# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 08:52:53 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 2-[(1R,2S)-2-{5-[(2S)-azetidin-2-ylmethoxy]pyridin-3-yl}cyclopropyl]ethanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC[C@H]1C[C@@H]1c2cncc(OC[C@@H]3CCN3)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
 SW4  SW4  2-[(1R,2S)-2-{5-[(2S)-azetidin-2-ylmethoxy]pyridin-3-yl}cyclopropyl]ethanol  ligand  38  18  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SW4
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
 SW4  O01   O  OH1   0  -0.675   6.7623  -2.0743   0.3005
 SW4  C02   C  CH2   0  -0.136   5.9853  -0.9071   0.4654
 SW4  C03   C  CH2   0  -0.469   4.5550  -1.2080   0.0582
 SW4  C04   C  CH1   0  -0.227   3.6746   0.0036   0.2173
 SW4  C05   C  CH2   0  -0.467   3.6487   1.0600  -0.8343
 SW4  C06   C  CH1   0  -0.393   2.4530   0.1607  -0.6509
 SW4  C07   C  CR6   0   0.160   1.1800   0.6706  -0.0976
 SW4  C08   C  CR16  0  -0.162   1.1249   1.6940   0.8545
 SW4  N09   N  N     0  -0.382  -0.0049   2.1512   1.3624
 SW4  C10   C  CR16  0  -0.206  -1.1613   1.6308   0.9634
 SW4  C11   C  CR6   0   0.341  -1.2235   0.6098   0.0179
 SW4  O12   O  O2    0  -0.472  -2.3563   0.0461  -0.4295
 SW4  C13   C  CH2   0  -0.171  -3.5993   0.4966   0.0888
 SW4  C14   C  C     0  -0.097  -4.6892  -0.3150  -0.5583
 SW4  C15   C  C     0  -0.501  -6.1127  -0.1099  -0.0162
 SW4  C16   C  C     0  -0.274  -6.2177  -1.6432  -0.0326
 SW4  N17   N  N     0  -0.605  -4.7521  -1.7227  -0.1416
 SW4  C18   C  CR16  0  -0.333  -0.0270   0.1308  -0.5118
 SW4  H01   H  HOH1  0   0.452   7.6632  -1.8747   0.5694
 SW4  H021  H  HCH2  0   0.190   6.0005  -0.5597   1.5072
 SW4  H022  H  HCH2  0   0.193   6.3657  -0.0797  -0.1483
 SW4  H031  H  HCH2  0   0.228   4.5343  -1.5409  -0.9842
 SW4  H032  H  HCH2  0   0.236   4.1640  -2.0310   0.6637
 SW4  H04   H  HCH1  0   0.259   3.5597   0.3508   1.2407
 SW4  H051  H  HCH2  0   0.257   3.5561   2.0963  -0.5331
 SW4  H052  H  HCH2  0   0.260   4.2471   0.9089  -1.7252
 SW4  H06   H  HCH1  0   0.261   2.3242  -0.6036  -1.4105
 SW4  H08   H  HCR6  0   0.249   2.0345   2.1619   1.2179
 SW4  H18   H  HCR6  0   0.269  -0.0514  -0.6646  -1.2481
 SW4  H10   H  HCR6  0   0.273  -2.0543   2.0473   1.4144
 SW4  H131  H  HCH2  0   0.219  -3.6340   0.3625   1.1762
 SW4  H132  H  HCH2  0   0.228  -3.7471   1.5608  -0.1300
 SW4  H14   H  H     0   0.230  -4.6528  -0.1807  -1.6467
 SW4  H151  H  H     0   0.239  -6.1256   0.3078   0.9913
 SW4  H152  H  H     0   0.248  -6.8053   0.4486  -0.6414
 SW4  H17   H  H     0   0.343  -4.4092  -2.3848  -0.8250
 SW4  H161  H  H     0   0.218  -6.6376  -2.1242   0.8535
 SW4  H162  H  H     0   0.214  -6.7546  -2.0113  -0.9120

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
 SW4  O01  C02   single    1.412  0.020  1.412
 SW4  C02  C03   single    1.517  0.020  1.517
 SW4  C03  C04   single    1.506  0.020  1.506
 SW4  C04  C05   single    1.491  0.020  1.491
 SW4  C04  C06   single    1.507  0.020  1.507
