# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 21:29:24 2021
#   Inital geometry file: a 81 line input string
#   Ligand name: 2-[4-[(3~{S})-pyrazolidin-3-yl]phenoxy]pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1C[C@H](NN1)c2ccc(Oc3ncccn3)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
 S9D  S9D  2-[4-[(3~{S})-pyrazolidin-3-yl]phenoxy]pyrimidine  ligand  32  18  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_S9D
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
 S9D  C10  C  CH1   0  -0.107  -27.5031  100.2865  134.0887
 S9D  C15  C  CR16  0  -0.302  -27.6615  101.2001  136.4340
 S9D  C01  C  CR16  0  -0.363  -30.0505   98.4597  142.0257
 S9D  C02  C  CR16  0  -0.004  -30.2106   98.5882  140.6584
 S9D  C04  C  CR6   0   0.579  -28.0890   99.2873  140.4556
 S9D  C06  C  CR6   0   0.342  -27.2136   99.8358  138.3471
 S9D  C07  C  CR16  0  -0.287  -26.9374   98.7581  137.5253
 S9D  C08  C  CR16  0  -0.305  -27.0178   98.9152  136.1494
 S9D  C09  C  CR6   0   0.058  -27.3760  100.1351  135.5805
 S9D  C11  C  CH2   0  -0.505  -26.5582   99.4097  133.2290
 S9D  C12  C  CH2   0  -0.285  -26.1606  100.3546  132.0856
 S9D  C16  C  CR16  0  -0.290  -27.5780  101.0582  137.8116
 S9D  C18  C  CR16  0  -0.016  -28.7999   98.7903  142.5237
 S9D  N03  N  N     0  -0.438  -29.2308   99.0039  139.8633
 S9D  N13  N  NH1   0  -0.490  -27.0945  101.4724  132.2493
 S9D  N14  N  NH1   0  -0.471  -27.2511  101.6560  133.6489
 S9D  N17  N  N     0  -0.426  -27.8110   99.2055  141.7454
 S9D  H1   H  HCH1  0   0.264  -28.5354  100.0489  133.8085
 S9D  H2   H  HCR6  0   0.261  -27.9556  102.1575  136.0246
 S9D  H4   H  HCR6  0   0.284  -31.1540   98.3515  140.1805
 S9D  H5   H  HCR6  0   0.271  -26.6492   97.8048  137.9496
 S9D  H6   H  HCR6  0   0.262  -26.7974   98.0632  135.5191
 S9D  H7   H  HCH2  0   0.248  -27.0621   98.5114  132.8733
 S9D  H8   H  HCH2  0   0.242  -25.6797   99.0912  133.7913
 S9D  H9   H  HCH2  0   0.233  -26.2735   99.9050  131.0986
 S9D  H10  H  HCH2  0   0.212  -25.1139  100.6637  132.1964
 S9D  H11  H  HCR6  0   0.270  -27.7907  101.8981  138.4609
 S9D  H12  H  HCR6  0   0.285  -28.5844   98.7194  143.5835
 S9D  H13  H  HNH1  0   0.360  -26.7441  102.3316  131.8462
 S9D  H14  H  HNH1  0   0.332  -26.3536  101.9342  134.0554
 S9D  O05  O  O2    0  -0.499  -27.0574   99.7119  139.7130
 S9D  H3   H  HCR6  0   0.285  -30.8513   98.1227  142.6662

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
 S9D  C12  N13  single    1.466  0.020  1.466
 S9D  C12  C11  single    1.536  0.020  1.536
 S9D  N13  N14  single    1.420  0.020  1.420
 S9D  C11  C10  single    1.549  0.020  1.549
 S9D  N14  C10  single    1.460  0.020  1.460
 S9D  C10  C09  single    1.505  0.020  1.505
 S9D  C09  C08  aromatic  1.393  0.020  1.393
