0  0
 SWS  CONST_09  C18  C17  C22  C21    0.00   0.0  0
 SWS  CONST_10  C14  C23  C22  C21  180.00   0.0  0
 SWS  CONST_11  C18  C19  N20  C21    0.00   0.0  0
 SWS  CONST_12  C19  C18  C17  C22    0.00   0.0  0
 SWS  CONST_13  C19  N20  C21  C22    0.00   0.0  0
 SWS  CONST_14  C23  C22  C17  C18  180.00   0.0  0
 SWS  CONST_15  N16  C17  C18  C19  180.00   0.0  0
 SWS  CONST_16  N16  C15  C14  C23    0.00   0.0  0
 SWS  CONST_17  N16  C17  C22  C23    0.00   0.0  0
 SWS  CONST_18  N20  C21  C22  C23  180.00   0.0  0
 SWS  CONST_19  N24  C19  C18  C17  180.00   0.0  0
 SWS  CONST_20  N24  C19  N20  C21  180.00   0.0  0
 SWS  CONST_21  C12  C14  C23  C22  180.00   0.0  0
 SWS  CONST_22  N16  C15  C14  C12  180.00   0.0  0
 SWS  CONST_23  H22  C23  C14  C15  180.00   0.0  0
 SWS  CONST_24  H3   C15  N16  C17  180.00   0.0  0
 SWS  CONST_25  H4   C21  C22  C17  180.00   0.0  0
 SWS  CONST_26  H21  C18  C17  C22  180.00   0.0  0
 SWS  CONST_27  C14  C12  N11  C08  180.00   0.0  0
 SWS  CONST_28  O13  C12  N11  C08    0.00   0.0  0
 SWS  CONST_29  H27  N11  C12  C14    0.00   0.0  0
 SWS  Var_01    C25  N24  C27  C26   -4.69  30.0  1
 SWS  Var_02    C08  C07  C06  C05  -57.46  30.0  1
 SWS  Var_03    C08  C09  C10  C05   56.22  30.0  1
 SWS  Var_04    O13  C12  C14  C15  -28.14  30.0  2
 SWS  Var_05    H7   C01  C02  C05  -64.53  30.0  3
 SWS  Var_06    H10  C03  C02  C05   66.46  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
 SWS  chir_01  C05  C06  C02  C10  positiv
 SWS  chir_02  C08  N11  C09  C07  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
 SWS  plan-1  C08  0.020
 SWS  plan-1  C14  0.020
 SWS  plan-1  N11  0.020
 SWS  plan-1  O13  0.020
 SWS  plan-1  H27  0.020
 SWS  plan-1  C12  0.020
 SWS  plan-2  C15  0.020
 SWS  plan-2  C17  0.020
 SWS  plan-2  C21  0.020
 SWS  plan-2  C22  0.020
 SWS  plan-2  C14  0.020
 SWS  plan-2  C18  0.020
 SWS  plan-2  C19  0.020
 SWS  plan-2  C23  0.020
 SWS  plan-2  N16  0.020
 SWS  plan-2  N20  0.020
 SWS  plan-2  N24  0.020
 SWS  plan-2  H4   0.020
 SWS  plan-2  H21  0.020
 SWS  plan-2  H22  0.020
 SWS  plan-2  C12  0.020
 SWS  plan-2  H3   0.020