 SW4  C05  C06   single    1.507  0.020  1.507
 SW4  C06  C07   single    1.479  0.020  1.479
 SW4  C07  C08   aromatic  1.399  0.020  1.399
 SW4  C07  C18   aromatic  1.385  0.020  1.385
 SW4  C08  N09   aromatic  1.320  0.020  1.320
 SW4  N09  C10   aromatic  1.329  0.020  1.329
 SW4  C10  C11   aromatic  1.393  0.020  1.393
 SW4  C11  O12   single    1.342  0.020  1.342
 SW4  C11  C18   aromatic  1.393  0.020  1.393
 SW4  O12  C13   single    1.420  0.020  1.420
 SW4  C13  C14   single    1.505  0.020  1.505
 SW4  C14  C15   single    1.537  0.020  1.537
 SW4  C14  N17   single    1.469  0.020  1.469
 SW4  C15  C16   single    1.537  0.020  1.537
 SW4  C16  N17   single    1.472  0.020  1.472
 SW4  O01  H01   single    0.850  0.020  0.980
 SW4  C02  H021  single    0.970  0.020  1.090
 SW4  C02  H022  single    0.970  0.020  1.090
 SW4  C03  H031  single    0.970  0.020  1.090
 SW4  C03  H032  single    0.970  0.020  1.090
 SW4  C04  H04   single    0.970  0.020  1.090
 SW4  C05  H051  single    0.970  0.020  1.090
 SW4  C05  H052  single    0.970  0.020  1.090
 SW4  C06  H06   single    0.970  0.020  1.090
 SW4  C08  H08   single    0.930  0.020  1.080
 SW4  C18  H18   single    0.930  0.020  1.080
 SW4  C10  H10   single    0.930  0.020  1.080
 SW4  C13  H131  single    0.970  0.020  1.090
 SW4  C13  H132  single    0.970  0.020  1.090
 SW4  C14  H14   single    0.970  0.020  1.090
 SW4  C15  H151  single    0.970  0.020  1.090
 SW4  C15  H152  single    0.970  0.020  1.090
 SW4  N17  H17   single    0.890  0.020  1.040
 SW4  C16  H161  single    0.970  0.020  1.090
 SW4  C16  H162  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
 SW4  H01   O01  C02   108.15  3.000
 SW4  H022  C02  H021  106.68  3.000
 SW4  H022  C02  C03   109.02  3.000
 SW4  H021  C02  C03   109.29  3.000
 SW4  H022  C02  O01   111.53  3.000
 SW4  H021  C02  O01   111.39  3.000
 SW4  C03   C02  O01   108.88  3.000
 SW4  H032  C03  H031  106.95  3.000
 SW4  H032  C03  C04   109.74  3.000
 SW4  H031  C03  C04   109.53  3.000
 SW4  H032  C03  C02   109.73  3.000
 SW4  H031  C03  C02   109.50  3.000
 SW4  C04   C03  C02   111.30  3.000
 SW4  H04   C04  C06   115.05  3.000
 SW4  H04   C04  C05   115.85  3.000
 SW4  C06   C04  C05    60.37  3.000
 SW4  H04   C04  C03   114.73  3.000
 SW4  C06   C04  C03   119.79  3.000
 SW4  C05   C04  C03   120.37  3.000
 SW4  H052  C05  H051  114.16  3.000
 SW4  H052  C05  C06   117.05  3.000
 SW4  H051  C05  C06   117.98  3.000
 SW4  H052  C05  C04   118.13  3.000
 SW4  H051  C05  C04   118.90  3.000
 SW4  C06   C05  C04    60.34  3.000
 SW4  H06   C06  C07   113.73  3.000
 SW4  H06   C06  C05   115.42  3.000
 SW4  C07   C06  C05   121.51  3.000
 SW4  H06   C06  C04   115.22  3.000
 SW4  C07   C06  C04   121.22  3.000
 SW4  C05   C06  C04    59.29  3.000
 SW4  C18   C07  C08   117.01  3.000
 SW4  C18   C07  C06   120.25  3.000
 SW4  C08   C07  C06   122.74  3.000
 SW4  H08   C08  N09   116.03  3.000
 SW4  H08   C08  C07   120.68  3.000
 SW4  N09   C08  C07   123.29  3.000