 S9D  C09  C15  aromatic  1.394  0.020  1.394
 S9D  C08  C07  aromatic  1.387  0.020  1.387
 S9D  C15  C16  aromatic  1.387  0.020  1.387
 S9D  C07  C06  aromatic  1.383  0.020  1.383
 S9D  C16  C06  aromatic  1.383  0.020  1.383
 S9D  C06  O05  single    1.380  0.020  1.380
 S9D  N03  C02  aromatic  1.328  0.020  1.328
 S9D  N03  C04  aromatic  1.317  0.020  1.317
 S9D  O05  C04  single    1.340  0.020  1.340
 S9D  C02  C01  aromatic  1.383  0.020  1.383
 S9D  C04  N17  aromatic  1.322  0.020  1.322
 S9D  C01  C18  aromatic  1.386  0.020  1.386
 S9D  N17  C18  aromatic  1.325  0.020  1.325
 S9D  C10  H1   single    0.970  0.020  1.090
 S9D  C15  H2   single    0.930  0.020  1.080
 S9D  C01  H3   single    0.930  0.020  1.080
 S9D  C02  H4   single    0.930  0.020  1.080
 S9D  C07  H5   single    0.930  0.020  1.080
 S9D  C08  H6   single    0.930  0.020  1.080
 S9D  C11  H7   single    0.970  0.020  1.090
 S9D  C11  H8   single    0.970  0.020  1.090
 S9D  C12  H9   single    0.970  0.020  1.090
 S9D  C12  H10  single    0.970  0.020  1.090
 S9D  C16  H11  single    0.930  0.020  1.080
 S9D  C18  H12  single    0.930  0.020  1.080
 S9D  N13  H13  single    0.890  0.020  1.040
 S9D  N14  H14  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
 S9D  H1   C10  N14  106.79  3.000
 S9D  H1   C10  C11  108.05  3.000
 S9D  N14  C10  C11  104.97  3.000
 S9D  H1   C10  C09  108.13  3.000
 S9D  N14  C10  C09  112.23  3.000
 S9D  C11  C10  C09  116.21  3.000
 S9D  H2   C15  C16  118.85  3.000
 S9D  H2   C15  C09  119.99  3.000
 S9D  C16  C15  C09  121.16  3.000
 S9D  H3   C01  C18  122.05  3.000
 S9D  H3   C01  C02  122.00  3.000
 S9D  C18  C01  C02  115.95  3.000
 S9D  H4   C02  N03  116.52  3.000
 S9D  H4   C02  C01  121.10  3.000
 S9D  N03  C02  C01  122.38  3.000
 S9D  O05  C04  N17  113.47  3.000
 S9D  N17  C04  N03  127.43  3.000
 S9D  O05  C04  N03  119.10  3.000
 S9D  O05  C06  C16  119.49  3.000
 S9D  O05  C06  C07  119.69  3.000
 S9D  C16  C06  C07  120.74  3.000
 S9D  H5   C07  C08  120.26  3.000
 S9D  H5   C07  C06  120.43  3.000
 S9D  C08  C07  C06  119.31  3.000
 S9D  H6   C08  C09  120.25  3.000
 S9D  H6   C08  C07  118.46  3.000
 S9D  C09  C08  C07  121.28  3.000
 S9D  C08  C09  C15  118.13  3.000
 S9D  C15  C09  C10  120.84  3.000
 S9D  C08  C09  C10  120.98  3.000
 S9D  H8   C11  H7   107.46  3.000
 S9D  H8   C11  C12  110.79  3.000
 S9D  H7   C11  C12  112.58  3.000
 S9D  H8   C11  C10  111.74  3.000
 S9D  H7   C11  C10  111.45  3.000
 S9D  C12  C11  C10  102.88  3.000
 S9D  H10  C12  H9   107.84  3.000
 S9D  H10  C12  N13  112.44  3.000
 S9D  H9   C12  N13  110.46  3.000
 S9D  H10  C12  C11  110.20  3.000
 S9D  H9   C12  C11  113.17  3.000
 S9D  N13  C12  C11  102.77  3.000
 S9D  H11  C16  C06  120.33  3.000