 SW4  C10   N09  C08   119.56  3.000
 SW4  H10   C10  C11   121.83  3.000
 SW4  H10   C10  N09   116.20  3.000
 SW4  C11   C10  N09   121.97  3.000
 SW4  C18   C11  O12   116.98  3.000
 SW4  C18   C11  C10   118.14  3.000
 SW4  O12   C11  C10   124.88  3.000
 SW4  C13   O12  C11   118.94  3.000
 SW4  H132  C13  H131  108.21  3.000
 SW4  H132  C13  C14   109.88  3.000
 SW4  H131  C13  C14   109.73  3.000
 SW4  H132  C13  O12   110.67  3.000
 SW4  H131  C13  O12   110.54  3.000
 SW4  C14   C13  O12   107.81  3.000
 SW4  H14   C14  N17   113.58  3.000
 SW4  H14   C14  C15   111.36  3.000
 SW4  N17   C14  C15    89.32  3.000
 SW4  H14   C14  C13   109.66  3.000
 SW4  N17   C14  C13   115.19  3.000
 SW4  C15   C14  C13   116.56  3.000
 SW4  H152  C15  H151  109.07  3.000
 SW4  H152  C15  C16   117.56  3.000
 SW4  H151  C15  C16   113.02  3.000
 SW4  H152  C15  C14   117.11  3.000
 SW4  H151  C15  C14   112.82  3.000
 SW4  C16   C15  C14    85.78  3.000
 SW4  H162  C16  H161  108.37  3.000
 SW4  H162  C16  N17   114.27  3.000
 SW4  H161  C16  N17   114.78  3.000
 SW4  H162  C16  C15   112.19  3.000
 SW4  H161  C16  C15   117.19  3.000
 SW4  N17   C16  C15    89.24  3.000
 SW4  H17   N17  C16   115.02  3.000
 SW4  H17   N17  C14   114.90  3.000
 SW4  C16   N17  C14    90.68  3.000
 SW4  H18   C18  C11   119.41  3.000
 SW4  H18   C18  C07   120.56  3.000
 SW4  C11   C18  C07   120.03  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
 SW4  CONST_01  C10  N09  C08  C07     0.00   0.0  0
 SW4  CONST_02  C10  C11  C18  C07     0.00   0.0  0
 SW4  CONST_03  C11  C18  C07  C08     0.00   0.0  0
 SW4  CONST_04  C11  C10  N09  C08     0.00   0.0  0
 SW4  CONST_05  C18  C07  C08  N09     0.00   0.0  0
 SW4  CONST_06  C18  C11  C10  N09     0.00   0.0  0
 SW4  CONST_07  N09  C08  C07  C06   180.00   0.0  0
 SW4  CONST_08  C11  C18  C07  C06   180.00   0.0  0
 SW4  CONST_09  O12  C11  C18  C07   180.00   0.0  0
 SW4  CONST_10  O12  C11  C10  N09   180.00   0.0  0
 SW4  CONST_11  H08  C08  C07  C06     0.00   0.0  0
 SW4  CONST_12  H18  C18  C07  C06     0.00   0.0  0
 SW4  CONST_13  H10  C10  N09  C08   180.00   0.0  0
 SW4  Var_01    C07  C06  C05  C04   110.05  30.0  1
 SW4  Var_02    C08  C07  C06  C04    38.34  30.0  2
 SW4  Var_03    N17  C16  C15  C14    16.41  30.0  1
 SW4  Var_04    C06  C05  C04  C03   109.22  30.0  1
 SW4  Var_05    C05  C04  C03  C02    81.53  30.0  3
 SW4  Var_06    C14  C13  O12  C11  -178.90  30.0  3
 SW4  Var_07    C18  C11  O12  C13   179.60  30.0  2
 SW4  Var_08    C04  C03  C02  O01   179.83  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
 SW4  chir_03  C14  C13  C15  N17  positiv
 SW4  chir_04  C04  C03  C05  C06  both
 SW4  chir_05  C06  C04  C05  C07  both

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
 SW4  plan-1  C06  0.020
 SW4  plan-1  C07  0.020
 SW4  plan-1  C08  0.020
 SW4  plan-1  N09  0.020
 SW4  plan-1  C10  0.020
 SW4  plan-1  C11  0.020
 SW4  plan-1  O12  0.020
 SW4  plan-1  C18  0.020
 SW4  plan-1  H08  0.020
 SW4  plan-1  H18  0.020
 SW4  plan-1  H10  0.020