 S9D  H11  C16  C15  120.29  3.000
 S9D  C06  C16  C15  119.38  3.000
 S9D  H12  C18  N17  116.51  3.000
 S9D  H12  C18  C01  121.01  3.000
 S9D  N17  C18  C01  122.48  3.000
 S9D  C04  N03  C02  115.95  3.000
 S9D  H13  N13  N14  108.73  3.000
 S9D  H13  N13  C12  112.49  3.000
 S9D  N14  N13  C12  106.20  3.000
 S9D  H14  N14  N13  109.25  3.000
 S9D  H14  N14  C10  106.65  3.000
 S9D  N13  N14  C10  101.22  3.000
 S9D  C18  N17  C04  115.81  3.000
 S9D  C06  O05  C04  119.31  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
 S9D  CONST_01  C07  C08  C09  C15    0.00   0.0  0
 S9D  CONST_02  C07  C06  C16  C15    0.00   0.0  0
 S9D  CONST_03  C04  N03  C02  C01    0.00   0.0  0
 S9D  CONST_04  C04  N17  C18  C01    0.00   0.0  0
 S9D  CONST_05  N17  C04  N03  C02    0.00   0.0  0
 S9D  CONST_06  N17  C18  C01  C02    0.00   0.0  0
 S9D  CONST_07  C09  C08  C07  C06    0.00   0.0  0
 S9D  CONST_08  C09  C15  C16  C06    0.00   0.0  0
 S9D  CONST_09  C16  C15  C09  C08    0.00   0.0  0
 S9D  CONST_10  C16  C06  C07  C08    0.00   0.0  0
 S9D  CONST_11  N03  C02  C01  C18    0.00   0.0  0
 S9D  CONST_12  N03  C04  N17  C18    0.00   0.0  0
 S9D  CONST_13  C07  C08  C09  C10  180.00   0.0  0
 S9D  CONST_14  C16  C15  C09  C10  180.00   0.0  0
 S9D  CONST_15  O05  C06  C16  C15  180.00   0.0  0
 S9D  CONST_16  O05  C04  N03  C02  180.00   0.0  0
 S9D  CONST_17  O05  C06  C07  C08  180.00   0.0  0
 S9D  CONST_18  O05  C04  N17  C18  180.00   0.0  0
 S9D  CONST_19  H6   C08  C09  C10    0.00   0.0  0
 S9D  CONST_20  H2   C15  C09  C10    0.00   0.0  0
 S9D  CONST_21  H12  C18  C01  C02  180.00   0.0  0
 S9D  CONST_22  H4   C02  N03  C04  180.00   0.0  0
 S9D  CONST_23  H11  C16  C06  C07  180.00   0.0  0
 S9D  CONST_24  H5   C07  C08  C09  180.00   0.0  0
 S9D  CONST_25  H3   C01  C02  N03  180.00   0.0  0
 S9D  Var_01    N13  C12  C11  C10  -11.59  30.0  1
 S9D  Var_02    C12  N13  N14  C10  -48.36  30.0  1
 S9D  Var_03    N14  N13  C12  C11   37.36  30.0  1
 S9D  Var_04    C07  C06  O05  C04  -89.52  30.0  3
 S9D  Var_05    N03  C04  O05  C06   -0.30  30.0  2

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
 S9D  chir_01  C10  C11  N14  C09  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
 S9D  plan-1  C10  0.020
 S9D  plan-1  C15  0.020
 S9D  plan-1  C06  0.020
 S9D  plan-1  C07  0.020
 S9D  plan-1  C08  0.020
 S9D  plan-1  C09  0.020
 S9D  plan-1  C16  0.020
 S9D  plan-1  H2   0.020
 S9D  plan-1  H5   0.020
 S9D  plan-1  H6   0.020
 S9D  plan-1  H11  0.020
 S9D  plan-1  O05  0.020
 S9D  plan-2  C01  0.020
 S9D  plan-2  C02  0.020
 S9D  plan-2  C04  0.020
 S9D  plan-2  C18  0.020
 S9D  plan-2  N03  0.020
 S9D  plan-2  N17  0.020
 S9D  plan-2  H4   0.020
 S9D  plan-2  H12  0.020
 S9D  plan-2  O05  0.020
 S9D  plan-2  H3   0.020

